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broadinstitute / viral-core
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master: 66%

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LAST BUILD BRANCH: ct-swiftseq-demux-integration
DEFAULT BRANCH: master
Repo Added 10 Sep 2019 08:19PM UTC
Files 24
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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
  • ct-add-ncbi-datasets
  • ct-add-read-filtering-cli-cmd
  • ct-align_and_fix_without_supplementary_alignments
  • ct-barcode-helper-ntc-counting
  • ct-barcode-i5-single-index-bugfix
  • ct-bugfix-idxstats-fns
  • ct-bugfix-minimap2_idxstats
  • ct-bump-baseimage
  • ct-bump-baseimage-0.2.3
  • ct-bump-pysam
  • ct-bump-pytest
  • ct-bump-python-version
  • ct-bump-viral-baseimage-0.2.4
  • ct-gh-actions-jvm-heap-decrease
  • ct-ghactions-update-ubuntu
  • ct-github-actions
  • ct-help-text-correction
  • ct-option-to-include-dup-reads-in-filtering
  • ct-set-default-threads
  • ct-swiftseq-demux-integration
  • ct-update-baseimage
  • ct-update-docker-base
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  • ct-update-testing
  • ct-version-read-fix
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  • ll-add_swiftseq_demux
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  • v2.4.1
  • v2.4.2
  • v2.4.3

12 Mar 2024 03:03PM UTC coverage: 0.0%. Remained the same
8251169825

push

github

web-flow
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

0 of 0 relevant lines covered (NaN%)

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Build:
Build:
0 RELEVANT LINES 0 COVERED LINES
0.0 HITS PER LINE
Source Files on v2.3.1
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  • Changed 0
  • Source Changed 0
  • Coverage Changed 0
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Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
8251169825 v2.3.1 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 m... push 12 Mar 2024 03:15PM UTC web-flow github
0.0
8145966302 v2.3.1 help text correction for filter_to_proper_primary_mapped_reads (#92) push 04 Mar 2024 07:43PM UTC web-flow github
0.0
8145966422 v2.3.1 help text correction for filter_to_proper_primary_mapped_reads (#92) push 04 Mar 2024 07:43PM UTC web-flow github
0.0
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