From a1fcf90ec7aae3374add766c392b6f4c01e64f56 Mon Sep 17 00:00:00 2001 From: vsoch Date: Tue, 4 Apr 2023 23:43:15 -0600 Subject: [PATCH 01/10] original update to clean up repo metadata Signed-off-by: vsoch --- .github/scripts/clean-database.py | 113 +++ .github/workflows/clean.yaml | 72 ++ README.md | 7 +- .../github/LSARP/ProteomicsQC/metadata.json | 0 .../github/cran/irtplay/metadata.json | 0 .../csbioinfopk/iSumoK-PseAAC/metadata.json | 0 .../iopenshell/ezSpectrum/metadata.json | 0 .../github/zhwm/SparsePro_Paper/metadata.json | 0 .../0x0f0f0f/Metatheory.jl/metadata.json | 3 +- database/github/AA-ALERT/AMBER/metadata.json | 2 +- .../github/AA-ALERT/AstroData/metadata.json | 2 +- .../AA-ALERT/Dedispersion/metadata.json | 2 +- .../github/AA-ALERT/frbcat-web/metadata.json | 2 +- .../github/AA-ALERT/frbcatdb/metadata.json | 2 +- .../github/BenWibking/quokka/metadata.json | 3 +- .../BioMeCIS-Lab/OpenOmics/metadata.json | 3 +- .../cmstatr/metadata.json | 2 +- .../EcologicalNetworks.jl/metadata.json | 3 +- .../EcoJulia/SimpleSDMLayers.jl/metadata.json | 3 +- .../Effective-Quadratures/metadata.json | 2 +- .../ExpansionHunterDenovo/metadata.json | 2 +- database/github/Illumina/canvas/metadata.json | 2 +- .../Jane110111107/IsoTree/metadata.json | 2 +- .../JetBrains-Research/spbla/metadata.json | 3 +- .../BandedMatrices.jl/metadata.json | 3 +- .../BlockBandedMatrices.jl/metadata.json | 3 +- .../LazyBandedMatrices.jl/metadata.json | 3 +- .../github/JuliaPlots/Makie.jl/metadata.json | 3 +- .../github/Julian/jsonschema/metadata.json | 3 +- database/github/Krona/wiki/metadata.json | 2 +- .../MrMinimal64/multivar_horner/metadata.json | 3 +- database/github/MrOlm/drep/metadata.json | 2 +- .../PyTorchLightning/metrics/metadata.json | 3 +- .../github/TransDecoder/wiki/metadata.json | 2 +- .../github/alex-b-davis/gubas/metadata.json | 3 +- .../github/andersen-lab/html/metadata.json | 2 +- .../atmos-cloud-sim-uj/PyMPDATA/metadata.json | 3 +- .../atmos-cloud-sim-uj/PySDM/metadata.json | 3 +- .../github/bihealth/sodar_core/metadata.json | 3 +- .../github/biocore/sortmerna/metadata.json | 3 +- database/github/bpp/bpp/metadata.json | 2 +- .../github/cheginit/HyRiver/metadata.json | 3 +- .../christopherburke/tess-point/metadata.json | 3 +- .../github/cl3425/Clairvoyance/metadata.json | 3 +- .../cosmo-epfl/chemiscope/metadata.json | 2 +- .../github/deeptools/deepTools/metadata.json | 2 +- .../dgarrimar/sqtlseeker2-nf/metadata.json | 2 +- .../eggnogdb/eggnog-mapper/metadata.json | 2 +- database/github/gagneurlab/drop/metadata.json | 4 +- database/github/giswqs/leafmap/metadata.json | 3 +- database/github/giswqs/lidar/metadata.json | 3 +- .../github/he2016012996/CABnet/metadata.json | 3 +- .../github/jkbonfield/crumble/metadata.json | 5 +- .../CategoricalTimeSeries.jl/metadata.json | 3 +- .../github/jonschwenk/RivGraph/metadata.json | 3 +- .../github/jteutenberg/downpore/metadata.json | 2 +- database/github/katholt/Kaptive/metadata.json | 3 +- .../github/katholt/Kleborate/metadata.json | 3 +- database/github/kboone/parsnip/metadata.json | 3 +- database/github/kkjawz/coref-ee/metadata.json | 2 +- database/github/mirnylab/cooler/metadata.json | 2 +- .../mrvollger/fibertools-rs/metadata.json | 3 +- .../nanoporetech/index.html#/metadata.json | 12 - database/github/nh13/DWGSIM/metadata.json | 2 +- .../nilearn/nilearnhub.io/metadata.json | 2 +- database/github/nlesc-nano/Moka/metadata.json | 3 +- .../nlesc-nano/insilico-server/metadata.json | 3 +- database/github/patscott/ddcalc/metadata.json | 3 +- .../github/pinellolab/CRISPRitz/metadata.json | 2 +- .../poldracklab/nitransforms/metadata.json | 3 +- .../github/rordenlab/dcm2niix/metadata.json | 2 +- .../ruta-k/uGMRT-pipeline/metadata.json | 3 +- database/github/scrm/scrmhub.io/metadata.json | 2 +- .../github/shenwei356/csvtk/metadata.json | 2 +- .../thegenemyers/DALIGNER/metadata.json | 2 +- .../thegenemyers/DEXTRACTOR/metadata.json | 2 +- database/github/timoast/signac/metadata.json | 2 +- .../trinotate/trinotatehub.io/metadata.json | 2 +- .../varlociraptorhub.io/metadata.json | 2 +- .../github/vcftools/index.html/metadata.json | 21 - database/github/vpc-ccg/calib/metadata.json | 2 +- .../github/weizhongli/cdhit/metadata.json | 2 +- .../github/wiki/Install-macs2/metadata.json | 2 +- .../williamjameshandley/fgivenx/metadata.json | 3 +- repos.txt | 667 +++++++++++++++++- 85 files changed, 963 insertions(+), 118 deletions(-) create mode 100755 .github/scripts/clean-database.py create mode 100644 .github/workflows/clean.yaml rename {database => archive}/github/LSARP/ProteomicsQC/metadata.json (100%) rename {database => archive}/github/cran/irtplay/metadata.json (100%) rename {database => archive}/github/csbioinfopk/iSumoK-PseAAC/metadata.json (100%) rename {database => archive}/github/iopenshell/ezSpectrum/metadata.json (100%) rename {database => archive}/github/zhwm/SparsePro_Paper/metadata.json (100%) delete mode 100644 database/github/nanoporetech/index.html#/metadata.json delete mode 100644 database/github/vcftools/index.html/metadata.json diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py new file mode 100755 index 000000000..6885a412c --- /dev/null +++ b/.github/scripts/clean-database.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 + +import json +import os +import fnmatch +import requests +import shutil +import sys +import time + + +def recursive_find(base, pattern="*.json"): + """recursive find will yield python files in all directory levels + below a base path. + + Arguments: + - base (str) : the base directory to search + - pattern: a pattern to match, defaults to *.py + """ + for root, _, filenames in os.walk(base): + for filename in fnmatch.filter(filenames, pattern): + yield os.path.join(root, filename) + + +def read_json(path): + """ + Read json into dict! + """ + with open(path, "r") as fd: + content = json.loads(fd.read()) + return content + + +def save_json(meta, path): + with open(path, "w") as fd: + fd.write(json.dumps(meta, indent=4)) + + +def clean(database, archive): + """ + Clean the database + """ + archives = set() + for path in recursive_find(database, "*metadata.json"): + meta = read_json(path) + + if meta["url"] is None: + meta["url"] = meta["data"]["url"] + save_json(meta, path) + + try: + res = requests.head(meta.get("html_url") or meta.get("url")) + except: + print("Issue with {path}") + continue + + relpath = os.path.relpath(path, database) + if res.status_code == 200: + continue + + elif res.status_code == 404: + print(f"Found repository no longer present at {relpath}, archiving") + newpath = os.path.join(archive, relpath) + newdir = os.path.dirname(newpath) + shutil.move(os.path.dirname(path), newdir) + archives.add(os.path.dirname(relpath)) + + elif res.status_code in [301, 302]: + if "gitlab" in res.url: + import IPython + + IPython.embed() + sys.exit() + print(f"Found repository {relpath} with moved location, updating") + new_location = requests.head(res.headers["Location"]) + meta["html_url"] = new_location.url + save_json(meta, path) + + # Read in repos.txt and remove archived + with open("repos.txt", "r") as fd: + repos = fd.readlines() + repos = set([x.strip() for x in repos if x.strip()]) + for to_remove in archives: + repos.remove(to_remove) + + # Save back to file + with open("repos.txt", "w") as fd: + fd.write("\n".join(list(repos))) + + import IPython + + IPython.embed() + sys.exit() + + +def main(): + + # python .github/scripts/clean-database.py $(pwd) + if len(sys.argv) < 2: + sys.exit("Please provide a root path with the database and argument") + + root = os.path.abspath(sys.argv[1]) + database = os.path.join(root, "database") + archive = os.path.join(root, "archive") + for path in database, archive: + if not os.path.exists(path): + sys.exit(f"{path} does not exist.") + + clean(database, archive) + + +if __name__ == "__main__": + main() diff --git a/.github/workflows/clean.yaml b/.github/workflows/clean.yaml new file mode 100644 index 000000000..3c0d89753 --- /dev/null +++ b/.github/workflows/clean.yaml @@ -0,0 +1,72 @@ +name: clean-software + +on: + workflow_dispatch: + pull_request: [] + schedule: + # Weekly + - cron: 0 7 * * 0 + +jobs: + clean: + runs-on: ubuntu-latest + steps: + - name: Checkout Repository + uses: actions/checkout@v3 + - name: Install Research Software Encyclopedia + run: | + sudo apt-get update && sudo apt-get install -y python3 python3-pip python3-setuptools + git clone https://github.com/rseng/rse /tmp/rse + cd /tmp/rse + sudo pip3 install .[all] + rse --version + - name: Clean Repos + env: + RSE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + python .github/scripts/clean-database.py + rse export repos.txt --force + + - name: Export site to docs/ + uses: rseng/rse-action@0.0.13 + with: + config: rse.ini + export_dir: docs + force: true + prefix: software + host: https://rseng.github.io + + - name: Checkout New Branch + if: (github.event_name == 'pull_request') + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + BRANCH_AGAINST: "master" + run: | + printf "GitHub Actor: ${GITHUB_ACTOR}\n" + export BRANCH_FROM="update/software-$(date '+%Y-%m-%d')" + git remote set-url origin "https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" + git branch + git checkout -b "${BRANCH_FROM}" || git checkout "${BRANCH_FROM}" + git branch + + git config --global user.name "github-actions" + git config --global user.email "github-actions@users.noreply.github.com" + + git add database/* + git add docs/* + + if git diff-index --quiet HEAD --; then + printf "No changes\n" + else + printf "Changes\n" + git commit -m "Automated deployment to update software database $(date '+%Y-%m-%d')" + git push origin "${BRANCH_FROM}" + fi + echo "PULL_REQUEST_FROM_BRANCH=${BRANCH_FROM}" >> $GITHUB_ENV + + - name: Open Pull Request + if: (github.event_name == 'pull_request') + uses: vsoch/pull-request-action@master + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + PULL_REQUEST_BRANCH: "master" diff --git a/README.md b/README.md index 90f28e6d5..1a3200279 100644 --- a/README.md +++ b/README.md @@ -71,8 +71,11 @@ rse export --type static-web docs/ rse export --type static-web docs/ --force # if exists ``` -Further, a static API is exported to [https://rseng.github.io/software/data.json](https://rseng.github.io/software/data.json) that provides a listing of your software repositories -for some programmatic usage. +Further, a static API is exported to [https://rseng.github.io/software/data.json](https://rseng.github.io/software/data.json) that provides a listing of your software repositories for some programmatic usage. We also clean (and [archive](archive)) repositories that are no longer found: + +```bash +$ python .github/scripts/clean-database.py $(pwd) +``` # Development Work diff --git a/database/github/LSARP/ProteomicsQC/metadata.json b/archive/github/LSARP/ProteomicsQC/metadata.json similarity index 100% rename from database/github/LSARP/ProteomicsQC/metadata.json rename to archive/github/LSARP/ProteomicsQC/metadata.json diff --git a/database/github/cran/irtplay/metadata.json b/archive/github/cran/irtplay/metadata.json similarity index 100% rename from database/github/cran/irtplay/metadata.json rename to archive/github/cran/irtplay/metadata.json diff --git a/database/github/csbioinfopk/iSumoK-PseAAC/metadata.json b/archive/github/csbioinfopk/iSumoK-PseAAC/metadata.json similarity index 100% rename from database/github/csbioinfopk/iSumoK-PseAAC/metadata.json rename to archive/github/csbioinfopk/iSumoK-PseAAC/metadata.json diff --git a/database/github/iopenshell/ezSpectrum/metadata.json b/archive/github/iopenshell/ezSpectrum/metadata.json similarity index 100% rename from database/github/iopenshell/ezSpectrum/metadata.json rename to archive/github/iopenshell/ezSpectrum/metadata.json diff --git a/database/github/zhwm/SparsePro_Paper/metadata.json b/archive/github/zhwm/SparsePro_Paper/metadata.json similarity index 100% rename from database/github/zhwm/SparsePro_Paper/metadata.json rename to archive/github/zhwm/SparsePro_Paper/metadata.json diff --git a/database/github/0x0f0f0f/Metatheory.jl/metadata.json b/database/github/0x0f0f0f/Metatheory.jl/metadata.json index 0462ffeb6..150d176dc 100644 --- a/database/github/0x0f0f0f/Metatheory.jl/metadata.json +++ b/database/github/0x0f0f0f/Metatheory.jl/metadata.json @@ -46,5 +46,6 @@ "compiler-construction" ] }, - "doi": "https://doi.org/10.5281/zenodo.4646136" + "doi": "https://doi.org/10.5281/zenodo.4646136", + "html_url": "https://github.com/JuliaSymbolics/Metatheory.jl" } \ No newline at end of file diff --git a/database/github/AA-ALERT/AMBER/metadata.json b/database/github/AA-ALERT/AMBER/metadata.json index f700f4791..032fe75c6 100644 --- a/database/github/AA-ALERT/AMBER/metadata.json +++ b/database/github/AA-ALERT/AMBER/metadata.json @@ -36,7 +36,7 @@ }, "name": "AMBER", "full_name": "AA-ALERT/AMBER", - "html_url": "https://github.com/AA-ALERT/AMBER", + "html_url": "https://github.com/TRASAL/AMBER", "private": false, "description": "A many-core transient searching pipeline, designed to search in real-time for Fast Radio Bursts.", "created_at": "2015-03-27T14:59:41Z", diff --git a/database/github/AA-ALERT/AstroData/metadata.json b/database/github/AA-ALERT/AstroData/metadata.json index e4b4a974f..7ecda3497 100644 --- a/database/github/AA-ALERT/AstroData/metadata.json +++ b/database/github/AA-ALERT/AstroData/metadata.json @@ -36,7 +36,7 @@ }, "name": "AstroData", "full_name": "AA-ALERT/AstroData", - "html_url": "https://github.com/AA-ALERT/AstroData", + "html_url": "https://github.com/TRASAL/AstroData", "private": false, "description": "Set of C++ classes to operate on radio astronomical data.", "created_at": "2012-10-31T14:04:56Z", diff --git a/database/github/AA-ALERT/Dedispersion/metadata.json b/database/github/AA-ALERT/Dedispersion/metadata.json index ad03783a4..c53f0e9a5 100644 --- a/database/github/AA-ALERT/Dedispersion/metadata.json +++ b/database/github/AA-ALERT/Dedispersion/metadata.json @@ -36,7 +36,7 @@ }, "name": "Dedispersion", "full_name": "AA-ALERT/Dedispersion", - "html_url": "https://github.com/AA-ALERT/Dedispersion", + "html_url": "https://github.com/TRASAL/Dedispersion", "private": false, "description": "Radio astronomy dedispersion algorithm implemented for many-core accelerators.", "created_at": "2013-09-20T14:09:03Z", diff --git a/database/github/AA-ALERT/frbcat-web/metadata.json b/database/github/AA-ALERT/frbcat-web/metadata.json index 7d9df78f1..ef84ba30a 100644 --- a/database/github/AA-ALERT/frbcat-web/metadata.json +++ b/database/github/AA-ALERT/frbcat-web/metadata.json @@ -37,7 +37,7 @@ "doi": "10.5281/zenodo.1051033", "name": "frbcat-web", "full_name": "AA-ALERT/frbcat-web", - "html_url": "https://github.com/AA-ALERT/frbcat-web", + "html_url": "https://github.com/TRASAL/frbcat-web", "private": false, "description": "FRBCat web", "created_at": "2017-05-29T10:54:37Z", diff --git a/database/github/AA-ALERT/frbcatdb/metadata.json b/database/github/AA-ALERT/frbcatdb/metadata.json index ac43fd0d0..8e66132cb 100644 --- a/database/github/AA-ALERT/frbcatdb/metadata.json +++ b/database/github/AA-ALERT/frbcatdb/metadata.json @@ -37,7 +37,7 @@ "doi": "10.5281/zenodo.1051039", "name": "frbcatdb", "full_name": "AA-ALERT/frbcatdb", - "html_url": "https://github.com/AA-ALERT/frbcatdb", + "html_url": "https://github.com/TRASAL/frbcatdb", "private": false, "description": "Fast Radio Burst (FRB) Catalogue DB management", "created_at": "2016-08-17T10:05:56Z", diff --git a/database/github/BenWibking/quokka/metadata.json b/database/github/BenWibking/quokka/metadata.json index 5b698c751..118fd9feb 100644 --- a/database/github/BenWibking/quokka/metadata.json +++ b/database/github/BenWibking/quokka/metadata.json @@ -44,5 +44,6 @@ ], "timestamp": "2022-07-17 16:50:12.100697", "avatar": "https://avatars.githubusercontent.com/u/1781919?v=4" - } + }, + "html_url": "https://github.com/quokka-astro/quokka" } \ No newline at end of file diff --git a/database/github/BioMeCIS-Lab/OpenOmics/metadata.json b/database/github/BioMeCIS-Lab/OpenOmics/metadata.json index 80912f1f2..a1b4d521f 100644 --- a/database/github/BioMeCIS-Lab/OpenOmics/metadata.json +++ b/database/github/BioMeCIS-Lab/OpenOmics/metadata.json @@ -41,5 +41,6 @@ "data-manipulation" ] }, - "doi": "https://doi.org/10.5281/zenodo.4731011" + "doi": "https://doi.org/10.5281/zenodo.4731011", + "html_url": "https://github.com/JonnyTran/OpenOmics" } \ No newline at end of file diff --git a/database/github/ComtekAdvancedStructures/cmstatr/metadata.json b/database/github/ComtekAdvancedStructures/cmstatr/metadata.json index 6a7a30d73..579b39f11 100644 --- a/database/github/ComtekAdvancedStructures/cmstatr/metadata.json +++ b/database/github/ComtekAdvancedStructures/cmstatr/metadata.json @@ -37,7 +37,7 @@ "doi": "https://doi.org/10.5281/zenodo.3930475", "name": "cmstatr", "full_name": "ComtekAdvancedStructures/cmstatr", - "html_url": "https://github.com/ComtekAdvancedStructures/cmstatr", + "html_url": "https://github.com/cmstatr/cmstatr", "private": false, "description": "An R Package for Statistical Analysis of Composite Material Data", "created_at": "2016-09-07T17:33:12Z", diff --git a/database/github/EcoJulia/EcologicalNetworks.jl/metadata.json b/database/github/EcoJulia/EcologicalNetworks.jl/metadata.json index 0e16b4c06..7306931b4 100644 --- a/database/github/EcoJulia/EcologicalNetworks.jl/metadata.json +++ b/database/github/EcoJulia/EcologicalNetworks.jl/metadata.json @@ -39,5 +39,6 @@ "networks" ] }, - "doi": "https://doi.org/10.5281/zenodo.4716483" + "doi": "https://doi.org/10.5281/zenodo.4716483", + "html_url": "https://github.com/PoisotLab/EcologicalNetworks.jl" } \ No newline at end of file diff --git a/database/github/EcoJulia/SimpleSDMLayers.jl/metadata.json b/database/github/EcoJulia/SimpleSDMLayers.jl/metadata.json index 237923dd9..6b885d8ba 100644 --- a/database/github/EcoJulia/SimpleSDMLayers.jl/metadata.json +++ b/database/github/EcoJulia/SimpleSDMLayers.jl/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "https://doi.org/10.5281/zenodo.4472905" + "doi": "https://doi.org/10.5281/zenodo.4472905", + "html_url": "https://github.com/PoisotLab/SimpleSDMLayers.jl" } \ No newline at end of file diff --git a/database/github/Effective-Quadratures/Effective-Quadratures/metadata.json b/database/github/Effective-Quadratures/Effective-Quadratures/metadata.json index 63d1e433d..b557aa03f 100644 --- a/database/github/Effective-Quadratures/Effective-Quadratures/metadata.json +++ b/database/github/Effective-Quadratures/Effective-Quadratures/metadata.json @@ -36,7 +36,7 @@ }, "name": "Effective-Quadratures", "full_name": "Effective-Quadratures/Effective-Quadratures", - "html_url": "https://github.com/Effective-Quadratures/Effective-Quadratures", + "html_url": "https://github.com/equadratures/equadratures", "private": false, "description": null, "created_at": "2016-03-23T10:15:19Z", diff --git a/database/github/Illumina/ExpansionHunterDenovo/metadata.json b/database/github/Illumina/ExpansionHunterDenovo/metadata.json index 0f3e7b0c7..a1a4bc618 100644 --- a/database/github/Illumina/ExpansionHunterDenovo/metadata.json +++ b/database/github/Illumina/ExpansionHunterDenovo/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/Illumina/ExpansionHunterDenovo", - "url": null, + "url": "https://github.com/Illumina/ExpansionHunterDenovo", "data": { "title": "ExpansionHunter Denovo", "url": "https://github.com/Illumina/ExpansionHunterDenovo", diff --git a/database/github/Illumina/canvas/metadata.json b/database/github/Illumina/canvas/metadata.json index d432f61c5..0c0c88ef4 100644 --- a/database/github/Illumina/canvas/metadata.json +++ b/database/github/Illumina/canvas/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/Illumina/canvas", - "url": null, + "url": "https://github.com/Illumina/canvas", "data": { "title": "Canvas", "url": "https://github.com/Illumina/canvas", diff --git a/database/github/Jane110111107/IsoTree/metadata.json b/database/github/Jane110111107/IsoTree/metadata.json index 89131cc37..593eedf76 100644 --- a/database/github/Jane110111107/IsoTree/metadata.json +++ b/database/github/Jane110111107/IsoTree/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/Jane110111107/IsoTree", - "url": null, + "url": "https://github.com/Jane110111107/IsoTree", "data": { "title": "IsoTree", "url": "https://github.com/Jane110111107/IsoTree", diff --git a/database/github/JetBrains-Research/spbla/metadata.json b/database/github/JetBrains-Research/spbla/metadata.json index aec28b44e..1c217ea35 100644 --- a/database/github/JetBrains-Research/spbla/metadata.json +++ b/database/github/JetBrains-Research/spbla/metadata.json @@ -45,5 +45,6 @@ ], "timestamp": "2022-08-21 00:38:37.212756", "avatar": "https://avatars.githubusercontent.com/u/10167268?v=4" - } + }, + "html_url": "https://github.com/SparseLinearAlgebra/spbla" } \ No newline at end of file diff --git a/database/github/JuliaMatrices/BandedMatrices.jl/metadata.json b/database/github/JuliaMatrices/BandedMatrices.jl/metadata.json index 94b71cdb1..6e55f5497 100644 --- a/database/github/JuliaMatrices/BandedMatrices.jl/metadata.json +++ b/database/github/JuliaMatrices/BandedMatrices.jl/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "rsotm": "2022-02" + "rsotm": "2022-02", + "html_url": "https://github.com/JuliaLinearAlgebra/BandedMatrices.jl" } \ No newline at end of file diff --git a/database/github/JuliaMatrices/BlockBandedMatrices.jl/metadata.json b/database/github/JuliaMatrices/BlockBandedMatrices.jl/metadata.json index fc5eec172..21060967e 100644 --- a/database/github/JuliaMatrices/BlockBandedMatrices.jl/metadata.json +++ b/database/github/JuliaMatrices/BlockBandedMatrices.jl/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "rsotm": "2022-02" + "rsotm": "2022-02", + "html_url": "https://github.com/JuliaLinearAlgebra/BlockBandedMatrices.jl" } \ No newline at end of file diff --git a/database/github/JuliaMatrices/LazyBandedMatrices.jl/metadata.json b/database/github/JuliaMatrices/LazyBandedMatrices.jl/metadata.json index 70d5bb83f..42bd2da25 100644 --- a/database/github/JuliaMatrices/LazyBandedMatrices.jl/metadata.json +++ b/database/github/JuliaMatrices/LazyBandedMatrices.jl/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "rsotm": "2022-02" + "rsotm": "2022-02", + "html_url": "https://github.com/JuliaLinearAlgebra/LazyBandedMatrices.jl" } \ No newline at end of file diff --git a/database/github/JuliaPlots/Makie.jl/metadata.json b/database/github/JuliaPlots/Makie.jl/metadata.json index 77caedeb0..afe247f77 100644 --- a/database/github/JuliaPlots/Makie.jl/metadata.json +++ b/database/github/JuliaPlots/Makie.jl/metadata.json @@ -42,5 +42,6 @@ "graphics" ] }, - "doi": "https://doi.org/10.5281/zenodo.5106448" + "doi": "https://doi.org/10.5281/zenodo.5106448", + "html_url": "https://github.com/MakieOrg/Makie.jl" } \ No newline at end of file diff --git a/database/github/Julian/jsonschema/metadata.json b/database/github/Julian/jsonschema/metadata.json index 03959d629..53fb8bc46 100644 --- a/database/github/Julian/jsonschema/metadata.json +++ b/database/github/Julian/jsonschema/metadata.json @@ -34,5 +34,6 @@ "type": "User" }, "topics": [] - } + }, + "html_url": "https://github.com/python-jsonschema/jsonschema" } \ No newline at end of file diff --git a/database/github/Krona/wiki/metadata.json b/database/github/Krona/wiki/metadata.json index 08c7d03cb..2c37455fb 100644 --- a/database/github/Krona/wiki/metadata.json +++ b/database/github/Krona/wiki/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/Krona/wiki", - "url": null, + "url": "https://github.com/marbl/Krona", "data": { "title": "Krona Tools", "url": "https://github.com/marbl/Krona/wiki", diff --git a/database/github/MrMinimal64/multivar_horner/metadata.json b/database/github/MrMinimal64/multivar_horner/metadata.json index f4417340a..ed4ef389e 100644 --- a/database/github/MrMinimal64/multivar_horner/metadata.json +++ b/database/github/MrMinimal64/multivar_horner/metadata.json @@ -50,5 +50,6 @@ "evaluation" ] }, - "doi": "https://doi.org/10.5281/zenodo.4062422" + "doi": "https://doi.org/10.5281/zenodo.4062422", + "html_url": "https://github.com/jannikmi/multivar_horner" } \ No newline at end of file diff --git a/database/github/MrOlm/drep/metadata.json b/database/github/MrOlm/drep/metadata.json index 3384c8201..ea2f3b993 100644 --- a/database/github/MrOlm/drep/metadata.json +++ b/database/github/MrOlm/drep/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/MrOlm/drep", - "url": null, + "url": "https://github.com/MrOlm/drep", "data": { "title": "dRep", "url": "https://github.com/MrOlm/drep", diff --git a/database/github/PyTorchLightning/metrics/metadata.json b/database/github/PyTorchLightning/metrics/metadata.json index 1de918dee..620be7e83 100644 --- a/database/github/PyTorchLightning/metrics/metadata.json +++ b/database/github/PyTorchLightning/metrics/metadata.json @@ -43,5 +43,6 @@ "analyses" ] }, - "doi": "https://doi.org/10.5281/zenodo.6037875" + "doi": "https://doi.org/10.5281/zenodo.6037875", + "html_url": "https://github.com/Lightning-AI/torchmetrics" } \ No newline at end of file diff --git a/database/github/TransDecoder/wiki/metadata.json b/database/github/TransDecoder/wiki/metadata.json index ea0ad65c9..7790e0989 100644 --- a/database/github/TransDecoder/wiki/metadata.json +++ b/database/github/TransDecoder/wiki/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/TransDecoder/wiki", - "url": null, + "url": "https://github.com/TransDecoder/TransDecoder", "data": { "title": "TransDecoder", "url": "https://github.com/TransDecoder/TransDecoder/wiki", diff --git a/database/github/alex-b-davis/gubas/metadata.json b/database/github/alex-b-davis/gubas/metadata.json index b99753b26..4da8fa509 100644 --- a/database/github/alex-b-davis/gubas/metadata.json +++ b/database/github/alex-b-davis/gubas/metadata.json @@ -35,5 +35,6 @@ }, "timestamp": "2022-07-17 17:11:29.641588", "avatar": "https://avatars.githubusercontent.com/u/54447759?v=4" - } + }, + "html_url": "https://github.com/meyeralexj/gubas" } \ No newline at end of file diff --git a/database/github/andersen-lab/html/metadata.json b/database/github/andersen-lab/html/metadata.json index af4f636b7..e006d6ffe 100644 --- a/database/github/andersen-lab/html/metadata.json +++ b/database/github/andersen-lab/html/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/andersen-lab/html", - "url": null, + "url": "https://github.com/andersen-lab/ivar", "data": { "title": "ivar", "url": "https://andersen-lab.github.io/ivar/html/", diff --git a/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json b/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json index 325e16c29..f6368bbbb 100644 --- a/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json +++ b/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json @@ -45,5 +45,6 @@ ], "timestamp": "2022-09-11 00:43:13.573293", "avatar": "https://avatars.githubusercontent.com/u/48702007?v=4" - } + }, + "html_url": "https://github.com/open-atmos/PyMPDATA" } \ No newline at end of file diff --git a/database/github/atmos-cloud-sim-uj/PySDM/metadata.json b/database/github/atmos-cloud-sim-uj/PySDM/metadata.json index 7809f102c..88e299a99 100644 --- a/database/github/atmos-cloud-sim-uj/PySDM/metadata.json +++ b/database/github/atmos-cloud-sim-uj/PySDM/metadata.json @@ -52,5 +52,6 @@ "pypi-package" ] }, - "doi": "https://doi.org/10.5281/zenodo.6321270" + "doi": "https://doi.org/10.5281/zenodo.6321270", + "html_url": "https://github.com/open-atmos/PySDM" } \ No newline at end of file diff --git a/database/github/bihealth/sodar_core/metadata.json b/database/github/bihealth/sodar_core/metadata.json index d1837ca48..17422436c 100644 --- a/database/github/bihealth/sodar_core/metadata.json +++ b/database/github/bihealth/sodar_core/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "https://doi.org/10.5281/zenodo.4269347" + "doi": "https://doi.org/10.5281/zenodo.4269347", + "html_url": "https://github.com/bihealth/sodar-core-legacy" } \ No newline at end of file diff --git a/database/github/biocore/sortmerna/metadata.json b/database/github/biocore/sortmerna/metadata.json index 58d49d91b..d8057de85 100644 --- a/database/github/biocore/sortmerna/metadata.json +++ b/database/github/biocore/sortmerna/metadata.json @@ -44,5 +44,6 @@ ], "timestamp": "2022-07-18 17:46:59.982010", "avatar": "https://avatars.githubusercontent.com/u/6241857?v=4" - } + }, + "html_url": "https://github.com/sortmerna/sortmerna" } \ No newline at end of file diff --git a/database/github/bpp/bpp/metadata.json b/database/github/bpp/bpp/metadata.json index 220bb5960..12c1bb361 100644 --- a/database/github/bpp/bpp/metadata.json +++ b/database/github/bpp/bpp/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/bpp/bpp", - "url": null, + "url": "https://github.com/bpp/bpp", "data": { "title": "bpp", "url": "https://github.com/bpp/bpp", diff --git a/database/github/cheginit/HyRiver/metadata.json b/database/github/cheginit/HyRiver/metadata.json index 82f035696..a90bfc498 100644 --- a/database/github/cheginit/HyRiver/metadata.json +++ b/database/github/cheginit/HyRiver/metadata.json @@ -41,5 +41,6 @@ "data" ] }, - "doi": "https://doi.org/10.5281/zenodo.5602114" + "doi": "https://doi.org/10.5281/zenodo.5602114", + "html_url": "https://github.com/hyriver/hyriver.github.io" } \ No newline at end of file diff --git a/database/github/christopherburke/tess-point/metadata.json b/database/github/christopherburke/tess-point/metadata.json index 526f24b1d..398397bed 100644 --- a/database/github/christopherburke/tess-point/metadata.json +++ b/database/github/christopherburke/tess-point/metadata.json @@ -37,5 +37,6 @@ }, "timestamp": "2022-07-17 17:14:50.258288", "avatar": "https://avatars.githubusercontent.com/u/12038053?v=4" - } + }, + "html_url": "https://github.com/tessgi/tess-point" } \ No newline at end of file diff --git a/database/github/cl3425/Clairvoyance/metadata.json b/database/github/cl3425/Clairvoyance/metadata.json index 16c045801..033ff95aa 100644 --- a/database/github/cl3425/Clairvoyance/metadata.json +++ b/database/github/cl3425/Clairvoyance/metadata.json @@ -29,5 +29,6 @@ }, "timestamp": "2022-07-17 17:21:03.595811", "avatar": "https://avatars.githubusercontent.com/u/16911363?v=4" - } + }, + "html_url": "https://github.com/exoclam/Clairvoyance" } \ No newline at end of file diff --git a/database/github/cosmo-epfl/chemiscope/metadata.json b/database/github/cosmo-epfl/chemiscope/metadata.json index 8b0945070..970e2dee0 100644 --- a/database/github/cosmo-epfl/chemiscope/metadata.json +++ b/database/github/cosmo-epfl/chemiscope/metadata.json @@ -37,7 +37,7 @@ "doi": "https://doi.org/10.5281/zenodo.3909400", "name": "chemiscope", "full_name": "cosmo-epfl/chemiscope", - "html_url": "https://github.com/cosmo-epfl/chemiscope", + "html_url": "https://github.com/lab-cosmo/chemiscope", "private": false, "description": "An interactive structure/property explorer for materials and molecules", "created_at": "2019-10-03T09:59:42Z", diff --git a/database/github/deeptools/deepTools/metadata.json b/database/github/deeptools/deepTools/metadata.json index e9c8739f3..39e218ed1 100644 --- a/database/github/deeptools/deepTools/metadata.json +++ b/database/github/deeptools/deepTools/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/deeptools/deepTools", - "url": null, + "url": "https://github.com/deeptools/deepTools", "data": { "title": "deepTools", "url": "https://github.com/deeptools/deepTools", diff --git a/database/github/dgarrimar/sqtlseeker2-nf/metadata.json b/database/github/dgarrimar/sqtlseeker2-nf/metadata.json index 08084a6cf..6140845cb 100644 --- a/database/github/dgarrimar/sqtlseeker2-nf/metadata.json +++ b/database/github/dgarrimar/sqtlseeker2-nf/metadata.json @@ -37,7 +37,7 @@ "doi": "10.1038/ncomms5698", "name": "sqtlseeker2-nf", "full_name": "dgarrimar/sqtlseeker2-nf", - "html_url": "https://github.com/dgarrimar/sqtlseeker2-nf", + "html_url": "https://github.com/guigolab/sqtlseeker2-nf", "private": false, "description": "An automated sQTL mapping pipeline using Nextflow", "created_at": "2017-11-28T17:07:19Z", diff --git a/database/github/eggnogdb/eggnog-mapper/metadata.json b/database/github/eggnogdb/eggnog-mapper/metadata.json index 70ce287a3..0286da672 100644 --- a/database/github/eggnogdb/eggnog-mapper/metadata.json +++ b/database/github/eggnogdb/eggnog-mapper/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/eggnogdb/eggnog-mapper", - "url": null, + "url": "https://github.com/eggnogdb/eggnog-mapper", "data": { "title": "EggNOG\u2011mapper", "url": "https://github.com/eggnogdb/eggnog-mapper", diff --git a/database/github/gagneurlab/drop/metadata.json b/database/github/gagneurlab/drop/metadata.json index d575c892a..d78f1dd91 100644 --- a/database/github/gagneurlab/drop/metadata.json +++ b/database/github/gagneurlab/drop/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/gagneurlab/drop", - "url": null, + "url": "https://github.com/gagneurlab/drop", "data": { "title": "DROP", "url": "https://github.com/gagneurlab/drop", @@ -43,4 +43,4 @@ ], "timestamp": "2022-07-18 17:43:39.955895" } -} \ No newline at end of file +} diff --git a/database/github/giswqs/leafmap/metadata.json b/database/github/giswqs/leafmap/metadata.json index fa12e7947..f9297c819 100644 --- a/database/github/giswqs/leafmap/metadata.json +++ b/database/github/giswqs/leafmap/metadata.json @@ -49,5 +49,6 @@ "geospatial-analysis" ] }, - "doi": "https://doi.org/10.5281/zenodo.5137372" + "doi": "https://doi.org/10.5281/zenodo.5137372", + "html_url": "https://github.com/opengeos/leafmap" } \ No newline at end of file diff --git a/database/github/giswqs/lidar/metadata.json b/database/github/giswqs/lidar/metadata.json index 45673ced2..7f9ecc77c 100644 --- a/database/github/giswqs/lidar/metadata.json +++ b/database/github/giswqs/lidar/metadata.json @@ -44,5 +44,6 @@ "hydrological" ] }, - "doi": "https://doi.org/10.5281/zenodo.4571011" + "doi": "https://doi.org/10.5281/zenodo.4571011", + "html_url": "https://github.com/opengeos/lidar" } \ No newline at end of file diff --git a/database/github/he2016012996/CABnet/metadata.json b/database/github/he2016012996/CABnet/metadata.json index 3a135ee10..096d1e5cf 100644 --- a/database/github/he2016012996/CABnet/metadata.json +++ b/database/github/he2016012996/CABnet/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "10.1109/TMI.2020.3023463" + "doi": "10.1109/TMI.2020.3023463", + "html_url": "https://github.com/NKUhealong/CABnet" } \ No newline at end of file diff --git a/database/github/jkbonfield/crumble/metadata.json b/database/github/jkbonfield/crumble/metadata.json index 970e8ab41..55b06a088 100644 --- a/database/github/jkbonfield/crumble/metadata.json +++ b/database/github/jkbonfield/crumble/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/jkbonfield/crumble", - "url": null, + "url": "https://github.com/jkbonfield/crumble", "data": { "title": "Crumble", "url": "https://github.com/jkbonfield/crumble", @@ -35,5 +35,6 @@ "type": "User" }, "timestamp": "2022-07-18 17:43:36.923298" - } + }, + "html_url": "https://github.com/stuart-lab/signac" } \ No newline at end of file diff --git a/database/github/johncwok/CategoricalTimeSeries.jl/metadata.json b/database/github/johncwok/CategoricalTimeSeries.jl/metadata.json index a932492e5..9ed20c50f 100644 --- a/database/github/johncwok/CategoricalTimeSeries.jl/metadata.json +++ b/database/github/johncwok/CategoricalTimeSeries.jl/metadata.json @@ -39,5 +39,6 @@ "julia" ] }, - "doi": "https://doi.org/10.6084/m9.figshare.16917625" + "doi": "https://doi.org/10.6084/m9.figshare.16917625", + "html_url": "https://github.com/CNelias/CategoricalTimeSeries.jl" } \ No newline at end of file diff --git a/database/github/jonschwenk/RivGraph/metadata.json b/database/github/jonschwenk/RivGraph/metadata.json index 482f8d9ca..4225d6827 100644 --- a/database/github/jonschwenk/RivGraph/metadata.json +++ b/database/github/jonschwenk/RivGraph/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "https://doi.org/10.5281/zenodo.4591559" + "doi": "https://doi.org/10.5281/zenodo.4591559", + "html_url": "https://github.com/VeinsOfTheEarth/RivGraph" } \ No newline at end of file diff --git a/database/github/jteutenberg/downpore/metadata.json b/database/github/jteutenberg/downpore/metadata.json index 6418d8b6d..127e0d8c2 100644 --- a/database/github/jteutenberg/downpore/metadata.json +++ b/database/github/jteutenberg/downpore/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/jteutenberg/downpore", - "url": null, + "url": "https://github.com/jteutenberg/downpore", "data": { "title": "downpore", "url": "https://github.com/jteutenberg/downpore", diff --git a/database/github/katholt/Kaptive/metadata.json b/database/github/katholt/Kaptive/metadata.json index db265065c..9455bc5a3 100644 --- a/database/github/katholt/Kaptive/metadata.json +++ b/database/github/katholt/Kaptive/metadata.json @@ -34,5 +34,6 @@ }, "timestamp": "2022-07-20 17:26:12.360666", "avatar": "https://avatars.githubusercontent.com/u/832158?v=4" - } + }, + "html_url": "https://github.com/klebgenomics/Kaptive" } \ No newline at end of file diff --git a/database/github/katholt/Kleborate/metadata.json b/database/github/katholt/Kleborate/metadata.json index 00516cd01..79ee23c1a 100644 --- a/database/github/katholt/Kleborate/metadata.json +++ b/database/github/katholt/Kleborate/metadata.json @@ -34,5 +34,6 @@ }, "timestamp": "2022-07-20 17:26:13.553044", "avatar": "https://avatars.githubusercontent.com/u/832158?v=4" - } + }, + "html_url": "https://github.com/klebgenomics/Kleborate" } \ No newline at end of file diff --git a/database/github/kboone/parsnip/metadata.json b/database/github/kboone/parsnip/metadata.json index a303bf6e7..ff27e1d97 100644 --- a/database/github/kboone/parsnip/metadata.json +++ b/database/github/kboone/parsnip/metadata.json @@ -37,5 +37,6 @@ }, "timestamp": "2022-07-17 16:50:12.815389", "avatar": "https://avatars.githubusercontent.com/u/789873?v=4" - } + }, + "html_url": "https://github.com/LSSTDESC/parsnip" } \ No newline at end of file diff --git a/database/github/kkjawz/coref-ee/metadata.json b/database/github/kkjawz/coref-ee/metadata.json index cb7477b40..56057ec90 100644 --- a/database/github/kkjawz/coref-ee/metadata.json +++ b/database/github/kkjawz/coref-ee/metadata.json @@ -36,7 +36,7 @@ }, "name": "coref-ee", "full_name": "kkjawz/coref-ee", - "html_url": "https://github.com/kkjawz/coref-ee", + "html_url": "https://github.com/bkntr/coref-ee", "private": false, "description": "Coreference Resolution With Entity Equalization", "created_at": "2019-06-03T08:11:48Z", diff --git a/database/github/mirnylab/cooler/metadata.json b/database/github/mirnylab/cooler/metadata.json index f549c7fb6..ef2ef218d 100644 --- a/database/github/mirnylab/cooler/metadata.json +++ b/database/github/mirnylab/cooler/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/mirnylab/cooler", - "url": null, + "url": "https://github.com/mirnylab/cooler", "data": { "title": "cooler", "url": "https://github.com/mirnylab/cooler", diff --git a/database/github/mrvollger/fibertools-rs/metadata.json b/database/github/mrvollger/fibertools-rs/metadata.json index b55c9cbbe..1571058bc 100644 --- a/database/github/mrvollger/fibertools-rs/metadata.json +++ b/database/github/mrvollger/fibertools-rs/metadata.json @@ -30,5 +30,6 @@ }, "timestamp": "2022-11-27 00:42:35.979054", "avatar": "https://avatars.githubusercontent.com/u/6935283?v=4" - } + }, + "html_url": "https://github.com/fiberseq/fibertools-rs" } \ No newline at end of file diff --git a/database/github/nanoporetech/index.html#/metadata.json b/database/github/nanoporetech/index.html#/metadata.json deleted file mode 100644 index b9980bd37..000000000 --- a/database/github/nanoporetech/index.html#/metadata.