8000 License, GHA CI, Dockerfile by etal · Pull Request #1 · formbio/laava · GitHub
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License, GHA CI, Dockerfile #1

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Merged
merged 6 commits into from
Sep 13, 2023
Merged

License, GHA CI, Dockerfile #1

merged 6 commits into from
Sep 13, 2023

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etal
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@etal etal commented Aug 30, 2023 •
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Adding some conveniences on top of the upstream source:

  • Add an OSI-compatible public license (Apache 2.0)
  • Add a Dockerfile to capture the conda environment and scripts
  • Set up GitHub Actions for basic automated testing (in this PR, just static checks)

Notes:

  • Python 3.11 and 3.7 can't be fully supported since some dependencies are unavailable for those versions (details in the commit log)
  • I left the original script code alone and updated the conda environment specification just a little bit.
  • The Docker image hasn't been published anywhere yet.

@etal etal marked this pull request as draft August 30, 2023 02:11
etal added 4 commits August 30, 2023 13:32
@etal
Add Dockerfile to capture conda environment and scripts
f7f35c3 
Include 'less' so the R interpreter's docs work.
@etal
Add GHA config for CI testing and dev conda environment
a314165 
Configure static error-checking with lintr for R and flake8 for Python.

Streamline CI conda environment to reduce dependency conflicts.
@etal
Reduce dependencies for CI conda packages
cf4c301 
In GHA, drop Python 3.7 and 3.11 from test matrix because:
- pysam isn't available for Python 3.11 yet
- parasail-python>=1.3.4 isn't available for Python 3.7

CI conda env:
- Remove 'anaconda' and 'r' channels -- they weren't used
- Remove explicit r-dplyr and r-ggplot2 -- included with r-tidyverse
- Specify r-base instead of r per official guidance
@etal
AAV,dev.conda_env.yml: clean up like CI environment
8d06238
@etal etal marked this pull request as ready for review August 30, 2023 20:34
@etal etal requested a review from bcantarel September 13, 2023 19:07
@bcantarel bcantarel merged commit 87fbade into main Sep 13, 2023
@etal etal deleted the oss-1 branch April 30, 2024 14:50
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@alphabdiallo alphabdiallo Awaiting requested review from alphabdiallo

@mcrocker-bioborg mcrocker-bioborg Awaiting requested review from mcrocker-bioborg

@Magdoll Magdoll Awaiting requested review from Magdoll

@bcantarel bcantarel Awaiting requested review from bcantarel

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