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Merge branch 'master' of github.com:stemangiola/HCAquery Conflicts: DESCRIPTION
2 parents 27580bc + 5484756 commit 9dace73

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‎.github/workflows/check-bioc.yml

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@@ -39,6 +39,7 @@ env:
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run_pkgdown: 'true'
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has_RUnit: 'false'
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cache-version: 'cache-v1'
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run_docker: 'false'
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jobs:
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build-check:
@@ -48,12 +49,14 @@ jobs:
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## Environment variables unique to this job.
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strategy:
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fail-fast: true
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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- { os: macOS-latest, r: '4.2', bioc: '3.16'}
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- { os: windows-latest, r: '4.2', bioc: '3.16'}
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- { os: ubuntu-latest, r: '4.3', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
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- { os: macOS-latest, r: '4.3', bioc: '3.18'}
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- { os: windows-latest, r: '4.3', bioc: '3.18'}
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## Check https://github.com/r-lib/actions/tree/master/examples
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## for examples using the http-user-agent
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
@@ -76,14 +79,15 @@ jobs:
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- name: Checkout Repository
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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## R is already included in the Bioconductor docker images
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- name: Setup R from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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## pandoc is already included in the Bioconductor docker images
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- name: Setup pandoc from r-lib
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Cache R packages
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- name: Restore R package cache
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: ${{ env.R_LIBS_USER }}
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key: "${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}r-{{ matrix.config.r }}"
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-
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- name: Cache R packages on Linux
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: /home/runner/work/_temp/Library
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key: "${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}r-{{ matrix.config.r }}"
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
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echo $sysreqs
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sudo -s eval "$sysreqs"
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# - name: Install Linux system dependencies
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# if: runner.os == 'Linux'
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# run: |
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# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
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# echo $sysreqs
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# sudo -s eval "$sysreqs"
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- name: Install macOS system dependencies
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if: matrix.config.os == 'macOS-latest'
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## For installing usethis's dependency gert
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brew install libgit2
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## To fix x11/cairo error with tidyHeatmap/Complexheatmap here https://github.com/stemangiola/tidybulk/runs/1388237421?check_suite_focus=true#step:14:2134
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## Suggested here https://stackoverflow.com/questions/63648591/how-to-install-x11-before-testing-with-github-actions-for-macos
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brew install --cask xquartz
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## Required for tcltk
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brew install xquartz --cask
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- name: Install Windows system dependencies
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if: runner.os == 'Windows'
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- name: Install BiocManager
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run: |
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message(paste('****', Sys.time(), 'installing BiocManager ****'))
150-
remotes::install_github("Bioconductor/BiocManager")
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remotes::install_cran("BiocManager")
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shell: Rscript {0}
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- name: Set BiocVersion
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run: |
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
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shell: Rscript {0}
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- name: Install dependencies pass 1
@@ -164,6 +169,10 @@ jobs:
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## https://github.com/r-lib/remotes/issues/296
165170
## Ideally, all dependencies should get installed in the first pass.
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
174+
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
175+
167176
## Pass #1 at installing dependencies
168177
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
169178
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
@@ -174,12 +183,7 @@ jobs:
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run: |
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## Pass #2 at installing dependencies
176185
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
177-
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
178-
179-
## For running the checks
180-
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
181-
remotes::install_cran("rcmdcheck")
182-
BiocManager::install("BiocCheck")
186+
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
183187
shell: Rscript {0}
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- name: Install BiocGenerics
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shell: Rscript {0}
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- name: Install covr
193-
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
197+
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
194198
run: |
195199
remotes::install_cran("covr")
196200
shell: Rscript {0}
197201

198202
- name: Install pkgdown
199-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
203+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
200204
run: |
201-
remotes::install_cran("pkgdown")
205+
remotes::install_github("r-lib/pkgdown")
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shell: Rscript {0}
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- name: Session info
@@ -211,10 +215,12 @@ jobs:
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- name: Run CMD check
212216
env:
213217
_R_CHECK_CRAN_INCOMING_: false
218+
DISPLAY: 99.0
214219
run: |
220+
options(crayon.enabled = TRUE)
215221
rcmdcheck::rcmdcheck(
216-
args = c("--no-manual", "--timings"),
217-
build_args = c("--no-manual", "--no-resave-data"),
222+
args = c("--no-manual", "--no-vignettes", "--timings"),
223+
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
218224
error_on = "warning",
219225
check_dir = "check"
220226
)
@@ -232,45 +238,101 @@ jobs:
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shell: Rscript {0}
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234240
- name: Run BiocCheck
241+
env:
242+
DISPLAY: 99.0
235243
run: |
236244
BiocCheck::BiocCheck(
237245
dir('check', 'tar.gz$', full.names = TRUE),
238246
`quit-with-status` = TRUE,
239247
`no-check-R-ver` = TRUE,
240-
`no-check-bioc-help` = TRUE,
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`new-package` = TRUE
248+
`no-check-bioc-help` = TRUE
242249
)
243250
shell: Rscript {0}
244251