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "parser": "github", - "uid": "github/nanoporetech/index.html#", - "url": null, - "data": { - "title": "Tombo", - "url": "https://nanoporetech.github.io/tombo/index.html#", - "credit": [], - "description": "a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.", - "timestamp": "2022-07-18 17:47:14.852532" - } -} \ No newline at end of file diff --git a/database/github/nh13/DWGSIM/metadata.json b/database/github/nh13/DWGSIM/metadata.json index b6c5195c3..5a7144200 100644 --- a/database/github/nh13/DWGSIM/metadata.json +++ b/database/github/nh13/DWGSIM/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/nh13/DWGSIM", - "url": null, + "url": "https://github.com/nh13/DWGSIM", "data": { "title": "DWGSIM", "url": "https://github.com/nh13/DWGSIM", diff --git a/database/github/nilearn/nilearnhub.io/metadata.json b/database/github/nilearn/nilearnhub.io/metadata.json index a637ffb2e..5c3c14aa1 100644 --- a/database/github/nilearn/nilearnhub.io/metadata.json +++ b/database/github/nilearn/nilearnhub.io/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/nilearn/nilearnhub.io", - "url": null, + "url": "https://github.com/nilearn/nilearn", "data": { "title": "nilearn", "url": "https://nilearn.github.io/", diff --git a/database/github/nlesc-nano/Moka/metadata.json b/database/github/nlesc-nano/Moka/metadata.json index d807c60d0..d7e3dccf6 100644 --- a/database/github/nlesc-nano/Moka/metadata.json +++ b/database/github/nlesc-nano/Moka/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "10.5281/zenodo.4241144" + "doi": "10.5281/zenodo.4241144", + "html_url": "https://github.com/nlesc-nano/ceiba-cli" } \ No newline at end of file diff --git a/database/github/nlesc-nano/insilico-server/metadata.json b/database/github/nlesc-nano/insilico-server/metadata.json index f3e245a9b..b876feb5a 100644 --- a/database/github/nlesc-nano/insilico-server/metadata.json +++ b/database/github/nlesc-nano/insilico-server/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "10.5281/zenodo.4240374" + "doi": "10.5281/zenodo.4240374", + "html_url": "https://github.com/nlesc-nano/ceiba" } \ No newline at end of file diff --git a/database/github/patscott/ddcalc/metadata.json b/database/github/patscott/ddcalc/metadata.json index fd0c68011..522ce5648 100644 --- a/database/github/patscott/ddcalc/metadata.json +++ b/database/github/patscott/ddcalc/metadata.json @@ -37,5 +37,6 @@ }, "timestamp": "2022-07-17 17:13:20.053220", "avatar": "https://avatars.githubusercontent.com/u/1249657?v=4" - } + }, + "html_url": "https://github.com/GambitBSM/DDCalc" } \ No newline at end of file diff --git a/database/github/pinellolab/CRISPRitz/metadata.json b/database/github/pinellolab/CRISPRitz/metadata.json index 7fc3a57de..e0c0caee0 100644 --- a/database/github/pinellolab/CRISPRitz/metadata.json +++ b/database/github/pinellolab/CRISPRitz/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/pinellolab/CRISPRitz", - "url": null, + "url": "https://github.com/pinellolab/CRISPRitz", "data": { "title": "CRISPRitz", "url": "https://github.com/pinellolab/CRISPRitz", diff --git a/database/github/poldracklab/nitransforms/metadata.json b/database/github/poldracklab/nitransforms/metadata.json index 10e6343b4..a65e91547 100644 --- a/database/github/poldracklab/nitransforms/metadata.json +++ b/database/github/poldracklab/nitransforms/metadata.json @@ -35,5 +35,6 @@ }, "topics": [] }, - "doi": "https://doi.org/10.5281/zenodo.5499694" + "doi": "https://doi.org/10.5281/zenodo.5499694", + "html_url": "https://github.com/nipy/nitransforms" } \ No newline at end of file diff --git a/database/github/rordenlab/dcm2niix/metadata.json b/database/github/rordenlab/dcm2niix/metadata.json index aa3b8b758..9a7ba6285 100644 --- a/database/github/rordenlab/dcm2niix/metadata.json +++ b/database/github/rordenlab/dcm2niix/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/rordenlab/dcm2niix", - "url": null, + "url": "https://github.com/rordenlab/dcm2niix", "data": { "title": "dcm2niix", "url": "https://github.com/rordenlab/dcm2niix", diff --git a/database/github/ruta-k/uGMRT-pipeline/metadata.json b/database/github/ruta-k/uGMRT-pipeline/metadata.json index 3e67e2369..750d8e65a 100644 --- a/database/github/ruta-k/uGMRT-pipeline/metadata.json +++ b/database/github/ruta-k/uGMRT-pipeline/metadata.json @@ -29,5 +29,6 @@ }, "timestamp": "2022-07-17 17:13:37.135364", "avatar": "https://avatars.githubusercontent.com/u/38125415?v=4" - } + }, + "html_url": "https://github.com/ruta-k/uGMRT-pipeline-outdated" } \ No newline at end of file diff --git a/database/github/scrm/scrmhub.io/metadata.json b/database/github/scrm/scrmhub.io/metadata.json index c24b3ad59..07522cfcd 100644 --- a/database/github/scrm/scrmhub.io/metadata.json +++ b/database/github/scrm/scrmhub.io/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/scrm/scrmhub.io", - "url": null, + "url": "https://github.com/scrm/scrm", "data": { "title": "scrm", "url": "https://scrm.github.io/", diff --git a/database/github/shenwei356/csvtk/metadata.json b/database/github/shenwei356/csvtk/metadata.json index 2a494e8a1..4445fe083 100644 --- a/database/github/shenwei356/csvtk/metadata.json +++ b/database/github/shenwei356/csvtk/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/shenwei356/csvtk", - "url": null, + "url": "https://github.com/shenwei356/csvtk", "data": { "title": "csvtk", "url": "https://github.com/shenwei356/csvtk", diff --git a/database/github/thegenemyers/DALIGNER/metadata.json b/database/github/thegenemyers/DALIGNER/metadata.json index 2e4e3dc14..a7fd15353 100644 --- a/database/github/thegenemyers/DALIGNER/metadata.json +++ b/database/github/thegenemyers/DALIGNER/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/thegenemyers/DALIGNER", - "url": null, + "url": "https://github.com/thegenemyers/DALIGNER", "data": { "title": "daligner", "url": "https://github.com/thegenemyers/DALIGNER", diff --git a/database/github/thegenemyers/DEXTRACTOR/metadata.json b/database/github/thegenemyers/DEXTRACTOR/metadata.json index f24cfe981..15f948c4b 100644 --- a/database/github/thegenemyers/DEXTRACTOR/metadata.json +++ b/database/github/thegenemyers/DEXTRACTOR/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/thegenemyers/DEXTRACTOR", - "url": null, + "url": "https://github.com/thegenemyers/DEXTRACTOR", "data": { "title": "Dextractor", "url": "https://github.com/thegenemyers/DEXTRACTOR", diff --git a/database/github/timoast/signac/metadata.json b/database/github/timoast/signac/metadata.json index 610851a14..b996fa6a8 100644 --- a/database/github/timoast/signac/metadata.json +++ b/database/github/timoast/signac/metadata.json @@ -36,7 +36,7 @@ }, "name": "signac", "full_name": "timoast/signac", - "html_url": "https://github.com/timoast/signac", + "html_url": "https://github.com/stuart-lab/signac", "private": false, "description": "R toolkit for the analysis of single-cell chromatin data", "created_at": "2019-05-09T22:32:26Z", diff --git a/database/github/trinotate/trinotatehub.io/metadata.json b/database/github/trinotate/trinotatehub.io/metadata.json index 497c0a409..b48896d8b 100644 --- a/database/github/trinotate/trinotatehub.io/metadata.json +++ b/database/github/trinotate/trinotatehub.io/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/trinotate/trinotatehub.io", - "url": null, + "url": "https://github.com/Trinotate/Trinotate", "data": { "title": "Trinotate", "url": "https://trinotate.github.io/", diff --git a/database/github/varlociraptor/varlociraptorhub.io/metadata.json b/database/github/varlociraptor/varlociraptorhub.io/metadata.json index d34a1e6e2..665e92185 100644 --- a/database/github/varlociraptor/varlociraptorhub.io/metadata.json +++ b/database/github/varlociraptor/varlociraptorhub.io/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/varlociraptor/varlociraptorhub.io", - "url": null, + "url": "https://github.com/varlociraptor/varlociraptor", "data": { "title": "varlociraptor", "url": "https://varlociraptor.github.io", diff --git a/database/github/vcftools/index.html/metadata.json b/database/github/vcftools/index.html/metadata.json deleted file mode 100644 index 02f54fa1c..000000000 --- a/database/github/vcftools/index.html/metadata.json +++ /dev/null @@ -1,21 +0,0 @@ -{ - "parser": "github", - "uid": "github/vcftools/index.html", - "url": null, - "data": { - "title": "VCFtools", - "url": "https://vcftools.github.io/index.html", - "credit": [ - "Adam Auton", - "Petr Danecek", - "Tony Marcketta" - ], - "tags": [ - "high-throughput-sequencing", - "variant-aggregation/summarization", - "wgs-analysis" - ], - "description": "a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.", - "timestamp": "2022-07-18 17:47:26.260239" - } -} \ No newline at end of file diff --git a/database/github/vpc-ccg/calib/metadata.json b/database/github/vpc-ccg/calib/metadata.json index d56ad6653..3bf9177b6 100644 --- a/database/github/vpc-ccg/calib/metadata.json +++ b/database/github/vpc-ccg/calib/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/vpc-ccg/calib", - "url": null, + "url": "https://github.com/vpc-ccg/calib", "data": { "title": "calib", "url": "https://github.com/vpc-ccg/calib", diff --git a/database/github/weizhongli/cdhit/metadata.json b/database/github/weizhongli/cdhit/metadata.json index d57c18e3d..648e80c3c 100644 --- a/database/github/weizhongli/cdhit/metadata.json +++ b/database/github/weizhongli/cdhit/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/weizhongli/cdhit", - "url": null, + "url": "https://github.com/weizhongli/cdhit", "data": { "title": "cd\u2011hit", "url": "https://github.com/weizhongli/cdhit", diff --git a/database/github/wiki/Install-macs2/metadata.json b/database/github/wiki/Install-macs2/metadata.json index 7958e1c9e..897b685da 100644 --- a/database/github/wiki/Install-macs2/metadata.json +++ b/database/github/wiki/Install-macs2/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/wiki/Install-macs2", - "url": null, + "url": "https://github.com/taoliu/MACS", "data": { "title": "MACS2", "url": "https://github.com/taoliu/MACS/wiki/Install-macs2", diff --git a/database/github/williamjameshandley/fgivenx/metadata.json b/database/github/williamjameshandley/fgivenx/metadata.json index d01ece611..4d1b3bc11 100644 --- a/database/github/williamjameshandley/fgivenx/metadata.json +++ b/database/github/williamjameshandley/fgivenx/metadata.json @@ -48,5 +48,6 @@ ], "timestamp": "2022-07-17 17:15:51.474703", "avatar": "https://avatars.githubusercontent.com/u/3708486?v=4" - } + }, + "html_url": "https://github.com/handley-lab/fgivenx" } \ No newline at end of file diff --git a/repos.txt b/repos.txt index a496104f9..083e08ac9 100644 --- a/repos.txt +++ b/repos.txt @@ -11,6 +11,7 @@ gitlab/random-quintessence/random-quintessence gitlab/gmamon/MAMPOSSt gitlab/ezlab/busco gitlab/cracklet/cracklet +gitlab/ProjectRHEA/flowsolverrhea gitlab/octopus-code/octopus gitlab/andrea-tango/ficos gitlab/picos-api/picos @@ -20,42 +21,59 @@ gitlab/metafundev/metafun gitlab/ztzou/phydl gitlab/BioimageInformaticsGroup/openphi gitlab/LouisLab/PiVR +gitlab/ags-data-format-wg/ags-python-library gitlab/pipe3d/pyPipe3D gitlab/joseaher/astroplotlib +gitlab/aegge/comet-emu gitlab/eleonoraalei/exo-mercat-gui gitlab/Molcas/OpenMolcas gitlab/bu_cnio/vulcanspot gitlab/thartwig/asloth gitlab/ffaucher/hawen +gitlab/InspectorCell/inspectorcell gitlab/gims-developers/gims gitlab/astron-idg/idg gitlab/moerman1/fhi-cc4s gitlab/etienne.behar/menura +gitlab/multigris/mgris gitlab/RKIBioinformaticsPipelines/QCumber +gitlab/petsc/petsc gitlab/rki_bioinformatics/purple gitlab/rki_bioinformatics/IDeFIX gitlab/rki_bioinformatics/HiLive2 gitlab/eduardo-vitral/balrogo gitlab/vibes-developers/vibes +gitlab/AstroVian/bmarxiv +gitlab/jesseds/apav gitlab/project-dare/dare-platform gitlab/ostrokach/proteinsolver gitlab/magnumpi/magnumpi gitlab/gpagano/lensinggw +gitlab/permafrostnet/teaspoon gitlab/ampere2/metalwalls gitlab/remram44/taguette gitlab/jason-rumengan/pyarma +gitlab/esa/pyxel gitlab/andreas.andrusch/paipline gitlab/german.tischler/libmaus2 gitlab/german.tischler/biobambam2 gitlab/mbiagetti/persistent_homology_lss +gitlab/fibreglass/pivc +gitlab/dglaeser/fieldcompare gitlab/sevecekp/sph gitlab/souvlaki/thalassa +gitlab/programgreg/tagginglatencyestimator +gitlab/mcfuman/SpectraPy gitlab/fduchate/predihood gitlab/mainlabwsu/bims gitlab/imoralc/malu-ifs-visualization-tool gitlab/treangenlab/emu +gitlab/treangenlab/vulcan gitlab/ChemBioHub/tpmap +gitlab/ENKI-portal/ThermoEngine +gitlab/ENKI-portal/vaporock gitlab/chrjan/seq-seq-pan +gitlab/remikz/nccmp gitlab/clairedavies/sedbys gitlab/loic.cg.rossi/pymiedap gitlab/jerrytheo16/exoplanet @@ -64,20 +82,31 @@ gitlab/aroffringa/wsclean gitlab/aroffringa/aoflagger gitlab/vincent-sater/umigen gitlab/chjordan/sslf +gitlab/leelamichaels/Burning_Arrow +gitlab/leelamichaels/Infinity +gitlab/leelamichaels/Elysium +gitlab/leelamichaels/Tranquillity +gitlab/leelamichaels/Omega gitlab/casi-project/casi-3d gitlab/casi-project/casi-2d +gitlab/dsbowen/conditional-inference gitlab/aceteam.kaist/ACE-Molecule gitlab/elsi_project/elsi_interface +gitlab/wpettersson/kep_solver gitlab/geekysquirrel/bigx gitlab/polmag/PORTA gitlab/dalton/dalton +gitlab/mauricemolli/petitRADTRANS github/rabrahm/zaspe github/rabrahm/ceres +github/databio/GenomicDistributions github/jiujiezz/tsnad github/ester-project/ester github/fastpm/fastpm github/jakobherpich/pyICs github/Someone789/galax2d +github/iipharma/pharmamind-molminer +github/valentineap/pyprop8 github/twopin/CAMP github/kkjawz/coref-ee github/williamjameshandley/anesthetic @@ -86,17 +115,21 @@ github/barentsen/dave github/barentsen/k2flix github/PolymerGuy/recolo github/ekaterinailin/AltaiPony -github/csbioinfopk/iSumoK-PseAAC +github/stillwater-sc/universal github/evanoconnor/GR1D +github/wdecoster/nanoQC github/wdecoster/nanolyse github/wdecoster/nanofilt github/wdecoster/nanocomp +github/wdecoster/NanoComp github/wdecoster/nanopack github/wdecoster/nanoget github/wdecoster/NanoPlot github/wdecoster/nanomath +github/wdecoster/chopper github/wdecoster/nano-snakemake github/wdecoster/nanostat +github/lsncibb/microbiomeGWAS github/upb-lea/openmodelica-microgrid-gym github/upb-lea/gym-electric-motor github/cobilab/RFSC @@ -115,6 +148,7 @@ github/dcorre/otrain github/ynop/audiomate github/GabrielaCR/AGNfitter github/nsoranzo/sspace_basic +github/riatelab/osrm github/jdswinbank/Comet github/adigenova/wengan github/toddy15/medicalterms @@ -140,6 +174,8 @@ github/SimonPfeifer/cows github/ArnaudCassan/microlensing github/fwhigh/stellar-locus-regression github/esperlman/JetCurry +github/tolkit/telomeric-identifier +github/BioHPC/MegaD github/astromb/PICsar2D github/cosmo-ethz/hide github/cosmo-ethz/seek @@ -147,12 +183,17 @@ github/cosmo-ethz/CosmoHammer github/DarkQuestCosmology/dark_emulator_public github/Kuifje02/vrpy github/nlesc-dirac/sagecal +github/Ge-Lab/USAT github/tensorflow/tensorflow github/ZhaiLab-SUSTech/FLEPSeq +github/single-cell-genetics/cellsnp-lite +github/maickrau/MBG +github/maickrau/GraphAligner github/ocean-eddy-cpt/gcm-filters github/leraman/Hopla github/christopherburke/tess-point github/iquasere/UPIMAPI +github/gmbrandt/xwavecal github/gmbrandt/HTOF github/spicy-oil/hfs_fit github/bio-phys/BioEn @@ -167,6 +208,7 @@ github/dmey/synthia github/spinicist/riesling github/hcdenbakker/sepia github/hcdenbakker/SalmID +github/natir/rustyread github/natir/yacrd github/pytorch/vision github/parklab/LiRA @@ -175,19 +217,26 @@ github/ideasrule/platon github/JDabringhausen/BiPoS1 github/onnela-lab/beiwe-backend github/ndrakos/ICICLE +github/dazhwu/pydynpd +github/LangeLab/SQuAPP github/sdnjly/WSDL-AD github/minkailin/stratsi github/FSEC-Photovoltaics/pvrpm-lcoe github/isoverse/isoreader github/chrisaberson/BetterReg +github/XGI-MSU/PyIMRPhenomD +github/XGI-MSU/WDMWaveletTransforms +github/zheng-lh/UBER github/bmvdgeijn/WASP github/ericagol/TTVFaster github/Pas-Kapli/mptp github/byuflowlab/GXBeam.jl +github/BiomedSciAI/fuse-med-ml github/VeinsOfTheEarth/rabpro github/vincentvaneylen/k2photometry github/phenology/cgc github/surf-eds/one-button-compute +github/lberaldoesilva/naif github/rferdman/afr github/jeffzhen/omnical github/vprusso/toqito @@ -196,6 +245,7 @@ github/mwhosek/extlaw_H18 github/JSB-UCLA/scPNMF github/jamescasbon/PyVCF github/debbiemarkslab/plmc +github/D-Crake/HEADSS github/egpbos/barcode github/CHRF-Genomics/Paratype github/jbuisine/macop @@ -223,9 +273,12 @@ github/theislab/scanpy github/atomneb/AtomNeb-py github/CosmoStat/shapepipe github/CosmoStat/Glimpse +github/CosmoStat/score +github/CosmoStat/mccd github/eScatter/pyelsepa github/cjbarrie/academictwitteR github/jczarnowski/DeepFactors +github/pavanvyn/triple-stability github/JelfsMaterialsGroup/stk github/jarvist/Julia-Phonons github/gogrean/PyXel @@ -239,18 +292,25 @@ github/kadyb/rgugik github/MRCIEU/metaboprep github/MRCIEU/PHESANT github/cistib/origami +github/LoganAMorrison/Hazma github/HenrykHaniewicz/PSRVoid github/AusSRC/SoFiAX github/icb-dcm/pyabc github/anuwu/DAGN-Blindtest github/anuwu/GOTHIC github/entangled/entangled +github/SwiftVISA/SwiftVISASwift github/OpenGene/fastp github/OpenGene/fastv github/geospace-code/h5fortran +github/polca/unfold +github/JianjunTan-Beijing/LPI-CSFFR +github/callendeprieto/ferre github/matthiasfabry/spinOS github/lijing28101/maize_pyrpipe +github/mkelley/calviacat github/mkelley/zchecker +github/karlotness/adrt github/cancerit/alleleCount github/OrlandoLam/SAMT github/cl3425/Clairvoyance @@ -268,10 +328,14 @@ github/oschwengers/bakta github/hillerlab/GenomeAlignmentTools github/yangxiaolinyn/Lemon github/AstraZeneca/kallisto +github/johnschwenck/bp github/zblz/naima github/vojtech-sidorin/quickclump github/mscroggs/symfem +github/IPK-BIT/divbrowse +github/cumbof/honto github/fredstro/hilbertmodgroup +github/MaudeDavidLab/GMEmbeddings github/Magritte-code/Magritte github/ejhigson/nestcheck github/ejhigson/perfectns @@ -286,28 +350,44 @@ github/zd1/telseq github/MoreiraLAB/mensadb-open github/MoreiraLAB/or github/cadop/seg1d +github/msaland/THInCR-Suite github/smoh/kinesis github/luizfelippesr/galmag github/luizfelippesr/magnetizer +github/migp11/pyfastcore github/pni-lab/mlconfound github/holmescao/ANTS_marking_and_analysis_tools +github/Dfupa/meTAline github/ivastar/clear github/elwinter/nnde github/PENTACLE-Team/PENTACLE +github/rzellem/EXOTIC github/lyf222/alpconv +github/fkiwy/unTimely_Catalog_explorer +github/fkiwy/Finder_charts github/fkiwy/AstroToolBox -github/iopenshell/ezSpectrum github/mdsteiner/EFAtools +github/exobssim/rapoc-public github/azizka/IUCNN github/BioGearsEngine/core +github/Hoecker-Lab/atligator +github/mlinderm/npsv +github/PNNL-m-q/mza +github/ylxu05/HN-PPISP github/DrDaveShaw/INCHEM-Py github/SJLeo/FFSD +github/flyaflya/causact github/rudeboybert/forestecology github/msm550/DMATIS github/bommert/stabm github/remi-adam/minot +github/peikuan/WBBC +github/surhh/nfitsview +github/javicarron/mtneedlet +github/pymedphys/pymedphys github/mchalela/GriSPy github/hsergi/Roman_Coronagraph_ETC +github/jonathanHuwP/CrystalGrowthTracker github/Yomguithereal/talisman github/caseyjlaw/tpipe github/caseyjlaw/rtpipe @@ -317,11 +397,13 @@ github/t-brandt/orvara github/t-brandt/acorns-adi github/grazianoucci/game github/grazianoucci/cosmic_variance +github/quantling/pyndl github/mariogrs/Simfast21 github/isovic/graphmap github/ashleefv/ACEInhibPKPD github/firedrakeproject/gusto github/firedrakeproject/firedrake +github/WangLabTHU/DeSP github/simd-everywhere/simde github/mcfrith/tandem-genotypes github/mcfrith/dnarrange @@ -329,7 +411,11 @@ github/faircloth-lab/phyluce github/jbrakensiek/CORBITS github/dawolfgang/MRrelation github/carpyncho/carpyncho-py +github/ArgonneCPAC/diffmah +github/ArgonneCPAC/diffstar +github/ArgonneCPAC/dsps github/jharno/cubep3m +github/ianfhunter/GNOLL github/atakan/KeplerSolver github/AlphonsG/Rainbow-Optical-Flow-For-ALI github/vimc/dettl @@ -339,7 +425,9 @@ github/lime-rt/lime github/AstrobioMike/GToTree github/mbhall88/rasusa github/NielsenBerkeleyLab/sconce +github/thachnguyen/CRISPRnano github/GeoffDuniam/FITS-Code-Examples +github/CMU-SAFARI/BLEND github/mofanv/darknetz github/vgteam/vg github/vgteam/vg#vg @@ -352,6 +440,8 @@ github/thetisproject/thetis github/AllenInstitute/bmtk github/hpgem/nanomesh github/ylab-hi/ScanITD +github/ylab-hi/ScanExitronLR +github/JensUweUlrich/ReadBouncer github/mattpitkin/psrqpy github/mattpitkin/lintegrate github/ANTsX/ANTs @@ -363,14 +453,17 @@ github/koenderks/jaspAudit github/genouest/biomaj-daemon github/genouest/biomaj-cli github/pyspeckit/pyspeckit +github/open2c/pairtools github/donaldRwilliams/GGMnonreg github/donaldRwilliams/BGGM github/mpc-bioinformatics/CalibraCurve +github/mlarichardson/CosmosCanvas github/mlarichardson/ramses2hsim github/neuralgraphs/diman github/IMS-MAXIMS/openMAXIMS github/rickhelmus/patRoon github/moble/GWFrames +github/moble/scri github/kpenev/poet github/poldracklab/nitransforms github/poldracklab/mriqc @@ -381,9 +474,11 @@ github/abonaldi/TRECS github/tariqdaouda/CAMAP github/hallamlab/TreeSAPP github/reality/klarigi +github/doriancazeneuve/ODNet github/max0x7ba/atomic_queue github/jpahlers/LASR github/OxES/k2sc +github/tmcclintock/cluster_toolkit github/tmcclintock/AReconstructionTool github/synchrofit/synchrofit github/Narayana-Rao/SAR-tools @@ -397,7 +492,9 @@ github/su2code/SU2 github/alexander-shen/rtest github/wvanzeist/riroriro github/getzlab/rnaseqc +github/kavir1698/EvoDynamics.jl github/FiorenSt/AutoSourceID-Light +github/liuhao-cn/fastSHT github/jeremysanders/dsdeproj github/jeremysanders/ggm github/jeremysanders/mbproj2 @@ -407,10 +504,13 @@ github/jeremysanders/xspec_emcee github/MD-Studio/MDStudio github/MD-Studio/cerulean github/MD-Studio/cerise +github/bic-nirrh/precocity github/bertrandplez/Turbospectrum2019 github/flemingtonlab/SpliceV +github/HITS-AIN/GPCC.jl github/HITS-AIN/PINK github/MNiwano/Eclaire +github/MOSAICS-NIH/MOSAICS github/ismaelpessa/PyMUSE github/TPI-Immunogenetics/igmat github/climate-machine/Oceananigans.jl @@ -420,6 +520,7 @@ github/WGLab/InterVar github/philres/catfishq github/philres/ngmlr github/Martinsos/edlib +github/xinyiguan/py2lispIDyOM github/nlesc-ave/ave-rest-service github/XuhanLiu/DrugEx github/ncbi/vadr @@ -428,6 +529,7 @@ github/ncbi/SKESA github/ncbi/BAMscale github/ncbi/ngs github/ncbi/sra-tools +github/ncbi/datasets github/ncbi/igblast github/ncbi/TPMCalculator github/RafiKueng/SpaghettiLens @@ -440,10 +542,13 @@ github/Sulstice/cocktail-shaker github/virgesmith/neworder github/rajeshrinet/pystokes github/bow/fsnviz +github/bow/crimson github/engyasin/Offline_MOT +github/tkonolige/city2ba github/RealTimeGenomics/rtg-tools github/coccoinomane/zelda github/coccoinomane/song +github/shergreen/SatGen github/jamesaird/FAST github/mjuric/galfast github/auranic/ClinTrajan @@ -455,19 +560,25 @@ github/jonathansick/starfish github/jonathansick/MoAstro github/C-Briddon/SELCIE github/vavrines/Kinetic.jl +github/theia-dev/Qiber3D github/ziyewang/MetaBinner github/ziyewang/ARG_SHINE github/galtay/sphray github/galtay/urchin -github/zhwm/SparsePro_Paper +github/ebmonson/2DFFTUtils-Module +github/Beuth-Erdelt/DBMS-Benchmarker +github/sosl/H-FISTA github/meenakshi-kushwaha/mmaqshiny github/connectomicslab/connectomemapper3 github/cmzmasek/forester github/GalletFlorian/TATOO github/aconley/simple_cosfitter github/aconley/mbb_emcee +github/tlancian/bio_cs github/sibirrer/hierArc github/sibirrer/lenstronomy +github/sibirrer/psfr +github/stinefm/relsad github/kuadrat/data_slicer github/jradcliffe5/multi_self_cal github/mazzalab/pyntacle @@ -477,12 +588,12 @@ github/rodluger/planetplanet github/rodluger/starry_process github/Yida-Lin/libxdf github/light-curve/light-curve +github/ggonnella/fastsubtrees github/ggonnella/gfapy github/ggonnella/rgfa github/nanoporetech/qcat github/nanoporetech/pychopper github/nanoporetech/scrappie -github/nanoporetech/index.html# github/nanoporetech/pomoxis github/nanoporetech/tombo github/nanoporetech/flappie @@ -490,14 +601,17 @@ github/nanoporetech/megalodon github/nanoporetech/pinfish github/nanoporetech/medaka github/nanoporetech/ont_fast5_api +github/pydemull/activAnalyzer github/research-software-directory/research-software-directory github/zpenoyre/CausticFrog github/zpenoyre/OoT github/tudelft3d/3dfier github/rkiman/wdwarfdate github/shengjin/Nii +github/jacksund/simmate github/ouyang-lab/PRAS github/r-cas/caracas +github/DavidT3/XGA github/LucaMalavolta/CCFpams github/LucaMalavolta/PyORBIT github/brian-lau/MatlabAUC @@ -508,10 +622,12 @@ github/katholt/Kleborate github/HajimeKawahara/exojax github/HajimeKawahara/sot github/HajimeKawahara/juwvid +github/dkoslicki/TAMPA github/changhoonhahn/pySpectrum github/mlpack/mlpack github/rjtanner/StarburstPy github/villrv/SuperRAENN +github/JuliaHEP/UnROOT.jl github/yaml2sbml-dev/yaml2sbml github/achaikova/frbmclust github/dwkim78/ASTRiDE @@ -526,10 +642,11 @@ github/srdc/onfhir github/matteolucchini1/BHJet github/ocxtal/minialign github/jianghuaijie/scLRTC +github/ToHanwei/Genome2OR github/morriscb/The-wiZZ github/ladsantos/p-winds github/ladsantos/flatstar -github/vcftools/index.html +github/tessgi/tvguide github/cog-imperial/entmoot github/cog-imperial/suspect github/cog-imperial/GPdoemd @@ -541,6 +658,7 @@ github/HWang-Summit/HCGrid github/bhi-kimlab/StressGenePred github/moscibrodzka/ipole github/gagneurlab/drop +github/vferat/pycrostates github/stamatak/ExaML github/stamatak/AxPcoords.dist github/davtsang/slimplectic @@ -549,9 +667,11 @@ github/compomics/DeepLC github/compomics/COSS github/compomics/xilmass github/dlakaplan/pulsarsurveyscraper +github/pandegroup/openmm github/KiranLDA/PAMLr github/BartoszBartmanski/StoSpa2 github/temuller/piscola +github/temuller/hostphot github/NarlikarLab/exoDIVERSITY github/mgalardini/pyseer github/xiaotiand/FunFor @@ -585,23 +705,33 @@ github/saeyslab/CytoNorm_Figures github/shbhuk/mrexo github/shbhuk/barycorrpy github/Quantum-Dynamics-Hub/libra-code +github/MIAnalyzer/MIA +github/sstadick/perbase +github/ZJUFanLab/bulk2space github/ZJUFanLab/scTITANS github/SunilAnandatheertha/PXO +github/JulianKarlBauer/mechkit github/zarr-developers/zarr-python github/chandra-marx/marxs github/duetosymmetry/qnm +github/rivasiker/PhaseTypeR github/tnakazato/priism github/lrnv/cort github/basp-group/sopt github/basp-group/Optical-Interferometry-Trilinear github/basp-group/SARA-dimensionality-reduction +github/basp-group/Puri-Psi github/basp-group/purify github/basp-group/SARA-PPD github/lydialucchesi/Vizumap +github/bluefoxr/COINr +github/DLR-RM/BlenderProc github/lammps/lammps +github/fforster/delight github/reproducible-biomedical-modeling/Biosimulations github/telatin/covtobed github/telatin/qax +github/telatin/bamtocov github/telatin/seqfu2 github/ConorMacBride/mcalf github/gperezs/StarcNet @@ -615,9 +745,12 @@ github/SCM-NV/qmflows-namd github/SCM-NV/qmflows github/SCM-NV/pyZacros github/tcassanelli/pywpf +github/napakalas/casbert +github/Merck/pkglite github/Merck/BioPhi github/arq5x/lumpy-sv github/arq5x/grabix +github/arq5x/poretools github/arq5x/bedtools2 github/TransDecoder/wiki github/nnssa/gallumi_public @@ -626,8 +759,10 @@ github/ChristopherWilks/megadepth github/Sydney-Informatics-Hub/OmixLitMiner github/loneknightpy/idba github/stemangiola/tidyHeatmap +github/AnthonyOfSeattle/pyAscoreValidation github/bihealth/sodar_core github/JuliaSmoothOptimizers/DCISolver.jl +github/JuliaSmoothOptimizers/PDENLPModels.jl github/thomasorb/orbs github/thomasorb/orcs github/benstahl92/deepSIP @@ -636,37 +771,49 @@ github/jan-rybizki/Galaxia_wrap github/jan-rybizki/gdr2_completeness github/jan-rybizki/Chempy github/EOSC-LOFAR/lofar-ld +github/davidpamos/MultiModes github/ewanbarr/peasoup github/pandas-dev/pandas github/JanCBrammer/biopeaks +github/eleniadam/npgreat +github/yymao/abundancematching github/keck-datareductionpipelines/MosfireDRP github/varlociraptor/varlociraptorhub.io github/ArtificialStellarPopulations/ArtPop github/DeltaRCM/pyDeltaRCM github/gkulkarni/QLF +github/statgen/popscle +github/statgen/demuxlet github/statgen/Minimac4 github/martibosch/detectree github/AdmiralenOla/Scoary github/fripon/freeture github/mischaschirmer/nebular +github/TNEL-UCSD/autolfads-deploy github/Rohit-Kundu/ET-NET_Covid-Detection github/rbturnbull/ausdex github/cboursnell/crb-blast github/astrobrent/mappings github/astrobrent/itera +github/wasserman-group/pyCADMium github/HHTpy/HHTpywrapper github/reizio/reiz.io github/DICP1810/SpotLink +github/DICP1810/ComMap github/A-Davies/LensCNN github/abatten/fruitbat +github/cgrudz/DataAssimilationBenchmarks.jl github/jdonnert/WVTICs github/adamgayoso/totalVI_reproducibility github/mikhailklassen/protostellar_evolution github/PathwayCommons/grounding-search github/sczesla/PyAstronomy +github/FofanovLab/mtsv_tools github/fabiopardo/tonic github/fabiopardo/qmap github/PabloVD/21cmDeepLearning +github/PabloVD/HaloGraphNet +github/sebastien-plutniak/archeofrag github/temken/obscura github/temken/DaMaSCUS github/temken/DarkARC @@ -684,6 +831,8 @@ github/astrom-tom/dfitspy github/johncwok/CategoricalTimeSeries.jl github/jdidion/atropos github/LabTranslationalArchitectomics/riboWaltz +github/OpenBioLink/Explorer +github/bokulich-lab/q2-fondue github/qmarcou/IGoR github/dnonatar/Sequoia github/ViennaRNA/RNAblueprint @@ -709,23 +858,33 @@ github/theosanderson/chronumental github/exoclime/THOR github/exoclime/HELIOS github/exoclime/HELIOS-K +github/exoclime/Helios-r2 github/exoclime/VULCAN github/exoclime/FastChem +github/matteobreschi/bajes github/lucaborsato/trades github/daissi/thesias github/hippke/tls github/hippke/PyOSE +github/hippke/pandora github/hippke/wotan +github/hippke/communication github/SeamusClarke/FragMent github/SeamusClarke/BTS +github/pangenome/smoothxg github/Parsl/parsl github/SciLifeLab/TIDDIT +github/fatmasevinck/enetLTS +github/Cadaei-Yuvxvs/OSHy-X github/babelomics/impuSARS github/ParBLiSS/FastANI github/fair-data/fairdatapoint-client github/ryokbys/nap +github/RafaelSdeSouza/qrpca github/epruesse/SINA github/UUDigitalHumanitieslab/texcavator +github/Keck-DataReductionPipelines/KcwiDRP +github/Keck-DataReductionPipelines/KCWI_DRP github/thejackal360/OpenPelt-Public github/PetroFit/petrofit github/mzemp/halogen @@ -750,6 +909,7 @@ github/davidemms/OrthoFinder github/minzastro/unidam github/fair-software/fairtally github/fair-software/howfairis +github/kwkx/IPRP github/QuantEcon/QuantEcon.py github/spacetx/starfish github/bwa-mem2/bwa-mem2 @@ -758,10 +918,14 @@ github/KeplerGO/kadenza github/KeplerGO/k2mosaic github/KeplerGO/K2fov github/lanl/PyBNF +github/lanl/CosmicEmu +github/lanl/GLUE github/lanl/spiner +github/lanl/scico github/xfangcosmo/2DFFTLog github/xfangcosmo/FFTLog-and-beyond github/beckermr/calclens +github/nickk124/RCR github/andreaminio/haplosync github/scipy/scipy github/fair-workflows/NanopubJL @@ -785,13 +949,17 @@ github/EoRImaging/FHD github/dokester/BayesicFitting github/Ramialison-Lab-ARMI/3DCardiomics github/0satoken/Eclairs +github/swagnercarena/ovejero +github/swagnercarena/paltas github/LiuJJ0327/CCPE github/vembrane/vembrane github/jameschapman19/cca_zoo +github/IBMTRostock/GIFT github/interactivereport/OmicsView0 github/csabiu/kstat github/saphir746/BiobankRead-Bash github/yiwenstat/MCPCA_PopGen +github/computational-chemical-biology/ChemWalker github/hoechenberger/questplus github/kd0kfo/cosmology github/HUST-DataMan/FRMC @@ -812,6 +980,7 @@ github/bcgov/bcdata github/snakemake/snakemake github/multiwavelength/redshifts github/multiwavelength/gleam +github/Pranab-JD/LeXInt github/BrianAronson/birankr github/biomedia-mira/istn github/biomedia-mira/masf @@ -823,17 +992,20 @@ github/guangtunbenzhu/NonnegMFPy github/hover2pi/SEDkit github/yuansliu/minirmd github/hmtabernero/SteParSyn +github/DESI-UR/VAST github/BenWibking/quokka github/nonlocalmodels/NLMech github/hishamhm/htop +github/yogi-tud/space_gpu github/glis-glis/loci github/rabix/cwl-format github/Alcampopiano/hypothesize github/niemasd/CoaTran github/ShubhadeepSadhukhan1993/fastSF github/AstroVPK/kali -github/cran/irtplay +github/tbisbas/PDFchem github/robashaw/libecpint +github/SharmaLlama/ticktack github/AA-ALERT/AMBER github/AA-ALERT/AstroData github/AA-ALERT/frbcat-web @@ -853,9 +1025,12 @@ github/wf4ever/astrotaverna github/JLiangLab/TransVW github/AstroUGent/shadowfax github/DLTK/DLTK +github/yair111/AnalyticLC github/ExeClim/Isca github/ryansmcgee/seirsplus +github/TRIQS/solid_dmft github/hongwanliu/DarkHistory +github/martinlackner/abcvoting github/uedaLabR/nanoDoc github/kostergroup/SIMsalabim github/cameron314/concurrentqueue @@ -880,19 +1055,25 @@ github/fccoelho/epimodels github/ArenA-Crowds/Crowds github/d-tear/SIAL github/parallelwindfarms/byteparsing +github/cosimameyer/overviewR github/sibyllema/Fast-Multiscale-Diffusion-on-Graphs