broadinstitute / viral-core

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LAST BUILD ON BRANCH v2.3.1

branch: v2.3.1

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• v2.3.1
• ct-add-fgbio
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• ct-bump-baseimage
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• ct-bump-pysam
• ct-bump-pytest
• ct-bump-python-version
• ct-bump-viral-baseimage-0.2.4
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• ct-github-actions
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• ct-set-default-threads
• ct-swiftseq-demux-integration
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Build # 8251169825

Build Type

push

github

Committed by web-flow

Commit Message

bump python version 3.8 -> 3.10 (#98)

* python bumped to 3.12 for Docker image, docs build, and GitHub Actions env

* change lz4 pin to allow newer versions

* let's try not restricting pytest to <=8

* try more flexible pinning for a few more dependencies

* verbose mamba install

* remove defaults conda channel

remove defaults conda channel as it is now noted to be incompatible with conda-forge; see: https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#mixing-the-defaults-and-conda-forge-channels

* set CONDA_ENVS_PATH env var (dir containing conda envs subdirs)

https://conda.io/projects/conda/en/latest/user-guide/configuration/settings.html#envs-dirs-specify-environment-directories

* set number of threads for conda to fetch repodata

set number of threads for conda to fetch repodata , via repodata_threads; see: https://conda.io/projects/conda/en/latest/user-guide/configuration/settings.html#configuring-number-of-threads

* bump pigz

* print dependency trees for packages specified (individually)

* set python to 3.10

set python to 3.10, as this is the most recent version in the bioconda build matrix; see: https://github.com/bioconda/bioconda-utils/blob/master/bioconda_utils/bioconda_utils-conda_build_config.yaml#L40

* add $CONDA_CHANNEL_STRING to mamba repodata depends call

* unpin lz4-c

* avoid syntax warning using "is" with a string literal

* add DEBUG variable-based toggle of verbose output during conda install script

* quote python version

* actions/setup-python@v4 -> v5

* more flexible pin of matplotlib for building docs

* viral-baseimage to 0.2.2

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