245252
- name: Test coverage
246-
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
253+
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
247254
run: |
248255
covr::codecov()
249256
shell: Rscript {0}
250257

251258
- name: Install package
252-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
259+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
253260
run: R CMD INSTALL .
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255-
- name: Deploy package
256-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
257-
run: |
258-
## Temporary workaround for https://github.com/actions/checkout/issues/766
259-
git config --global --add safe.directory "$GITHUB_WORKSPACE"
260-
261-
git config --local user.email "[email protected]"
262-
git config --local user.name "GitHub Actions"
263-
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
264-
shell: bash {0}
262+
- name: Build pkgdown site
263+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
264+
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
265+
shell: Rscript {0}
265266
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
266267
## at least one locally before this will work. This creates the gh-pages
267268
## branch (erasing anything you haven't version controlled!) and
268269
## makes the git history recognizable by pkgdown.
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271+
- name: Install deploy dependencies
272+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
274+
apt-get update && apt-get -y install rsync
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- name: Deploy pkgdown site to GitHub pages 🚀
277+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
278+
uses: JamesIves/github-pages-deploy-action@releases/v4
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with:
280+
clean: false
281+
branch: gh-pages
282+
folder: docs
283+
270284
- name: Upload check results
271285
if: failure()
272-
uses: actions/upload-artifact@v2
286+
uses: actions/upload-artifact@master
273287
with:
274-
name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
288+
name: ${{ runner.os }}-biocversion-devel-r-4.3-results
275289
path: check
276-
290+
291+
292+
## Code adapted from
293+
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
294+
docker-build-and-push:
295+
runs-on: ubuntu-latest
296+
needs: build-check
297+
steps:
298+
- name: Checkout Repository
299+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
300+
uses: actions/checkout@v3
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302+
- name: Register repo name
303+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
304+
id: reg_repo_name
305+
run: |
306+
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
307+
308+
- name: Set up QEMU
309+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
310+
uses: docker/setup-qemu-action@v2
311+
312+
- name: Set up Docker Buildx
313+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
314+
uses: docker/setup-buildx-action@v2
315+
316+
- name: Login to Docker Hub
317+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
318+
uses: docker/login-action@v2
319+
with:
320+
username: ${{ secrets.DOCKERHUB_USERNAME }}
321+
password: ${{ secrets.DOCKERHUB_TOKEN }}
322+
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
323+
## account, not your actual dockerhub account password. You can get it
324+
## from https://hub.docker.com/settings/security.
325+
## Check https://github.com/docker/build-push-action/tree/v4.0.0
326+
## for more details.
327+
## Alternatively, try checking
328+
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
329+
330+
- name: Build and Push Docker
331+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
332+
uses: docker/build-push-action@v4
333+
with:
334+
context: .
335+
push: true
336+
tags: >
337+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
338+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

‎DESCRIPTION

Lines changed: 12 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
Type: Package
22
Package: CuratedAtlasQueryR
33
Title: Queries the Human Cell Atlas
4-
Version: 0.99.3
4+
Version: 1.1.3
55
Authors@R: c(
66
person(
77
"Stefano",
@@ -93,7 +93,8 @@ Imports:
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utils,
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dbplyr (>= 2.3.0),
9595
duckdb,
96-
stringr
96+
stringr,
97+
checkmate
9798
Suggests:
9899
zellkonverter,
99100
rmarkdown,
@@ -106,7 +107,10 @@ Suggests:
106107
forcats,
107108
ggplot2,
108109
tidySingleCellExperiment,
109-
rprojroot
110+
rprojroot,
111+
openssl,
112+
scuttle,
113+
DelayedArray
110114
Biarch: true
111115
biocViews:
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AssayDomain,
@@ -121,7 +125,7 @@ biocViews:
121125
Transcription,
122126
Transcriptomics
123127
Encoding: UTF-8
124-
RoxygenNote: 7.2.3
128+
RoxygenNote: 7.3.1
125129
LazyDataCompression: xz
126130
URL: https://github.com/stemangiola/CuratedAtlasQueryR
127131
BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
@@ -130,9 +134,13 @@ Roxygen: list(markdown = TRUE)
130134
Collate:
131135
'utils.R'
132136
'counts.R'
137+
'counts_per_million.R'
138+
'data.R'
133139
'dev.R'
140+
'import_metadata_and_counts.R'
134141
'metadata.R'
135142
'seurat.R'
136143
'unharmonised.R'
137144
'zzz.R'
138145
Language: en-US
146+
LazyData: true

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