github/mtazzari/galario github/mtazzari/uvplot github/mtazzari/binary +github/siavash-saki/tesspy github/sonjageorgievska/CClusTera github/JunTaoLuo/mctreesearch4j github/jfarek/xatlas github/jfarek/alignstats github/weecology/retriever github/tomasstolker/ARTES +github/tomasstolker/pycrires +github/IPIS-XieLei/CNTSeg github/xstarkit/mpi_xstar +github/psheehan/pdspy github/mackelab/sbi github/danhey/maelstrom +github/danhey/echelle github/peterk87/sistr_cmd github/deepmedic/deepmedic github/arangrhie/merfin @@ -901,8 +1082,10 @@ github/nwchemgit/nwchem github/PaulMcMillan-Astro/Torus github/PaulMcMillan-Astro/GalPot github/DrMarc/slab +github/Gaiana/nirdust github/scrook/neuroml-db github/lh3/bioawk +github/lh3/wgsim github/lh3/minimap2 github/lh3/fermi-lite github/lh3/bgt @@ -910,8 +1093,10 @@ github/lh3/seqtk github/lh3/miniasm github/freelawproject/eyecite github/jianlin-cheng/DRCon +github/jonaselgammal/GPry github/Dulab2020/ARMT github/mrtommyb/ktransit +github/QuantumPlasma/SFQEDtoolkit github/online-behaviour/find-journalists github/online-behaviour/machine-learning github/tdaylan/pcat @@ -938,24 +1123,35 @@ github/cwru-pat/cosmograph github/cwru-pat/cmb-multipole_vectors github/dfujim/bfit github/OncoRNALab/CiLiQuant +github/wiederm/transformato github/ariedel/lacewing github/TianlaiProject/tlpipe github/AbeelLab/lorikeet +github/bancaditalia/black-it github/pfaucon/PBSIM-PacBio-Simulator github/ProjectPyRhO/PyRhO +github/morispi/LRez +github/keatonb/Pyriod +github/keatonb/TESS_PRF github/LindleyLentati/Cobra github/traja-team/traja github/widdowquinn/pyani +github/kevin218/Eureka github/tinglabs/scAIDE github/fraserw/TRIPPy github/andersen-lab/html github/andersen-lab/ivar +github/ABard0/MDGF-MCEC +github/csuhjhjhj/GCNCMI github/afeinstein20/stella github/afeinstein20/eleanor github/mengyao/Complete-Striped-Smith-Waterman-Library github/cdslaborg/paramonte +github/blind-contours/CVtreeMLE github/VMBoehm/MADLens github/indrops/indrops +github/chocoteam/choco-solver +github/nickelnine37/pykronecker github/meinardmueller/synctoolbox github/meinardmueller/libfmp github/nextstrain/auspice @@ -970,6 +1166,7 @@ github/wmglab-duke/ascent github/SWIFTSIM/emulator github/shihyuntang/igrins_rv github/LucaJRossi/NIGO +github/inrae/RCaNmodel github/tool-bin/ukbcc github/MCTwo/MCMAC github/alexdobin/STAR @@ -977,6 +1174,7 @@ github/bpp/bpp github/orcasgit/python-fitbit github/KIT-MBS/pyREX github/fhcrc/seqmagick +github/JieZheng-ShanghaiTech/PiLSL github/joe-antognini/kozai github/AndreaCaldiroli/ATES-Code github/rasg-affiliates/healvis @@ -986,14 +1184,19 @@ github/dtanoglidis/DeepShadows github/leprojetcastor/castor github/igmhub/picca github/igmhub/baofit +github/ICESat2-SlideRule/paper +github/SciOmicsLab/PhenoComb github/weizhongli/cdhit github/nilearn/nilearnhub.io +github/tud-hri/joan github/tud-hri/travia github/debian-tex/biber github/debian-tex/texlive-nonbin +github/pedro-acunha/SHEEP github/EcoJulia/EcologicalNetworks.jl github/EcoJulia/Microbiome.jl github/EcoJulia/SimpleSDMLayers.jl +github/XSLiuLab/Seq2Neo github/brandonckelly/carma_pack github/libdynd/dynd-python github/milicolazo/Pyedra @@ -1001,7 +1204,10 @@ github/metawards/MetaWards github/zachetienne/nrpytutorial github/Multiversario/satcand github/galaxyproject/galaxy-lib +github/cosmostat/pmclib github/cosmostat/CosmoPMC +github/cosmostat/nicaea +github/ronshnapp/MyPTV github/SPARTA-dev/SPARTA github/MRChemSoft/mrchem github/bokeh/bokeh @@ -1019,11 +1225,14 @@ github/sPaMFouR/RedPipe github/indraniel/fqgrep github/cb-geo/mpm github/Muhammad-Arif-NUST/BVP_Pred_Unb +github/cdanielmachado/reframed github/nbarbey/TomograPy github/radio-astro-tools/pvextractor +github/radio-astro-tools/uvcombine github/radio-astro-tools/spectral-cube github/jsh58/Genrich github/umbramortem/nProFit +github/danielemelini/ALMA3 github/SandoghdarLab/PiSCAT github/4dn-dcic/pairix github/PeterBartram/TES @@ -1042,24 +1251,30 @@ github/mikessh/vdjtools github/FourierFlows/GeophysicalFlows.jl github/illumina/pyflow github/maxbernyk/lightcone +github/austinpeel/herculens github/spyder-ide/spyder github/christopherlovell/sengi github/rauschenberger/joinet +github/rauschenberger/transreg github/mkenworthy/exorings github/CityU-AIM-Group/HTD github/pscicluna/precision +github/facebookresearch/faiss github/mriener/gausspyplus github/jo276/EvapMass github/dalya/WeirdestGalaxies github/rhyspoulton/OrbWeaver github/rhyspoulton/WhereWolf +github/abeelen/powspec github/RTIP/artip github/CAMI-challenge/CAMITAX github/bcerutti/Zeltron-code +github/LiesaSalzer/MobilityTransformR github/HingeAssembler/HINGE github/PCMSolver/pcmsolver github/AemulusProject/bias_emulator github/bokunoBike/m6AGE +github/li-yangyang/lotus github/cylammarco/ASPIRED github/cylammarco/WDPhotTools github/gymreklab/GangSTR @@ -1073,9 +1288,11 @@ github/mbursa/disk-models github/mbursa/sim5 github/jfoster17/extinction-distances github/SMTG-UCL/surfaxe +github/SMTG-UCL/ShakeNBreak github/ziotom78/Healpix.jl github/ziotom78/libpolycomp github/ziotom78/dacapo_calibration +github/putonti/virmine github/dynamicslab/pysindy github/ChileanVirtualObservatory/indexing_utfsm github/maayane/catsHTM @@ -1095,11 +1312,13 @@ github/savage13/sacio github/gerddie/maxflow github/jaimedelacruz/stic github/tmux/tmux +github/danielenricocahall/elephas github/lehtiolab/msstitch +github/idruglab/hignn +github/brunettsp/myosothes github/patscott/pippi github/patscott/ddcalc github/patscott/gambit_1.3 -github/LSARP/ProteomicsQC github/biobakery/halla github/chapmanb/bcbio.prioritize github/chapmanb/bcbb @@ -1107,6 +1326,7 @@ github/chapmanb/bcbio.variation github/akcochrane/TEfits github/BasilioRuiz/SIR-code github/bcalden/ClusterPyXT +github/mrempel/geohexviz github/pysat/pysat github/neuroanatomy/reorient github/matchms/matchms @@ -1115,10 +1335,13 @@ github/emossoux/LIFELINE github/johnh2o2/cuvarbase github/nu-radio/NuRadioMC github/florisvb/PyNumDiff +github/kibokov/grumpy +github/mzytnicki/srnaMapper github/mp3guy/ElasticFusion github/vipinagrawal25/MeMC github/BogdanCiambur/PROFILER github/elsner/arkcos +github/dparks1134/RefineM github/kendomaniac/docker4seq github/kendomaniac/rCASC github/cupy/cupy @@ -1126,7 +1349,9 @@ github/OSU-BMBL/IDAM github/WorkflowConversion/CTDConverter github/WorkflowConversion/CTDopts github/agombolay/ribose-map +github/MicGrasso/bigonlight github/RajLabMSSM/echolocatoR +github/minaskar/pocomc github/minaskar/zeus github/minaskar/hankl github/qpv-research-group/solcore5 @@ -1140,6 +1365,7 @@ github/drupke/ifsred github/drupke/ifsfit github/drupke/questfit github/samtools/bcftools +github/samtools/samtools github/samtools/htslib github/samtools/htsjdk github/kdmurray91/axe @@ -1181,6 +1407,8 @@ github/surhudm/aum github/surhudm/savitzky_golay_with_errors github/haoharryfeng/NeuCA github/HajkD/LTRpred +github/torluca/morphofit +github/RavenGan/GR2D2 github/etempel/Bisous github/flosalbizziae/kataegis github/timoast/signac @@ -1205,6 +1433,7 @@ github/kboone/avocado github/mlower/rmnest github/mikesmitka/truvot github/eblur/dust +github/USU-Analytics-Solution-Center/Bruno.jl github/Oftatkofta/cellocity github/caracal-pipeline/caracal github/arabic-digital-humanities/adhtools @@ -1218,7 +1447,10 @@ github/NLESC-JCER/EigenCuda github/NLESC-JCER/Fortran_Davidson github/NLESC-JCER/QMCblip github/msolpera/pyUPMASK +github/wullm/fastdf github/wullm/zwindstroom +github/mrvollger/rustybam +github/mrvollger/fibertools-rs github/puregome/notebooks github/exomishra/kobe github/jendelel/PrankWebApp @@ -1226,22 +1458,30 @@ github/ScialdoneLab/MitoHEAR github/lucydot/effmass github/liulei/volks2 github/ejeschke/ginga +github/winger/hawking_net github/davideamato/NAPLES github/joshspeagle/dynesty +github/lpfworld/DMPNet github/fdebras/ECLIPS3D +github/ComputationalPhysiology/simcardems github/Vini2/GraphBin github/combine-lab/salmon +github/SAIL-Labs/AMICAL github/sarrvesh/cuFFS github/florian-lienhard/MM-LSD github/xenon-middleware/xenon github/xenon-middleware/pyxenon github/kehrlab/PopDel +github/Rocsg/FijiRelax github/mc-imperial/jfs github/mc-imperial/multicore-test-harness github/mc-imperial/gpuverify github/krober10nd/SeismicMesh +github/yukiteruono/pbsim2 github/grant-m-s/astronomicAL github/dtamayo/reboundx +github/LTeinturier/Cloud-Killer- +github/yangfangs/KPP github/yangfangs/test_GFICLEE github/ConnorStoneAstro/AutoProf github/MesserLab/SLiM @@ -1275,6 +1515,7 @@ github/McMahonCosmologyGroup/holosim-ml github/ebellm/pyraf-dbsp github/Ashod/garli github/antoinemarchal/ROHSA +github/ThomasMBury/ewstools github/glenco/lensed github/jdhenshaw/scousepy github/jdhenshaw/SCOUSE @@ -1292,6 +1533,8 @@ github/mishioo/tesliper github/grahambell/pymoc github/GunzIvan28/rMAP github/exafmm/exafmm-t +github/heuermh/dishevelled-bio +github/cistrome/MIRA github/rdpstaff/TaxonomyTree github/rdpstaff/AlignmentTools github/rdpstaff/ReadSeq @@ -1305,6 +1548,7 @@ github/vedantchandra/wdtools github/vreverdy/magrathea-pathfinder github/phillippro/pexo github/phillippro/agatha +github/CederGroupHub/smol github/pymatting/pymatting github/tlverse/hal9001 github/pratheesh3780/grapesAgri1 @@ -1330,14 +1574,18 @@ github/snowformatics/macrobot github/USEPA/nsink github/SKA-INAF/caesar-rest github/ColemanRHarris/mxnorm +github/jkimlab/msPIPE github/jianhuupenn/SpaGCN github/pyro-ppl/pyro +github/annajenul/UBayFS +github/ZjuLiangsl/mmkp github/eggplantbren/Exoplanet github/eggplantbren/RJObject github/eggplantbren/DNest3 github/eggplantbren/DNest4 github/eggplantbren/RMHB github/Climdyn/qgs +github/floodlight-sports/floodlight github/diCenzo-GC/Tn-Core-webserver github/annayqho/TheCannon github/PeterDenton/ANA @@ -1351,27 +1599,43 @@ github/dnafinder/uroccomp github/PynPoint/PynPoint github/PeterKamphuis/FAT github/NeoGeographyToolkit/StereoPipeline +github/CSUBioGroup/GraphLncLoc github/netsiphd/netrd +github/lucabaldini/ixpeobssim github/argiopetech/base github/vpc-ccg/svict github/vpc-ccg/calib +github/vpc-ccg/genion github/FelixKrueger/TrimGalore github/dgobbi/vtk-dicom +github/E3SM-Project/gdess github/aneeshnaik/spam github/lantunes/cellpylib github/schlafly/crowdsource github/li-shaochuan/SEDIM +github/LuisScoccola/persistable github/DeepRegNet/DeepReg github/musevlt/origin github/musevlt/muse-psfr github/vincentlab/PyFR github/alphaparrot/ExoPlaSim +github/el2718/FastQSL +github/sfarrens/sf_deconvolve github/sfarrens/sfof github/mbillingr/libgdf +github/nathanael-fijalkow/DeepSynth +github/mdlreyes/void-dwarf-analysis +github/masadcv/FastGeodis +github/TeamPerie/CellDestiny +github/VIB-PSB/MINI-EX github/Ensembl/ensembl-vep github/Ensembl/WiggleTools github/r-spatialecology/shar +github/MartianColonist/POSEIDON +github/simoncasassus/ConeRot +github/marcelauliano/MitoHiFi github/nithyanandan/PRISim +github/podondra/eidein github/podondra/bayesian-sznet github/TriPed-Robot/TriP github/mikegrudic/pytreegrav @@ -1379,7 +1643,9 @@ github/mikegrudic/MakeCloud github/Effective-Quadratures/Effective-Quadratures github/jydu/maffilter github/jydu/physamp +github/olivecha/guitarsounds github/bioinform/somaticseq +github/hildebra/sdm github/adamjermyn/Skye github/icrar/daliuge github/jakeown/astroclover @@ -1391,13 +1657,18 @@ github/ropensci-org/roblog github/rgerum/pylustrator github/marbl/Mash github/marbl/Krona +github/marbl/Winnowmap github/gerthmicha/wolbachia-mlst github/lanzen/ampliconnoise github/Social-Evolution-and-Behavior/anTraX +github/stevenweaver/seqcomplexity github/astroCV/astroCV github/lasseignelab/CINmetrics +github/LiShuTJ/NDNet github/kiyo-masui/bitshuffle github/logological/gpp +github/agshumate/LiftoffTools +github/mjshao06/pdifFinder github/Imperial-visualizations/Physics-Visualizations github/0xCoto/Virgo github/rordenlab/dcm2niix @@ -1430,18 +1701,23 @@ github/barnabytprowe/imcom github/pezmaster31/bamtools github/atomec-project/atoMEC github/elkebir-group/Jumper +github/max-little/GRAPL github/jonzink/EDI-Vetter github/jonzink/EDI_Vetter_unplugged github/jhparkastro/gpcal +github/insilicomedicine/GENTRL github/backyardworlds/wiseview github/chervias/DustFilaments github/Azeret/galIMF github/scipion-em/scipion-em-continuousflex +github/rmaphoh/AutoMorph github/scikit-image/scikit-image github/dansarie/sboxgates github/SWAT-Sheffield/SAC github/kegiljarhus/pyBEMT +github/ZacharyJia/opsdn github/uclchem/Chemulator +github/xiaofengsong/pHisPred github/csj607/STaRS github/lcpp-org/RustBCA github/fabiorigamonti/bang @@ -1449,6 +1725,7 @@ github/nmslib/hnswlib github/mmp2/megaman github/asmusskar/ALVA github/nhejazi/txshift +github/nhejazi/haldensify github/nhejazi/medoutcon github/Circuitscape/Omniscape.jl github/astrostat/LIRA @@ -1457,6 +1734,7 @@ github/astrostat/Automark github/yanzhanglab/Graph2GO github/astrosmili/smili github/tony-travis/PIQUE +github/dunnkers/fseval github/astronomyk/SimCADO github/darrencroton/sage github/equipeGST/RiboDoc @@ -1471,13 +1749,17 @@ github/forceflow1049/phast github/aspuru-guzik-group/funsies github/gridap/Gridap.jl github/aviadpi/SparseBLS +github/flu-crew/smot github/ferdymercury/amide github/numba/numba github/linDing-groups/Deep-4mCW2V github/YihanWangAstro/SpaceHub github/CosmoLike/CosmoCov +github/webbjj/m2mcluster +github/yuansh3354/CaSee github/arviz-devs/arviz github/vhaasteren/piccard +github/jiwoncpark/baobab github/JannisHoch/copro github/AbbasAlameer/geoCancerPrognosticDatasetsRetriever github/918particle/AskaryanModule @@ -1489,10 +1771,16 @@ github/SegataLab/lefse github/jonschwenk/RivGraph github/ComparativeGenomicsToolkit/cactus github/Pithikos/C-Thread-Pool +github/ELELAB/RosettaDDGPrediction +github/ELELAB/LipidDyn +github/ELELAB/cancermuts github/ELELAB/CAncer-bioMarker-Prediction-Pipeline-CAMPP +github/JanLeppert/GasChromatographySimulator.jl github/ndaniel/fusioncatcher +github/xuanxu/starmatrix github/EnricoCorsaro/DIAMONDS github/EnricoCorsaro/FAMED +github/ericsteinbring/World_Observatory github/infer-actively/pymdp github/FAIR-data-for-CAPACITY/FHIR-to-CAPACITY github/mneeleman/qubefit @@ -1512,6 +1800,10 @@ github/yesint/EnCurv github/JuliaMatrices/BandedMatrices.jl github/JuliaMatrices/LazyBandedMatrices.jl github/JuliaMatrices/BlockBandedMatrices.jl +github/Eventdisplay/Eventdisplay +github/Onogi/VIGoR +github/shinichiroando/sashimi-c +github/shinichiroando/sashimi-w github/Johannes-Sahlmann/pygacs github/guilledufort/EnanoFASTQ github/tvwenger/wisp @@ -1523,6 +1815,7 @@ github/tvwenger/kd github/ruanjue/wtdbg2 github/constantAmateur/SoupX github/kno10/python-kmedoids +github/nemesiscode/radtrancode github/nickhand/pyRSD github/veg/tn93 github/christophuv/PeakBot_example @@ -1531,6 +1824,7 @@ github/djbard/ccogs github/KALMUS-Color-Toolkit/KALMUS github/ryanhausen/fitsmap github/aboucaud/pypher +github/apcamargo/prodigal-gv github/jcibanezm/DustCharge github/MikeSWang/HorizonGRound github/MikeSWang/Harmonia @@ -1540,22 +1834,28 @@ github/mbaes/SpheCow github/robertwissing/EOS github/sbird/fake_spectra github/sbird/GenPK +github/Aarhus-Psychiatry-Research/timeseriesflattener github/ewatercycle/era5cli github/DataIntellSystLab/KARGA github/netrias/rnassist github/mdruett/COCOPLOT github/deeprob/ThioesteraseEnzymeSpecificity github/pvlib/pvlib-python +github/DrJCarson/BoundedCoalescent github/BD2KGenomics/toil github/adammoss/supernovae github/IBM/fold2seq github/phelelani/nf-rnaSeqCount github/phelelani/nf-rnaSeqMetagen +github/fbreitwieser/krakenuniq +github/MIC-DKFZ/HD-BET github/MIC-DKFZ/TractSeg github/vdemichev/DiaNN +github/Xia-Yijie/Xponge github/hemanthpruthvi/PyAstroPol github/afd-illinois/grim github/MolecularAI/DockStreamCommunity +github/jfowkes/pycutest github/ratschlab/metagraph github/matthiaslee/Xmatch github/pnnl/interflow @@ -1567,6 +1867,7 @@ github/barbagroup/geoclaw-landspill github/jteutenberg/downpore github/mary77/scQcut github/rafaeleufrasio/lightning +github/EMBL-Hentze-group/htseq-clip github/gt1/bambamc github/rorybarnes/EqTide github/EGaraldi/ZInCo @@ -1574,12 +1875,18 @@ github/JEFworks-Lab/STdeconvolve github/nlesc/embodied-emotions-scripts github/nlesc/scriptcwl github/linqs/psl +github/anuradhawick/LRBinner github/SpaceML/GalaxyGAN github/drcandacemakedamoore/cleanX +github/Hoohm/CITE-seq-Count github/pwry/lextes +github/UM-Bridge/umbridge +github/lu-yizhou/ClusterSeg github/adrijd/beamconv github/silburt/DeepMoon +github/viromelab/tracespipe github/AFD-Illinois/ebhlight +github/AFD-Illinois/iharm3d github/COINtoolbox/ActSNClass github/COINtoolbox/DRACULA github/COINtoolbox/CosmoPhotoz @@ -1598,6 +1905,7 @@ github/abelson-lab/smMIP-tools github/morpheus-project/morpheus github/tfwillems/HipSTR github/danielreardon/scintools +github/marziarivi/RadioLensfit2 github/nrao/UniPOPS github/ashleychontos/pySYD github/carlosborca/CrystaLattE @@ -1613,6 +1921,7 @@ github/Planet-AI-GmbH/tfaip github/chfeder/turbulence_generator github/zonca/python-qucs github/zonca/dst +github/jmejia8/Metaheuristics.jl github/ADThomas-astro/oxaf github/Acellera/htmd github/jpcoles/mosaic @@ -1632,11 +1941,14 @@ github/joergbuchwald/joss_ogs6py_VTUinterface github/blackrim/phyutility github/mirnylab/pairtools github/mirnylab/cooler +github/reggiebernardo/PTAfast github/zhanglabtools/CASAVA github/ukoethe/vigra +github/freesurfer/freesurfer github/abs-tudelft/variant-calling-at-scale github/CFSAN-Biostatistics/SeroTools github/roban/CosmoloPy +github/watts-dev/watts github/ernewton/tellrv github/rvaser/bioparser github/rvaser/spoa @@ -1644,16 +1956,20 @@ github/rvaser/sword github/rvaser/thread_pool github/rvaser/rampler github/binzhulab/SUITOR +github/kathlandgren/SWAMPE github/chrishales/pieflag github/henrikju/resolve +github/Qiskit/rustworkx github/EISy-as-Py/hardy github/nicolet5/DiffCapAnalyzer github/aobr/gsf github/GRIT-RBSim/GRIT github/medema-group/bigslice github/egonw/bacting +github/stefanoMP/massiveGST github/mattyowl/astLib github/ageller/firefly +github/SDXorg/pysd github/mirochaj/ares github/mirochaj/sedop github/Samreay/Marz @@ -1671,11 +1987,14 @@ github/FlowModelingControl/flowtorch github/lgrcia/prose github/silx-kit/pyFAI github/openmm/openmm +github/shangguandong1996/FindIT2 github/JuliaPlots/Makie.jl github/ggmichael/craterstats github/andreasmang/claire github/gabraham/flashpca github/biocore/emperor +github/biocore/unifrac-binaries +github/biocore/deblur github/biocore/sortmerna github/biocore/scikit-bio github/biocore/unifrac @@ -1683,6 +2002,7 @@ github/VarStarDetect/varstardetect github/EddyRivasLab/hmmer github/JGCRI/ambrosia github/JGCRI/rfasst +github/JGCRI/rmap github/JGCRI/plutus github/kritiyer/AngioNet github/scrm/scrmhub.io @@ -1690,10 +2010,13 @@ github/plazar/coast_guard github/plazar/TOASTER github/EpistasisLab/tpot github/EpistasisLab/regens +github/desihub/fastspecfit +github/desihub/desitarget github/joglekara/VlaPy github/duffell/Disco github/duffell/RT1D github/MDAnalysis/mdanalysis +github/henrycousins/gspa github/anmolter/XLUR github/pyxnat/pyxnat github/jpierel14/sntd @@ -1712,6 +2035,7 @@ github/dpalmasan/TRUNAJOD2.0 github/PyPSA/atlite github/tekpinar/correlationplus github/ucl-exoplanets/pylightcurve +github/ucl-exoplanets/TauREx3_public github/ucl-exoplanets/ExoTETHyS github/ucl-exoplanets/ExoGAN_public github/ruta-k/uGMRT-pipeline @@ -1723,6 +2047,7 @@ github/shenlab-sinai/ngsplot github/skyfielders/python-skyfield github/gwastro/pycbc github/dparkins/CosmoNest +github/pyccel/pyccel github/rambaut/jebl2 github/exosports/transit github/exosports/MARGE @@ -1736,29 +2061,37 @@ github/barnesgroupICL/Driftfusion github/ArneTillmann/AuDoLab github/UAMCAntwerpen/LEADD github/pw31/GGchem +github/fkeruzore/panco2 +github/sebastian-zieba/PACMAN github/Bahler-Lab/pyphe github/bulik/ldsc github/mpi4jax/mpi4jax github/casaluca/bolometric-corrections +github/chhylp123/hifiasm github/tbronzwaer/raptor github/seeh/surprise github/smith-chem-wisc/ProteaseGuru github/ProfessorBrunner/rc3-pipeline +github/delphes/delphes github/sahasuparna/DeMoS github/deepsphere/deepsphere-cosmo-tf1 github/arvados/arvados github/RaRe-Technologies/gensim github/longfei8533/SDC +github/CliMA/EnsembleKalmanProcesses.jl github/TomKellyGenetics/graphsim github/sap218/jabberwocky github/Zafiirah13/meercrab github/chemfiles/chemfiles +github/joshuakt/Oxygen-False-Positives github/ExoSim/ExoSimPublic github/VU-BEAM-Lab/GENRE github/astro-friedel/CADRE github/valboz/VBBinaryLensing +github/zhoulinumass/ML-wPBE github/taehoryu/TDEmass github/dentalfloss1/transients-simulations +github/dolaver/calsagos github/leishenggit/CircleBase github/edwardoughton/itmlogic github/xfcui/onn4arg @@ -1770,15 +2103,20 @@ github/xinglunju/pyAmor github/cconroy20/fsps github/icecube/FIRESONG github/icecube/TauRunner +github/icecube/toise github/HillLab/SomaticSiMu +github/gbernstein/pixmappy +github/gbernstein/gbdes github/jollejolles/pirecorder github/genotoul-bioinfo/dgenies +github/JetBrains-Research/spbla github/jakevdp/wpca github/latrop/DECA github/arnauqb/Qwind.jl github/arnauqb/qwind github/JoeMcEwen/FAST-PT github/tresoldi/ngesh +github/ppsp-team/PyNM github/oscaribv/pyaneti github/oscaribv/citlalicue github/oscaribv/exotrending @@ -1786,18 +2124,26 @@ github/beckrob/Photo-z-SQL github/margudo/LSSGALPY github/cgarraffo/StelNet github/ogotoh/spaln +github/cpinte/mcfost +github/cpinte/pymcfost +github/cpinte/casa_cube github/damocles-code/damocles +github/travisseymour/EPICpy github/ahmedmagds/GNUVID github/YuLab-SMU/treeio github/sonwell/biotools +github/sparks-baird/xtal2png github/petigura/terra github/MikeHeiber/Excimontec github/iancze/PSOAP github/iancze/DiskJockey github/MAnalytics/opitools github/MAnalytics/akmedoids +github/egjergo/galcem +github/parkus/ffd github/parkus/fiducial_flare github/parkus/scicatalog +github/firefly-cpp/NiaARM github/aimalz/qp github/ropensci-archive/reviewer github/ropensci-archive/monkeylearn @@ -1815,8 +2161,11 @@ github/leonzheng2/butterfly github/torognes/vsearch github/torognes/swarm github/elixir-luxembourg/daisy +github/tobiasrausch/wally github/tobiasrausch/alfred +github/tobiasrausch/lorax github/dgbowl/yadg +github/bionlplab/GlaucomaNet github/lucian-ilie/DELPHI github/dixonlab/hic_breakfinder github/RudolfCardinal/camcops @@ -1837,6 +2186,7 @@ github/tkerscher/blast github/scottleedavis/googleearthtoolbox github/AdrianA-T/cytomorph github/iobio-zjut/IPTDFold +github/cire-thk/BifacialSimu github/wesleyburr/subMaldi github/SouthGreenPlatform/PyRice github/he2016012996/CABnet @@ -1846,6 +2196,7 @@ github/pysal/pysal github/daler/gffutils github/daler/pybedtools github/sinc-lab/miRe2e +github/matthiasdemuzere/w2w github/adithirgis/pollucheck github/pacificbiosciences/bam2fastx github/astro-datalab/noaosourcecatalog @@ -1889,6 +2240,7 @@ github/mateidavid/fast5 github/natashabatalha/picaso github/natashabatalha/PandExo github/philbull/RadioFisher +github/cnes/EleFits github/BIC-MNI/libminc github/tgrimes/SeqNet github/vsquicciarini/madys @@ -1896,12 +2248,17 @@ github/abs2k12/COCOA github/staphopia/staphopia-paper github/KVSlab/turtleFSI github/DistrictDataLabs/yellowbrick +github/planck-npipe/hillipop +github/planck-npipe/lollipop +github/hydrosolutions/riversCentralAsia github/nanakiksc/zerone github/abacusorg/zeldovich-PLT github/gausspy/gausspy github/abinit/abinit +github/genostats/LowKi github/dingyaozhang/Evitar github/Bonfanti88/MCMCI +github/AMSSwanglab/SpecVar github/sheneman/clearcut github/pytoolz/toolz github/emhuff/Balrog @@ -1913,6 +2270,7 @@ github/Starlink/ORAC-DR github/Starlink/starjava github/Starlink/hds-v5 github/FCS-analysis/multipletau +github/snugel/cas-offinder github/teuben/QAC github/teuben/nemo github/GalacticDynamics-Oxford/Agama @@ -1923,14 +2281,18 @@ github/PDB-REDO/cif-tools github/PDB-REDO/libpdb-redo github/PDB-REDO/density-fitness github/PDB-REDO/dssp +github/tonhingm/PHOTOe-v1 github/tidyverse/glue github/ahoward-cf/ppmap +github/micahvista/MAMnet +github/reznik-lab/MIRTH github/cedrus-opensource/pyxid github/pengweixing/FACT github/dstansby/pfsspy github/Taywee/args github/alexander-pastukhov/bistablehistory github/carlosandrepaes/GaPP +github/txopen/histoc github/danxhuber/galclassify github/danxhuber/evolstate github/fabian-sp/GGLasso @@ -1940,11 +2302,14 @@ github/tramarobin/fctSPM github/gheald/rmclean github/vmplacco/linemake github/ejikeugba/serp +github/ejikeugba/gofcat github/BitSeq/BitSeq +github/calebclass/Shiny-NanoTube github/cinemascience/cinema_snap github/KarrLab/de_sim github/davidebolo1993/TRiCoLOR github/davidebolo1993/VISOR +github/jeschaef/Graph4Med github/arnikz/PIQMIe github/obreschkow/dftools github/spacetelescope/imexam @@ -1957,12 +2322,15 @@ github/spacetelescope/synphot_refactor github/spacetelescope/specviz github/spacetelescope/stginga github/spacetelescope/specview +github/sjbeckett/localcovid19now github/jlenain/flaapluc github/amkram/shusher github/semaphoreP/whereistheplanet github/aranyics/ReDCM github/pokynmr/ipick +github/YesselmanLab/rna_map github/akdeniz-uzay/A-Track +github/SietzeN/glottospace github/cheginit/HyRiver github/lbcb-sci/graphmap2 github/lbcb-sci/racon @@ -1970,19 +2338,24 @@ github/lbcb-sci/raven github/brainglobe/bg-atlasapi github/rae-holcomb/SpinSpotter github/SoFiA-Admin/SoFiA-2 +github/ridgelab/rampAtlas github/ridgelab/ExtRampOnline github/patrickfuchs/buildH +github/LTLA/basilisk github/python-hydro/pyro2 github/qutip/qutip github/jacobmerson/model-traits github/pjcigan/multicolorfits +github/bjmorgan/py-sc-fermi github/NASA-PDS/naif-pds4-bundler github/Kambrian/HBTplus github/cma2015/iwa-miRNA github/UFParLab/aces4 github/yatiml/yatiml +github/NorwegianVeterinaryInstitute/ALPPACA github/SteveMacenski/slam_toolbox github/osallou/cassiopee-c +github/BiodataAnalysisGroup/UMIc github/dvallesp/vortex github/dvallesp/asohf github/jboynyc/textnets @@ -2003,7 +2376,9 @@ github/Michalychforever/AsPy github/lumen-org/lumen github/ElsevierSoftwareX/SOFTX_2020_119 github/neuralhydrology/neuralhydrology +github/CouncilDataProject/speakerbox github/CouncilDataProject/cookiecutter-cdp-deployment +github/rqtl/qtl2 github/dynamics-of-stellar-systems/dynamite_release github/mggg/ecological-inference github/esheldon/ngmix @@ -2015,6 +2390,7 @@ github/comprna/reorientexpress github/comprna/SUPPA github/mmahmoudian/sivs github/neeravkaushal/RIDs-in-WCDs +github/MIT-STARLab/deconfuser github/KULL-Centre/DEERpredict github/pydata/xarray github/Kamuish/archi @@ -2025,9 +2401,11 @@ github/MrOlm/drep github/GRChombo/GRChombo github/brinckmann/montepython_public github/seshnadathur/Revolver +github/siavashk/pycpd github/wtraylor/modular_megafauna_model github/sdrastro/NWelch github/drzeeshanahmed/JWES-Visual +github/jgieseler/solarmach github/Singh-Lab/DeMaSk github/Singh-Lab/uKIN github/linbox-team/linbox @@ -2037,6 +2415,7 @@ github/R-Vessel-X/SlicerRVXLiverSegmentation github/tikk3r/legacystamps github/kennethcarrell/ATARRI github/fury-gl/fury +github/dartoon/galight github/ebachelet/pyLIMA github/COVID-IWG/epimargin github/rhenanbartels/hrv @@ -2045,6 +2424,7 @@ github/christophmschaefer/miluphcuda github/ParaFly/ParaFly github/GenomicParisCentre/toulligQC github/wiki/Install-macs2 +github/Bishop-Laboratory/RLoop-QC-Meta-Analysis-Miller-2022 github/sandmanns/CopyDetective github/freebayes/freebayes github/tariks/peakachu @@ -2053,19 +2433,23 @@ github/ywx649999311/EzTao github/idptools/metapredict github/bio-ontology-research-group/deepgoplus github/SHTOOLS/SHTOOLS +github/yyZhang14/dbEssLnc github/SwissClinicalTrialOrganisation/secuTrialR github/coleygroup/pyscreener github/xcompact3d/Incompact3d github/BGPS/distance-omnibus +github/domenico-simone/rmlst_api github/msalibian/RBF github/NKI-AI/direct github/zgazak/TAP +github/cvbuchem/LavAtmos github/valerio-marra/CalPriorSNIa github/acbecker/hotpants github/IndrajeetPatil/ggstatsplot github/IndrajeetPatil/statsExpressions github/potassco/clingo github/lmfit/lmfit-py +github/refresh-bio/agc github/refresh-bio/whisper github/vwesselkamp/ernie-extension github/daehwankimlab/hisat2 @@ -2081,12 +2465,14 @@ github/cameronliang/BayesVP github/NctuICLab/PredCRP github/IMB-Computational-Genomics-Lab/scGPS github/ThomasEdwardRiley/xpsi-pre-transfer +github/bezuidenhoutmc/SeeKAT github/sensein/etelemetry-client github/sourmash-bio/sourmash github/Julian/jsonschema github/SchmollerLab/Cell_ACDC github/ireis/PRF github/lastz/lastz +github/neuroneural/brainchop github/jeffdaily/parasail-python github/jeffdaily/parasail github/amrex-astro/MAESTRO @@ -2097,12 +2483,16 @@ github/seawander/centerRadon github/seawander/DebrisDiskFM github/abhisrkckl/GWecc github/IMMM-SFA/gamut +github/IMMM-SFA/tell github/IMMM-SFA/mosartwmpy github/ICRAR/libprofit github/ICRAR/ProFit github/ICRAR/shark github/cosmo-epfl/chemiscope +github/RECETOX/RIAssigner +github/RECETOX/MSMetaEnhancer github/imperialchem/mrd-demo +github/tiberioap/grav_waldo github/tzhu-bio/UMI-ATAC-seq github/networkx/networkx github/thegenemyers/DEXTRACTOR @@ -2114,28 +2504,35 @@ github/jupyter/notebook github/AlexanderBartholomaeus/smORFer github/ahwkuepper/mcluster github/vbakis/mrs +github/agsreejith/CONTROL github/rhdtownsend/gyre github/aasensio/sicon github/aasensio/hazel github/SJTU-CGM/ivTerm github/VBlesius/RHRT github/nextflow-io/nextflow +github/bcjaeger/aorsf github/Pizzuti92/MG-MAMPOSSt github/vaexio/vaex github/mikaelLEROY/AxionNS_RayTracing github/bengeof/QPoweredCompound2DeNovoDrugPropMax +github/candebellavita/vkompth github/rgmyr/corebreakout +github/cbio-astar-tools/GeneCloudOmics github/datalad/datalad github/ablab/TandemTools github/ablab/nerpa github/clauswilke/PeptideBuilder github/jw-lin/lightbeam +github/biocircuits/bioscrape github/dankelley/oce github/PyDL/cat-puma github/tcherninceline/PPInteractions github/SNEWS2/snewpy github/CarlosCoba/XookSuut-code github/StephenJHardy/SL1M +github/RosettaCommons/RFDesign +github/RosettaCommons/RoseTTAFold github/tylunel/pvpumpingsystem github/iomega/zenodo-upload github/iomega/paired-data-form @@ -2148,6 +2545,7 @@ github/avigan/SPHERE github/avigan/pyZELDA github/dellytools/delly github/dellytools/sansa +github/copasi/COPASI github/GeneDx/scramble github/tumcms/Open-Infra-Platform github/ismael-mendoza/ShapeMeasurementFisherFormalism @@ -2162,30 +2560,39 @@ github/Trovemaster/exocross github/Trovemaster/TROVE github/Hegghammer/daiR github/wadpac/GGIR +github/perfanalytics/pose2sim github/SterlingYM/astroPIPS +github/Nic5472K/ScientificData2021_HealthGym github/Dfam-consortium/RepeatModeler github/CrowdTruth/CrowdTruth github/jiffyclub/palettable github/stammler/simframe +github/stammler/dustpy github/cmateu/PyMGC3 github/cmateu/galstreams github/icbm-iupui/STAFF github/eggnogdb/eggnog-mapper github/mithun218/GiNaCDE +github/tanner-trickle/EXCEED-DM github/jdeast/EXOFASTv2 github/pkugyf/MST github/chenjj2/forecaster +github/atmos-cloud-sim-uj/PyMPDATA github/atmos-cloud-sim-uj/PySDM github/davek44/Glimmer-MG +github/ccsosa/GOCompare github/N-BodyShop/smooth github/dpseidel/stmove +github/JorenSix/Panako github/ucberkeleyseti/turbo_seti github/ucberkeleyseti/blimpy github/ml-evs/matador github/alejandrobll/py-sphviewer +github/gasparl/possa github/samb8s/PsrPopPy github/openscm/openscm-twolayermodel github/DrafProject/elmada +github/jjmccollum/teiphy github/toros-astro/corral github/toros-astro/astroalign-legacy github/nlesc-nano/swan @@ -2216,11 +2623,14 @@ github/uw-comphys/opencmp github/anwarbio/bioassays github/PaulSt/NGSTrefftz github/potree/PotreeConverter +github/LucyMcGowan/tipr github/kushaltirumala/WaldoInSky github/mpievolbio-scicomp/cancer_sim github/Stuermer/EchelleSimulator github/nboley/idr github/grburgess/popsynth +github/grburgess/ronswanson +github/Robaina/Pynteny github/amerand/CANDID github/amerand/PMOIRED github/amerand/SPIPS @@ -2239,14 +2649,17 @@ github/stedolan/jq github/michaeltouati/ESVM github/pencil-code/pencil-code github/0x0f0f0f/Metatheory.jl +github/MonashSmartStructures/ospgrillage github/cespinosa/pyHIIexplorerV2 github/ParisAstronomicalDataCentre/OPUS github/xavierdidelot/ClonalFrameML github/xavierdidelot/clonalorigin github/mlares/hearsay +github/valeriabonapersona/repair github/csb5/lofreq github/pyomeca/ezc3d github/pyomeca/biorbd +github/pyomeca/biosiglive github/kblin/ncbi-acc-download github/jeffcsauer/arcos_arcospy_information github/Krona/wiki @@ -2260,6 +2673,7 @@ github/wilkelab/Opfi github/afarahi/kllr github/afarahi/PoPE github/afarahi/tatter +github/arjunsavel/SImMER github/lomereiter/sambamba github/jorisparet/partycls github/bmorris3/aesop @@ -2275,19 +2689,24 @@ github/yjx1217/RecombineX github/vcflib/vcflib github/vcflib/bio-vcf github/riogroup/SORA +github/nebblu/ReACT github/feature-engine/feature_engine github/JohannesBuchner/nway github/JohannesBuchner/PyMultiNest github/JohannesBuchner/UltraNest github/JohannesBuchner/BXA github/mjacob1002/Eir +github/jdiasn/lidarSuit +github/AWehrhahn/SME github/expressionanalysis/ea-utils github/PolyChord/PolyChordLite github/gear-genomics/tracy +github/ajwheeler/korg.jl github/UK-Digital-Heart-Project/4Dsegment github/UK-Digital-Heart-Project/4Dsurvival github/chianti-atomic/ChiantiPy github/venkateshgopinath/FAlCon-DNS +github/yrjia1015/CRISPRCasStack github/sapearson/HSS github/eucp-project/storyboards github/eucp-project/atlas @@ -2297,9 +2716,13 @@ github/1313e/PRISM github/TeamLEGWORK/LEGWORK github/drphilmarshall/Pangloss github/drphilmarshall/HumVI +github/pierfied/karmma github/shandley/hecatomb +github/mtakahiro/gsf +github/markheckmann/OpenRepGrid.ic github/astroboylrx/PLAN github/astroboylrx/Rubble +github/n8thangreen/BCEA github/alex-b-davis/gubas github/nevrome/bleiglas github/regonzar/paravt @@ -2318,11 +2741,14 @@ github/Illumina/ExpansionHunterDenovo github/vijayvarma392/binaryBHexp github/pmelsted/pizzly github/RussellJurek/busy-function-fitting +github/prioritizr/wdpar github/bempp/bempp-cl +github/hytrac/amber github/stevengj/nlopt github/colour-science/colour github/bcbio/bcbio.variation.recall github/bcbio/bcbio-nextgen +github/s-abbas/robnptests github/cbottrell/realsim_ifs github/nh13/DWGSIM github/HERA-Team/aipy @@ -2330,17 +2756,21 @@ github/HERA-Team/hera_opm github/DKMS/hapl-o-Mat_WinBin github/kartheikiyer/dense_basis github/ArtRand/signalAlign +github/dsheward-astro/pynaple github/teoxxx/rlos github/dgrun/FateID github/raredd/kmdata +github/free1234hm/CLAM github/realfastvla/rfpipe github/cieslar/Indri github/creaneroDIAS/beamModelTester github/fulcrumgenomics/fgbio +github/JacobBumgarner/VesselVio github/nworbde/dStar github/TommasoRonconi/scampy github/phac-nml/mob-suite github/phac-nml/biohansel +github/phac-nml/staramr github/ModellingWebLab/chaste-codegen github/OSSOS/SurveySimulator github/ExaScience/elprep @@ -2348,6 +2778,7 @@ github/HorvathLab/ReQTL github/qianlivan/RPPPS github/aomlomics/tourmaline github/ValeevGroup/mpqc +github/CatarinaMMarques/FisherCosmology github/nyusngroup/pyMCZ github/DeepRank/deeprank-core github/DeepRank/DeepRank-GNN @@ -2359,6 +2790,10 @@ github/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework github/athulpg007/AMAT github/sachsmc/cosinor github/Jammy2211/PyAutoLens +github/Jammy2211/PyAutoGalaxy +github/andresmegias/radex-python +github/andresmegias/gildas-class-python +github/andresmegias/richvalues github/HIPS/autograd github/damcb/tyssue github/shirtsgroup/physical_validation @@ -2368,6 +2803,7 @@ github/bfarr/kombine github/eelregit/covdisc github/eelregit/mcfit github/beastraban/INSANE +github/UrbanRuralSystems/ur-scape github/DreamCloud-Project/McSim-Cycle-accurate-NoC github/DreamCloud-Project/AMALTHEA-Microworkload-Generator github/DreamCloud-Project/McSim-Cycle-accurate-Xbar @@ -2383,9 +2819,12 @@ github/tensorlayer/tensorlayer github/johnlees/PopPUNK github/johnlees/seer github/johnlees/pp-sketchlib +github/LondonBiofoundry/basicsynbio github/sieunhanbom04/support-exploration-matrix-factorization github/ruggiero/clustep github/ruggiero/galstep +github/hues-platform/cesar-p-core +github/shadden/celmech github/einsteinpy/einsteinpy github/CadenArmstrong/simuTrans github/hannorein/rebound @@ -2415,7 +2854,10 @@ github/mavrix93/LightCurvesClassifier github/EC-Earth/ece2cmor3 github/panoptes-organization/panoptes github/dsoave/JLS +github/swiftbiosciences/primerclip github/weizhouUMICH/SAIGE +github/NiallJeffrey/BornRaytrace +github/NiallJeffrey/DeepMass github/esoPanda/FTbg github/mrc-ide/PhyDyn github/mrc-ide/odin @@ -2450,23 +2892,29 @@ github/medvedevgroup/TwoPaCo github/medvedevgroup/varmatch github/lmcinnes/umap github/bccp/nbodykit +github/zhongqiu1245/CCS-Net github/KTH-Nek5000/UQit github/artic-network/fieldbioinformatics github/artic-network/readucks github/maxpumperla/hyperas github/SirSharpest/NarrowEscapeSimulator +github/j-faria/kima github/rvalieris/parallel-fastq-dump github/mes5k/amap-align github/simon-prunet/defringe +github/esa/NIDN github/esa/pagmo2-paper github/cov-ert/gofasta +github/huiwenke/MineProt github/mayuresh159/starsense_algorithms github/SISPO-developers/sispo +github/wouterpeere/GHEtool github/sbailey/empca github/jstjohn/SeqPrep github/manodeep/Corrfunc github/manodeep/TesseRACt github/mne-tools/mne-python +github/mne-tools/mne-icalabel github/PhaseTracer/PhaseTracer github/warrickball/tomso github/astroumd/miriad @@ -2475,8 +2923,10 @@ github/htjb/maxsmooth github/htjb/globalemu github/FDPS/FDPS github/frarei312/ExceS-A-An-Exon-Centric-Split-Aligner +github/astrorama/sourcextractorplusplus github/federicomarulli/CosmoBolognaLib github/supernnova/SuperNNova +github/sihanjiao/j-comb github/DataBiosphere/wdl-parsers github/skovaka/UNCALLED github/sevimcengiz/Oryx-MRSI @@ -2492,8 +2942,12 @@ github/CPM-project/MCPM github/MASILab/pyPheWAS github/seung-lab/FlyWirePaper github/MorgansLab/OSCILOS_Long +github/aabdurrouf/piXedfit +github/zizroc/villager github/ITA-Solar/rh +github/CRPropa/CRPropa3 github/CRPropa/CRPropa2 +github/kazewong/flowMC github/bmoster/emerge github/ymocquar/HOODESolver.jl github/kutaslab/fitgrid @@ -2505,6 +2959,7 @@ github/ClusterMonteCarlo/CMC-COSMIC github/rathnakumars/difference-smoothing github/NathanSkene/MAGMA_Celltyping github/NathanSkene/EWCE +github/seheonoh/baygaud github/seheonoh/2dbat github/nanograv/enterprise github/nanograv/PINT @@ -2513,7 +2968,9 @@ github/yuliang419/AstroNet-Triage github/yuliang419/AstroNet-Vetting github/soerendip/ms-mint github/NicolasHug/Surprise +github/GreiffLab/immuneREF github/milnus/Magphi +github/milnus/Corekaburra github/astromer-science/main-code github/hsinnan75/MapCaller github/hsinnan75/GSAlign @@ -2535,6 +2992,8 @@ github/3D-e-Chem/kripodb github/3D-e-Chem/knime-gpcrdb github/3D-e-Chem/knime-klifs github/indralab/pybiopax +github/moead-framework/framework +github/Griffan/VerifyBamID github/esteinig/nanoq github/benvanwerkhoven/kernel_tuner github/BenNordick/HiLoop @@ -2546,19 +3005,24 @@ github/PrincetonUniversity/Athena-Cversion github/spokenlanguage/platalea github/jmackereth/orbit-estimation github/benjaminbolling/DynaGUI +github/benjaminbolling/RSW github/biolab/orange3 github/biolab/orange-bio github/biolab/orange3-network github/LindaNab/mecor github/LQYoLH/CnnCrispr +github/openmsi/openmsistream github/NKI-CCB/PRECISE github/Blosc/c-blosc github/biod/sambamba +github/mpeel/fastcc github/BioMedIA/MIRTK github/Astroua/SCIMES github/Astroua/TurbuStat +github/QingyuLiaib/PLA-MoRe github/gui11aume/starcode github/learningsimulator/learningsimulator +github/OBrink/RanDepict github/CornellLabofOrnithology/auk github/RuthAngus/stardate github/RuthAngus/SIPK2 @@ -2566,6 +3030,9 @@ github/RuthAngus/gprotation github/sylabs/singularity github/RozanskiT/suppnet github/NREL/OpenOA +github/NREL/graph-env +github/bhorowitz/HyPhy-public +github/ABM4ALL/Melodie github/twesterhout/lattice-symmetries github/SMI/SmiServices github/oorb/oorb @@ -2577,6 +3044,7 @@ github/sfeeney/hh0 github/sfeeney/ddspectra github/nathanchara/l1periodogram github/RadioAstronomySoftwareGroup/pyuvdata +github/lorenzo-rovigatti/oxDNA github/snad-space/zwad github/snad-space/ztf-viewer github/matplotlib/matplotlib @@ -2594,6 +3062,7 @@ github/tardis-sn/carsus github/opimwue/ddop github/andresGranadosC/GalRotpy github/SNOwGLoBES/snowglobes +github/AprilYuge/ResPAN github/radiocosmology/draco github/jakeret/abcpmc github/jakeret/tf_unet @@ -2612,6 +3081,8 @@ github/gotsunami/Youpi github/rdicosmo/parmap github/TeraTrees/TIPP github/datngu/Circall +github/MeasureTransport/MParT +github/xpsi-group/xpsi github/eliotayache/GAMMA github/kbarbary/extinction github/kbarbary/nestle @@ -2619,6 +3090,7 @@ github/kbarbary/sep github/jupyterlab/jupyterlab github/rega-cev/virulign github/CEED/libCEED +github/mgm8/pyngham github/klho/FLAM github/mostanes/umbrella2 github/rohinkumar/correlcalc @@ -2628,12 +3100,18 @@ github/rajewsky-lab/spacemake github/elnjensen/Tapir github/herjy/SLIT github/WatsonGroupTCD/J2suscep +github/kingyin3613/RingsPy +github/korcsmarosgroup/TFlink github/korcsmarosgroup/CytokineLink github/narunlifescience/runcircos-gui +github/MichaelAbdul-Masih/SPAMMS github/dcjones/quip github/dask/dask github/H-E-L-P/XID_plus github/CosmoStatGW/DarkSirensStat +github/CosmoStatGW/MGCosmoPop +github/CosmoStatGW/WF4Py +github/CosmoStatGW/gwfast github/ckm3/Py-PDM github/spectralcode/OCTproZ github/abmantz/lmc @@ -2648,6 +3126,7 @@ github/gigjozsa/tirific github/muLAn-project/muLAn github/semiautomaticgit/SemiAutomaticClassificationPlugin github/JuliaDynamics/DrWatson.jl +github/JuliaDynamics/TimeseriesSurrogates.jl github/pyBRAvo/pyBRAvo github/davidkipping/MAH github/davidkipping/MACULA @@ -2668,10 +3147,15 @@ github/cytham/nanovar github/cdalvaro/machine-learning-master-thesis github/cochran4/GEMB github/mihanke/athos +github/OceanGenomics/mudskipper github/hanyue36/nanoplexer +github/cwentland0/perform github/dstndstn/astrometry.net github/dstndstn/tractor +github/statdivlab/rigr +github/YenWenWang/HapDipKinship github/AP6YC/AdaptiveResonance.jl +github/AP6YC/ClusterValidityIndices.jl github/aalhossary/pyemgpipeline github/low-sky/cprops github/migueldvb/cine @@ -2679,6 +3163,7 @@ github/drwaseemsheikh/audiometry github/moustakas/iSEDfit github/AntonelliLab/seqcap_processor github/YeoLab/clipper +github/dgerosa/gwdet github/dgerosa/surrkick github/dgerosa/spops github/alekseyzimin/ufasta @@ -2694,6 +3179,7 @@ github/pcubillos/rate github/pcubillos/mc3 github/pcubillos/repack github/pcubillos/pyratbay +github/ajshajib/LensingETC github/ajshajib/dolphin github/ratt-ru/CubiCal github/ratt-ru/PyMORESANE @@ -2702,6 +3188,7 @@ github/ratt-ru/montblanc github/delve-team/delve github/aztekas-code/aztekas-main github/bencebeky/spotrod +github/dengzhuo-AI/Real-Fundus github/eXtremeGravityInstitute/QuickCBC github/aarondotter/iso github/savila/halogen @@ -2722,17 +3209,21 @@ github/mslonina/Mechanic github/nservant/HiC-Pro github/wokast/PyCactus github/wokast/RePrimAnd +github/10XGenomics/bamtofastq github/herrsalmi/FConverter github/subisarkar/JexoSim +github/Pinlyu3/LRLoop github/ixkael/3DEX github/ixkael/QuickSip github/demorest/nanopipe +github/njcuk9999/apero-drs github/statOmics/satuRnPaper github/statOmics/tradeSeqPaper github/alan-turing-institute/DetectorChecker github/alan-turing-institute/Palaeoanalytics github/alan-turing-institute/monitoring-ecosystem-resilience github/alan-turing-institute/MLJ.jl +github/DOnghiaGroup/MGwave github/eWaterCycle/eWaterleaf github/eWaterCycle/grpc4bmi github/eWaterCycle/setup-grpc @@ -2741,21 +3232,25 @@ github/eWaterCycle/ewatercycle github/eWaterCycle/experiment-launcher github/eWaterCycle/setup-singularity github/eWaterCycle/jupyterlab_thredds +github/myfang2021/VIPPID github/eaobservatory/jcmt_coadd github/MiguelEA/nudec_BSM github/SSDataLab/vetting github/smsharma/fermi-gce-flows github/smsharma/dark-photons-perturbations github/smsharma/mining-for-substructure-lens +github/kungfugo/BellDiagonalQudits.jl github/DirectDM/directdm-mma github/DirectDM/directdm-py github/josegit88/SCORPIO github/google/caliban github/google/jax +github/google/best github/AlexanderLabWHOI/EUKulele github/forrest-lab/scMatch github/OP2/PyOP2 github/yqiuu/starduster +github/YuRui8879/MRASleepNet github/klee/klee github/gilestrolab/ethoscope github/gilestrolab/pySolo @@ -2764,6 +3259,8 @@ github/dh4gan/oberon github/dh4gan/grapus github/dh4gan/taktent github/MESAHub/mesa +github/yangyanli/DO-Conv +github/SimCab-CHU/ifCNVR github/skendrew/milkywayproject_triggering github/skendrew/midIR_sensitivity github/MingBit/PySCNet @@ -2776,8 +3273,10 @@ github/soedinglab/mmseqs2 github/soedinglab/spacepharer github/soedinglab/metaeuk github/enthought/mayavi +github/enthought/vpsearch github/tloredo/CUDAHM github/PfizerRD/sit2standpy +github/Natsiopoulos/ARDL github/landlab/landlab github/daniel-muthukrishna/astrodash github/pierrepo/autoclassweb @@ -2785,6 +3284,7 @@ github/circuitgraph/circuitgraph github/cole-trapnell-lab/cufflinks github/palumbom/grass github/sib-swiss/pftools3 +github/TRASAL/AMBER github/TRASAL/psrdada-python github/aertslab/pySCENIC github/fredericlemoine/goalign @@ -2809,7 +3309,10 @@ github/LSSTDESC/sacc github/emerge-erc/ALminer github/ELeeAstro/gCMCRT github/ckay314/OSPREI +github/SotaYoshida/NuclearToolkit.jl +github/ICAMS/strucscan github/geopandas/geopandas +github/ExObsSim/ExoRad2-public github/yuliadm/mixComp github/nexml/nexml.java github/CajoterBraak/demc2 @@ -2819,6 +3322,7 @@ github/JulianZDing/UniMAP github/mpound/comb github/mpound/pdrtpy github/lskatz/SneakerNet +github/igvteam/igv-reports github/teamPSG/kNN_Sleep_Scorer_kNNSS github/londumas/redvsblue github/rfeldmann/leopy @@ -2837,6 +3341,7 @@ github/Open-ET/flux-data-qaqc github/odb9402/CNNPeaks github/linneas/condetri github/KathrynJones1/catwoman +github/SysBioUAB/hpi_predictor github/mrteetoe/HOI github/ebundhoo/TAGOPSIN github/ropensci/trufflesniffer @@ -2927,6 +3432,7 @@ github/ropensci/ots github/ropensci/graphql github/ropensci/rbhl github/ropensci/arkdb +github/ropensci/spiro github/ropensci/terrainr github/ropensci/hunspell github/ropensci/paleobioDB @@ -3034,6 +3540,7 @@ github/ropensci/rnaturalearth github/ropensci/rbace github/ropensci/ssh github/ropensci/rentrez +github/ropensci/rb3 github/ropensci/ijtiff github/ropensci/rorcid github/ropensci/NLMR @@ -3046,6 +3553,7 @@ github/ropensci/rtweet github/ropensci/rusda github/ropensci/robotstxt github/ropensci/DataSpaceR +github/ropensci/daiquiri github/ropensci/rnassqs github/ropensci/charlatan github/ropensci/riem @@ -3182,6 +3690,7 @@ github/NLeSC/case-law-app github/NLeSC/eAstroViz github/NLeSC/compressing-the-sky github/NLeSC/ShiCo +github/NLeSC/litstudy github/NLeSC/pycoeman github/NLeSC/OCTSegmentation github/NLeSC/ahn-pointcloud-viewer-ws @@ -3210,16 +3719,23 @@ github/psi4/psi4 github/PopMedNet-Team/popmednet github/WelbornGroup/ELECTRIC github/meta-logic/sequoia +github/xfengnefx/hifiasm-meta github/mfruzan/HaploMaker +github/AndreinaCastillo/Genie_manuscript_data_analysis github/stevengiacalone/triceratops github/fcastagna/preprofit github/fcastagna/JoXSZ github/BiocomputeLab/paraSBOLv github/astronomical-data-processing/RAPP +github/phipsonlab/propeller-paper-analysis +github/ExoCTK/exoctk +github/Mat-dp/mat-dp-core github/GooglingTheCancerGenome/sv-gen github/GooglingTheCancerGenome/sv-callers +github/GooglingTheCancerGenome/sv-channels github/ReGIS-org/regis-v2 github/DJArmstrong/TransitSOM +github/jmcbroome/BTE github/epiforecasts/covidregionaldata github/CLARIAH/grlc github/TimothyADavis/KinMSpy @@ -3230,9 +3746,13 @@ github/mlaparie/phidget-tools github/deepmind/alphafold github/mkargo/pipeline github/smithlabcode/preseq +github/smithlabcode/falco github/KBNLresearch/ochre github/portsmouth/cmbview +github/thomaspinder/GPJax github/QZH2022/germline_flow +github/opengenomebrowser/opengenomebrowser +github/astrosupriyo/pyTANSPEC github/tschad/pycelp github/bids-standard/bids-validator github/plotly/dash @@ -3250,8 +3770,11 @@ github/21cmFAST/21cmFAST github/miguelzuma/hi_class_public github/reneshbedre/bioinfokit github/benallard/galileo +github/nickrodd/HDMSpectra +github/Basvanstein/GSAreport github/sklasfeld/DANPOS3 github/keflavich/HiGal_SEDfitter +github/bodenlab/GRASP github/carpenterphysics/DarkFlux github/scottgigante/picopore github/cthoyt/bel-resources @@ -3268,17 +3791,23 @@ github/lilyminium/psiresp github/freemed/freeshim github/nbellomo/Multi_CLASS github/sblunt/orbitize +github/cns-iu/HRA-supporting-information github/casacore/casacore github/ci-for-research/self-hosted-runners github/SuLab/Wikidata-phenomizer github/cbalbin-FIU/Epitopedia github/OpenWaterAnalytics/pyswmm github/mlhutchins/LWPC +github/lynx-x-ray-observatory/soxs +github/blebon/directChillFoam github/cullanhowlett/l-picola github/pilon/wiki +github/cgobat/asymmetric_uncertainty github/dnarayanan/powderday github/zhoux85/scAdapt +github/ruizengalways/FOD-Net github/najoshi/sickle +github/koszullab/pareidolia github/dpryan79/MethylDackel github/dpryan79/pyBigWig github/dpryan79/libBigWig @@ -3286,6 +3815,7 @@ github/ramadatta/CPgeneProfiler github/Smith42/pix2prof github/Smith42/astroddpm github/Smith42/XDF-GAN +github/Gaius-Augustus/GALBA github/Gaius-Augustus/BRAKER github/devitocodes/pyrevolve github/devitocodes/devito @@ -3302,6 +3832,7 @@ github/al-mcintyre/mCaller github/jls713/tact github/kateharborne/SimSpin github/chasmani/piecewise-regression +github/tamarervin/SolAster github/bretthandrews/flexCE github/llt1836/TE-HI-GCN github/ComputationalRegulatoryGenomicsICL/TFBS @@ -3310,6 +3841,7 @@ github/cajohare/NeutrinoFog github/asntech/intervene github/gorpipe/gor github/FireflySpectra/firefly_release +github/tensorly/viz github/nluetts/NoisySignalIntegration.jl github/keckert7/codes github/benhid/Sequoya @@ -3325,10 +3857,13 @@ github/AMReX-Astro/Nyx github/tidymodels/infer github/tidymodels/stacks github/Martindelosrios/ROGER +github/Martindelosrios/cosmic-kite +github/Martindelosrios/MeSsI github/QibangLiu/PDLSM-FEM_mpi github/wangsiwei2010/FPMVS-CAG github/amoradinejad/limHaloPT github/lauralwatkins/cjam +github/cheng-zhao/FCFC github/shaniAmare/long_read_tools github/broadinstitute/cromwell github/broadinstitute/CellBender @@ -3338,6 +3873,7 @@ github/broadinstitute/wot github/baiwenjia/ukbb_cardiac github/BASTAcode/BASTA github/Via-Appia/via-appia-online-viewer +github/aL3x-O-o-Hung/CAT-Net github/svi-opensource/libics github/SynthSys/pyOmeroUpload github/econ-ark/HARK @@ -3345,18 +3881,22 @@ github/PaulHancock/Robbie github/PaulHancock/Aegean github/AgentM-GEG/residual_feature_extraction github/qboxcode/qbox-public +github/JiangFangzhou/SIDM github/Peppags/CNN-SVR +github/maximewack/viroCapt github/nedRad88/SCALAR github/HARMONI-ELT/HSIM github/jakelever/civicmine github/pixixiaonaogou/MLSDR github/kimberg/voxbo +github/CNIC-Proteomics/TurboPutative-web github/CoolWorlds/exoinformatics github/CoolWorlds/ExoPriors github/DorianDepriester/mtex2Gmsh github/ihrke/pypillometry github/yuhaoran/CUBE github/Glogobyte/miRGalaxy +github/EESI/Complet-Plus github/Leo-Simpson/c-lasso github/mirapy-org/mirapy github/labsquare/CutePeaks @@ -3365,21 +3905,27 @@ github/tbep-tech/tbeptools github/johnpaulett/python-hl7 github/quadram-institute-bioscience/dadaist2 github/cmillion/gPhoton +github/NickSwainston/pulsar_spectra github/CRG-CNAG/anubis github/swiftsim/swiftsimio github/biswajitmb/DarpanX github/fstrozzi/Fastool github/rizkg/BBHash github/sheryl-ai/MetaPred +github/cwinpy/cwinpy github/djsutherland/py-sdm github/bxia888/CEFCIG github/codidact/qpixel github/ska-sa/hibayes github/maxibor/sam2lca +github/haiyang1986/TVAR +github/miracum/ahd2fhir github/jenniferlu717/Bracken +github/zengzhenhuan/GFNet github/girder/viime github/phenomecentre/nPYc-Toolbox github/HaowenZhang/TRINITY +github/JesusTorrado/extrapops github/dutilh/CAT github/a-griffiths/AutoSpec github/jesford/cluster-lensing @@ -3396,11 +3942,13 @@ github/julia-wrobel/registr github/bwvdnbro/CMacIonize github/bwvdnbro/HydroCode1D github/rhenkin/visxhclust +github/Jacks0nJ/PyFPT github/dmentipl/plonk github/dsavransky/EXOSIMS github/icredd-cheminfo/CGRdb2 github/ColdThunder/NR-code github/BackmanLab/PWSpy +github/SciML/GlobalSensitivity.jl github/alicia-ziying-yang/conTEXT-explorer github/kgullikson88/Telluric-Fitter github/kgullikson88/Companion-Finder @@ -3421,11 +3969,15 @@ github/pkgw/pwkit github/kerkelae/disimpy github/junkoda/sidm-nbody github/healytwin1/HISS +github/Ruiz-HCI-Lab/ggMOB github/reneheller/pile-up github/erikhom/aida github/dzesmin/TEA github/buschlab/fhirspark github/christopher-vollmers/C3POa +github/andreyshabalin/TwinEQTL +github/yangyongsan-bio/GREAP +github/N-Wouda/ALNS github/tripathi/Atmospheric-Athena github/ialopezt/GalLenspy github/amkozlov/raxml-ng @@ -3433,6 +3985,7 @@ github/hope-data-science/tidyfst github/wajidarshad/ESIDE github/szpiech/selscan github/ggobi/ggobi +github/SYalouz/QuantNBody github/MICCoM/SSAGES-public github/alexfields/ORF-RATER github/BIMSBbioinfo/pigx_scrnaseq @@ -3442,6 +3995,7 @@ github/ejsafron/SATCHEL github/justincfeng/PoMiN github/bbuchfink/diamond github/epfl-radio-astro/LiSA +github/epfl-radio-astro/PINION github/COSMIC-PopSynth/COSMIC github/asgr/celestial github/asgr/ProFuse @@ -3449,14 +4003,18 @@ github/asgr/NFWdist github/asgr/ProFound github/asgr/hyper.fit github/asgr/ProSpect +github/CMakePP/CMinx github/FastMLC/fMLC github/christinahedges/contaminante +github/ptiede/Comrade.jl github/devries/analytic_infall github/wathela/FIRST-CLASSIFIER github/atchekho/harmpi github/tofflemire/saphires github/alexander-mead/HMcode github/alexander-mead/collapse +github/LCOGT/banzai +github/LCOGT/banzai-nres github/ctSkennerton/minced github/ctSkennerton/crass github/fermisurfaces/IFermi @@ -3474,31 +4032,42 @@ github/jtksai/PyCOOL github/IFB-ElixirFr/edam-browser github/wmalab/EnHiC github/shilpagarg/WHdenovo +github/domschrei/mallob +github/BGI-Qingdao/TGS-GapCloser github/Varnani/pywd2015-qt5 github/e-mental-health/data-processing github/e-mental-health/orange-hackathon +github/astro-informatics/sleplet github/astro-informatics/s2 github/astro-informatics/comb github/astro-informatics/RequiSim github/astro-informatics/s2let github/astro-informatics/flag-archive +github/astro-informatics/massmappy +github/astro-informatics/ssht github/yangao07/abPOA github/yangao07/TideHunter github/s4hts/HTStream github/segasai/q3c github/segasai/rvspecfit +github/bcgsc/btllib +github/bcgsc/arcs github/bcgsc/NanoSim github/bcgsc/ntHash github/bcgsc/longstitch +github/bcgsc/TMBur github/bcgsc/abyss github/bcgsc/ntCard github/mgckind/SparsePz github/mgckind/easyaccess github/ahcm/ffindex github/devsim/devsim +github/huchiayu/ParticleGridMapper.jl +github/szhorvat/IGraphM github/kkrismer/scansite4 github/panoptes/POCS github/GabrielNakamura/FishPhyloMaker +github/ParkvilleData/MetaGenePipe github/ekg/fastahack github/ekg/seqwish github/ekg/freebayes @@ -3506,12 +4075,16 @@ github/ekg/tabixpp github/ekg/smithwaterman github/AnitaPetzler/AMOEBA github/alesantuz/musclesyneRgies +github/cwieder/py-ssPA github/plumed/plumed2 github/Libsharp/libsharp github/bthorne93/PySM_public +github/DrSoulain/PREVIS github/syasini/AstroPaint +github/kircherlab/ReMM github/cdw9bf/CompactGroup github/bwengals/CCSNMultivar +github/adriancorrendo/metrica github/rpoleski/MulensModel github/matvii/ADAM github/rcarragh/c212 @@ -3542,6 +4115,7 @@ github/bramvandijk88/cacatoo github/seqan/lara github/seqan/flexbar github/seqan/lambda +github/BorgwardtLab/simbsig github/mwvgroup/pwv_kpno github/astropy/astroplan github/astropy/halotools @@ -3565,24 +4139,34 @@ github/trevisanj/PFANT github/mzechmeister/viper github/mzechmeister/serval github/nye17/javelin +github/RitchieLab/hudson github/uwssg/APS +github/galizia-lab/pyview github/NCAS-CMS/cfdm github/lnasellentin/DALI github/jmschrei/pomegranate github/mengaldo/PySPOD +github/RBrearton/islatu github/snystrom/memes +github/cagrikymk/JAX-ReaxFF github/gokalpcelik/ROHMMCLI github/biboyd/SALSA github/eEcoLiDAR/Laserfarm github/eEcoLiDAR/laserchicken +github/fjprichard/PyAFBF +github/schochastics/signnet +github/schochastics/netrankr github/sethspjohnso/satmc github/HUST-NingKang-Lab/ONN4MST github/aberer/RogueNaRok +github/freqtrade/freqtrade +github/BaroudLab/Griottes github/SCECcode/pycsep github/RWTH-EBC/AixCaliBuHA github/pmelchior/skymapper github/pmelchior/skylens github/pmelchior/scarlet +github/pmelchior/spender github/pmelchior/shear-stacking github/pmelchior/des-exp-checker github/pmelchior/shapelens @@ -3590,6 +4174,7 @@ github/pmelchior/epsnoise github/pmelchior/pyGMMis github/brentp/vcfanno github/brentp/gsort +github/brentp/smoove github/brentp/goleft github/brentp/cyvcf2 github/brentp/somalier @@ -3608,7 +4193,9 @@ github/antoinediez/Sisyphe github/vishwas1984/LaplaceInterpolation.jl github/klevis-a/kinematics-vis github/MannLabs/alphapept +github/iAART/aart github/mbonav/Exo_DMC +github/YinanZhao21/SOAP_GPU github/FePhyFoFum/phyx github/IftachSadeh/ANNZ github/CTU-Bern/presize @@ -3618,12 +4205,15 @@ github/BritishGeologicalSurvey/pyvolcans github/EMResearch/EvoMaster github/ronnyerrmann/HiFLEx github/bio-tools/biotoolsSum +github/phineasng/DECODE github/carronj/lenspyx github/carronj/plancklens github/openjournals/joss github/HEML/HEML github/FluidityProject/fluidity +github/SpaceOdyssey/Blobby3D github/tronsgaard/barycorr +github/raddleverse/MimiBRICK.jl github/aprsa/ebai github/aprsa/dips github/DynaSlum/satsense @@ -3631,20 +4221,28 @@ github/intake/intake github/fairdataihub/SPARClink github/MichielCottaar/velbin github/nlppln/nlppln +github/dusanmarceta/Synthetic-Population-of-Interstellar-Objects +github/dusanmarceta/Synthetic-Population-of-Interstellar-Obejcts +github/tyo-nu/MINE-app github/actris-cloudnet/cloudnetpy github/IanevskiAleksandr/sc-type +github/JakobBD/pounce github/soylentdeen/MoogStokes github/soylentdeen/CounterPoint github/opencobra/cobrapy +github/VChristiaens/special github/lifs-tools/jmzTab-m github/sjteresi/TE_Density github/genome/bam-readcount github/genome/somatic-sniper +github/parmoo/parmoo github/danielacarrasco/GLACiAR +github/ycwu1030/EvoEMD github/ZhaoXM-Lab/metaMIC github/fruzsinaagocs/oscode github/hposborn/MonoTools github/saezlab/PHONEMeS +github/ConnorDonegan/geostan github/liulizhi1996/HPODNets github/sanger-pathogens/snp-sites github/sanger-pathogens/Fastaq @@ -3662,7 +4260,9 @@ github/m-a-d-n-e-s-s/madness github/guynir42/radon github/AndreNicolasChene/DRAGRACES github/kylemede/ExoSOFT +github/mmore500/hstrat github/ProSolo/prosolo +github/Ajstros/pyripherals github/nkhorshid/simab github/EmmanuelSchaan/ThumbStack github/EmmanuelSchaan/LaSSI @@ -3682,11 +4282,15 @@ github/ijuric/MAPS github/UBC-Astrophysics/kd-match github/nivha/three_body_integration github/sambit-giri/tools21cm +github/FergusDonnan/PAHDecomp github/FergusDonnan/PyROA github/FergusDonnan/Running-Optimal-Average github/YangLab/CIRCexplorer2 +github/YangLab/RNAlight github/jadexter/grtrans github/rsnemmen/BCES +github/zpliulab/GENELink +github/connor-lab/vapor github/Electrostatics/apbs github/CavendishAstrophysics/anmap github/CavendishAstrophysics/postmortem @@ -3712,6 +4316,7 @@ github/xoopR/set6 github/farhanferoz/SkyNet github/farhanferoz/BAMBI github/farhanferoz/MultiNest +github/hpparvi/MuSCAT2_transit_pipeline github/hpparvi/opents github/hpparvi/ldtk github/hpparvi/PyTransit @@ -3733,10 +4338,13 @@ github/arhstevens/DarkSage github/coljac/sensie github/FreBio/komics github/BU-hammerTeam/PyHammer +github/RemoteSensingTools/vSmartMOM.jl github/elizabethnewman/hessQuik github/stan-dev/stan github/twinl/website github/vsoch/gridtest +github/vsoch/citelang +github/maize-genetics/rTASSEL github/DReichLab/EIG github/wanpinglee/MOSAIK github/pec27/lizard @@ -3748,7 +4356,10 @@ github/nlesc-sherlock/emma github/nlesc-sherlock/Rig github/ecological-cities/home2park github/aewallin/allantools +github/ltlancas/walter +github/SuperKogito/spafe github/raspishake/rsudp +github/justinmathias/isocalcR github/rmjarvis/TreeCorr github/rmjarvis/Piff github/rice-solar-physics/EBTEL @@ -3763,6 +4374,7 @@ github/dhubber/seren github/gtonkinhill/fastbaps github/YosefLab/scvi-tools github/STAR-Fusion/STAR-Fusion +github/nand1155/CausNet github/MelanieKahl/MechAnalyze github/ERA-URBAN/fm128_radar github/ERA-URBAN/netcdf2littler @@ -3771,16 +4383,23 @@ github/iraf-community/pyraf github/calboo/TAWAS github/calboo/wigglewave github/calboo/Potential_Field_Calculator +github/coolneighbors/unwise-verse github/JASHunt/Snapdragons +github/paumard/cubefit +github/RomainFeron/mwga-utils +github/difuture-lmu/dsBinVal github/achael/eht-imaging github/saltastro/pyhrs +github/blackjax-devs/blackjax github/Crompulence/cpl-library +github/dbuscher/pois github/bluesky/bluesky github/sagepublishing/rejected_article_tracker_pkg github/editeodoro/Bbarolo github/ledatelescope/bifrost github/paulmorio/gincco github/cicirello/Chips-n-Salsa +github/cicirello/rho-mu github/danielkoll/tidally-locked-coordinates github/danielkoll/PyRADS github/SIOSlab/exodetbox @@ -3788,12 +4407,15 @@ github/andizq/sf3dmodels github/winni2k/abeona github/nf-core/viralrecon github/nf-core/mag +github/nf-core/sarek github/AlexandrosAntoniadis/ODUSSEAS github/luxsrc/gray +github/Liltsliverfish/A-time-series-reconstruction-method-of-massive-astronomical-catalogues-based-on-Spark github/citation-file-format/cffconvert-github-action github/citation-file-format/cff-initializer-javascript github/citation-file-format/cff-converter-python github/citation-file-format/citation-file-format +github/starkit/wsynphot github/gnave/Xgremlin github/TrackerControl/tracker-control-android github/mentatpsi/OSGenome @@ -3806,6 +4428,7 @@ github/ropenscilabs/r2readthedocs github/ropenscilabs/qcoder github/arcaldwell49/SimplyAgree github/desmid/mview +github/alexriss/SpmImageTycoon.jl github/j-erler/pymf github/moranegg/deposit-template github/moranegg/AffectationRO @@ -3816,17 +4439,22 @@ github/AshleySpindler/AstroVaDEr-Public github/vgl-hub/gfastats github/davemlz/eemont github/aakepley/autobox +github/jgrembi/riskCommunicator github/cjneely10/EukMetaSanity +github/AnantharamanLab/vRhyme github/DidierMurilloF/FielDHub +github/palaimon/ipyannotator github/qtltools/qtltools github/Crick-CancerGenomics/ascat github/sebhaan/geobo github/Starfish-develop/Starfish +github/mh-skjelvareid/synaptus github/VincentAlcazer/StatAid github/erikbern/ann-benchmarks github/B-UMMI/chewBBACA github/yuhuan-wu/mobilesal github/CGATOxford/UMI-tools +github/weiliu123/PCLassoReg github/gxiaolab/scAllele github/pennsignals/chime github/timchurches/NetEpi-Analysis @@ -3841,6 +4469,7 @@ github/cosmicrays/hermes github/cosmicrays/DRAGON github/simonsobs/pixell github/simonsobs/so_noise_models +github/ChenYangyao/hipp github/bd-j/prospector github/bd-j/sedpy github/jobovy/extreme-deconvolution @@ -3858,6 +4487,7 @@ github/chanzuckerberg/idseq-dag github/chanzuckerberg/shasta github/zkdtc/MLC_ELGs github/EliabCanul/nauyaca +github/mad-lab-fau/tpcp github/mad-lab-fau/imucal github/daeken/Emokit github/JuliaDiff/ForwardDiff.jl @@ -3870,6 +4500,7 @@ github/ropensci-review-tools/autotest github/ropensci-review-tools/srr github/ropensci-review-tools/pkgcheck github/ropensci-review-tools/pkgstats +github/Dylan-Aliberti/Kepler-Collisions github/samhforbes/PupillometryR github/abrupt-climate/hyper-canny github/natelust/least_asymmetry @@ -3878,12 +4509,15 @@ github/caselawanalytics/CaseLawAnalytics github/COMBINE-lab/RapMap github/COMBINE-lab/cuttlefish github/COMBINE-lab/salmon +github/COMBINE-lab/terminus github/COMBINE-lab/pufferfish +github/COMBINE-lab/alevin-fry github/COMBINE-lab/libgff github/adrn/pyia github/adrn/SuperFreq github/adrn/schwimmbad github/adbar/htmldate +github/OnroerendErfgoed/atramhasis github/ot483/NetCom github/myrafproject/myrafproject github/enveda/RPath @@ -3894,7 +4528,9 @@ github/maserlib/ExPRES github/legolason/PyQSOFit github/openmopac/MOPAC github/lazzati-astro/MCRaT +github/krab1k/ChargeFW2 github/cblakeastro/intensitypower +github/V-Bernal/GeneNetTools github/BradGreig/21CMMC github/pypeit/PypeIt github/marcelm/tinyalign @@ -3912,12 +4548,14 @@ github/AlgoLab/shark github/BDI-pathogens/OpenABM-Covid19-model-paper github/TingMAC/FrMLNet github/ckarako/RRATtrap +github/ajohnson-uoregon/llvm-project github/tcollett/LensPop github/marius311/cosmoslik github/marius311/pypico github/Jonathanfreundlich/CuspCore github/optuna/optuna github/vibbits/phyd3 +github/gourabghoshroy/MPVNN github/danielhuson/dendroscope3 github/danielhuson/jloda github/danielhuson/malt @@ -3925,11 +4563,13 @@ github/danielhuson/megan-ce github/mourisl/Lighter github/FarnazFouladi/HashSeq_Manuscript github/apertif/apercal +github/jolie/tquery github/Midnighter/dependency-info github/singularityhub/sregistry github/singularityhub/singularity-compose github/singularityhub/singularity-hpc github/gramos/imagetooth +github/DeepMIALab/UC-NfNet github/tseemann/snippy github/tseemann/abricate github/tseemann/snp-dists @@ -3944,10 +4584,16 @@ github/abschneider/StrainHub github/insilico/cncv github/prajwel/curvit github/zoometh/iconr +github/barricklab/pLannotate +github/hnikaein/stark github/csdms/bmi github/FrancesBW/bellamy +github/fjankowsk/scatfit +github/rochoa85/NTDHealth_Forms github/cas-bioinf/rboAnalyzer +github/klb2/qmkpy github/kernsuite-debian/parseltongue +github/gnudatalanguage/gdl github/aidenlab/juicer github/cweniger/swordfish github/davidgardenier/frbpoppy @@ -3957,12 +4603,15 @@ github/TearsWaiting/MIMML github/samuelefiorini/tangle github/martinsparre/XSHPipelineManager github/masoncarney/stepped_luneburg +github/sylvainprigent/napari-tracks-reader github/jessecambon/tidygeocoder +github/zjupgx/modig github/INCEPTdk/adaptr github/juliotux/astropop github/sanjibs/bmcmc github/Adamtaranto/Yanagiba github/creanero/locus +github/seamusclarke/rjplots github/damonge/CUTE github/damonge/CoLoRe github/damonge/schNell @@ -3974,6 +4623,7 @@ github/PyTables/PyTables github/zhouzilu/DENDRO github/labjg/fibmeasure github/sciapp/sampledb +github/BioGenies/AMPBenchmark github/tp2vis/distribute github/cheerfuluser/tessreduce github/utrillalab/repromin @@ -3988,15 +4638,18 @@ github/libgamera/GAMERA github/siara-cc/Unishox2 github/deweylab/RSEM github/PacificBiosciences/pbalign +github/PacificBiosciences/IsoSeq github/PacificBiosciences/pbmm2 github/PacificBiosciences/pbcopper github/PacificBiosciences/FALCON github/PacificBiosciences/kineticsTools +github/PacificBiosciences/minorseq github/PacificBiosciences/blasr github/PacificBiosciences/pbbam github/PacificBiosciences/pbcore github/PacificBiosciences/pbbioconda github/julblarod/SOPHISM +github/c-white/blacklight github/BU-ISCIII/taranis github/BU-ISCIII/iSkyLIMS github/BU-ISCIII/plasmidID From 7670598f694c10f1860157595a6fe9cf91348aab Mon Sep 17 00:00:00 2001 From: vsoch Date: Tue, 4 Apr 2023 23:44:24 -0600 Subject: [PATCH 02/10] original update to clean up repo metadata Signed-off-by: vsoch --- .github/scripts/clean-database.py | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py index 6885a412c..4e5811be5 100755 --- a/.github/scripts/clean-database.py +++ b/.github/scripts/clean-database.py @@ -66,14 +66,9 @@ def clean(database, archive): archives.add(os.path.dirname(relpath)) elif res.status_code in [301, 302]: - if "gitlab" in res.url: - import IPython - - IPython.embed() - sys.exit() print(f"Found repository {relpath} with moved location, updating") new_location = requests.head(res.headers["Location"]) - meta["html_url"] = new_location.url + meta["html_url"] = new_location.url save_json(meta, path) # Read in repos.txt and remove archived @@ -87,12 +82,6 @@ def clean(database, archive): with open("repos.txt", "w") as fd: fd.write("\n".join(list(repos))) - import IPython - - IPython.embed() - sys.exit() - - def main(): # python .github/scripts/clean-database.py $(pwd) From ddb749883ca5837e2e5e761e9f8c3c38e2b60cdc Mon Sep 17 00:00:00 2001 From: Vanessasaurus <814322+vsoch@users.noreply.github.com> Date: Tue, 4 Apr 2023 23:47:33 -0600 Subject: [PATCH 03/10] Update metadata.json --- .../github/williamjameshandley/fgivenx/metadata.json | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/database/github/williamjameshandley/fgivenx/metadata.json b/database/github/williamjameshandley/fgivenx/metadata.json index 4d1b3bc11..5d351eefa 100644 --- a/database/github/williamjameshandley/fgivenx/metadata.json +++ b/database/github/williamjameshandley/fgivenx/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", - "uid": "github/williamjameshandley/fgivenx", - "url": "https://github.com/williamjameshandley/fgivenx", + "uid": "github.com/handley-lab/fgivenx", + "url": "https://github.com/handley-lab/fgivenx", "data": { "doi": [ "https://ui.adsabs.harvard.edu/abs/2019PhRvD.100b3501H", @@ -9,7 +9,7 @@ "https://ui.adsabs.harvard.edu/abs/2019ascl.soft09014H/abstract" ], "title": "fgivenx: Functional posterior plotter", - "url": "https://github.com/williamjameshandley/fgivenx", + "url": "https://github.com/handley-lab/fgivenx" "name": "fgivenx", "full_name": "williamjameshandley/fgivenx", "html_url": "https://github.com/williamjameshandley/fgivenx", @@ -48,6 +48,5 @@ ], "timestamp": "2022-07-17 17:15:51.474703", "avatar": "https://avatars.githubusercontent.com/u/3708486?v=4" - }, - "html_url": "https://github.com/handley-lab/fgivenx" -} \ No newline at end of file + } +} From 882a2edaa3bdbba045ce97ac78ecb388fa491c7b Mon Sep 17 00:00:00 2001 From: vsoch Date: Tue, 4 Apr 2023 23:59:43 -0600 Subject: [PATCH 04/10] fix renames Signed-off-by: vsoch --- .github/scripts/clean-database.py | 32 +- .../pilon/wiki/metadata.json | 2 +- .../cufflinks/metadata.json | 2 +- .../21cmFAST/metadata.json | 0 .../3D-e-Chem/3D-e-Chem-VM/metadata.json | 5 +- .../3D-e-Chem/knime-gpcrdb/metadata.json | 5 +- .../3D-e-Chem/knime-klifs/metadata.json | 5 +- .../3D-e-Chem/knime-kripodb/metadata.json | 5 +- .../3D-e-Chem/knime-molviewer/metadata.json | 5 +- .../knime-pharmacophore/metadata.json | 5 +- .../3D-e-Chem/knime-plants/metadata.json | 5 +- .../knime-python-node-archetype/metadata.json | 5 +- .../knime-python-wrapper/metadata.json | 5 +- .../3D-e-Chem/knime-silicos-it/metadata.json | 5 +- .../3D-e-Chem/knime-sstea/metadata.json | 5 +- .../3D-e-Chem/knime-sygma/metadata.json | 5 +- .../3D-e-Chem/knime-testflow/metadata.json | 5 +- .../github/3D-e-Chem/kripodb/metadata.json | 5 +- database/github/3D-e-Chem/sygma/metadata.json | 5 +- .../tycho-knime-node-archetype/metadata.json | 5 +- .../ADAH-EviDENce/evidence/metadata.json | 5 +- .../grim/metadata.json | 0 .../Castro}/Castro/metadata.json | 0 .../MAESTRO/metadata.json | 0 .../Nyx}/Nyx/metadata.json | 0 .../REBOUND_fragmentation}/metadata.json | 0 .../{adrijd => AdriJD}/beamconv/metadata.json | 0 .../Alcampopiano/hypothesize/metadata.json | 5 +- .../NarrowEscapeSimulator/metadata.json | 0 .../github/ArenA-Crowds/Crowds/metadata.json | 5 +- .../github/B-UMMI/chewBBACA/metadata.json | 2 +- .../BartoszBartmanski/StoSpa2/metadata.json | 5 +- .../SeeKAT/metadata.json | 0 database/github/Blosc/c-blosc/metadata.json | 5 +- .../github/BrianAronson/birankr/metadata.json | 5 +- .../toppred/metadata.json | 0 database/github/CLARIAH/grlc/metadata.json | 5 +- .../{cnes => CNES}/EleFits/metadata.json | 0 .../CategoricalTimeSeries.jl/metadata.json | 7 +- .../COMBINE-lab/cuttlefish/metadata.json | 2 +- .../salmon}/salmon/metadata.json | 0 .../{csb5 => CSB5}/lofreq/metadata.json | 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.../github/NLeSC/PattyAnalytics/metadata.json | 5 +- database/github/NLeSC/PattyData/metadata.json | 5 +- .../{pattyvis => PattyVis}/metadata.json | 5 +- .../SalientDescriptor-matlab/metadata.json | 5 +- .../SalientDetector-matlab/metadata.json | 5 +- .../SalientDetector-python/metadata.json | 5 +- database/github/NLeSC/ShiCo/metadata.json | 5 +- .../UncertaintyVisualization/metadata.json | 5 +- .../ahn-pointcloud-viewer-ws/metadata.json | 5 +- database/github/NLeSC/baklava/metadata.json | 5 +- database/github/NLeSC/boatswain/metadata.json | 5 +- .../github/NLeSC/case-law-app/metadata.json | 5 +- .../NLeSC/compressing-the-sky/metadata.json | 5 +- database/github/NLeSC/cptm/metadata.json | 5 +- .../NLeSC/docker-couch-admin/metadata.json | 5 +- database/github/NLeSC/eAstroViz/metadata.json | 5 +- .../eEcology-Annotation-WS/metadata.json | 5 +- .../eEcology-Classification/metadata.json | 5 +- .../NLeSC/eEcology-SMS-reciever/metadata.json | 5 +- .../eEcology-script-wrapper/metadata.json | 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ClonalOrigin}/metadata.json (100%) rename database/github/{Yida-Lin => xdf-modules}/libxdf/metadata.json (100%) rename database/github/{NLeSC => xenon-middleware}/osmium/metadata.json (91%) rename database/github/{NLeSC => xenon-middleware}/xenon-cli/metadata.json (91%) rename database/github/{NLeSC => xenon-middleware}/xenon-flow/metadata.json (91%) rename database/github/{NLeSC => xenon-middleware}/xenon-grpc/metadata.json (91%) rename database/github/xstarkit/{mpi_xstar => MPI_XSTAR}/metadata.json (100%) rename database/github/yuhuan-wu/{mobilesal => MobileSal}/metadata.json (100%) rename database/github/yuliang419/{AstroNet-Triage => Astronet-Triage}/metadata.json (100%) rename database/github/yuliang419/{AstroNet-Vetting => Astronet-Vetting}/metadata.json (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-absence.