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feat: Update dependencies to latest versions #1054

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Merged
merged 9 commits into from
Aug 1, 2025
Merged

feat: Update dependencies to latest versions #1054

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1964c27
feat: Update dependencies to latest versions
mencian Jul 17, 2025
d6f13e9
use 2nd most recent conda-forge-pinning
mencian Jul 17, 2025
2e7e9bc
Update bioconda_utils-requirements.txt
mencian Jul 17, 2025
1470a7c
Update bioconda_utils-requirements.txt
mencian Jul 17, 2025
24a6d31
Update bioconda_utils-requirements.txt
mencian Jul 18, 2025
55e84c9
Update bioconda_utils-requirements.txt
mencian Jul 18, 2025
6e4cb2c
Update bioconda_utils-requirements.txt
mencian Jul 18, 2025
0daf3df
Update bioconda_utils-requirements.txt
mencian Jul 24, 2025
f82875e
bump aiohttp to >=3.12.14
mencian Jul 31, 2025
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2 changes: 1 addition & 1 deletion bioconda_utils/bioconda_utils-conda_build_config.yaml
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Expand Up @@ -21,7 +21,7 @@ MACOSX_DEPLOYMENT_TARGET: # [osx]
- 10.13 # [osx and x86_64]

bamtools:
- "2.5.2"
- "2.5.3"

# NOTE: Workaround https://github.com/conda/conda-build/issues/3974 we slightly alter the values
# from conda-forge-pinnings here (inserting '.*' or ' ' which should be ignored later on).
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35 changes: 17 additions & 18 deletions bioconda_utils/bioconda_utils-requirements.txt
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Expand Up @@ -6,30 +6,29 @@
conda-forge-pinning=2024.11.29.12.37.53

# basics
python=3.10.*
conda=24.9.*
conda-libmamba-solver=24.1.*
conda-build=24.7.*
conda-index=0.5.*
conda-package-streaming=0.11.*
python=3.12.*
conda=24.11.*
conda-libmamba-solver=24.9.*
conda-build=24.9.*
conda-index=0.6.*
conda-package-streaming=0.12.*
mamba=1.5.*
#boa=0.17.*

argh=0.31.* # CLI
colorlog=6.* # Logging
tqdm=4.66.* # Progress monitor
yaspin=2.* #
tqdm=4.67.* # Progress monitor
yaspin=3.* #
ruamel.yaml=0.18.* # Recipe YAML parsing
pyaml=24.04.* # Faster YAML parser (deprecate?)
networkx=3.3.* # (networkx>3.3 needs python>=3.10)
pandas=2.2.* #
pyaml=24.12.* # Faster YAML parser (deprecate?)
networkx=3.4.* # (networkx>3.3 needs python>=3.10)
pandas=2.3.* #
libblas=*=*openblas # Avoid large mkl package (pulled in by pandas)
boltons=24.0.* #
jsonschema=4.22.* # JSON schema verification
boltons=25.0.* #
jsonschema=4.24.* # JSON schema verification
jinja2=3.1.* #

anaconda-client=1.12.* # anaconda_upload
galaxy-tool-util=24.* # mulled test and container build
anaconda-client=1.13.* # anaconda_upload
galaxy-tool-util=25.* # mulled test and container build
involucro=1.1.* # mulled test and container build
skopeo=1.15.* # docker upload
findutils # find/xargs copy built packages from container
Expand All @@ -39,12 +38,12 @@ git=2.* # well - git
regex=2024.* #

# asyncio
aiohttp>=3.10.11 # HTTP lib; pinning to reflect dependabot alert
aiohttp>=3.12.14 # HTTP lib; pinning to reflect dependabot alert
aiohttp-jinja2 # jinja2 renderer for aiohttp.web
aiohttp-session #
aiohttp-security #
aiofiles=23.* # async open
aioftp=0.22.* # FTP lib
aioftp=0.26.* # FTP lib
backoff=2.2.* # retrying of failed API calls
cachetools=5.3.* # request caching (NEEDED?)

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