Migrate CI from Travis CI to GitHub Actions #241
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Pull request overview
This PR migrates the CI pipeline from Travis CI to GitHub Actions while preserving existing test and Docker publishing behavior.
Changes:
- Removes the legacy
.travis.ymlconfiguration. - Adds a GitHub Actions workflow (
.github/workflows/ci.yml) to run tests on Python 3.9 and 3.12, including genome setup and integration tests. - Reimplements the conditional Docker image build and push to GHCR on
masterpushes (Python 3.12 matrix entry) using GitHub Actions context and secrets.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| .travis.yml | Removes the old Travis CI configuration, including test execution and Docker deployment logic. |
| .github/workflows/ci.yml | Introduces a GitHub Actions workflow that mirrors the previous Travis CI steps for testing, genome installation, and Docker image build/push. |
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.github/workflows/ci.yml
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| - name: Download GRCh37.tar.gz if not present | ||
| run: | | ||
| if [ ! -f ./src/GRCh37.tar.gz ]; then | ||
| wget --connect-timeout=10 --tries=20 ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/ | ||
| fi | ||
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| - name: Cache src directory | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: ./src/ | ||
| key: ${{ runner.os }}-src-grch37 | ||
| restore-keys: | | ||
| ${{ runner.os }}-src- |
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The cache for ./src/ is restored and saved after the Download GRCh37.tar.gz step, which means the download will run on every job even when a cache hit is available, and the restored cache may overwrite the just-downloaded file. To actually benefit from caching and avoid unnecessary network calls, the cache step should run before the download/install step so that a hit restores ./src/ first, and the download is only performed on a cache miss.
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@copilot open a new pull request to apply changes based on this feedback
|
@mdbarnesUCSD I've opened a new pull request, #242, to work on those changes. Once the pull request is ready, I'll request review from you. |
Co-authored-by: mdbarnesUCSD <22506723+mdbarnesUCSD@users.noreply.github.com>
Fix cache ordering in CI workflow to avoid redundant downloads
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