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-citation.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-domain-intention.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-question-intention.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-research-intention.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/criteria-RSE-usage.tsv (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/metadata.json (100%) rename database/gitlab/LouisLab/{PiVR => pivr}/taxonomy.tsv (100%) rename database/{github/sanger-pathogens => sanger-pathogens.github.io}/circlator/metadata.json (97%) rename database/{github => trinityrnaseq}/trinityrnaseq/wiki/metadata.json (92%) diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py index 4e5811be5..cc58ffd52 100755 --- a/.github/scripts/clean-database.py +++ b/.github/scripts/clean-database.py @@ -40,10 +40,16 @@ def clean(database, archive): """ Clean the database """ - archives = set() + # Read in repos.txt and remove archived + with open("repos.txt", "r") as fd: + repos = fd.readlines() + repos = set([x.strip() for x in repos if x.strip()]) + + relpath = os.path.relpath(path, database) for path in recursive_find(database, "*metadata.json"): meta = read_json(path) + # Spurious bug with empty url if meta["url"] is None: meta["url"] = meta["data"]["url"] save_json(meta, path) @@ -54,7 +60,6 @@ def clean(database, archive): print("Issue with {path}") continue - relpath = os.path.relpath(path, database) if res.status_code == 200: continue @@ -63,20 +68,27 @@ def clean(database, archive): newpath = os.path.join(archive, relpath) newdir = os.path.dirname(newpath) shutil.move(os.path.dirname(path), newdir) - archives.add(os.path.dirname(relpath)) + uid = os.path.dirname(relpath) + if uid in repos: + repos.remove(uid) elif res.status_code in [301, 302]: print(f"Found repository {relpath} with moved location, updating") new_location = requests.head(res.headers["Location"]) - meta["html_url"] = new_location.url + meta["url"] = new_location.url save_json(meta, path) - # Read in repos.txt and remove archived - with open("repos.txt", "r") as fd: - repos = fd.readlines() - repos = set([x.strip() for x in repos if x.strip()]) - for to_remove in archives: - repos.remove(to_remove) + # Ensure UID is correct + uid = meta['url'].rsplit('/', 3) + uid = "/".join(uid[1:]).replace('.com', '') + + if uid not in relpath: + old_uid = os.path.dirname(relpath) + shutil.move(os.path.dirname(path), os.path.join(database, uid)) + print(f"{relpath} should be {uid}") + if old_uid in repos: + repos.remove(old_uid) + repos.add(uid) # Save back to file with open("repos.txt", "w") as fd: diff --git a/database/github/pilon/wiki/metadata.json b/database/broadinstitute/pilon/wiki/metadata.json similarity index 89% rename from database/github/pilon/wiki/metadata.json rename to database/broadinstitute/pilon/wiki/metadata.json index 380b7c2e5..3c3cfeb7d 100644 --- a/database/github/pilon/wiki/metadata.json +++ b/database/broadinstitute/pilon/wiki/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/pilon/wiki", - "url": null, + "url": "https://github.com/broadinstitute/pilon/wiki", "data": { "title": "Pilon", "url": "https://github.com/broadinstitute/pilon/wiki", diff --git a/database/github/cole-trapnell-lab/cufflinks/metadata.json b/database/cole-trapnell-lab.github.io/cufflinks/metadata.json similarity index 96% rename from database/github/cole-trapnell-lab/cufflinks/metadata.json rename to database/cole-trapnell-lab.github.io/cufflinks/metadata.json index 61ce4a917..fa94a6fc1 100644 --- a/database/github/cole-trapnell-lab/cufflinks/metadata.json +++ b/database/cole-trapnell-lab.github.io/cufflinks/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/cole-trapnell-lab/cufflinks", - "url": null, + "url": "http://cole-trapnell-lab.github.io/cufflinks/", "data": { "title": "Cufflinks", "url": "http://cole-trapnell-lab.github.io/cufflinks/", diff --git a/database/github/21cmFAST/21cmFAST/metadata.json b/database/github/21cmfast/21cmFAST/metadata.json similarity index 100% rename from database/github/21cmFAST/21cmFAST/metadata.json rename to database/github/21cmfast/21cmFAST/metadata.json diff --git a/database/github/3D-e-Chem/3D-e-Chem-VM/metadata.json b/database/github/3D-e-Chem/3D-e-Chem-VM/metadata.json index a5aa60ff7..8269ea794 100644 --- a/database/github/3D-e-Chem/3D-e-Chem-VM/metadata.json +++ b/database/github/3D-e-Chem/3D-e-Chem-VM/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/3D-e-Chem-VM", - "url": "https://api.github.com/repos/3D-e-Chem/3D-e-Chem-VM", + "url": "https://github.com/3D-e-Chem/3D-e-Chem-VM", "data": { "timestamp": "2020-07-05 00:17:07.943003", "name": "3D-e-Chem-VM", - "url": "https://api.github.com/repos/3D-e-Chem/3D-e-Chem-VM", + "url": "https://github.com/3D-e-Chem/3D-e-Chem-VM", "full_name": "3D-e-Chem/3D-e-Chem-VM", "html_url": "https://github.com/3D-e-Chem/3D-e-Chem-VM", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.594559", "name": "3D-e-Chem-VM", "full_name": "3D-e-Chem/3D-e-Chem-VM", - "html_url": "https://github.com/3D-e-Chem/3D-e-Chem-VM", "private": false, "description": "Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows", "created_at": "2016-01-11T21:10:05Z", diff --git a/database/github/3D-e-Chem/knime-gpcrdb/metadata.json b/database/github/3D-e-Chem/knime-gpcrdb/metadata.json index 507ad0c69..648e6683d 100644 --- a/database/github/3D-e-Chem/knime-gpcrdb/metadata.json +++ b/database/github/3D-e-Chem/knime-gpcrdb/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-gpcrdb", - "url": "https://api.github.com/repos/3D-e-Chem/knime-gpcrdb", + "url": "https://github.com/3D-e-Chem/knime-gpcrdb", "data": { "timestamp": "2020-07-05 00:17:14.880978", "name": "knime-gpcrdb", - "url": "https://api.github.com/repos/3D-e-Chem/knime-gpcrdb", + "url": "https://github.com/3D-e-Chem/knime-gpcrdb", "full_name": "3D-e-Chem/knime-gpcrdb", "html_url": "https://github.com/3D-e-Chem/knime-gpcrdb", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597174", "name": "knime-gpcrdb", "full_name": "3D-e-Chem/knime-gpcrdb", - "html_url": "https://github.com/3D-e-Chem/knime-gpcrdb", "private": false, "description": "GPCRDB nodes for Knime", "created_at": "2016-01-12T13:31:10Z", diff --git a/database/github/3D-e-Chem/knime-klifs/metadata.json b/database/github/3D-e-Chem/knime-klifs/metadata.json index 8cd8a6aa7..ae5c50cf6 100644 --- a/database/github/3D-e-Chem/knime-klifs/metadata.json +++ b/database/github/3D-e-Chem/knime-klifs/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-klifs", - "url": "https://api.github.com/repos/3D-e-Chem/knime-klifs", + "url": "https://github.com/3D-e-Chem/knime-klifs", "data": { "timestamp": "2020-07-05 00:17:15.027377", "name": "knime-klifs", - "url": "https://api.github.com/repos/3D-e-Chem/knime-klifs", + "url": "https://github.com/3D-e-Chem/knime-klifs", "full_name": "3D-e-Chem/knime-klifs", "html_url": "https://github.com/3D-e-Chem/knime-klifs", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.595324", "name": "knime-klifs", "full_name": "3D-e-Chem/knime-klifs", - "html_url": "https://github.com/3D-e-Chem/knime-klifs", "private": false, "description": "Knime nodes to interact with KLIFS", "created_at": "2016-05-11T11:00:29Z", diff --git a/database/github/3D-e-Chem/knime-kripodb/metadata.json b/database/github/3D-e-Chem/knime-kripodb/metadata.json index c919c8914..42250ec27 100644 --- a/database/github/3D-e-Chem/knime-kripodb/metadata.json +++ b/database/github/3D-e-Chem/knime-kripodb/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-kripodb", - "url": "https://api.github.com/repos/3D-e-Chem/knime-kripodb", + "url": "https://github.com/3D-e-Chem/knime-kripodb", "data": { "timestamp": "2020-07-05 00:17:06.490235", "name": "knime-kripodb", - "url": "https://api.github.com/repos/3D-e-Chem/knime-kripodb", + "url": "https://github.com/3D-e-Chem/knime-kripodb", "full_name": "3D-e-Chem/knime-kripodb", "html_url": "https://github.com/3D-e-Chem/knime-kripodb", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597262", "name": "knime-kripodb", "full_name": "3D-e-Chem/knime-kripodb", - "html_url": "https://github.com/3D-e-Chem/knime-kripodb", "private": false, "description": "Knime node for KripoDB package", "created_at": "2016-02-12T11:12:39Z", diff --git a/database/github/3D-e-Chem/knime-molviewer/metadata.json b/database/github/3D-e-Chem/knime-molviewer/metadata.json index f482cdffb..01a34251f 100644 --- a/database/github/3D-e-Chem/knime-molviewer/metadata.json +++ b/database/github/3D-e-Chem/knime-molviewer/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-molviewer", - "url": "https://api.github.com/repos/3D-e-Chem/knime-molviewer", + "url": "https://github.com/3D-e-Chem/knime-molviewer", "data": { "timestamp": "2020-07-05 00:17:15.191079", "name": "knime-molviewer", - "url": "https://api.github.com/repos/3D-e-Chem/knime-molviewer", + "url": "https://github.com/3D-e-Chem/knime-molviewer", "full_name": "3D-e-Chem/knime-molviewer", "html_url": "https://github.com/3D-e-Chem/knime-molviewer", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597231", "name": "knime-molviewer", "full_name": "3D-e-Chem/knime-molviewer", - "html_url": "https://github.com/3D-e-Chem/knime-molviewer", "private": false, "description": "KNIME node which launches a web browser with moleculer viewer powered by webgl", "created_at": "2016-08-12T19:13:57Z", diff --git a/database/github/3D-e-Chem/knime-pharmacophore/metadata.json b/database/github/3D-e-Chem/knime-pharmacophore/metadata.json index 3aa67e67a..644dfed89 100644 --- a/database/github/3D-e-Chem/knime-pharmacophore/metadata.json +++ b/database/github/3D-e-Chem/knime-pharmacophore/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-pharmacophore", - "url": "https://api.github.com/repos/3D-e-Chem/knime-pharmacophore", + "url": "https://github.com/3D-e-Chem/knime-pharmacophore", "data": { "timestamp": "2020-07-05 00:17:06.675589", "name": "knime-pharmacophore", - "url": "https://api.github.com/repos/3D-e-Chem/knime-pharmacophore", + "url": "https://github.com/3D-e-Chem/knime-pharmacophore", "full_name": "3D-e-Chem/knime-pharmacophore", "html_url": "https://github.com/3D-e-Chem/knime-pharmacophore", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.997332", "name": "knime-pharmacophore", "full_name": "3D-e-Chem/knime-pharmacophore", - "html_url": "https://github.com/3D-e-Chem/knime-pharmacophore", "private": false, "description": "KNIME nodes to read/write pharmacophore files", "created_at": "2017-06-23T15:10:14Z", diff --git a/database/github/3D-e-Chem/knime-plants/metadata.json b/database/github/3D-e-Chem/knime-plants/metadata.json index 51d9b4fc9..dccdacdac 100644 --- a/database/github/3D-e-Chem/knime-plants/metadata.json +++ b/database/github/3D-e-Chem/knime-plants/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-plants", - "url": "https://api.github.com/repos/3D-e-Chem/knime-plants", + "url": "https://github.com/3D-e-Chem/knime-plants", "data": { "timestamp": "2020-07-05 00:17:06.840344", "name": "knime-plants", - "url": "https://api.github.com/repos/3D-e-Chem/knime-plants", + "url": "https://github.com/3D-e-Chem/knime-plants", "full_name": "3D-e-Chem/knime-plants", "html_url": "https://github.com/3D-e-Chem/knime-plants", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.997272", "name": "knime-plants", "full_name": "3D-e-Chem/knime-plants", - "html_url": "https://github.com/3D-e-Chem/knime-plants", "private": false, "description": "KNIME nodes to configure, run and analyze PLANTS protein-ligand docking", "created_at": "2016-11-29T09:55:05Z", diff --git a/database/github/3D-e-Chem/knime-python-node-archetype/metadata.json b/database/github/3D-e-Chem/knime-python-node-archetype/metadata.json index bf26a194e..787bf856e 100644 --- a/database/github/3D-e-Chem/knime-python-node-archetype/metadata.json +++ b/database/github/3D-e-Chem/knime-python-node-archetype/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-python-node-archetype", - "url": "https://api.github.com/repos/3D-e-Chem/knime-python-node-archetype", + "url": "https://github.com/3D-e-Chem/knime-python-node-archetype", "data": { "timestamp": "2020-07-05 00:17:07.000894", "name": "knime-python-node-archetype", - "url": "https://api.github.com/repos/3D-e-Chem/knime-python-node-archetype", + "url": "https://github.com/3D-e-Chem/knime-python-node-archetype", "full_name": "3D-e-Chem/knime-python-node-archetype", "html_url": "https://github.com/3D-e-Chem/knime-python-node-archetype", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597226", "name": "knime-python-node-archetype", "full_name": "3D-e-Chem/knime-python-node-archetype", - "html_url": "https://github.com/3D-e-Chem/knime-python-node-archetype", "private": false, "description": "Knime Python node archetype", "created_at": "2016-07-11T15:36:03Z", diff --git a/database/github/3D-e-Chem/knime-python-wrapper/metadata.json b/database/github/3D-e-Chem/knime-python-wrapper/metadata.json index 507e659cb..a7c604b66 100644 --- a/database/github/3D-e-Chem/knime-python-wrapper/metadata.json +++ b/database/github/3D-e-Chem/knime-python-wrapper/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-python-wrapper", - "url": "https://api.github.com/repos/3D-e-Chem/knime-python-wrapper", + "url": "https://github.com/3D-e-Chem/knime-python-wrapper", "data": { "timestamp": "2020-07-05 00:17:07.148367", "name": "knime-python-wrapper", - "url": "https://api.github.com/repos/3D-e-Chem/knime-python-wrapper", + "url": "https://github.com/3D-e-Chem/knime-python-wrapper", "full_name": "3D-e-Chem/knime-python-wrapper", "html_url": "https://github.com/3D-e-Chem/knime-python-wrapper", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597238", "name": "knime-python-wrapper", "full_name": "3D-e-Chem/knime-python-wrapper", - "html_url": "https://github.com/3D-e-Chem/knime-python-wrapper", "private": false, "description": "Utilities for development of KNIME nodes calling Python scripts.", "created_at": "2016-07-11T12:11:54Z", diff --git a/database/github/3D-e-Chem/knime-silicos-it/metadata.json b/database/github/3D-e-Chem/knime-silicos-it/metadata.json index 10cc9cb59..90147d469 100644 --- a/database/github/3D-e-Chem/knime-silicos-it/metadata.json +++ b/database/github/3D-e-Chem/knime-silicos-it/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-silicos-it", - "url": "https://api.github.com/repos/3D-e-Chem/knime-silicos-it", + "url": "https://github.com/3D-e-Chem/knime-silicos-it", "data": { "timestamp": "2020-07-05 00:17:07.332748", "name": "knime-silicos-it", - "url": "https://api.github.com/repos/3D-e-Chem/knime-silicos-it", + "url": "https://github.com/3D-e-Chem/knime-silicos-it", "full_name": "3D-e-Chem/knime-silicos-it", "html_url": "https://github.com/3D-e-Chem/knime-silicos-it", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597793", "name": "knime-silicos-it", "full_name": "3D-e-Chem/knime-silicos-it", - "html_url": "https://github.com/3D-e-Chem/knime-silicos-it", "private": false, "description": "KNIME nodes and example workflows for software made by Silicos-it, ie. align-it, shape-it", "created_at": "2017-04-19T09:52:58Z", diff --git a/database/github/3D-e-Chem/knime-sstea/metadata.json b/database/github/3D-e-Chem/knime-sstea/metadata.json index a6820ec08..1b202a76a 100644 --- a/database/github/3D-e-Chem/knime-sstea/metadata.json +++ b/database/github/3D-e-Chem/knime-sstea/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-sstea", - "url": "https://api.github.com/repos/3D-e-Chem/knime-sstea", + "url": "https://github.com/3D-e-Chem/knime-sstea", "data": { "timestamp": "2020-07-05 00:17:15.362481", "name": "knime-sstea", - "url": "https://api.github.com/repos/3D-e-Chem/knime-sstea", + "url": "https://github.com/3D-e-Chem/knime-sstea", "full_name": "3D-e-Chem/knime-sstea", "html_url": "https://github.com/3D-e-Chem/knime-sstea", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597241", "name": "knime-sstea", "full_name": "3D-e-Chem/knime-sstea", - "html_url": "https://github.com/3D-e-Chem/knime-sstea", "private": false, "description": "Knime node to calculate ss-TEA score of sequence alignment and subfamily members.", "created_at": "2016-05-04T15:08:06Z", diff --git a/database/github/3D-e-Chem/knime-sygma/metadata.json b/database/github/3D-e-Chem/knime-sygma/metadata.json index 1311dfe35..6a5f8075e 100644 --- a/database/github/3D-e-Chem/knime-sygma/metadata.json +++ b/database/github/3D-e-Chem/knime-sygma/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-sygma", - "url": "https://api.github.com/repos/3D-e-Chem/knime-sygma", + "url": "https://github.com/3D-e-Chem/knime-sygma", "data": { "timestamp": "2020-07-05 00:17:07.480646", "name": "knime-sygma", - "url": "https://api.github.com/repos/3D-e-Chem/knime-sygma", + "url": "https://github.com/3D-e-Chem/knime-sygma", "full_name": "3D-e-Chem/knime-sygma", "html_url": "https://github.com/3D-e-Chem/knime-sygma", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1033752", "name": "knime-sygma", "full_name": "3D-e-Chem/knime-sygma", - "html_url": "https://github.com/3D-e-Chem/knime-sygma", "private": false, "description": "KNIME nodes for Sygma", "created_at": "2016-07-12T08:27:52Z", diff --git a/database/github/3D-e-Chem/knime-testflow/metadata.json b/database/github/3D-e-Chem/knime-testflow/metadata.json index b8668eeaf..120785c40 100644 --- a/database/github/3D-e-Chem/knime-testflow/metadata.json +++ b/database/github/3D-e-Chem/knime-testflow/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/3D-e-Chem/knime-testflow", - "url": "https://api.github.com/repos/3D-e-Chem/knime-testflow", + "url": "https://github.com/3D-e-Chem/knime-testflow", "data": { "timestamp": "2020-07-05 00:17:15.509928", "name": "knime-testflow", - "url": "https://api.github.com/repos/3D-e-Chem/knime-testflow", + "url": "https://github.com/3D-e-Chem/knime-testflow", "full_name": "3D-e-Chem/knime-testflow", "html_url": "https://github.com/3D-e-Chem/knime-testflow", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.55805", "name": "knime-testflow", "full_name": "3D-e-Chem/knime-testflow", - "html_url": "https://github.com/3D-e-Chem/knime-testflow", "private": false, 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database/github/amrex-astro/Castro/metadata.json rename to database/github/AMReX-Astro/Castro/Castro/metadata.json diff --git a/database/github/amrex-astro/MAESTRO/metadata.json b/database/github/AMReX-Astro/MAESTRO/metadata.json similarity index 100% rename from database/github/amrex-astro/MAESTRO/metadata.json rename to database/github/AMReX-Astro/MAESTRO/metadata.json diff --git a/database/github/amrex-astro/Nyx/metadata.json b/database/github/AMReX-Astro/Nyx/Nyx/metadata.json similarity index 100% rename from database/github/amrex-astro/Nyx/metadata.json rename to database/github/AMReX-Astro/Nyx/Nyx/metadata.json diff --git a/database/github/annacrnn/rebound_fragmentation/metadata.json b/database/github/ANNACRNN/REBOUND_fragmentation/metadata.json similarity index 100% rename from database/github/annacrnn/rebound_fragmentation/metadata.json rename to database/github/ANNACRNN/REBOUND_fragmentation/metadata.json diff --git a/database/github/adrijd/beamconv/metadata.json b/database/github/AdriJD/beamconv/metadata.json similarity index 100% rename from database/github/adrijd/beamconv/metadata.json rename to database/github/AdriJD/beamconv/metadata.json diff --git a/database/github/Alcampopiano/hypothesize/metadata.json b/database/github/Alcampopiano/hypothesize/metadata.json index a517be042..addcb0fca 100644 --- a/database/github/Alcampopiano/hypothesize/metadata.json +++ b/database/github/Alcampopiano/hypothesize/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/Alcampopiano/hypothesize", - "url": "https://api.github.com/repos/Alcampopiano/hypothesize", + "url": "https://github.com/Alcampopiano/hypothesize", "data": { "timestamp": "2020-07-04 13:22:10.361063", "name": "hypothesize", - "url": "https://api.github.com/repos/Alcampopiano/hypothesize", + "url": "https://github.com/Alcampopiano/hypothesize", "full_name": "Alcampopiano/hypothesize", "html_url": "https://github.com/Alcampopiano/hypothesize", "private": false, @@ -36,7 +36,6 @@ }, "name": "hypothesize", "full_name": "Alcampopiano/hypothesize", - "html_url": "https://github.com/Alcampopiano/hypothesize", "private": false, "description": "Robust statistics in Python", "created_at": "2020-03-04T20:39:34Z", diff --git a/database/github/SirSharpest/NarrowEscapeSimulator/metadata.json b/database/github/AoifeHughes/NarrowEscapeSimulator/metadata.json similarity index 100% rename from database/github/SirSharpest/NarrowEscapeSimulator/metadata.json rename to database/github/AoifeHughes/NarrowEscapeSimulator/metadata.json diff --git a/database/github/ArenA-Crowds/Crowds/metadata.json b/database/github/ArenA-Crowds/Crowds/metadata.json index d3840b4fe..df979bc62 100644 --- a/database/github/ArenA-Crowds/Crowds/metadata.json +++ b/database/github/ArenA-Crowds/Crowds/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ArenA-Crowds/Crowds", - "url": "https://api.github.com/repos/ArenA-Crowds/Crowds", + "url": "https://github.com/ArenA-Crowds/Crowds", 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"full_name": "Blosc/c-blosc", "html_url": "https://github.com/Blosc/c-blosc", "private": false, @@ -30,7 +30,6 @@ }, "name": "c-blosc", "full_name": "Blosc/c-blosc", - "html_url": "https://github.com/Blosc/c-blosc", "private": false, "description": "A blocking, shuffling and loss-less compression library that can be faster than `memcpy()`.", "created_at": "2011-07-03T11:38:39Z", diff --git a/database/github/BrianAronson/birankr/metadata.json b/database/github/BrianAronson/birankr/metadata.json index 7c72c7aae..2e116e21e 100644 --- a/database/github/BrianAronson/birankr/metadata.json +++ b/database/github/BrianAronson/birankr/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/BrianAronson/birankr", - "url": "https://api.github.com/repos/BrianAronson/birankr", + "url": "https://github.com/BrianAronson/birankr", "data": { "timestamp": "2020-07-12 00:26:29.717920", "name": "birankr", - "url": "https://api.github.com/repos/BrianAronson/birankr", + "url": 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database/github/combine-lab/salmon/metadata.json rename to database/github/COMBINE-lab/salmon/salmon/metadata.json diff --git a/database/github/csb5/lofreq/metadata.json b/database/github/CSB5/lofreq/metadata.json similarity index 100% rename from database/github/csb5/lofreq/metadata.json rename to database/github/CSB5/lofreq/metadata.json diff --git a/database/github/Cantera/cantera/metadata.json b/database/github/Cantera/cantera/metadata.json index b0869430f..0f447440a 100644 --- a/database/github/Cantera/cantera/metadata.json +++ b/database/github/Cantera/cantera/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/Cantera/cantera", - "url": "https://api.github.com/repos/Cantera/cantera", + "url": "https://github.com/Cantera/cantera", "data": { "timestamp": "2020-07-04 13:22:26.048044", "name": "cantera", - "url": "https://api.github.com/repos/Cantera/cantera", + "url": "https://github.com/Cantera/cantera", "full_name": "Cantera/cantera", "html_url": 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"url": "https://api.github.com/repos/DreamCloud-Project/AMALTHEA-SimGrid", + "url": "https://github.com/DreamCloud-Project/AMALTHEA-SimGrid", "data": { "timestamp": "2020-07-05 00:17:52.705331", "name": "AMALTHEA-SimGrid", - "url": "https://api.github.com/repos/DreamCloud-Project/AMALTHEA-SimGrid", + "url": "https://github.com/DreamCloud-Project/AMALTHEA-SimGrid", "full_name": "DreamCloud-Project/AMALTHEA-SimGrid", "html_url": "https://github.com/DreamCloud-Project/AMALTHEA-SimGrid", "private": false, @@ -36,7 +36,6 @@ }, "name": "AMALTHEA-SimGrid", "full_name": "DreamCloud-Project/AMALTHEA-SimGrid", - "html_url": "https://github.com/DreamCloud-Project/AMALTHEA-SimGrid", "private": false, "description": "Simulator for cloud applications described using the Amalthea application model on top of SimGrid", "created_at": "2015-10-26T18:35:34Z", diff --git a/database/github/DreamCloud-Project/McSim-Cycle-accurate-NoC/metadata.json b/database/github/DreamCloud-Project/McSim-Cycle-accurate-NoC/metadata.json index 14460080a..e5f71d7ac 100644 --- a/database/github/DreamCloud-Project/McSim-Cycle-accurate-NoC/metadata.json +++ b/database/github/DreamCloud-Project/McSim-Cycle-accurate-NoC/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/DreamCloud-Project/McSim-Cycle-accurate-NoC", - 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"url": "https://api.github.com/repos/ERA-URBAN/fm128_radar", + "url": "https://github.com/ERA-URBAN/fm128_radar", "data": { "timestamp": "2020-07-05 00:17:25.673934", "name": "fm128_radar", - "url": "https://api.github.com/repos/ERA-URBAN/fm128_radar", + "url": "https://github.com/ERA-URBAN/fm128_radar", "full_name": "ERA-URBAN/fm128_radar", "html_url": "https://github.com/ERA-URBAN/fm128_radar", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1420223", "name": "fm128_radar", "full_name": "ERA-URBAN/fm128_radar", - "html_url": "https://github.com/ERA-URBAN/fm128_radar", "private": false, "description": null, "created_at": "2016-12-21T11:50:04Z", diff --git a/database/github/ERA-URBAN/netcdf2littler/metadata.json b/database/github/ERA-URBAN/netcdf2littler/metadata.json index 9350c4969..bb89e9394 100644 --- a/database/github/ERA-URBAN/netcdf2littler/metadata.json +++ b/database/github/ERA-URBAN/netcdf2littler/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ERA-URBAN/netcdf2littler", - 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"url": "https://github.com/JuliaMatrices/LazyBandedMatrices.jl", + "url": "https://github.com/JuliaLinearAlgebra/LazyBandedMatrices.jl", "data": { "timestamp": "2022-05-12 03:43:41.410548", "name": "LazyBandedMatrices.jl", - "url": "https://api.github.com/repos/JuliaMatrices/LazyBandedMatrices.jl", + "url": "https://github.com/JuliaLinearAlgebra/LazyBandedMatrices.jl", "full_name": "JuliaMatrices/LazyBandedMatrices.jl", "html_url": "https://github.com/JuliaMatrices/LazyBandedMatrices.jl", "private": false, @@ -35,6 +35,5 @@ }, "topics": [] }, - "rsotm": "2022-02", - "html_url": "https://github.com/JuliaLinearAlgebra/LazyBandedMatrices.jl" + "rsotm": "2022-02" } \ No newline at end of file diff --git a/database/github/0x0f0f0f/Metatheory.jl/metadata.json b/database/github/JuliaSymbolics/Metatheory.jl/metadata.json similarity index 86% rename from database/github/0x0f0f0f/Metatheory.jl/metadata.json rename to database/github/JuliaSymbolics/Metatheory.jl/metadata.json index 150d176dc..2419a046a 100644 --- a/database/github/0x0f0f0f/Metatheory.jl/metadata.json +++ b/database/github/JuliaSymbolics/Metatheory.jl/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/0x0f0f0f/Metatheory.jl", - 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"url": "https://api.github.com/repos/NLeSC/ShiCo", + "url": "https://github.com/NLeSC/ShiCo", "data": { "timestamp": "2020-07-05 00:17:21.308467", "name": "ShiCo", - "url": "https://api.github.com/repos/NLeSC/ShiCo", + "url": "https://github.com/NLeSC/ShiCo", "full_name": "NLeSC/ShiCo", "html_url": "https://github.com/NLeSC/ShiCo", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1187089", "name": "ShiCo", "full_name": "NLeSC/ShiCo", - "html_url": "https://github.com/NLeSC/ShiCo", "private": false, "description": "Netherlands eScience Center - Shifting Concepts Through Time project", "created_at": "2015-11-04T09:06:02Z", diff --git a/database/github/NLeSC/UncertaintyVisualization/metadata.json b/database/github/NLeSC/UncertaintyVisualization/metadata.json index f134e2876..2d48e1413 100644 --- a/database/github/NLeSC/UncertaintyVisualization/metadata.json +++ b/database/github/NLeSC/UncertaintyVisualization/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/UncertaintyVisualization", - "url": "https://api.github.com/repos/NLeSC/UncertaintyVisualization", + "url": "https://github.com/NLeSC/UncertaintyVisualization", "data": { "timestamp": "2020-07-05 00:17:21.797713", "name": "UncertaintyVisualization", - "url": "https://api.github.com/repos/NLeSC/UncertaintyVisualization", + "url": "https://github.com/NLeSC/UncertaintyVisualization", "full_name": "NLeSC/UncertaintyVisualization", "html_url": "https://github.com/NLeSC/UncertaintyVisualization", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.996323", "name": "UncertaintyVisualization", "full_name": "NLeSC/UncertaintyVisualization", - "html_url": "https://github.com/NLeSC/UncertaintyVisualization", "private": false, "description": null, "created_at": "2015-07-30T09:06:11Z", diff --git a/database/github/NLeSC/ahn-pointcloud-viewer-ws/metadata.json b/database/github/NLeSC/ahn-pointcloud-viewer-ws/metadata.json index 5aacf9c7d..6c76b47e5 100644 --- a/database/github/NLeSC/ahn-pointcloud-viewer-ws/metadata.json +++ b/database/github/NLeSC/ahn-pointcloud-viewer-ws/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/ahn-pointcloud-viewer-ws", - "url": "https://api.github.com/repos/NLeSC/ahn-pointcloud-viewer-ws", + "url": "https://github.com/NLeSC/ahn-pointcloud-viewer-ws", "data": { "timestamp": "2020-07-05 00:17:08.189008", "name": "ahn-pointcloud-viewer-ws", - "url": "https://api.github.com/repos/NLeSC/ahn-pointcloud-viewer-ws", + "url": "https://github.com/NLeSC/ahn-pointcloud-viewer-ws", "full_name": "NLeSC/ahn-pointcloud-viewer-ws", "html_url": "https://github.com/NLeSC/ahn-pointcloud-viewer-ws", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.909307", "name": "ahn-pointcloud-viewer-ws", "full_name": "NLeSC/ahn-pointcloud-viewer-ws", - "html_url": "https://github.com/NLeSC/ahn-pointcloud-viewer-ws", "private": false, "description": "Webservice for ahn pointcloud viewer", "created_at": "2015-06-08T12:58:19Z", diff --git a/database/github/NLeSC/baklava/metadata.json b/database/github/NLeSC/baklava/metadata.json index 7a07c1581..78c73f366 100644 --- a/database/github/NLeSC/baklava/metadata.json +++ b/database/github/NLeSC/baklava/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/baklava", - "url": "https://api.github.com/repos/NLeSC/baklava", + "url": "https://github.com/NLeSC/baklava", "data": { "timestamp": "2020-07-05 00:17:27.341390", "name": "baklava", - "url": "https://api.github.com/repos/NLeSC/baklava", + "url": "https://github.com/NLeSC/baklava", "full_name": "NLeSC/baklava", "html_url": "https://github.com/NLeSC/baklava", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.3630355", "name": "baklava", "full_name": "NLeSC/baklava", - "html_url": "https://github.com/NLeSC/baklava", "private": false, "description": "Deploy a Kubernetes cluster and big data services on the cloud.", "created_at": "2019-05-08T09:54:45Z", diff --git a/database/github/NLeSC/boatswain/metadata.json b/database/github/NLeSC/boatswain/metadata.json index 2f43565b1..fd2ff0dd6 100644 --- a/database/github/NLeSC/boatswain/metadata.json +++ b/database/github/NLeSC/boatswain/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/boatswain", - "url": "https://api.github.com/repos/NLeSC/boatswain", + "url": "https://github.com/NLeSC/boatswain", "data": { "timestamp": "2020-07-05 00:17:09.269657", "name": "boatswain", - "url": "https://api.github.com/repos/NLeSC/boatswain", + "url": "https://github.com/NLeSC/boatswain", "full_name": "NLeSC/boatswain", "html_url": "https://github.com/NLeSC/boatswain", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1149010", "name": "boatswain", "full_name": "NLeSC/boatswain", - "html_url": "https://github.com/NLeSC/boatswain", "private": false, "description": "A simple build system for docker images", "created_at": "2017-02-02T12:23:44Z", diff --git a/database/github/NLeSC/case-law-app/metadata.json b/database/github/NLeSC/case-law-app/metadata.json index 647164026..7d051d574 100644 --- a/database/github/NLeSC/case-law-app/metadata.json +++ b/database/github/NLeSC/case-law-app/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/case-law-app", - "url": "https://api.github.com/repos/NLeSC/case-law-app", + "url": "https://github.com/NLeSC/case-law-app", "data": { "timestamp": "2020-07-05 00:17:09.586598", "name": "case-law-app", - "url": "https://api.github.com/repos/NLeSC/case-law-app", + "url": "https://github.com/NLeSC/case-law-app", "full_name": "NLeSC/case-law-app", "html_url": "https://github.com/NLeSC/case-law-app", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.596839", "name": "case-law-app", "full_name": "NLeSC/case-law-app", - "html_url": "https://github.com/NLeSC/case-law-app", "private": false, "description": null, "created_at": "2017-01-18T14:45:03Z", diff --git a/database/github/NLeSC/compressing-the-sky/metadata.json b/database/github/NLeSC/compressing-the-sky/metadata.json index a07871d87..0775cc09d 100644 --- a/database/github/NLeSC/compressing-the-sky/metadata.json +++ b/database/github/NLeSC/compressing-the-sky/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/compressing-the-sky", - "url": "https://api.github.com/repos/NLeSC/compressing-the-sky", + "url": "https://github.com/NLeSC/compressing-the-sky", "data": { "timestamp": "2020-07-05 00:17:10.882362", "name": "compressing-the-sky", - "url": "https://api.github.com/repos/NLeSC/compressing-the-sky", + "url": "https://github.com/NLeSC/compressing-the-sky", "full_name": "NLeSC/compressing-the-sky", "html_url": "https://github.com/NLeSC/compressing-the-sky", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1050368", "name": "compressing-the-sky", "full_name": "NLeSC/compressing-the-sky", - 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"url": "https://api.github.com/repos/NLeSC/docker-couch-admin", + "url": "https://github.com/NLeSC/docker-couch-admin", "data": { "timestamp": "2020-07-05 00:17:11.535657", "name": "docker-couch-admin", - "url": "https://api.github.com/repos/NLeSC/docker-couch-admin", + "url": "https://github.com/NLeSC/docker-couch-admin", "full_name": "NLeSC/docker-couch-admin", "html_url": "https://github.com/NLeSC/docker-couch-admin", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.61301", "name": "docker-couch-admin", "full_name": "NLeSC/docker-couch-admin", - "html_url": "https://github.com/NLeSC/docker-couch-admin", "private": false, "description": "Configures a web service using angular-schema-form and CouchDB", "created_at": "2016-01-07T14:04:01Z", diff --git a/database/github/NLeSC/eAstroViz/metadata.json b/database/github/NLeSC/eAstroViz/metadata.json index 638b4433a..61150d490 100644 --- a/database/github/NLeSC/eAstroViz/metadata.json +++ b/database/github/NLeSC/eAstroViz/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/eAstroViz", - 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"url": "https://api.github.com/repos/NLeSC/eEcology-Annotation-WS", + "url": "https://github.com/NLeSC/eEcology-Annotation-WS", "full_name": "NLeSC/eEcology-Annotation-WS", "html_url": "https://github.com/NLeSC/eEcology-Annotation-WS", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597984", "name": "eEcology-Annotation-WS", "full_name": "NLeSC/eEcology-Annotation-WS", - "html_url": "https://github.com/NLeSC/eEcology-Annotation-WS", "private": false, "description": "Webservice for eEcology Annotation project.", "created_at": "2013-08-28T10:59:18Z", diff --git a/database/github/NLeSC/eEcology-Classification/metadata.json b/database/github/NLeSC/eEcology-Classification/metadata.json index e5013f69c..377435dfa 100644 --- a/database/github/NLeSC/eEcology-Classification/metadata.json +++ b/database/github/NLeSC/eEcology-Classification/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/eEcology-Classification", - "url": "https://api.github.com/repos/NLeSC/eEcology-Classification", + "url": "https://github.com/NLeSC/eEcology-Classification", "data": { "timestamp": "2020-07-05 00:17:12.014307", "name": "eEcology-Classification", - "url": "https://api.github.com/repos/NLeSC/eEcology-Classification", + "url": "https://github.com/NLeSC/eEcology-Classification", "full_name": "NLeSC/eEcology-Classification", "html_url": "https://github.com/NLeSC/eEcology-Classification", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.594525", "name": "eEcology-Classification", "full_name": "NLeSC/eEcology-Classification", - "html_url": "https://github.com/NLeSC/eEcology-Classification", "private": false, "description": "Classification tool", "created_at": "2014-01-16T15:21:14Z", diff --git a/database/github/NLeSC/eEcology-SMS-reciever/metadata.json b/database/github/NLeSC/eEcology-SMS-reciever/metadata.json index b21fa7050..d0ab3d22f 100644 --- a/database/github/NLeSC/eEcology-SMS-reciever/metadata.json +++ b/database/github/NLeSC/eEcology-SMS-reciever/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/eEcology-SMS-reciever", - "url": "https://api.github.com/repos/NLeSC/eEcology-SMS-reciever", + "url": "https://github.com/NLeSC/eEcology-SMS-reciever", "data": { "timestamp": "2020-07-05 00:17:12.166766", "name": "eEcology-SMS-reciever", - "url": "https://api.github.com/repos/NLeSC/eEcology-SMS-reciever", + "url": "https://github.com/NLeSC/eEcology-SMS-reciever", "full_name": "NLeSC/eEcology-SMS-reciever", "html_url": "https://github.com/NLeSC/eEcology-SMS-reciever", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.598013", "name": "eEcology-SMS-reciever", "full_name": "NLeSC/eEcology-SMS-reciever", - "html_url": "https://github.com/NLeSC/eEcology-SMS-reciever", "private": false, "description": "Webservice to store SMS messages into a database table", "created_at": "2015-02-25T17:01:40Z", diff --git a/database/github/NLeSC/eEcology-script-wrapper/metadata.json b/database/github/NLeSC/eEcology-script-wrapper/metadata.json index 128904f18..3fb9975f5 100644 --- a/database/github/NLeSC/eEcology-script-wrapper/metadata.json +++ b/database/github/NLeSC/eEcology-script-wrapper/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/eEcology-script-wrapper", - "url": "https://api.github.com/repos/NLeSC/eEcology-script-wrapper", + "url": "https://github.com/NLeSC/eEcology-script-wrapper", "data": { "timestamp": "2020-07-05 00:17:12.344100", "name": "eEcology-script-wrapper", - "url": "https://api.github.com/repos/NLeSC/eEcology-script-wrapper", + "url": "https://github.com/NLeSC/eEcology-script-wrapper", "full_name": "NLeSC/eEcology-script-wrapper", "html_url": "https://github.com/NLeSC/eEcology-script-wrapper", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1034002", "name": "eEcology-script-wrapper", "full_name": "NLeSC/eEcology-script-wrapper", - "html_url": "https://github.com/NLeSC/eEcology-script-wrapper", "private": false, "description": "Web application to make Matlab, R scripts available.", "created_at": "2013-09-19T14:21:14Z", diff --git a/database/github/NLeSC/eSalsa-MPI/metadata.json b/database/github/NLeSC/eSalsa-MPI/metadata.json index 6fb72acce..e56b0ea38 100644 --- a/database/github/NLeSC/eSalsa-MPI/metadata.json +++ b/database/github/NLeSC/eSalsa-MPI/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/eSalsa-MPI", - "url": "https://api.github.com/repos/NLeSC/eSalsa-MPI", + "url": "https://github.com/NLeSC/eSalsa-MPI", "data": { "timestamp": "2020-07-05 00:17:16.107634", "name": "eSalsa-MPI", - "url": "https://api.github.com/repos/NLeSC/eSalsa-MPI", + "url": "https://github.com/NLeSC/eSalsa-MPI", "full_name": "NLeSC/eSalsa-MPI", "html_url": "https://github.com/NLeSC/eSalsa-MPI", "private": false, @@ -36,7 +36,6 @@ }, "name": "eSalsa-MPI", "full_name": "NLeSC/eSalsa-MPI", - "html_url": "https://github.com/NLeSC/eSalsa-MPI", "private": false, "description": "This project contains the wide area MPI used in the eSalsa project", "created_at": "2013-08-06T14:24:14Z", diff --git a/database/github/nlesc/embodied-emotions-scripts/metadata.json b/database/github/NLeSC/embodied-emotions-scripts/metadata.json similarity index 90% rename from database/github/nlesc/embodied-emotions-scripts/metadata.json rename to database/github/NLeSC/embodied-emotions-scripts/metadata.json index 0b17adaff..20a763f5d 100644 --- a/database/github/nlesc/embodied-emotions-scripts/metadata.json +++ b/database/github/NLeSC/embodied-emotions-scripts/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nlesc/embodied-emotions-scripts", - "url": "https://api.github.com/repos/NLeSC/embodied-emotions-scripts", + "url": "https://github.com/NLeSC/embodied-emotions-scripts", "data": { "timestamp": "2020-07-05 00:17:12.642187", "name": "embodied-emotions-scripts", - "url": "https://api.github.com/repos/NLeSC/embodied-emotions-scripts", + "url": "https://github.com/NLeSC/embodied-emotions-scripts", "full_name": "NLeSC/embodied-emotions-scripts", "html_url": "https://github.com/NLeSC/embodied-emotions-scripts", "private": false, @@ -36,7 +36,6 @@ }, "name": "embodied-emotions-scripts", "full_name": "NLeSC/embodied-emotions-scripts", - "html_url": "https://github.com/NLeSC/embodied-emotions-scripts", "private": false, "description": null, "created_at": "2015-10-02T08:46:50Z", diff --git a/database/github/NLeSC/esibayes/metadata.json b/database/github/NLeSC/esibayes/metadata.json index 33e89a283..a131601ac 100644 --- a/database/github/NLeSC/esibayes/metadata.json +++ b/database/github/NLeSC/esibayes/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/esibayes", - 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"url": "https://api.github.com/repos/NLeSC/fairdatapoint", + "url": "https://github.com/NLeSC/fairdatapoint", "full_name": "NLeSC/fairdatapoint", "html_url": "https://github.com/NLeSC/fairdatapoint", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1083950", "name": "fairdatapoint", "full_name": "NLeSC/fairdatapoint", - "html_url": "https://github.com/NLeSC/fairdatapoint", "private": false, "description": "Provide machine-readable descriptions of your data assets", "created_at": "2015-06-15T14:39:10Z", diff --git a/database/github/NLeSC/hadrianus-scripts/metadata.json b/database/github/NLeSC/hadrianus-scripts/metadata.json index 15db2845d..48d3542d6 100644 --- a/database/github/NLeSC/hadrianus-scripts/metadata.json +++ b/database/github/NLeSC/hadrianus-scripts/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/hadrianus-scripts", - "url": "https://api.github.com/repos/NLeSC/hadrianus-scripts", + "url": "https://github.com/NLeSC/hadrianus-scripts", "data": { "timestamp": "2020-07-05 00:17:14.302796", "name": "hadrianus-scripts", - "url": "https://api.github.com/repos/NLeSC/hadrianus-scripts", + "url": "https://github.com/NLeSC/hadrianus-scripts", "full_name": "NLeSC/hadrianus-scripts", "html_url": "https://github.com/NLeSC/hadrianus-scripts", "private": false, @@ -31,7 +31,6 @@ "doi": "10.5281/zenodo.1462264", "name": "hadrianus-scripts", "full_name": "NLeSC/hadrianus-scripts", - "html_url": "https://github.com/NLeSC/hadrianus-scripts", "private": false, "description": "Scripts used for the Hadrianus project", "created_at": "2016-02-09T12:25:08Z", diff --git a/database/github/NLeSC/lokum/metadata.json b/database/github/NLeSC/lokum/metadata.json index eb56d89ed..3166b24a0 100644 --- a/database/github/NLeSC/lokum/metadata.json +++ b/database/github/NLeSC/lokum/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/lokum", - "url": "https://api.github.com/repos/NLeSC/lokum", + "url": "https://github.com/NLeSC/lokum", "data": { "timestamp": "2020-07-05 00:17:27.467253", "name": "lokum", - "url": "https://api.github.com/repos/NLeSC/lokum", + "url": "https://github.com/NLeSC/lokum", "full_name": "NLeSC/lokum", "html_url": "https://github.com/NLeSC/lokum", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.3482938", "name": "lokum", "full_name": "NLeSC/lokum", - 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"url": "https://api.github.com/repos/AA-ALERT/AstroData", + "url": "https://github.com/TRASAL/AstroData", "data": { "timestamp": "2020-07-05 00:17:08.985805", "name": "AstroData", - "url": "https://api.github.com/repos/AA-ALERT/AstroData", + "url": "https://github.com/TRASAL/AstroData", "full_name": "AA-ALERT/AstroData", "html_url": "https://github.com/AA-ALERT/AstroData", "private": false, @@ -36,7 +36,6 @@ }, "name": "AstroData", "full_name": "AA-ALERT/AstroData", - "html_url": "https://github.com/TRASAL/AstroData", "private": false, "description": "Set of C++ classes to operate on radio astronomical data.", "created_at": "2012-10-31T14:04:56Z", diff --git a/database/github/AA-ALERT/AstroData/taxonomy.tsv b/database/github/TRASAL/AstroData/taxonomy.tsv similarity index 100% rename from database/github/AA-ALERT/AstroData/taxonomy.tsv rename to database/github/TRASAL/AstroData/taxonomy.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-absence.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-absence.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-absence.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-absence.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-citation.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-citation.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-citation.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-citation.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-domain-intention.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-domain-intention.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-domain-intention.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-domain-intention.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-question-intention.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-question-intention.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-question-intention.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-question-intention.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-research-intention.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-research-intention.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-research-intention.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-research-intention.tsv diff --git a/database/github/AA-ALERT/Dedispersion/criteria-RSE-usage.tsv b/database/github/TRASAL/Dedispersion/criteria-RSE-usage.tsv similarity index 100% rename from database/github/AA-ALERT/Dedispersion/criteria-RSE-usage.tsv rename to database/github/TRASAL/Dedispersion/criteria-RSE-usage.tsv diff --git a/database/github/AA-ALERT/Dedispersion/metadata.json b/database/github/TRASAL/Dedispersion/metadata.json similarity index 92% rename from database/github/AA-ALERT/Dedispersion/metadata.json rename to database/github/TRASAL/Dedispersion/metadata.json index c53f0e9a5..9b8826322 100644 --- a/database/github/AA-ALERT/Dedispersion/metadata.json +++ b/database/github/TRASAL/Dedispersion/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/AA-ALERT/Dedispersion", - 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"url": "https://api.github.com/repos/anmolter/XLUR", + "url": "https://github.com/anmolter/XLUR", "full_name": "anmolter/XLUR", "html_url": "https://github.com/anmolter/XLUR", "private": false, @@ -36,7 +36,6 @@ }, "name": "XLUR", "full_name": "anmolter/XLUR", - "html_url": "https://github.com/anmolter/XLUR", "private": false, "description": "A Python toolbox for ArcGIS Pro that enables the development and application of land use regression models.", "created_at": "2019-09-19T10:12:12Z", diff --git a/database/github/anuwu/DAGN-Blindtest/metadata.json b/database/github/anuwu/GOTHIC/DAGN-Blindtest/metadata.json similarity index 100% rename from database/github/anuwu/DAGN-Blindtest/metadata.json rename to database/github/anuwu/GOTHIC/DAGN-Blindtest/metadata.json diff --git a/database/github/JunTaoLuo/mctreesearch4j/metadata.json b/database/github/aqtech-ca/mctreesearch4j/metadata.json similarity index 100% rename from database/github/JunTaoLuo/mctreesearch4j/metadata.json rename to database/github/aqtech-ca/mctreesearch4j/metadata.json diff --git a/database/github/arabic-digital-humanities/adhtools/metadata.json b/database/github/arabic-digital-humanities/adhtools/metadata.json index e096a3d3c..531ac2e2b 100644 --- a/database/github/arabic-digital-humanities/adhtools/metadata.json +++ b/database/github/arabic-digital-humanities/adhtools/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/arabic-digital-humanities/adhtools", - "url": "https://api.github.com/repos/arabic-digital-humanities/adhtools", + "url": "https://github.com/arabic-digital-humanities/adhtools", "data": { "timestamp": "2020-07-05 00:17:25.968824", "name": "adhtools", - "url": "https://api.github.com/repos/arabic-digital-humanities/adhtools", + "url": "https://github.com/arabic-digital-humanities/adhtools", "full_name": "arabic-digital-humanities/adhtools", "html_url": "https://github.com/arabic-digital-humanities/adhtools", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.2633819", "name": "adhtools", "full_name": "arabic-digital-humanities/adhtools", - "html_url": "https://github.com/arabic-digital-humanities/adhtools", "private": false, "description": "Scripts for manipulating Arabic texts", "created_at": "2018-01-25T09:47:41Z", diff --git a/database/github/arviz-devs/arviz/metadata.json b/database/github/arviz-devs/arviz/metadata.json index 4814b868c..295c4c8dd 100644 --- a/database/github/arviz-devs/arviz/metadata.json +++ b/database/github/arviz-devs/arviz/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/arviz-devs/arviz", - "url": "https://api.github.com/repos/arviz-devs/arviz", + "url": "https://github.com/arviz-devs/arviz", "data": { "timestamp": "2020-07-04 13:22:20.416780", "name": "arviz", - "url": "https://api.github.com/repos/arviz-devs/arviz", + "url": "https://github.com/arviz-devs/arviz", "full_name": "arviz-devs/arviz", "html_url": "https://github.com/arviz-devs/arviz", "private": false, @@ -36,7 +36,6 @@ }, "name": "arviz", "full_name": "arviz-devs/arviz", - "html_url": "https://github.com/arviz-devs/arviz", "private": false, "description": "Exploratory analysis of Bayesian models with Python", "created_at": "2015-07-29T11:51:10Z", diff --git a/database/github/astroml/gatspy/metadata.json b/database/github/astroML/gatspy/gatspy/metadata.json similarity index 100% rename from database/github/astroml/gatspy/metadata.json rename to database/github/astroML/gatspy/gatspy/metadata.json diff --git a/database/github/astropy/astropy/metadata.json b/database/github/astropy/astropy/metadata.json index 898d19a2a..0cf0891d3 100644 --- a/database/github/astropy/astropy/metadata.json +++ b/database/github/astropy/astropy/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/astropy/astropy", - 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"url": "https://api.github.com/repos/c-martinez/BeyondTheBook", + "url": "https://github.com/c-martinez/BeyondTheBook", "data": { "timestamp": "2020-07-05 00:17:09.143818", "name": "BeyondTheBook", - "url": "https://api.github.com/repos/c-martinez/BeyondTheBook", + "url": "https://github.com/c-martinez/BeyondTheBook", "full_name": "c-martinez/BeyondTheBook", "html_url": "https://github.com/c-martinez/BeyondTheBook", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1436372", "name": "BeyondTheBook", "full_name": "c-martinez/BeyondTheBook", - "html_url": "https://github.com/c-martinez/BeyondTheBook", "private": false, "description": "Using Wikipedia to assess the translatability of text.", "created_at": "2014-08-14T11:30:21Z", diff --git a/database/github/c3s-magic/c3s-magic-wps/metadata.json b/database/github/c3s-magic/c3s-magic-wps/metadata.json index 8735b4f54..5c1f19d08 100644 --- a/database/github/c3s-magic/c3s-magic-wps/metadata.json +++ b/database/github/c3s-magic/c3s-magic-wps/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/c3s-magic/c3s-magic-wps", - "url": "https://api.github.com/repos/c3s-magic/c3s-magic-wps", + "url": "https://github.com/c3s-magic/c3s-magic-wps", "data": { "timestamp": "2020-07-05 00:17:26.616981", "name": "c3s-magic-wps", - "url": "https://api.github.com/repos/c3s-magic/c3s-magic-wps", + "url": "https://github.com/c3s-magic/c3s-magic-wps", "full_name": "c3s-magic/c3s-magic-wps", "html_url": "https://github.com/c3s-magic/c3s-magic-wps", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.3240041", "name": "c3s-magic-wps", "full_name": "c3s-magic/c3s-magic-wps", - "html_url": "https://github.com/c3s-magic/c3s-magic-wps", "private": false, "description": null, "created_at": "2019-04-30T12:02:23Z", diff --git a/database/github/calboo/wigglewave/metadata.json b/database/github/calboo/Wigglewave/metadata.json similarity index 100% rename from database/github/calboo/wigglewave/metadata.json rename to database/github/calboo/Wigglewave/metadata.json diff --git a/database/github/cameronliang/BayesVP/metadata.json b/database/github/cameronliang/bayesvp/metadata.json similarity index 100% rename from database/github/cameronliang/BayesVP/metadata.json rename to database/github/cameronliang/bayesvp/metadata.json diff --git a/database/github/candYgene/QTM/metadata.json b/database/github/candYgene/QTM/metadata.json index f761839ef..e272efe52 100644 --- a/database/github/candYgene/QTM/metadata.json +++ b/database/github/candYgene/QTM/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/candYgene/QTM", - "url": "https://api.github.com/repos/candYgene/QTM", + "url": "https://github.com/candYgene/QTM", "data": { "timestamp": "2020-07-05 00:17:19.302552", "name": "QTM", - "url": "https://api.github.com/repos/candYgene/QTM", + "url": "https://github.com/candYgene/QTM", "full_name": "candYgene/QTM", "html_url": "https://github.com/candYgene/QTM", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1193639", "name": "QTM", "full_name": "candYgene/QTM", - "html_url": "https://github.com/candYgene/QTM", "private": false, "description": "QTLTableMiner++ tool for mining tables in scientific articles", "created_at": "2019-08-28T09:17:12Z", diff --git a/database/github/candYgene/abg-ld/metadata.json b/database/github/candYgene/abg-ld/metadata.json index b765cb32f..80d122b13 100644 --- a/database/github/candYgene/abg-ld/metadata.json +++ b/database/github/candYgene/abg-ld/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/candYgene/abg-ld", - "url": "https://api.github.com/repos/candYgene/abg-ld", + "url": "https://github.com/candYgene/abg-ld", "data": { "timestamp": "2020-07-05 00:17:15.667804", "name": "abg-ld", - "url": "https://api.github.com/repos/candYgene/abg-ld", + "url": "https://github.com/candYgene/abg-ld", "full_name": "candYgene/abg-ld", "html_url": "https://github.com/candYgene/abg-ld", "private": false, @@ -36,7 +36,6 @@ }, "name": "abg-ld", "full_name": "candYgene/abg-ld", - "html_url": "https://github.com/candYgene/abg-ld", "private": false, "description": "Linked Data Platform for Animal Breeding & Genomics", "created_at": "2017-04-10T21:04:46Z", diff --git a/database/github/candYgene/pbg-ld/metadata.json b/database/github/candYgene/pbg-ld/metadata.json index 87ad216ea..39743e7d5 100644 --- a/database/github/candYgene/pbg-ld/metadata.json +++ b/database/github/candYgene/pbg-ld/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/candYgene/pbg-ld", - "url": "https://api.github.com/repos/candYgene/pbg-ld", + "url": "https://github.com/candYgene/pbg-ld", "data": { "timestamp": "2020-07-05 00:17:15.801817", "name": "pbg-ld", - "url": "https://api.github.com/repos/candYgene/pbg-ld", + "url": "https://github.com/candYgene/pbg-ld", "full_name": "candYgene/pbg-ld", "html_url": "https://github.com/candYgene/pbg-ld", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1458168", "name": "pbg-ld", "full_name": "candYgene/pbg-ld", - "html_url": "https://github.com/candYgene/pbg-ld", "private": false, "description": "Linked Data Platform for Plant Breeding & Genomics", "created_at": "2017-04-10T21:00:27Z", diff --git a/database/github/candYgene/siga/metadata.json b/database/github/candYgene/siga/metadata.json index 2e5cbfdd1..8d402998f 100644 --- a/database/github/candYgene/siga/metadata.json +++ b/database/github/candYgene/siga/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/candYgene/siga", - "url": "https://api.github.com/repos/candYgene/siga", + "url": "https://github.com/candYgene/siga", "data": { "timestamp": "2020-07-05 00:17:21.483907", "name": "siga", - "url": "https://api.github.com/repos/candYgene/siga", + "url": "https://github.com/candYgene/siga", "full_name": "candYgene/siga", "html_url": "https://github.com/candYgene/siga", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1076437", "name": "siga", "full_name": "candYgene/siga", - "html_url": "https://github.com/candYgene/siga", "private": false, "description": "Semantically Interoperable Genome Annotations", "created_at": "2017-04-10T22:10:29Z", diff --git a/database/github/caselawanalytics/CaseLawAnalytics/metadata.json b/database/github/caselawanalytics/CaseLawAnalytics/metadata.json index c2d9ac1b0..09e431d71 100644 --- a/database/github/caselawanalytics/CaseLawAnalytics/metadata.json +++ b/database/github/caselawanalytics/CaseLawAnalytics/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/caselawanalytics/CaseLawAnalytics", - "url": "https://api.github.com/repos/caselawanalytics/CaseLawAnalytics", + "url": "https://github.com/caselawanalytics/CaseLawAnalytics", "data": { "timestamp": "2020-07-05 00:17:09.733202", "name": "CaseLawAnalytics", - "url": "https://api.github.com/repos/caselawanalytics/CaseLawAnalytics", + "url": "https://github.com/caselawanalytics/CaseLawAnalytics", "full_name": "caselawanalytics/CaseLawAnalytics", "html_url": "https://github.com/caselawanalytics/CaseLawAnalytics", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.832894", "name": "CaseLawAnalytics", "full_name": "caselawanalytics/CaseLawAnalytics", - "html_url": "https://github.com/caselawanalytics/CaseLawAnalytics", "private": false, "description": null, "created_at": "2016-10-11T12:16:05Z", diff --git a/database/github/cb-geo/mpm/metadata.json b/database/github/cb-geo/mpm/metadata.json index bdd3d1e87..5a06b43d2 100644 --- a/database/github/cb-geo/mpm/metadata.json +++ b/database/github/cb-geo/mpm/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/cb-geo/mpm", - "url": "https://api.github.com/repos/cb-geo/mpm", + "url": "https://github.com/cb-geo/mpm", "data": { "timestamp": "2020-07-04 13:22:12.955367", "name": "mpm", - "url": "https://api.github.com/repos/cb-geo/mpm", + "url": "https://github.com/cb-geo/mpm", "full_name": "cb-geo/mpm", "html_url": "https://github.com/cb-geo/mpm", "private": false, @@ -36,7 +36,6 @@ }, "name": "mpm", "full_name": "cb-geo/mpm", - "html_url": "https://github.com/cb-geo/mpm", "private": false, "description": "CB-Geo High-Performance Material Point Method", "created_at": "2017-08-25T23:53:55Z", diff --git a/database/github/cbalbin-FIU/Epitopedia/metadata.json b/database/github/cbalbin-bio/Epitopedia/metadata.json similarity index 100% rename from database/github/cbalbin-FIU/Epitopedia/metadata.json rename to database/github/cbalbin-bio/Epitopedia/metadata.json diff --git a/database/github/cbirdferrer/collatrix/metadata.json b/database/github/cbirdferrer/collatrix/metadata.json index cf471d63b..44e19748e 100644 --- a/database/github/cbirdferrer/collatrix/metadata.json +++ b/database/github/cbirdferrer/collatrix/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/cbirdferrer/collatrix", - "url": "https://api.github.com/repos/cbirdferrer/collatrix", + "url": "https://github.com/cbirdferrer/collatrix", "data": { "timestamp": "2020-07-12 00:26:30.009788", "name": "collatrix", - "url": "https://api.github.com/repos/cbirdferrer/collatrix", + "url": "https://github.com/cbirdferrer/collatrix", "full_name": "cbirdferrer/collatrix", "html_url": "https://github.com/cbirdferrer/collatrix", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.5281/zenodo.3937611", "name": "collatrix", "full_name": "cbirdferrer/collatrix", - "html_url": "https://github.com/cbirdferrer/collatrix", "private": false, "description": "this tool collates the outputs of the MorphoMetriX photogrammetry tool", "created_at": "2020-02-26T23:10:26Z", diff --git a/database/github/cbrueffer/tophat-recondition/metadata.json b/database/github/cbrueffer/tophat-recondition/metadata.json index 45a2cfa68..0a6286734 100644 --- a/database/github/cbrueffer/tophat-recondition/metadata.json +++ b/database/github/cbrueffer/tophat-recondition/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/cbrueffer/tophat-recondition", - "url": "https://api.github.com/repos/cbrueffer/tophat-recondition", + "url": "https://github.com/cbrueffer/tophat-recondition", "data": { "timestamp": "2020-07-19 00:17:19.935707", "name": "tophat-recondition", - "url": "https://api.github.com/repos/cbrueffer/tophat-recondition", + "url": "https://github.com/cbrueffer/tophat-recondition", "full_name": "cbrueffer/tophat-recondition", "html_url": "https://github.com/cbrueffer/tophat-recondition", "private": false, @@ -37,7 +37,6 @@ "doi": "10.1186/s12859-016-1058-x", "name": "tophat-recondition", "full_name": "cbrueffer/tophat-recondition", - "html_url": "https://github.com/cbrueffer/tophat-recondition", "private": false, "description": "Post-processor for TopHat unmapped.bam files making them useable by downstream software.", "created_at": "2014-10-29T14:12:58Z", diff --git a/database/github/chanzuckerberg/cellxgene/metadata.json b/database/github/chanzuckerberg/cellxgene/metadata.json index 5a03a39a9..c7453b5bb 100644 --- a/database/github/chanzuckerberg/cellxgene/metadata.json +++ b/database/github/chanzuckerberg/cellxgene/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/chanzuckerberg/cellxgene", - "url": null, + "url": "https://github.com/chanzuckerberg/cellxgene", "data": { "title": "cellxgene", "url": "https://github.com/chanzuckerberg/cellxgene", diff --git a/database/github/chanzuckerberg/idseq-dag/metadata.json b/database/github/chanzuckerberg/czid-dag/metadata.json similarity index 100% rename from database/github/chanzuckerberg/idseq-dag/metadata.json rename to database/github/chanzuckerberg/czid-dag/metadata.json diff --git a/database/github/christopher-vollmers/C3POa/metadata.json b/database/github/christopher-vollmers/C3POa/metadata.json index 5fa8e052d..1f4df42c7 100644 --- a/database/github/christopher-vollmers/C3POa/metadata.json +++ b/database/github/christopher-vollmers/C3POa/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/christopher-vollmers/C3POa", - "url": null, + "url": "https://github.com/christopher-vollmers/C3POa", "data": { "title": "C3POa", "url": "https://github.com/christopher-vollmers/C3POa", diff --git a/database/github/christophuv/PeakBot_example/metadata.json b/database/github/christophuv/PeakBot_Example/metadata.json similarity index 100% rename from database/github/christophuv/PeakBot_example/metadata.json rename to database/github/christophuv/PeakBot_Example/metadata.json diff --git a/database/github/ci-for-research/self-hosted-runners/metadata.json b/database/github/ci-for-research/self-hosted-runners/metadata.json index 6fe0ba101..d4495d019 100644 --- a/database/github/ci-for-research/self-hosted-runners/metadata.json +++ b/database/github/ci-for-research/self-hosted-runners/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ci-for-science/self-hosted-runners", - "url": "https://api.github.com/repos/ci-for-research/self-hosted-runners", + "url": "https://github.com/ci-for-research/self-hosted-runners", "data": { "timestamp": "2020-07-05 00:17:29.666854", "name": "self-hosted-runners", - "url": "https://api.github.com/repos/ci-for-research/self-hosted-runners", + "url": "https://github.com/ci-for-research/self-hosted-runners", "full_name": "ci-for-research/self-hosted-runners", "html_url": "https://github.com/ci-for-research/self-hosted-runners", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.3904265", "name": "self-hosted-runners", "full_name": "ci-for-research/self-hosted-runners", - "html_url": "https://github.com/ci-for-research/self-hosted-runners", "private": false, "description": "Recipe to install and configure a GitHub action runner using Ansible", "created_at": "2019-11-26T14:03:16Z", diff --git a/database/github/ci-for-science/self-hosted-runners/metadata.json b/database/github/ci-for-research/self-hosted-runners/self-hosted-runners/metadata.json similarity index 100% rename from database/github/ci-for-science/self-hosted-runners/metadata.json rename to database/github/ci-for-research/self-hosted-runners/self-hosted-runners/metadata.json diff --git a/database/github/citation-file-format/cff-converter-python/metadata.json b/database/github/citation-file-format/cff-converter-python/metadata.json index fc1a809f8..6f1c00c48 100644 --- a/database/github/citation-file-format/cff-converter-python/metadata.json +++ b/database/github/citation-file-format/cff-converter-python/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/citation-file-format/cff-converter-python", - "url": "https://api.github.com/repos/citation-file-format/cff-converter-python", + "url": "https://github.com/citation-file-format/cff-converter-python", "data": { "timestamp": "2020-07-05 00:17:10.447070", "name": "cff-converter-python", - "url": "https://api.github.com/repos/citation-file-format/cff-converter-python", + "url": "https://github.com/citation-file-format/cff-converter-python", "full_name": "citation-file-format/cff-converter-python", "html_url": "https://github.com/citation-file-format/cff-converter-python", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1162057", "name": "cff-converter-python", "full_name": "citation-file-format/cff-converter-python", - "html_url": "https://github.com/citation-file-format/cff-converter-python", "private": false, "description": "Command line utility to read CITATION.cff file from a GitHub url or local file and convert it to BibTex and other formats.", "created_at": "2018-01-09T14:16:28Z", diff --git a/database/github/citation-file-format/cff-initializer-javascript/metadata.json b/database/github/citation-file-format/cff-initializer-javascript/metadata.json index 20fb9428f..5795cecfd 100644 --- a/database/github/citation-file-format/cff-initializer-javascript/metadata.json +++ b/database/github/citation-file-format/cff-initializer-javascript/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/citation-file-format/cff-initializer-javascript", - "url": "https://api.github.com/repos/citation-file-format/cff-initializer-javascript", + "url": "https://github.com/citation-file-format/cff-initializer-javascript", "data": { "timestamp": "2020-07-05 00:17:24.043016", "name": "cff-initializer-javascript", - "url": "https://api.github.com/repos/citation-file-format/cff-initializer-javascript", + "url": "https://github.com/citation-file-format/cff-initializer-javascript", "full_name": "citation-file-format/cff-initializer-javascript", "html_url": "https://github.com/citation-file-format/cff-initializer-javascript", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1404735", "name": "cff-initializer-javascript", "full_name": "citation-file-format/cff-initializer-javascript", - "html_url": "https://github.com/citation-file-format/cff-initializer-javascript", "private": false, "description": "Web form to initialize CITATION.cff files.", "created_at": "2018-08-02T13:14:06Z", diff --git a/database/github/clawpack/clawpack/metadata.json b/database/github/clawpack/clawpack/metadata.json index c90400cc2..1b886f20d 100644 --- a/database/github/clawpack/clawpack/metadata.json +++ b/database/github/clawpack/clawpack/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/clawpack/clawpack", - 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"url": "https://api.github.com/repos/drwaseemsheikh/audiometry", + "url": "https://github.com/drwaseemsheikh/audiometry", "data": { "timestamp": "2020-07-05 00:17:04.337685", "name": "audiometry", - "url": "https://api.github.com/repos/drwaseemsheikh/audiometry", + "url": "https://github.com/drwaseemsheikh/audiometry", "full_name": "drwaseemsheikh/audiometry", "html_url": "https://github.com/drwaseemsheikh/audiometry", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.5281/zenodo.3924784", "name": "audiometry", "full_name": "drwaseemsheikh/audiometry", - "html_url": "https://github.com/drwaseemsheikh/audiometry", "private": false, "description": "Audiometry is an application framework written in C# and based on WPF and .NET that enables accurate digital recording, search, analysis, graphical visualization, and reproduction of human audio-vestibular impairment test data to assist in hearing loss or disability diagnosis.", "created_at": "2019-10-06T20:45:03Z", diff --git a/database/github/dsheward-astro/pynaple/metadata.json b/database/github/dsheward-astro/PyNAPLE/metadata.json similarity index 100% rename from database/github/dsheward-astro/pynaple/metadata.json rename to database/github/dsheward-astro/PyNAPLE/metadata.json diff --git a/database/github/dvallesp/asohf/metadata.json b/database/github/dvallesp/ASOHF/metadata.json similarity index 100% rename from database/github/dvallesp/asohf/metadata.json rename to database/github/dvallesp/ASOHF/metadata.json diff --git a/database/github/eEcoLiDAR/laserchicken/metadata.json b/database/github/eEcoLiDAR/laserchicken/metadata.json index 3935e7c64..2da0534df 100644 --- a/database/github/eEcoLiDAR/laserchicken/metadata.json +++ b/database/github/eEcoLiDAR/laserchicken/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eEcoLiDAR/laserchicken", - "url": "https://api.github.com/repos/eEcoLiDAR/laserchicken", + "url": "https://github.com/eEcoLiDAR/laserchicken", "data": { "timestamp": "2020-07-05 00:17:27.196825", "name": "laserchicken", - "url": "https://api.github.com/repos/eEcoLiDAR/laserchicken", + "url": "https://github.com/eEcoLiDAR/laserchicken", "full_name": "eEcoLiDAR/laserchicken", "html_url": "https://github.com/eEcoLiDAR/laserchicken", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1219422", "name": "laserchicken", "full_name": "eEcoLiDAR/laserchicken", - "html_url": "https://github.com/eEcoLiDAR/laserchicken", "private": false, "description": null, "created_at": "2017-06-28T08:51:42Z", diff --git a/database/github/eScatter/pyelsepa/metadata.json b/database/github/eScatter/pyelsepa/metadata.json index 1d57fb5e5..f19dec100 100644 --- a/database/github/eScatter/pyelsepa/metadata.json +++ b/database/github/eScatter/pyelsepa/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eScatter/pyelsepa", - "url": "https://api.github.com/repos/eScatter/pyelsepa", + "url": "https://github.com/eScatter/pyelsepa", "data": { "timestamp": "2020-07-05 00:17:12.790499", "name": "pyelsepa", - "url": "https://api.github.com/repos/eScatter/pyelsepa", + "url": "https://github.com/eScatter/pyelsepa", "full_name": "eScatter/pyelsepa", "html_url": "https://github.com/eScatter/pyelsepa", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1045193", "name": "pyelsepa", "full_name": "eScatter/pyelsepa", - "html_url": "https://github.com/eScatter/pyelsepa", "private": false, "description": "A Python wrapper for ELSEPA", "created_at": "2016-09-08T12:30:15Z", diff --git a/database/github/eWaterCycle/Cesium-NcWMS/metadata.json b/database/github/eWaterCycle/Cesium-NcWMS/metadata.json index 9718f6e81..6947e8684 100644 --- a/database/github/eWaterCycle/Cesium-NcWMS/metadata.json +++ b/database/github/eWaterCycle/Cesium-NcWMS/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eWaterCycle/Cesium-NcWMS", - "url": "https://api.github.com/repos/eWaterCycle/Cesium-NcWMS", + "url": "https://github.com/eWaterCycle/Cesium-NcWMS", "data": { "timestamp": "2020-07-05 00:17:10.234220", "name": "Cesium-NcWMS", - "url": "https://api.github.com/repos/eWaterCycle/Cesium-NcWMS", + "url": "https://github.com/eWaterCycle/Cesium-NcWMS", "full_name": "eWaterCycle/Cesium-NcWMS", "html_url": "https://github.com/eWaterCycle/Cesium-NcWMS", "private": false, @@ -31,7 +31,6 @@ "doi": "10.5281/zenodo.60031", "name": "Cesium-NcWMS", "full_name": "eWaterCycle/Cesium-NcWMS", - "html_url": "https://github.com/eWaterCycle/Cesium-NcWMS", "private": false, "description": "Cesium angular directive with ncwms integration to display netcdf datasets", "created_at": "2015-04-07T08:46:55Z", diff --git a/database/github/eWaterCycle/eWaterleaf/metadata.json b/database/github/eWaterCycle/eWaterleaf/metadata.json index 73ad8a795..b8b7848ec 100644 --- a/database/github/eWaterCycle/eWaterleaf/metadata.json +++ b/database/github/eWaterCycle/eWaterleaf/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eWaterCycle/eWaterleaf", - 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"url": "https://api.github.com/repos/eWaterCycle/experiment-launcher", + "url": "https://github.com/eWaterCycle/experiment-launcher", "data": { "timestamp": "2020-07-05 00:17:24.649613", "name": "experiment-launcher", - "url": "https://api.github.com/repos/eWaterCycle/experiment-launcher", + "url": "https://github.com/eWaterCycle/experiment-launcher", "full_name": "eWaterCycle/experiment-launcher", "html_url": "https://github.com/eWaterCycle/experiment-launcher", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1453264", "name": "experiment-launcher", "full_name": "eWaterCycle/experiment-launcher", - "html_url": "https://github.com/eWaterCycle/experiment-launcher", "private": false, "description": "eWaterCycle Experiment Launcher", "created_at": "2018-04-03T11:05:19Z", diff --git a/database/github/eWaterCycle/grpc4bmi/metadata.json b/database/github/eWaterCycle/grpc4bmi/metadata.json index db215f257..b7e523e2f 100644 --- a/database/github/eWaterCycle/grpc4bmi/metadata.json +++ b/database/github/eWaterCycle/grpc4bmi/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eWaterCycle/grpc4bmi", - 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"url": "https://api.github.com/repos/eWaterCycle/jupyterlab_thredds", + "url": "https://github.com/eWaterCycle/jupyterlab_thredds", "data": { "timestamp": "2020-07-05 00:17:24.523294", "name": "jupyterlab_thredds", - "url": "https://api.github.com/repos/eWaterCycle/jupyterlab_thredds", + "url": "https://github.com/eWaterCycle/jupyterlab_thredds", "full_name": "eWaterCycle/jupyterlab_thredds", "html_url": "https://github.com/eWaterCycle/jupyterlab_thredds", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1241006", "name": "jupyterlab_thredds", "full_name": "eWaterCycle/jupyterlab_thredds", - "html_url": "https://github.com/eWaterCycle/jupyterlab_thredds", "private": false, "description": "JupyterLab dataset browser for THREDDS catalog", "created_at": "2018-04-10T15:43:36Z", diff --git a/database/github/eWaterCycle/setup-grpc/metadata.json b/database/github/eWaterCycle/setup-grpc/metadata.json index 1a57d402a..4bebf4e06 100644 --- a/database/github/eWaterCycle/setup-grpc/metadata.json +++ b/database/github/eWaterCycle/setup-grpc/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/eWaterCycle/setup-grpc", - 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"url": "https://api.github.com/repos/edwardoughton/itmlogic", + "url": "https://github.com/edwardoughton/itmlogic", "full_name": "edwardoughton/itmlogic", "html_url": "https://github.com/edwardoughton/itmlogic", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.5281/zenodo.3931350", "name": "itmlogic", "full_name": "edwardoughton/itmlogic", - "html_url": "https://github.com/edwardoughton/itmlogic", "private": false, "description": "Longley-Rice Irregular Terrain Model (itmlogic)", "created_at": "2019-06-13T14:38:00Z", diff --git a/database/github/egjergo/galcem/metadata.json b/database/github/egjergo/GalCEM/metadata.json similarity index 100% rename from database/github/egjergo/galcem/metadata.json rename to database/github/egjergo/GalCEM/metadata.json diff --git a/database/github/eltevo/steps/metadata.json b/database/github/eltevo/StePS/metadata.json similarity index 100% rename from database/github/eltevo/steps/metadata.json rename to database/github/eltevo/StePS/metadata.json diff --git a/database/github/entangled/entangled/metadata.json b/database/github/entangled/entangled/metadata.json index d8eb535a5..547983673 100644 --- a/database/github/entangled/entangled/metadata.json +++ b/database/github/entangled/entangled/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/entangled/entangled", - 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"url": "https://api.github.com/repos/Effective-Quadratures/Effective-Quadratures", + "url": "https://github.com/equadratures/equadratures", "data": { "timestamp": "2020-07-04 13:22:18.914509", "name": "Effective-Quadratures", - "url": "https://api.github.com/repos/Effective-Quadratures/Effective-Quadratures", + "url": "https://github.com/equadratures/equadratures", "full_name": "Effective-Quadratures/Effective-Quadratures", "html_url": "https://github.com/Effective-Quadratures/Effective-Quadratures", "private": false, @@ -36,7 +36,6 @@ }, "name": "Effective-Quadratures", "full_name": "Effective-Quadratures/Effective-Quadratures", - "html_url": "https://github.com/equadratures/equadratures", "private": false, "description": null, "created_at": "2016-03-23T10:15:19Z", diff --git a/database/github/Effective-Quadratures/Effective-Quadratures/taxonomy.tsv b/database/github/equadratures/equadratures/taxonomy.tsv similarity index 100% rename from database/github/Effective-Quadratures/Effective-Quadratures/taxonomy.tsv rename to database/github/equadratures/equadratures/taxonomy.tsv diff --git a/database/github/equib/equib/metadata.json b/database/github/equib/EQUIB/metadata.json similarity index 100% rename from database/github/equib/equib/metadata.json rename to database/github/equib/EQUIB/metadata.json diff --git a/database/github/etal/cnvkit/metadata.json b/database/github/etal/cnvkit/metadata.json index 1ab8f2f2f..dda7ee131 100644 --- a/database/github/etal/cnvkit/metadata.json +++ b/database/github/etal/cnvkit/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/etal/cnvkit", - 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"url": "https://github.com/cl3425/Clairvoyance", + "url": "https://github.com/exoclam/Clairvoyance", "name": "Clairvoyance", "full_name": "cl3425/Clairvoyance", "html_url": "https://github.com/cl3425/Clairvoyance", @@ -29,6 +29,5 @@ }, "timestamp": "2022-07-17 17:21:03.595811", "avatar": "https://avatars.githubusercontent.com/u/16911363?v=4" - }, - "html_url": "https://github.com/exoclam/Clairvoyance" + } } \ No newline at end of file diff --git a/database/github/exosports/homer/metadata.json b/database/github/exosports/HOMER/metadata.json similarity index 100% rename from database/github/exosports/homer/metadata.json rename to database/github/exosports/HOMER/metadata.json diff --git a/database/github/lsds/faasm/metadata.json b/database/github/faasm/faasm/metadata.json similarity index 100% rename from database/github/lsds/faasm/metadata.json rename to database/github/faasm/faasm/metadata.json diff --git a/database/github/Fermipy/fermipy/metadata.json b/database/github/fermiPy/fermipy/metadata.json similarity index 100% rename from database/github/Fermipy/fermipy/metadata.json rename to database/github/fermiPy/fermipy/metadata.json diff --git a/database/github/fforster/delight/metadata.json b/database/github/fforster/DELIGHT/metadata.json similarity index 100% rename from database/github/fforster/delight/metadata.json rename to database/github/fforster/DELIGHT/metadata.json diff --git a/database/github/JLiangLab/TransVW/metadata.json b/database/github/fhaghighi/TransVW/metadata.json similarity index 100% rename from database/github/JLiangLab/TransVW/metadata.json rename to database/github/fhaghighi/TransVW/metadata.json diff --git a/database/github/mrvollger/fibertools-rs/metadata.json b/database/github/fiberseq/fibertools-rs/metadata.json similarity index 86% rename from database/github/mrvollger/fibertools-rs/metadata.json rename to database/github/fiberseq/fibertools-rs/metadata.json index 1571058bc..4aaa61df6 100644 --- a/database/github/mrvollger/fibertools-rs/metadata.json +++ b/database/github/fiberseq/fibertools-rs/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", "uid": "github/mrvollger/fibertools-rs", - "url": "https://github.com/mrvollger/fibertools-rs", + "url": "https://github.com/fiberseq/fibertools-rs", "data": { "title": "fibertools\u2011rs", - "url": "https://github.com/mrvollger/fibertools-rs", + "url": "https://github.com/fiberseq/fibertools-rs", "credit": [], "tags": [ "high-throughput-sequencing" @@ -30,6 +30,5 @@ }, "timestamp": "2022-11-27 00:42:35.979054", "avatar": "https://avatars.githubusercontent.com/u/6935283?v=4" - }, - "html_url": "https://github.com/fiberseq/fibertools-rs" + } } \ No newline at end of file diff --git a/database/github/forceflow1049/phast/metadata.json b/database/github/forceflow1049/PhAst/metadata.json similarity index 100% rename from database/github/forceflow1049/phast/metadata.json rename to database/github/forceflow1049/PhAst/metadata.json diff --git a/database/github/fraserw/TRIPPy/metadata.json b/database/github/fraserw/trippy/metadata.json similarity index 100% rename from database/github/fraserw/TRIPPy/metadata.json rename to database/github/fraserw/trippy/metadata.json diff --git a/database/github/ekg/freebayes/metadata.json b/database/github/freebayes/freebayes/freebayes/metadata.json similarity index 100% rename from database/github/ekg/freebayes/metadata.json rename to database/github/freebayes/freebayes/freebayes/metadata.json diff --git a/database/github/genotoul-bioinfo/dgenies/metadata.json b/database/github/genotoul-bioinfo/dgenies/metadata.json index 288416f52..fe37f44d1 100644 --- a/database/github/genotoul-bioinfo/dgenies/metadata.json +++ b/database/github/genotoul-bioinfo/dgenies/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/genotoul-bioinfo/dgenies", - "url": "https://api.github.com/repos/genotoul-bioinfo/dgenies", + "url": "https://github.com/genotoul-bioinfo/dgenies", "data": { "timestamp": "2020-07-05 00:17:52.843773", "name": "dgenies", - "url": "https://api.github.com/repos/genotoul-bioinfo/dgenies", + "url": "https://github.com/genotoul-bioinfo/dgenies", "full_name": "genotoul-bioinfo/dgenies", "html_url": "https://github.com/genotoul-bioinfo/dgenies", "private": false, @@ -36,7 +36,6 @@ }, "name": "dgenies", "full_name": "genotoul-bioinfo/dgenies", - "html_url": "https://github.com/genotoul-bioinfo/dgenies", "private": false, "description": "Dotplot large Genomes in an Interactive, Efficient and Simple way", "created_at": "2018-02-20T13:42:27Z", diff --git a/database/github/geopandas/geopandas/metadata.json b/database/github/geopandas/geopandas/metadata.json index 708789093..51324fa4b 100644 --- a/database/github/geopandas/geopandas/metadata.json +++ b/database/github/geopandas/geopandas/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/geopandas/geopandas", - "url": "https://api.github.com/repos/geopandas/geopandas", + "url": "https://github.com/geopandas/geopandas", "data": { "timestamp": "2020-07-04 13:22:36.400025", "name": "geopandas", - "url": "https://api.github.com/repos/geopandas/geopandas", + "url": "https://github.com/geopandas/geopandas", "full_name": "geopandas/geopandas", "html_url": "https://github.com/geopandas/geopandas", "private": false, @@ -36,7 +36,6 @@ }, "name": "geopandas", "full_name": "geopandas/geopandas", - "html_url": "https://github.com/geopandas/geopandas", "private": false, "description": "Python tools for geographic data", "created_at": "2013-06-27T17:03:47Z", diff --git a/database/github/gijut/gnucash/metadata.json b/database/github/gijut/gnucash/metadata.json index 625926759..257497a53 100644 --- a/database/github/gijut/gnucash/metadata.json +++ b/database/github/gijut/gnucash/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/gijut/gnucash", - "url": "https://api.github.com/repos/gijut/gnucash", + "url": "https://github.com/gijut/gnucash", "data": { "timestamp": "2020-07-05 00:17:53.022588", "name": "gnucash", - "url": "https://api.github.com/repos/gijut/gnucash", + "url": "https://github.com/gijut/gnucash", "full_name": "gijut/gnucash", "html_url": "https://github.com/gijut/gnucash", "private": false, @@ -36,7 +36,6 @@ }, "name": "gnucash", "full_name": "gijut/gnucash", - "html_url": "https://github.com/gijut/gnucash", "private": false, "description": "Public Mirror of code.gnucash.org/gnucash", "created_at": "2016-01-26T13:17:43Z", diff --git a/database/github/giswqs/geemap/metadata.json b/database/github/giswqs/geemap/metadata.json index 05e89e037..ef34edf37 100644 --- a/database/github/giswqs/geemap/metadata.json +++ b/database/github/giswqs/geemap/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/giswqs/geemap", - "url": "https://api.github.com/repos/giswqs/geemap", + "url": "https://github.com/giswqs/geemap", "data": { "timestamp": "2020-07-19 00:17:13.571575", "name": "geemap", - "url": "https://api.github.com/repos/giswqs/geemap", + "url": "https://github.com/giswqs/geemap", "full_name": "giswqs/geemap", "html_url": "https://github.com/giswqs/geemap", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.6084/m9.figshare.12608834.v1", "name": "geemap", "full_name": "giswqs/geemap", - 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"url": "https://api.github.com/repos/dgarrimar/sqtlseeker2-nf", + "url": "https://github.com/guigolab/sqtlseeker2-nf", "data": { "timestamp": "2020-07-26 00:17:05.182459", "name": "sqtlseeker2-nf", - "url": "https://api.github.com/repos/dgarrimar/sqtlseeker2-nf", + "url": "https://github.com/guigolab/sqtlseeker2-nf", "full_name": "dgarrimar/sqtlseeker2-nf", "html_url": "https://github.com/dgarrimar/sqtlseeker2-nf", "private": false, @@ -37,7 +37,6 @@ "doi": "10.1038/ncomms5698", "name": "sqtlseeker2-nf", "full_name": "dgarrimar/sqtlseeker2-nf", - "html_url": "https://github.com/guigolab/sqtlseeker2-nf", "private": false, "description": "An automated sQTL mapping pipeline using Nextflow", "created_at": "2017-11-28T17:07:19Z", diff --git a/database/github/williamjameshandley/fgivenx/metadata.json b/database/github/handley-lab/fgivenx/metadata.json similarity index 97% rename from database/github/williamjameshandley/fgivenx/metadata.json rename to database/github/handley-lab/fgivenx/metadata.json index 5d351eefa..0602a8572 100644 --- a/database/github/williamjameshandley/fgivenx/metadata.json +++ b/database/github/handley-lab/fgivenx/metadata.json @@ -9,7 +9,7 @@ "https://ui.adsabs.harvard.edu/abs/2019ascl.soft09014H/abstract" ], "title": "fgivenx: Functional posterior plotter", - "url": "https://github.com/handley-lab/fgivenx" + "url": "https://github.com/handley-lab/fgivenx", "name": "fgivenx", "full_name": "williamjameshandley/fgivenx", "html_url": "https://github.com/williamjameshandley/fgivenx", diff --git a/database/github/haowenz/chromap/metadata.json b/database/github/haowenz/chromap/metadata.json index e03ab5932..e6381487e 100644 --- a/database/github/haowenz/chromap/metadata.json +++ b/database/github/haowenz/chromap/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/haowenz/chromap", - "url": null, + "url": "https://github.com/haowenz/chromap", "data": { "title": "Chromap", "url": "https://github.com/haowenz/chromap", diff --git a/database/github/herrsalmi/FConverter/metadata.json b/database/github/herrsalmi/FConverter/metadata.json index aeac93bab..e3057d4ef 100644 --- a/database/github/herrsalmi/FConverter/metadata.json +++ b/database/github/herrsalmi/FConverter/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/herrsalmi/FConverter", - "url": "https://api.github.com/repos/herrsalmi/FConverter", + "url": "https://github.com/herrsalmi/FConverter", "data": { "timestamp": "2020-07-19 00:17:20.071312", "name": "FConverter", - "url": "https://api.github.com/repos/herrsalmi/FConverter", + "url": "https://github.com/herrsalmi/FConverter", "full_name": "herrsalmi/FConverter", "html_url": "https://github.com/herrsalmi/FConverter", "private": false, @@ -36,7 +36,6 @@ }, "name": "FConverter", "full_name": "herrsalmi/FConverter", - "html_url": "https://github.com/herrsalmi/FConverter", "private": false, "description": "File format converter for FImpute2", "created_at": "2019-07-27T15:32:15Z", diff --git a/database/github/hippke/pandora/metadata.json b/database/github/hippke/Pandora/metadata.json similarity index 100% rename from database/github/hippke/pandora/metadata.json rename to database/github/hippke/Pandora/metadata.json diff --git a/database/github/hover2pi/SEDkit/metadata.json b/database/github/hover2pi/sedkit/metadata.json similarity index 100% rename from database/github/hover2pi/SEDkit/metadata.json rename to database/github/hover2pi/sedkit/metadata.json diff --git a/database/github/hrwakeford/ExoTiC-ISM/metadata.json b/database/github/hrwakeford/ExoTiC-ISM/metadata.json index be871da54..225e06aa0 100644 --- a/database/github/hrwakeford/ExoTiC-ISM/metadata.json +++ b/database/github/hrwakeford/ExoTiC-ISM/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/hrwakeford/ExoTiC-ISM", - "url": "https://api.github.com/repos/hrwakeford/ExoTiC-ISM", + "url": "https://github.com/hrwakeford/ExoTiC-ISM", "data": { "timestamp": "2020-07-12 00:26:30.737396", "name": "ExoTiC-ISM", - "url": "https://api.github.com/repos/hrwakeford/ExoTiC-ISM", + "url": "https://github.com/hrwakeford/ExoTiC-ISM", "full_name": "hrwakeford/ExoTiC-ISM", "html_url": "https://github.com/hrwakeford/ExoTiC-ISM", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.5281/zenodo.3923986", "name": "ExoTiC-ISM", "full_name": "hrwakeford/ExoTiC-ISM", - "html_url": "https://github.com/hrwakeford/ExoTiC-ISM", "private": false, "description": "This is a repository for the reduction pipeline detailed in Wakeford, et al., 2016, ApJ. 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"url": "https://api.github.com/repos/ihrke/pypillometry", + "url": "https://github.com/ihrke/pypillometry", "data": { "timestamp": "2020-07-05 00:17:04.062490", "name": "pypillometry", - "url": "https://api.github.com/repos/ihrke/pypillometry", + "url": "https://github.com/ihrke/pypillometry", "full_name": "ihrke/pypillometry", "html_url": "https://github.com/ihrke/pypillometry", "private": false, @@ -37,7 +37,6 @@ "doi": "https://doi.org/10.5281/zenodo.3925528", "name": "pypillometry", "full_name": "ihrke/pypillometry", - "html_url": "https://github.com/ihrke/pypillometry", "private": false, "description": "pupillometry with python", "created_at": "2019-10-14T09:46:03Z", diff --git a/database/github/iomega/paired-data-form/metadata.json b/database/github/iomega/paired-data-form/metadata.json index 5b2b3951f..2d746f871 100644 --- a/database/github/iomega/paired-data-form/metadata.json +++ b/database/github/iomega/paired-data-form/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/iomega/paired-data-form", - 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"url": "https://github.com/alex-b-davis/gubas", + "url": "https://github.com/meyeralexj/gubas", "data": { "doi": [ "https://ui.adsabs.harvard.edu/abs/2020Icar..34113439D", "https://ui.adsabs.harvard.edu/abs/2021ascl.soft07013D/abstract" ], "title": "GUBAS: General Use Binary Asteroid Simulator", - "url": "https://github.com/alex-b-davis/gubas", + "url": "https://github.com/meyeralexj/gubas", "name": "gubas", "full_name": "alex-b-davis/gubas", "html_url": "https://github.com/alex-b-davis/gubas", @@ -35,6 +35,5 @@ }, "timestamp": "2022-07-17 17:11:29.641588", "avatar": "https://avatars.githubusercontent.com/u/54447759?v=4" - }, - "html_url": "https://github.com/meyeralexj/gubas" + } } \ No newline at end of file diff --git a/database/github/mlpack/mlpack/metadata.json b/database/github/mlpack/mlpack/metadata.json index f2d48b4da..faa209c3c 100644 --- a/database/github/mlpack/mlpack/metadata.json +++ b/database/github/mlpack/mlpack/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/mlpack/mlpack", - "url": "https://api.github.com/repos/mlpack/mlpack", + "url": "https://github.com/mlpack/mlpack", "data": { "timestamp": "2020-07-04 13:22:06.255087", "name": "mlpack", - "url": "https://api.github.com/repos/mlpack/mlpack", + "url": "https://github.com/mlpack/mlpack", "full_name": "mlpack/mlpack", "html_url": "https://github.com/mlpack/mlpack", "private": false, @@ -36,7 +36,6 @@ }, "name": "mlpack", "full_name": "mlpack/mlpack", - "html_url": "https://github.com/mlpack/mlpack", "private": false, "description": "mlpack: a scalable C++ machine learning library -- ", "created_at": "2014-12-17T18:16:59Z", diff --git a/database/github/morriscb/The-wiZZ/metadata.json b/database/github/morriscb/the-wizz/metadata.json similarity index 100% rename from database/github/morriscb/The-wiZZ/metadata.json rename to database/github/morriscb/the-wizz/metadata.json diff --git a/database/github/multiscale/muscle3/metadata.json b/database/github/multiscale/muscle3/metadata.json index 6e43b10e6..a144da658 100644 --- a/database/github/multiscale/muscle3/metadata.json +++ b/database/github/multiscale/muscle3/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/multiscale/muscle3", - "url": "https://api.github.com/repos/multiscale/muscle3", + "url": "https://github.com/multiscale/muscle3", "data": { "timestamp": "2020-07-05 00:17:26.488992", "name": "muscle3", - "url": "https://api.github.com/repos/multiscale/muscle3", + "url": "https://github.com/multiscale/muscle3", "full_name": "multiscale/muscle3", "html_url": "https://github.com/multiscale/muscle3", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.3258864", "name": "muscle3", "full_name": "multiscale/muscle3", - "html_url": "https://github.com/multiscale/muscle3", "private": false, "description": "The third major version of the MUltiScale Coupling Library and Environment", "created_at": "2018-02-25T21:07:17Z", diff --git a/database/github/myinxd/mcrgnet/metadata.json b/database/github/myinxd/MCRGNet/metadata.json similarity index 100% rename from database/github/myinxd/mcrgnet/metadata.json rename to database/github/myinxd/MCRGNet/metadata.json diff --git a/database/github/mzy2240/ESA/metadata.json b/database/github/mzy2240/ESA/metadata.json index 6c063313c..253810496 100644 --- a/database/github/mzy2240/ESA/metadata.json +++ b/database/github/mzy2240/ESA/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/mzy2240/ESA", - "url": "https://api.github.com/repos/mzy2240/ESA", + "url": "https://github.com/mzy2240/ESA", "data": { "timestamp": "2020-07-04 13:22:39.528390", "name": "ESA", - "url": "https://api.github.com/repos/mzy2240/ESA", + "url": "https://github.com/mzy2240/ESA", "full_name": "mzy2240/ESA", "html_url": "https://github.com/mzy2240/ESA", "private": false, @@ -36,7 +36,6 @@ }, "name": "ESA", "full_name": "mzy2240/ESA", - "html_url": "https://github.com/mzy2240/ESA", "private": false, "description": "Easy SimAuto (ESA): An easy-to-use Python connector to PowerWorld Simulator Automation Server (SimAuto)", "created_at": "2019-10-08T21:37:23Z", diff --git a/database/github/networkx/networkx/metadata.json b/database/github/networkx/networkx/metadata.json index ab150cf79..e229842db 100644 --- a/database/github/networkx/networkx/metadata.json +++ b/database/github/networkx/networkx/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/networkx/networkx", - "url": "https://api.github.com/repos/networkx/networkx", + "url": "https://github.com/networkx/networkx", "data": { "timestamp": "2020-07-04 13:22:28.232907", "name": "networkx", - "url": "https://api.github.com/repos/networkx/networkx", + "url": "https://github.com/networkx/networkx", "full_name": "networkx/networkx", "html_url": "https://github.com/networkx/networkx", "private": false, @@ -36,7 +36,6 @@ }, "name": "networkx", "full_name": "networkx/networkx", - "html_url": "https://github.com/networkx/networkx", "private": false, "description": "Network Analysis in Python", "created_at": "2010-09-06T00:53:44Z", diff --git a/database/github/NathanSkene/MAGMA_Celltyping/metadata.json b/database/github/neurogenomics/MAGMA_Celltyping/metadata.json similarity index 100% rename from database/github/NathanSkene/MAGMA_Celltyping/metadata.json rename to database/github/neurogenomics/MAGMA_Celltyping/metadata.json diff --git a/database/github/nextflow-io/nextflow/metadata.json b/database/github/nextflow-io/nextflow/metadata.json index 75feeae64..5be0a8393 100644 --- a/database/github/nextflow-io/nextflow/metadata.json +++ b/database/github/nextflow-io/nextflow/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nextflow-io/nextflow", - "url": "https://api.github.com/repos/nextflow-io/nextflow", + "url": "https://github.com/nextflow-io/nextflow", "data": { "timestamp": "2020-07-04 13:22:29.189575", "name": "nextflow", - "url": "https://api.github.com/repos/nextflow-io/nextflow", + "url": "https://github.com/nextflow-io/nextflow", "full_name": "nextflow-io/nextflow", "html_url": "https://github.com/nextflow-io/nextflow", "private": false, @@ -36,7 +36,6 @@ }, "name": "nextflow", "full_name": "nextflow-io/nextflow", - "html_url": "https://github.com/nextflow-io/nextflow", "private": false, "description": "A DSL for data-driven computational pipelines", "created_at": "2013-03-27T11:17:33Z", diff --git a/database/github/sanger-pathogens/gubbins/metadata.json b/database/github/nickjcroucher/gubbins/metadata.json similarity index 100% rename from database/github/sanger-pathogens/gubbins/metadata.json rename to database/github/nickjcroucher/gubbins/metadata.json diff --git a/database/github/nigyta/dfast_core/metadata.json b/database/github/nigyta/dfast_core/metadata.json index cf4034292..4aea7bd9b 100644 --- a/database/github/nigyta/dfast_core/metadata.json +++ b/database/github/nigyta/dfast_core/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/nigyta/dfast_core", - "url": null, + "url": "https://github.com/nigyta/dfast_core", "data": { "title": "DFAST", "url": "https://github.com/nigyta/dfast_core", diff --git a/database/github/poldracklab/mriqc/metadata.json b/database/github/nipreps/mriqc/metadata.json similarity index 100% rename from database/github/poldracklab/mriqc/metadata.json rename to database/github/nipreps/mriqc/metadata.json diff --git a/database/github/poldracklab/nitransforms/metadata.json b/database/github/nipy/nitransforms/metadata.json similarity index 84% rename from database/github/poldracklab/nitransforms/metadata.json rename to database/github/nipy/nitransforms/metadata.json index a65e91547..cf393183d 100644 --- a/database/github/poldracklab/nitransforms/metadata.json +++ b/database/github/nipy/nitransforms/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/poldracklab/nitransforms", - "url": "https://github.com/poldracklab/nitransforms", + "url": "https://github.com/nipy/nitransforms", "data": { "timestamp": "2021-09-12 00:34:53.529735", "name": "nitransforms", - "url": "https://api.github.com/repos/poldracklab/nitransforms", + "url": "https://github.com/nipy/nitransforms", "full_name": "poldracklab/nitransforms", "html_url": "https://github.com/poldracklab/nitransforms", "private": false, @@ -35,6 +35,5 @@ }, "topics": [] }, - "doi": "https://doi.org/10.5281/zenodo.5499694", - "html_url": "https://github.com/nipy/nitransforms" + "doi": "https://doi.org/10.5281/zenodo.5499694" } \ No newline at end of file diff --git a/database/github/nkhorshid/simab/metadata.json b/database/github/nkhorshid/SimAb/metadata.json similarity index 100% rename from database/github/nkhorshid/simab/metadata.json rename to database/github/nkhorshid/SimAb/metadata.json diff --git a/database/github/nlesc-ave/ave-rest-service/metadata.json b/database/github/nlesc-ave/ave-rest-service/metadata.json index fe4ba88be..3ccc89025 100644 --- a/database/github/nlesc-ave/ave-rest-service/metadata.json +++ b/database/github/nlesc-ave/ave-rest-service/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nlesc-ave/ave-rest-service", - 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"url": "https://api.github.com/repos/nlesc-dirac/sagecal", + "url": "https://github.com/nlesc-dirac/sagecal", "data": { "timestamp": "2020-07-05 00:17:20.238519", "name": "sagecal", - "url": "https://api.github.com/repos/nlesc-dirac/sagecal", + "url": "https://github.com/nlesc-dirac/sagecal", "full_name": "nlesc-dirac/sagecal", "html_url": "https://github.com/nlesc-dirac/sagecal", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1051168", "name": "sagecal", "full_name": "nlesc-dirac/sagecal", - "html_url": "https://github.com/nlesc-dirac/sagecal", "private": false, "description": "SAGECal is a very fast, memory efficient and GPU accelerated radio interferometric calibration program. 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"html_url": "https://github.com/nlesc-nano/ceiba-cli" + "doi": "10.5281/zenodo.4241144" } \ No newline at end of file diff --git a/database/github/nlesc-nano/insilico-server/metadata.json b/database/github/nlesc-nano/ceiba/insilico-server/metadata.json similarity index 84% rename from database/github/nlesc-nano/insilico-server/metadata.json rename to database/github/nlesc-nano/ceiba/insilico-server/metadata.json index b876feb5a..fce9da014 100644 --- a/database/github/nlesc-nano/insilico-server/metadata.json +++ b/database/github/nlesc-nano/ceiba/insilico-server/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nlesc-nano/insilico-server", - "url": "https://github.com/nlesc-nano/insilico-server", + "url": "https://github.com/nlesc-nano/ceiba", "data": { "timestamp": "2020-11-08 00:20:30.649495", "name": "insilico-server", - "url": "https://api.github.com/repos/nlesc-nano/insilico-server", + "url": "https://github.com/nlesc-nano/ceiba", "full_name": "nlesc-nano/insilico-server", "html_url": "https://github.com/nlesc-nano/insilico-server", "private": false, @@ -35,6 +35,5 @@ }, "topics": [] }, - 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"url": "https://api.github.com/repos/nlesc-sherlock/Rig", + "url": "https://github.com/nlesc-sherlock/Rig", "data": { "timestamp": "2020-07-05 00:17:19.931027", "name": "Rig", - "url": "https://api.github.com/repos/nlesc-sherlock/Rig", + "url": "https://github.com/nlesc-sherlock/Rig", "full_name": "nlesc-sherlock/Rig", "html_url": "https://github.com/nlesc-sherlock/Rig", "private": false, @@ -36,7 +36,6 @@ }, "name": "Rig", "full_name": "nlesc-sherlock/Rig", - "html_url": "https://github.com/nlesc-sherlock/Rig", "private": false, "description": null, "created_at": "2016-02-16T09:51:31Z", diff --git a/database/github/nlesc-sherlock/emma/metadata.json b/database/github/nlesc-sherlock/emma/metadata.json index 1b5b015ce..02e2dad10 100644 --- a/database/github/nlesc-sherlock/emma/metadata.json +++ b/database/github/nlesc-sherlock/emma/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nlesc-sherlock/emma", - "url": "https://api.github.com/repos/nlesc-sherlock/emma", + "url": "https://github.com/nlesc-sherlock/emma", "data": { "timestamp": "2020-07-05 00:17:21.170967", "name": "emma", - "url": "https://api.github.com/repos/nlesc-sherlock/emma", + "url": "https://github.com/nlesc-sherlock/emma", "full_name": "nlesc-sherlock/emma", "html_url": "https://github.com/nlesc-sherlock/emma", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.996294", "name": "emma", "full_name": "nlesc-sherlock/emma", - "html_url": "https://github.com/nlesc-sherlock/emma", "private": false, "description": "Ansible playbook to create a cluster with GlusterFS, Docker, Spark and JupyterHub services", "created_at": "2017-02-12T19:57:58Z", diff --git a/database/github/nlppln/nlppln/metadata.json b/database/github/nlppln/nlppln/metadata.json index ccdf8453e..1f4a909cc 100644 --- a/database/github/nlppln/nlppln/metadata.json +++ b/database/github/nlppln/nlppln/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/nlppln/nlppln", - "url": "https://api.github.com/repos/nlppln/nlppln", + "url": "https://github.com/nlppln/nlppln", "data": { "timestamp": "2020-07-05 00:17:16.799272", "name": "nlppln", - "url": "https://api.github.com/repos/nlppln/nlppln", + "url": "https://github.com/nlppln/nlppln", "full_name": "nlppln/nlppln", "html_url": "https://github.com/nlppln/nlppln", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1116323", "name": "nlppln", "full_name": "nlppln/nlppln", - "html_url": "https://github.com/nlppln/nlppln", "private": false, "description": "NLP pipeline software using common workflow language", "created_at": "2016-08-08T11:29:33Z", diff --git a/database/github/numba/numba/metadata.json b/database/github/numba/numba/metadata.json index 44e46c06b..fde682fa8 100644 --- a/database/github/numba/numba/metadata.json +++ b/database/github/numba/numba/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/numba/numba", - "url": "https://api.github.com/repos/numba/numba", + "url": "https://github.com/numba/numba", "data": { "timestamp": "2020-07-04 13:22:19.857861", "name": "numba", - "url": "https://api.github.com/repos/numba/numba", + "url": "https://github.com/numba/numba", "full_name": "numba/numba", "html_url": "https://github.com/numba/numba", "private": false, @@ -36,7 +36,6 @@ }, "name": "numba", "full_name": "numba/numba", - 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"url": "https://api.github.com/repos/online-behaviour/find-journalists", + "url": "https://github.com/online-behaviour/find-journalists", "data": { "timestamp": "2020-07-05 00:17:13.604195", "name": "find-journalists", - "url": "https://api.github.com/repos/online-behaviour/find-journalists", + "url": "https://github.com/online-behaviour/find-journalists", "full_name": "online-behaviour/find-journalists", "html_url": "https://github.com/online-behaviour/find-journalists", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1045122", "name": "find-journalists", "full_name": "online-behaviour/find-journalists", - "html_url": "https://github.com/online-behaviour/find-journalists", "private": false, "description": null, "created_at": "2017-04-03T15:31:46Z", diff --git a/database/github/online-behaviour/machine-learning/metadata.json b/database/github/online-behaviour/machine-learning/metadata.json index 9b805ef7b..11f301c54 100644 --- a/database/github/online-behaviour/machine-learning/metadata.json +++ b/database/github/online-behaviour/machine-learning/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/online-behaviour/machine-learning", - "url": "https://api.github.com/repos/online-behaviour/machine-learning", + "url": "https://github.com/online-behaviour/machine-learning", "data": { "timestamp": "2020-07-05 00:17:17.384641", "name": "machine-learning", - "url": "https://api.github.com/repos/online-behaviour/machine-learning", + "url": "https://github.com/online-behaviour/machine-learning", "full_name": "online-behaviour/machine-learning", "html_url": "https://github.com/online-behaviour/machine-learning", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1045198", "name": "machine-learning", "full_name": "online-behaviour/machine-learning", - "html_url": "https://github.com/online-behaviour/machine-learning", "private": false, "description": "Python scripts for tweet retrieval and machine learning in the eScience project Automated Analysis of Online Behaviour on Social Media", "created_at": "2017-04-10T16:45:02Z", diff --git a/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json b/database/github/open-atmos/PyMPDATA/metadata.json similarity index 89% rename from database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json rename to database/github/open-atmos/PyMPDATA/metadata.json index f6368bbbb..5478cb7cb 100644 --- a/database/github/atmos-cloud-sim-uj/PyMPDATA/metadata.json +++ b/database/github/open-atmos/PyMPDATA/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/atmos-cloud-sim-uj/PyMPDATA", - "url": "https://github.com/atmos-cloud-sim-uj/PyMPDATA", + "url": "https://github.com/open-atmos/PyMPDATA", "data": { "doi": "https://doi.org/10.5281/zenodo.6934418", "name": "PyMPDATA", - "url": "https://github.com/atmos-cloud-sim-uj/PyMPDATA", + "url": "https://github.com/open-atmos/PyMPDATA", "full_name": "atmos-cloud-sim-uj/PyMPDATA", "html_url": "https://github.com/atmos-cloud-sim-uj/PyMPDATA", "description": "Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab", @@ -45,6 +45,5 @@ ], "timestamp": "2022-09-11 00:43:13.573293", "avatar": "https://avatars.githubusercontent.com/u/48702007?v=4" - }, - "html_url": "https://github.com/open-atmos/PyMPDATA" + } } \ No newline at end of file diff --git a/database/github/atmos-cloud-sim-uj/PySDM/metadata.json b/database/github/open-atmos/PySDM/metadata.json similarity index 88% rename from database/github/atmos-cloud-sim-uj/PySDM/metadata.json rename to database/github/open-atmos/PySDM/metadata.json index 88e299a99..683828458 100644 --- a/database/github/atmos-cloud-sim-uj/PySDM/metadata.json +++ b/database/github/open-atmos/PySDM/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/atmos-cloud-sim-uj/PySDM", - 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"url": "https://github.com/giswqs/leafmap", + "url": "https://github.com/opengeos/leafmap", "data": { "timestamp": "2021-08-08 00:31:57.508734", "name": "leafmap", - "url": "https://api.github.com/repos/giswqs/leafmap", + "url": "https://github.com/opengeos/leafmap", "full_name": "giswqs/leafmap", "html_url": "https://github.com/giswqs/leafmap", "private": false, @@ -49,6 +49,5 @@ "geospatial-analysis" ] }, - "doi": "https://doi.org/10.5281/zenodo.5137372", - "html_url": "https://github.com/opengeos/leafmap" + "doi": "https://doi.org/10.5281/zenodo.5137372" } \ No newline at end of file diff --git a/database/github/giswqs/lidar/metadata.json b/database/github/opengeos/lidar/metadata.json similarity index 87% rename from database/github/giswqs/lidar/metadata.json rename to database/github/opengeos/lidar/metadata.json index 7f9ecc77c..8ce1970fa 100644 --- a/database/github/giswqs/lidar/metadata.json +++ b/database/github/opengeos/lidar/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/giswqs/lidar", - 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"url": "https://api.github.com/repos/pandas-dev/pandas", + "url": "https://github.com/pandas-dev/pandas", "data": { "timestamp": "2020-07-04 13:22:08.390971", "name": "pandas", - "url": "https://api.github.com/repos/pandas-dev/pandas", + "url": "https://github.com/pandas-dev/pandas", "full_name": "pandas-dev/pandas", "html_url": "https://github.com/pandas-dev/pandas", "private": false, @@ -36,7 +36,6 @@ }, "name": "pandas", "full_name": "pandas-dev/pandas", - "html_url": "https://github.com/pandas-dev/pandas", "private": false, "description": "Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more", "created_at": "2010-08-24T01:37:33Z", diff --git a/database/github/phac-nml/biohansel/metadata.json b/database/github/phac-nml/biohansel/metadata.json index 1e53548a6..1ebd0e36e 100644 --- a/database/github/phac-nml/biohansel/metadata.json +++ b/database/github/phac-nml/biohansel/metadata.json @@ -1,7 +1,7 @@ { "parser": "github", "uid": "github/phac-nml/biohansel", - "url": null, + "url": "https://github.com/phac-nml/biohansel", "data": { "title": "BioHansel", "url": "https://github.com/phac-nml/biohansel", diff --git a/database/github/peterk87/sistr_cmd/metadata.json b/database/github/phac-nml/sistr_cmd/metadata.json similarity index 100% rename from database/github/peterk87/sistr_cmd/metadata.json rename to database/github/phac-nml/sistr_cmd/metadata.json diff --git a/database/github/plotly/dash/metadata.json b/database/github/plotly/dash/metadata.json index f495e36c1..8e1df381e 100644 --- a/database/github/plotly/dash/metadata.json +++ b/database/github/plotly/dash/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/plotly/dash", - "url": "https://api.github.com/repos/plotly/dash", + "url": "https://github.com/plotly/dash", "data": { "timestamp": "2020-07-04 13:22:40.042658", "name": "dash", - "url": "https://api.github.com/repos/plotly/dash", + "url": "https://github.com/plotly/dash", "full_name": "plotly/dash", "html_url": "https://github.com/plotly/dash", "private": false, @@ -36,7 +36,6 @@ }, "name": "dash", "full_name": "plotly/dash", - 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"url": "https://api.github.com/repos/potree/PotreeConverter", + "url": "https://github.com/potree/PotreeConverter", "full_name": "potree/PotreeConverter", "html_url": "https://github.com/potree/PotreeConverter", "private": false, @@ -36,7 +36,6 @@ }, "name": "PotreeConverter", "full_name": "potree/PotreeConverter", - "html_url": "https://github.com/potree/PotreeConverter", "private": false, "description": "Create multi res point cloud to use with potree", "created_at": "2014-02-08T09:23:58Z", diff --git a/database/github/putonti/virmine/metadata.json b/database/github/putonti/virMine/metadata.json similarity index 100% rename from database/github/putonti/virmine/metadata.json rename to database/github/putonti/virMine/metadata.json diff --git a/database/github/pvlib/pvlib-python/metadata.json b/database/github/pvlib/pvlib-python/metadata.json index a53cb7fe6..4ff50e0bb 100644 --- a/database/github/pvlib/pvlib-python/metadata.json +++ b/database/github/pvlib/pvlib-python/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/pvlib/pvlib-python", - "url": "https://api.github.com/repos/pvlib/pvlib-python", + "url": "https://github.com/pvlib/pvlib-python", "data": { "timestamp": "2020-07-04 13:22:20.875456", "name": "pvlib-python", - "url": "https://api.github.com/repos/pvlib/pvlib-python", + "url": "https://github.com/pvlib/pvlib-python", "full_name": "pvlib/pvlib-python", "html_url": "https://github.com/pvlib/pvlib-python", "private": false, @@ -36,7 +36,6 @@ }, "name": "pvlib-python", "full_name": "pvlib/pvlib-python", - "html_url": "https://github.com/pvlib/pvlib-python", "private": false, "description": "A set of documented functions for simulating the performance of photovoltaic energy systems.", "created_at": "2015-02-17T00:21:33Z", diff --git a/database/github/cthoyt/bel-resources/metadata.json b/database/github/pybel/bel-resources/metadata.json similarity index 100% rename from database/github/cthoyt/bel-resources/metadata.json rename to database/github/pybel/bel-resources/metadata.json diff --git a/database/github/pydata/xarray/metadata.json b/database/github/pydata/xarray/metadata.json index 6f91e6870..880255f02 100644 --- a/database/github/pydata/xarray/metadata.json +++ b/database/github/pydata/xarray/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/pydata/xarray", - 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"url": "https://api.github.com/repos/ropensci/opentripplanner", + "url": "https://github.com/ropensci/opentripplanner", "full_name": "ropensci/opentripplanner", "html_url": "https://github.com/ropensci/opentripplanner", "private": false, @@ -36,7 +36,6 @@ }, "name": "opentripplanner", "full_name": "ropensci/opentripplanner", - "html_url": "https://github.com/ropensci/opentripplanner", "private": false, "description": "An R package to set up and use OpenTripPlanner (OTP) as a local or remote multimodal trip planner.", "created_at": "2018-10-19T10:22:31Z", diff --git a/database/github/ropensci/plotly/metadata.json b/database/github/ropensci/plotly/metadata.json index 67fa950a1..63a061d0a 100644 --- a/database/github/ropensci/plotly/metadata.json +++ b/database/github/ropensci/plotly/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ropensci/plotly", - "url": "https://api.github.com/repos/ropensci/plotly", + "url": "https://github.com/ropensci/plotly", "data": { "timestamp": "2020-07-04 13:22:37.901769", "name": "plotly", - "url": "https://api.github.com/repos/ropensci/plotly", + "url": "https://github.com/ropensci/plotly", "full_name": "ropensci/plotly", "html_url": "https://github.com/ropensci/plotly", "private": false, @@ -36,7 +36,6 @@ }, "name": "plotly", "full_name": "ropensci/plotly", - "html_url": "https://github.com/ropensci/plotly", "private": false, "description": "An interactive graphing library for R", "created_at": "2013-11-21T05:56:51Z", diff --git a/database/github/ropensci/rtweet/metadata.json b/database/github/ropensci/rtweet/metadata.json index acbc15f84..582586fc7 100644 --- a/database/github/ropensci/rtweet/metadata.json +++ b/database/github/ropensci/rtweet/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ropensci/rtweet", - "url": "https://api.github.com/repos/ropensci/rtweet", + "url": "https://github.com/ropensci/rtweet", "data": { "timestamp": "2020-07-04 13:22:37.342918", "name": "rtweet", - "url": "https://api.github.com/repos/ropensci/rtweet", + "url": "https://github.com/ropensci/rtweet", "full_name": "ropensci/rtweet", "html_url": "https://github.com/ropensci/rtweet", "private": false, @@ -37,7 +37,6 @@ "doi": "10.21105/joss.01829", "name": "rtweet", "full_name": "ropensci/rtweet", - 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"url": "https://api.github.com/repos/stemangiola/tidyHeatmap", + "url": "https://github.com/stemangiola/tidyHeatmap", "data": { "timestamp": "2020-08-09 00:18:51.031454", "name": "tidyHeatmap", - "url": "https://api.github.com/repos/stemangiola/tidyHeatmap", + "url": "https://github.com/stemangiola/tidyHeatmap", "full_name": "stemangiola/tidyHeatmap", "html_url": "https://github.com/stemangiola/tidyHeatmap", "private": false, @@ -31,7 +31,6 @@ "doi": "https://doi.org/10.5281/zenodo.3966515", "name": "tidyHeatmap", "full_name": "stemangiola/tidyHeatmap", - "html_url": "https://github.com/stemangiola/tidyHeatmap", "private": false, "description": "Draw heatmap simply using a tidy data frame", "created_at": "2020-01-13T06:59:37Z", diff --git a/database/github/jkbonfield/crumble/metadata.json b/database/github/stuart-lab/signac/crumble/metadata.json similarity index 87% rename from database/github/jkbonfield/crumble/metadata.json rename to database/github/stuart-lab/signac/crumble/metadata.json index 55b06a088..7b11f81f0 100644 --- a/database/github/jkbonfield/crumble/metadata.json +++ b/database/github/stuart-lab/signac/crumble/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", "uid": "github/jkbonfield/crumble", - "url": "https://github.com/jkbonfield/crumble", + "url": "https://github.com/stuart-lab/signac", "data": { "title": "Crumble", - "url": "https://github.com/jkbonfield/crumble", + "url": "https://github.com/stuart-lab/signac", "credit": [], "tags": [ "high-throughput-sequencing" @@ -35,6 +35,5 @@ "type": "User" }, "timestamp": "2022-07-18 17:43:36.923298" - }, - "html_url": "https://github.com/stuart-lab/signac" + } } \ No newline at end of file diff --git a/database/github/timoast/signac/metadata.json b/database/github/stuart-lab/signac/metadata.json similarity index 92% rename from database/github/timoast/signac/metadata.json rename to database/github/stuart-lab/signac/metadata.json index b996fa6a8..b748e57d9 100644 --- a/database/github/timoast/signac/metadata.json +++ b/database/github/stuart-lab/signac/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/timoast/signac", - "url": "https://api.github.com/repos/timoast/signac", + "url": "https://github.com/stuart-lab/signac", "data": { "timestamp": "2020-07-04 13:22:16.732305", "name": "signac", - "url": "https://api.github.com/repos/timoast/signac", + "url": "https://github.com/stuart-lab/signac", "full_name": "timoast/signac", "html_url": "https://github.com/timoast/signac", "private": false, @@ -36,7 +36,6 @@ }, "name": "signac", "full_name": "timoast/signac", - "html_url": "https://github.com/stuart-lab/signac", "private": false, "description": "R toolkit for the analysis of single-cell chromatin data", "created_at": "2019-05-09T22:32:26Z", diff --git a/database/github/sunpy/sunpy/metadata.json b/database/github/sunpy/sunpy/metadata.json index c7b685780..70979ca99 100644 --- a/database/github/sunpy/sunpy/metadata.json +++ b/database/github/sunpy/sunpy/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/sunpy/sunpy", - "url": "https://api.github.com/repos/sunpy/sunpy", + "url": "https://github.com/sunpy/sunpy", "data": { "timestamp": "2020-07-04 13:22:44.509099", "name": "sunpy", - "url": "https://api.github.com/repos/sunpy/sunpy", + "url": "https://github.com/sunpy/sunpy", "full_name": "sunpy/sunpy", "html_url": "https://github.com/sunpy/sunpy", "private": false, @@ -36,7 +36,6 @@ }, "name": "sunpy", "full_name": "sunpy/sunpy", - "html_url": "https://github.com/sunpy/sunpy", "private": false, "description": "SunPy - Python for Solar Physics", "created_at": "2011-08-06T15:34:08Z", diff --git a/database/github/surf-eds/one-button-compute/metadata.json b/database/github/surf-eds/one-button-compute/metadata.json index 373cbd15f..35d339cbb 100644 --- a/database/github/surf-eds/one-button-compute/metadata.json +++ b/database/github/surf-eds/one-button-compute/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/surf-eds/one-button-compute", - "url": "https://api.github.com/repos/surf-eds/one-button-compute", + "url": "https://github.com/surf-eds/one-button-compute", "data": { "timestamp": "2020-07-05 00:17:21.928716", "name": "one-button-compute", - "url": "https://api.github.com/repos/surf-eds/one-button-compute", + "url": "https://github.com/surf-eds/one-button-compute", "full_name": "surf-eds/one-button-compute", "html_url": "https://github.com/surf-eds/one-button-compute", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1033816", "name": "one-button-compute", "full_name": "surf-eds/one-button-compute", - "html_url": "https://github.com/surf-eds/one-button-compute", "private": false, "description": "Web API for dynamic compute", "created_at": "2015-10-01T09:31:05Z", diff --git a/database/github/sverhoeven/docker-cartodb/metadata.json b/database/github/sverhoeven/docker-cartodb/metadata.json index 2792d5da1..c4bbea101 100644 --- a/database/github/sverhoeven/docker-cartodb/metadata.json +++ b/database/github/sverhoeven/docker-cartodb/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/sverhoeven/docker-cartodb", - "url": "https://api.github.com/repos/sverhoeven/docker-cartodb", + "url": "https://github.com/sverhoeven/docker-cartodb", "data": { "timestamp": "2020-07-05 00:17:09.441695", "name": "docker-cartodb", - "url": "https://api.github.com/repos/sverhoeven/docker-cartodb", + "url": "https://github.com/sverhoeven/docker-cartodb", "full_name": "sverhoeven/docker-cartodb", "html_url": "https://github.com/sverhoeven/docker-cartodb", "private": false, @@ -36,7 +36,6 @@ }, "name": "docker-cartodb", "full_name": "sverhoeven/docker-cartodb", - "html_url": "https://github.com/sverhoeven/docker-cartodb", "private": false, "description": "Dockerized CartoDB", "created_at": "2015-02-13T13:36:01Z", diff --git a/database/github/taoliu/MACS/metadata.json b/database/github/taoliu/MACS/metadata.json index 248b2f292..897b685da 100644 --- a/database/github/taoliu/MACS/metadata.json +++ b/database/github/taoliu/MACS/metadata.json @@ -1,48 +1,19 @@ { "parser": "github", - "uid": "github/taoliu/MACS", - "url": "https://github.com/macs3-project/MACS", + "uid": "github/wiki/Install-macs2", + "url": "https://github.com/taoliu/MACS", "data": { - "url": "https://github.com/macs3-project/MACS", - "title": "Macs", - "description": "MACS -- Model-based Analysis of ChIP-Seq", - "doi": "http://dx.doi.org/10.1186/gb-2008-9-9-r137", - "name": "MACS", - "full_name": "macs3-project/MACS", - "html_url": "https://github.com/macs3-project/MACS", - "created_at": "2011-03-02T19:40:25Z", - "updated_at": "2022-07-14T09:25:57Z", - "clone_url": "https://github.com/macs3-project/MACS.git", - 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database/github/tramarobin/fctSPM/metadata.json rename to database/github/tramarobin/fctSnPM/metadata.json diff --git a/database/github/tvwenger/wisp/metadata.json b/database/github/tvwenger/WISP/metadata.json similarity index 100% rename from database/github/tvwenger/wisp/metadata.json rename to database/github/tvwenger/WISP/metadata.json diff --git a/database/github/twinl/website/metadata.json b/database/github/twinl/website/metadata.json index 85be8d12d..cb357d877 100644 --- a/database/github/twinl/website/metadata.json +++ b/database/github/twinl/website/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/twinl/website", - "url": "https://api.github.com/repos/twinl/website", + "url": "https://github.com/twinl/website", "data": { "timestamp": "2020-07-05 00:17:22.375840", "name": "website", - "url": "https://api.github.com/repos/twinl/website", + "url": "https://github.com/twinl/website", "full_name": "twinl/website", "html_url": "https://github.com/twinl/website", 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b/database/github/xenon-middleware/osmium/metadata.json similarity index 91% rename from database/github/NLeSC/osmium/metadata.json rename to database/github/xenon-middleware/osmium/metadata.json index 54bc151b2..c8ff1e465 100644 --- a/database/github/NLeSC/osmium/metadata.json +++ b/database/github/xenon-middleware/osmium/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/osmium", - "url": "https://api.github.com/repos/xenon-middleware/osmium", + "url": "https://github.com/xenon-middleware/osmium", "data": { "timestamp": "2020-07-05 00:17:17.693720", "name": "osmium", - "url": "https://api.github.com/repos/xenon-middleware/osmium", + "url": "https://github.com/xenon-middleware/osmium", "full_name": "xenon-middleware/osmium", "html_url": "https://github.com/xenon-middleware/osmium", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1065435", "name": "osmium", "full_name": "xenon-middleware/osmium", - "html_url": 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100644 --- a/database/github/NLeSC/xenon-grpc/metadata.json +++ b/database/github/xenon-middleware/xenon-grpc/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/NLeSC/xenon-grpc", - "url": "https://api.github.com/repos/xenon-middleware/xenon-grpc", + "url": "https://github.com/xenon-middleware/xenon-grpc", "data": { "timestamp": "2020-07-05 00:17:23.204432", "name": "xenon-grpc", - "url": "https://api.github.com/repos/xenon-middleware/xenon-grpc", + "url": "https://github.com/xenon-middleware/xenon-grpc", "full_name": "xenon-middleware/xenon-grpc", "html_url": "https://github.com/xenon-middleware/xenon-grpc", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1043481", "name": "xenon-grpc", "full_name": "xenon-middleware/xenon-grpc", - "html_url": "https://github.com/xenon-middleware/xenon-grpc", "private": false, "description": "Xenon grpc based server", "created_at": "2017-05-12T15:27:28Z", diff --git a/database/github/xenon-middleware/xenon/metadata.json b/database/github/xenon-middleware/xenon/metadata.json index 3cac967a1..4a2f38e99 100644 --- a/database/github/xenon-middleware/xenon/metadata.json +++ b/database/github/xenon-middleware/xenon/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/xenon-middleware/xenon", - "url": "https://api.github.com/repos/xenon-middleware/xenon", + "url": "https://github.com/xenon-middleware/xenon", "data": { "timestamp": "2020-07-05 00:17:22.691274", "name": "xenon", - "url": "https://api.github.com/repos/xenon-middleware/xenon", + "url": "https://github.com/xenon-middleware/xenon", "full_name": "xenon-middleware/xenon", "html_url": "https://github.com/xenon-middleware/xenon", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.597993", "name": "xenon", "full_name": "xenon-middleware/xenon", - "html_url": "https://github.com/xenon-middleware/xenon", "private": false, "description": "A middleware abstraction library that provides a simple programming interface to various 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"full_name": "yatiml/yatiml", "html_url": "https://github.com/yatiml/yatiml", "private": false, @@ -37,7 +37,6 @@ "doi": "10.5281/zenodo.1478048", "name": "yatiml", "full_name": "yatiml/yatiml", - "html_url": "https://github.com/yatiml/yatiml", "private": false, "description": "Python library for YAML type inference, schema checking and syntactic sugar", "created_at": "2018-09-03T12:31:02Z", diff --git a/database/github/ylab-hi/ScanITD/metadata.json b/database/github/ylab-hi/ScanITD/metadata.json index 41ef036a2..1f1b75a4d 100644 --- a/database/github/ylab-hi/ScanITD/metadata.json +++ b/database/github/ylab-hi/ScanITD/metadata.json @@ -1,11 +1,11 @@ { "parser": "github", "uid": "github/ylab-hi/ScanITD", - "url": "https://api.github.com/repos/ylab-hi/ScanITD", + "url": "https://github.com/ylab-hi/ScanITD", "data": { "timestamp": "2020-08-02 16:35:31.291415", "name": "ScanITD", - "url": "https://api.github.com/repos/ylab-hi/ScanITD", + "url": "https://github.com/ylab-hi/ScanITD", 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+github/achael/eht-imaging +gitlab/andreas.andrusch/paipline +github/WGS-TB/MentaLiST +github/tatekawa-astron/PN +github/DreamCloud-Project/AMALTHEA-Microworkload-Generator +github/kadyb/rgugik +github/B-UMMI/chewBBACA +github/UCD4IDS/WaveletsExt.jl +github/bcerutti/Zeltron-code +github/ajohnson-uoregon/llvm-project +github/jkrogager/VoigtFit +gitlab/joseaher/astroplotlib +github/linksmart/thing-directory github/mrbell/fsclean -github/FRED-2/OptiType -github/gromacs/gromacs \ No newline at end of file +github/pyomeca/biosiglive +github/tp2vis/distribute +github/ToHanwei/Genome2OR +github/HCGB-IGTP/spaTyper +github/musevlt/origin +github/4dn-dcic/pairix +github/rmaphoh/AutoMorph +github/bommert/stabm +github/seheonoh/2dbat +github/Natsiopoulos/ARDL +github/ropensci/neotoma +github/ketch/RK-Opt +github/mgalardini/pyseer +github/fatmasevinck/enetLTS +github/hall-lab/bamkit +github/CosmoStat/CosmoPMC +github/paulhjkelly/taskgraph-metaprogramming +github/EISy-as-Py/hardy +github/VincentAlcazer/StatAid +github/ethankruse/koi3278 +github/vishwas1984/LaplaceInterpolation.jl +github/varlociraptor/varlociraptorhub.io +github/SciML/GlobalSensitivity.jl +github/stammler/simframe +github/nlesc-nano/flamingo +github/ropensci/oai +github/ropensci/riem +github/linnarsson-lab/loompy +github/yjx1217/RecombineX +github/KeplerGO/K2fov +github/raphael-group/hatchet +github/mommermi/photometrypipeline +github/lrnv/cort +github/Glogobyte/miRGalaxy \ No newline at end of file From 7eccc004ac071918053de02719adf7b05d7e199a Mon Sep 17 00:00:00 2001 From: Vanessasaurus <814322+vsoch@users.noreply.github.com> Date: Wed, 5 Apr 2023 00:15:19 -0600 Subject: [PATCH 05/10] Update clean.yaml --- .github/workflows/clean.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/clean.yaml b/.github/workflows/clean.yaml index 3c0d89753..fb5eb2b3d 100644 --- a/.github/workflows/clean.yaml +++ b/.github/workflows/clean.yaml @@ -24,7 +24,7 @@ jobs: env: RSE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: | - python .github/scripts/clean-database.py + python .github/scripts/clean-database.py $(pwd) rse export repos.txt --force - name: Export site to docs/ From 50e4e0f0db8c5836543d74b4541664b980ef023f Mon Sep 17 00:00:00 2001 From: vsoch Date: Wed, 5 Apr 2023 00:19:58 -0600 Subject: [PATCH 06/10] fix Signed-off-by: vsoch --- .github/scripts/clean-database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py index cc58ffd52..d750d7c14 100755 --- a/.github/scripts/clean-database.py +++ b/.github/scripts/clean-database.py @@ -45,9 +45,9 @@ def clean(database, archive): repos = fd.readlines() repos = set([x.strip() for x in repos if x.strip()]) - relpath = os.path.relpath(path, database) for path in recursive_find(database, "*metadata.json"): meta = read_json(path) + relpath = os.path.relpath(path, database) # Spurious bug with empty url if meta["url"] is None: From 8cb01ca6d2bf25fc9a198463429a66a3d85c2b84 Mon Sep 17 00:00:00 2001 From: vsoch Date: Wed, 5 Apr 2023 01:12:39 -0600 Subject: [PATCH 07/10] tweak cleanup Signed-off-by: vsoch --- repos.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repos.txt b/repos.txt index 9529ca828..51746141e 100644 --- a/repos.txt +++ b/repos.txt @@ -1694,7 +1694,7 @@ github/smithlabcode/falco github/johnpaulett/python-hl7 github/soedinglab/MMseqs2 github/joe-antognini/kozai -trinityrnaseq/trinityrnaseq/wiki +trinityrnaseq/trinityrnaseq github/planck-npipe/hillipop github/aarondotter/iso github/VeinsOfTheEarth/RivGraph @@ -2693,7 +2693,7 @@ github/ianfhunter/GNOLL github/SPARTA-dev/SPARTA github/ropensci/treestartr github/symmy596/Polypy -broadinstitute/pilon/wiki +broadinstitute/pilon github/jluastro/PopSyCLE github/RuthAngus/GProtation github/akcochrane/TEfits @@ -4634,4 +4634,4 @@ github/KeplerGO/K2fov github/raphael-group/hatchet github/mommermi/photometrypipeline github/lrnv/cort -github/Glogobyte/miRGalaxy \ No newline at end of file +github/Glogobyte/miRGalaxy From 661db98d83eab75ba2997790d99e24b84aef7fdb Mon Sep 17 00:00:00 2001 From: vsoch Date: Wed, 5 Apr 2023 17:03:20 -0600 Subject: [PATCH 08/10] test cleaning a subset Signed-off-by: vsoch --- .github/scripts/clean-database.py | 26 ++++++++++++++++++-------- .github/workflows/clean.yaml | 22 ++++++++++++++++++++-- 2 files changed, 38 insertions(+), 10 deletions(-) diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py index d750d7c14..d7c0ef976 100755 --- a/.github/scripts/clean-database.py +++ b/.github/scripts/clean-database.py @@ -36,19 +36,32 @@ def save_json(meta, path): fd.write(json.dumps(meta, indent=4)) -def clean(database, archive): +def clean(repos_file, database, archive): """ Clean the database """ # Read in repos.txt and remove archived + with open(repos_file, "r") as fd: + subset = fd.readlines() + with open("repos.txt", "r") as fd: repos = fd.readlines() + repos = set([x.strip() for x in repos if x.strip()]) + subset = set([x.strip() for x in subset if x.strip()]) for path in recursive_find(database, "*metadata.json"): meta = read_json(path) relpath = os.path.relpath(path, database) + # Ensure UID is correct + uid = meta['url'].rsplit('/', 3) + uid = "/".join(uid[1:]).replace('.com', '') + + # Only look at subset + if uid not in subset: + continue + # Spurious bug with empty url if meta["url"] is None: meta["url"] = meta["data"]["url"] @@ -78,10 +91,6 @@ def clean(database, archive): meta["url"] = new_location.url save_json(meta, path) - # Ensure UID is correct - uid = meta['url'].rsplit('/', 3) - uid = "/".join(uid[1:]).replace('.com', '') - if uid not in relpath: old_uid = os.path.dirname(relpath) shutil.move(os.path.dirname(path), os.path.join(database, uid)) @@ -97,17 +106,18 @@ def clean(database, archive): def main(): # python .github/scripts/clean-database.py $(pwd) - if len(sys.argv) < 2: - sys.exit("Please provide a root path with the database and argument") + if len(sys.argv) < 3: + sys.exit("Please provide a root path (with the database and argument) and a text file of repos.") root = os.path.abspath(sys.argv[1]) + repos_file = os.path.abspath(sys.argv[2]) database = os.path.join(root, "database") archive = os.path.join(root, "archive") for path in database, archive: if not os.path.exists(path): sys.exit(f"{path} does not exist.") - clean(database, archive) + clean(repos_file, database, archive) if __name__ == "__main__": diff --git a/.github/workflows/clean.yaml b/.github/workflows/clean.yaml index fb5eb2b3d..1b3d33cc5 100644 --- a/.github/workflows/clean.yaml +++ b/.github/workflows/clean.yaml @@ -20,11 +20,29 @@ jobs: cd /tmp/rse sudo pip3 install .[all] rse --version - - name: Clean Repos + + - name: Shpc Listing + run: | + # Remove default remote registry and add PWD + shpc config remove registry https://github.com/singularityhub/shpc-registry + shpc config add registry $(pwd) + shpc show > listing.txt + + # Run a specific letter matched to a day of the month A==1, Z==26 + - name: Calendar Updater + uses: vsoch/split-list-action@main + with: + ids_file: repos.txt + outfile: repos-subset.txt + + # One letter assigned to each day + calendar_split: true + + - name: Clean Repos Subset env: RSE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: | - python .github/scripts/clean-database.py $(pwd) + python .github/scripts/clean-database.py $(pwd) repos-subset.txt rse export repos.txt --force - name: Export site to docs/ From 835e2445da739938eac7f933a4ace9cbfbc3c0d1 Mon Sep 17 00:00:00 2001 From: vsoch Date: Wed, 5 Apr 2023 18:27:22 -0600 Subject: [PATCH 09/10] tweak Signed-off-by: vsoch --- .github/workflows/clean.yaml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/clean.yaml b/.github/workflows/clean.yaml index 1b3d33cc5..1e8ceeaae 100644 --- a/.github/workflows/clean.yaml +++ b/.github/workflows/clean.yaml @@ -21,13 +21,6 @@ jobs: sudo pip3 install .[all] rse --version - - name: Shpc Listing - run: | - # Remove default remote registry and add PWD - shpc config remove registry https://github.com/singularityhub/shpc-registry - shpc config add registry $(pwd) - shpc show > listing.txt - # Run a specific letter matched to a day of the month A==1, Z==26 - name: Calendar Updater uses: vsoch/split-list-action@main From f1bc7609a4dfe9b7afb24f5c82ae3ca3b7f982de Mon Sep 17 00:00:00 2001 From: vsoch Date: Tue, 18 Apr 2023 14:55:22 -0600 Subject: [PATCH 10/10] additional cleanup Signed-off-by: vsoch --- .github/scripts/clean-database.py | 25 +++++++++++-------- .../broadinstitute/pilon}/metadata.json | 8 +++--- .../cufflinks/metadata.json | 6 ++--- .../github/marbl/Krona/wiki/metadata.json | 16 ------------ .../circulator}/metadata.json | 6 ++--- database/github/taoliu/MACS/metadata.json | 6 ++--- .../trinityrnaseq}/metadata.json | 8 +++--- 7 files changed, 32 insertions(+), 43 deletions(-) rename database/{broadinstitute/pilon/wiki => github/broadinstitute/pilon}/metadata.json (73%) rename database/{cole-trapnell-lab.github.io => github/cole-trapnell-lab}/cufflinks/metadata.json (92%) delete mode 100644 database/github/marbl/Krona/wiki/metadata.json rename database/{sanger-pathogens.github.io/circlator => github/sanger-pathogens/circulator}/metadata.json (94%) rename database/{trinityrnaseq/trinityrnaseq/wiki => github/trinityrnaseq/trinityrnaseq}/metadata.json (81%) diff --git a/.github/scripts/clean-database.py b/.github/scripts/clean-database.py index d7c0ef976..e4bc4605e 100755 --- a/.github/scripts/clean-database.py +++ b/.github/scripts/clean-database.py @@ -55,8 +55,8 @@ def clean(repos_file, database, archive): relpath = os.path.relpath(path, database) # Ensure UID is correct - uid = meta['url'].rsplit('/', 3) - uid = "/".join(uid[1:]).replace('.com', '') + uid = meta["url"].rsplit("/", 3) + uid = "/".join(uid[1:]).replace(".com", "") # Only look at subset if uid not in subset: @@ -88,26 +88,31 @@ def clean(repos_file, database, archive): elif res.status_code in [301, 302]: print(f"Found repository {relpath} with moved location, updating") new_location = requests.head(res.headers["Location"]) - meta["url"] = new_location.url + meta["url"] = new_location.url save_json(meta, path) if uid not in relpath: - old_uid = os.path.dirname(relpath) - shutil.move(os.path.dirname(path), os.path.join(database, uid)) - print(f"{relpath} should be {uid}") - if old_uid in repos: - repos.remove(old_uid) - repos.add(uid) + old_uid = os.path.dirname(relpath) + shutil.move(os.path.dirname(path), os.path.join(database, uid)) + print(f"{relpath} should be {uid}") + if old_uid in repos: + repos.remove(old_uid) + repos.add(uid) # Save back to file + # This largely isn't needed because we re-generate with export + # But might as well try to maintain consistency here. with open("repos.txt", "w") as fd: fd.write("\n".join(list(repos))) + def main(): # python .github/scripts/clean-database.py $(pwd) if len(sys.argv) < 3: - sys.exit("Please provide a root path (with the database and argument) and a text file of repos.") + sys.exit( + "Please provide a root path (with the database and argument) and a text file of repos." + ) root = os.path.abspath(sys.argv[1]) repos_file = os.path.abspath(sys.argv[2]) diff --git a/database/broadinstitute/pilon/wiki/metadata.json b/database/github/broadinstitute/pilon/metadata.json similarity index 73% rename from database/broadinstitute/pilon/wiki/metadata.json rename to database/github/broadinstitute/pilon/metadata.json index 3c3cfeb7d..f93adec48 100644 --- a/database/broadinstitute/pilon/wiki/metadata.json +++ b/database/github/broadinstitute/pilon/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", - "uid": "github/pilon/wiki", - "url": "https://github.com/broadinstitute/pilon/wiki", + "uid": "github/broadinstitute/pilon", + "url": "https://github.com/broadinstitute/pilon", "data": { "title": "Pilon", - "url": "https://github.com/broadinstitute/pilon/wiki", + "url": "https://github.com/broadinstitute/pilon", "credit": [], "tags": [ "genome-assembly", @@ -13,4 +13,4 @@ "description": "Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection.", "timestamp": "2022-07-18 17:46:22.067066" } -} \ No newline at end of file +} diff --git a/database/cole-trapnell-lab.github.io/cufflinks/metadata.json b/database/github/cole-trapnell-lab/cufflinks/metadata.json similarity index 92% rename from database/cole-trapnell-lab.github.io/cufflinks/metadata.json rename to database/github/cole-trapnell-lab/cufflinks/metadata.json index fa94a6fc1..33b391c43 100644 --- a/database/cole-trapnell-lab.github.io/cufflinks/metadata.json +++ b/database/github/cole-trapnell-lab/cufflinks/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", "uid": "github/cole-trapnell-lab/cufflinks", - "url": "http://cole-trapnell-lab.github.io/cufflinks/", + "url": "https://github.com/cole-trapnell-lab/cufflinks", "data": { "title": "Cufflinks", - "url": "http://cole-trapnell-lab.github.io/cufflinks/", + "url": "https://github.com/cole-trapnell-lab/cufflinks", "credit": [ "Cole Trapnell", "Geo Pertea" @@ -42,4 +42,4 @@ }, "timestamp": "2022-07-18 17:43:37.311554" } -} \ No newline at end of file +} diff --git a/database/github/marbl/Krona/wiki/metadata.json b/database/github/marbl/Krona/wiki/metadata.json deleted file mode 100644 index 2c37455fb..000000000 --- a/database/github/marbl/Krona/wiki/metadata.json +++ /dev/null @@ -1,16 +0,0 @@ -{ - "parser": "github", - "uid": "github/Krona/wiki", - "url": "https://github.com/marbl/Krona", - "data": { - "title": "Krona Tools", - "url": "https://github.com/marbl/Krona/wiki", - "credit": [], - "tags": [ - "visualization", - "visualization" - ], - "description": "is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", - "timestamp": "2022-07-18 17:45:32.620098" - } -} \ No newline at end of file diff --git a/database/sanger-pathogens.github.io/circlator/metadata.json b/database/github/sanger-pathogens/circulator/metadata.json similarity index 94% rename from database/sanger-pathogens.github.io/circlator/metadata.json rename to database/github/sanger-pathogens/circulator/metadata.json index 5a8e4ea9a..03e846bc7 100644 --- a/database/sanger-pathogens.github.io/circlator/metadata.json +++ b/database/github/sanger-pathogens/circulator/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", "uid": "github/sanger-pathogens/circlator", - "url": "http://sanger-pathogens.github.io/circlator/", + "url": "https://github.com/sanger-pathogens/circlator", "data": { "title": "Circlator", - "url": "http://sanger-pathogens.github.io/circlator/", + "url": "https://github.com/sanger-pathogens/circlator", "credit": [], "tags": [ "genome-assembly", @@ -50,4 +50,4 @@ ], "timestamp": "2022-07-18 17:43:35.722068" } -} \ No newline at end of file +} diff --git a/database/github/taoliu/MACS/metadata.json b/database/github/taoliu/MACS/metadata.json index 897b685da..640fc1b32 100644 --- a/database/github/taoliu/MACS/metadata.json +++ b/database/github/taoliu/MACS/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", - "uid": "github/wiki/Install-macs2", + "uid": "github/taoliu/MACS", "url": "https://github.com/taoliu/MACS", "data": { "title": "MACS2", - "url": "https://github.com/taoliu/MACS/wiki/Install-macs2", + "url": "https://github.com/taoliu/MACS", "credit": [ "Tao Liu" ], @@ -16,4 +16,4 @@ "description": "(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.", "timestamp": "2022-07-18 17:45:38.076565" } -} \ No newline at end of file +} diff --git a/database/trinityrnaseq/trinityrnaseq/wiki/metadata.json b/database/github/trinityrnaseq/trinityrnaseq/metadata.json similarity index 81% rename from database/trinityrnaseq/trinityrnaseq/wiki/metadata.json rename to database/github/trinityrnaseq/trinityrnaseq/metadata.json index 6c9c9de5e..83bd130c6 100644 --- a/database/trinityrnaseq/trinityrnaseq/wiki/metadata.json +++ b/database/github/trinityrnaseq/trinityrnaseq/metadata.json @@ -1,10 +1,10 @@ { "parser": "github", - "uid": "github/trinityrnaseq/wiki", - "url": "https://github.com/trinityrnaseq/trinityrnaseq/wiki", + "uid": "github/trinityrnaseq/trinityrnaseq", + "url": "https://github.com/trinityrnaseq/trinityrnaseq", "data": { "title": "Trinity", - "url": "https://github.com/trinityrnaseq/trinityrnaseq/wiki", + "url": "https://github.com/trinityrnaseq/trinityrnaseq", "credit": [ "Alexie Papanicolaou", "Aviv Regev", @@ -23,4 +23,4 @@ "description": "a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.", "timestamp": "2022-07-18 17:47:19.602967" } -} \ No newline at end of file +}