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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| name: Test | ||
| on: | ||
| pull_request: | ||
| branches: ["main"] | ||
| push: | ||
| branches: ["main"] | ||
| env: | ||
| DISTRO: shotgun | ||
|
|
||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| latest-dev-tag: 2024.5.0.dev0 | ||
| latest-stable-tag: 2024.2.0 | ||
| commit-msg: ${{ steps.get-commit-msg.outputs.commit-msg }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Checkout utilities | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| repository: bokulich-lab/utilities | ||
| path: utilities | ||
|
|
||
| - name: Get last commit | ||
| id: get-commit-msg | ||
| run: | | ||
| echo "$(git log --pretty=%B -n 1 --skip 1)" | ||
| echo "commit-msg=$(git log --pretty=%B -n 1 --skip 1)" >> $GITHUB_OUTPUT | ||
| - name: Install dependencies | ||
| run: python -m pip install requests yq | ||
|
|
||
| - name: Create conda yaml | ||
| id: create-conda-yaml | ||
| run: | | ||
| commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}" | ||
| if [[ "$commit_msg" == *"[stable]"* ]] || [[ "$commit_msg" == *"[prod]"* ]]; then | ||
| tag="2024.2.0" | ||
| else | ||
| tag="2024.5.0.dev0" | ||
| fi | ||
| bash utilities/ci/get-dependencies.sh "$DISTRO" $tag utilities/ci/repositories.yaml | ||
| cat environment.yml >> $GITHUB_STEP_SUMMARY | ||
| echo "qiime-deps=$(tr '\n' ' ' < repo-urls.txt | xargs)" >> $GITHUB_OUTPUT | ||
| - name: Setup miniconda | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| python-version: 3.8 | ||
| mamba-version: "*" | ||
| channels: conda-forge,defaults | ||
| channel-priority: true | ||
| activate-environment: conda-env | ||
| condarc-file: utilities/ci/condarc | ||
| # use-only-tar-bz2: true | ||
|
|
||
| - name: Get date | ||
| id: get-date | ||
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | ||
| shell: bash | ||
|
|
||
| - name: Cache conda env | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/share/miniconda/envs | ||
| key: | ||
| conda-${{ runner.os }}--${{ runner.arch }}--${{ | ||
| steps.get-date.outputs.today }}-${{ | ||
| hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER | ||
| }} | ||
| env: | ||
| # Increase this value to reset cache if environment.yml has not changed | ||
| CACHE_NUMBER: 0 | ||
| id: cache | ||
|
|
||
| - name: Update environment | ||
| run: mamba env update -n conda-env -f environment.yml | ||
| if: steps.cache.outputs.cache-hit != 'true' | ||
|
|
||
| # - name: Install dev versions of QIIME repos | ||
| # run: mamba run -n conda-env pip install ${{ steps.create-conda-yaml.outputs.qiime-deps }} | ||
|
|
||
| - name: Update specific dependency, if requested | ||
| if: contains(${{ steps.get-commit-msg.outputs.commit-msg }}, '[add:') | ||
| run: | | ||
| commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}" | ||
| IFS=',' read -ra ADDR <<< "$commit_msg" | ||
| for i in "${ADDR[@]}"; do | ||
| pkg_name=$(echo "$i" | awk -F':' '/\[add/{print $2}') | ||
| commit_hash=$(echo "$i" | awk -F':' '/\[add/{print $3}' | awk -F']' '{print $1}') | ||
| if [[ $(yq '.repositories[].name' utilities/ci/repositories.yaml | grep -c $pkg_name) -eq 1 ]]; then | ||
| pkg_url=$(yq ".repositories[] | select(.name == \"$pkg_name\") | .url" utilities/ci/repositories.yaml | tr -d '"') | ||
| mamba run -n conda-env pip install "git+$pkg_url@$commit_hash" | ||
| fi | ||
| done | ||
| - name: Install plugin | ||
| run: | | ||
| mamba run -n conda-env pip install . | ||
| mamba run -n conda-env qiime dev refresh-cache | ||
| - name: Install dev dependencies | ||
| run: mamba run -n conda-env pip install pytest coverage parameterized | ||
|
|
||
| - name: Run tests | ||
| id: test | ||
| run: mamba run -n conda-env make test-cov | ||
|
|
||
| - name: Upload artifacts | ||
| uses: actions/upload-artifact@v4 | ||
| if: steps.test.outcome == 'success' | ||
| with: | ||
| name: coverage | ||
| path: coverage.xml |
22 changes: 15 additions & 7 deletions
22
.github/workflows/ci-dev.yaml → .github/workflows/q2-ci.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| name: Upload coverage report | ||
|
|
||
| on: | ||
| workflow_run: | ||
| workflows: ["Test"] | ||
| types: | ||
| - completed | ||
|
|
||
| jobs: | ||
| upload-coverage: | ||
| runs-on: ubuntu-latest | ||
| if: > | ||
| github.event.workflow_run.event == 'pull_request' && | ||
| github.event.workflow_run.conclusion == 'success' | ||
| steps: | ||
| - name: 'Download artifact' | ||
| uses: actions/[email protected] | ||
| with: | ||
| script: | | ||
| var artifacts = await github.rest.actions.listWorkflowRunArtifacts({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| run_id: ${{github.event.workflow_run.id }}, | ||
| }); | ||
| var matchArtifact = artifacts.data.artifacts.filter((artifact) => { | ||
| return artifact.name == "coverage" | ||
| })[0]; | ||
| var download = await github.rest.actions.downloadArtifact({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| artifact_id: matchArtifact.id, | ||
| archive_format: 'zip', | ||
| }); | ||
| var fs = require('fs'); | ||
| fs.writeFileSync('${{github.workspace}}/coverage.zip', Buffer.from(download.data)); | ||
| - run: unzip coverage.zip | ||
|
|
||
| - name: Find associated PR | ||
| id: pr | ||
| uses: actions/[email protected] | ||
| with: | ||
| script: | | ||
| const response = await github.rest.search.issuesAndPullRequests({ | ||
| q: 'repo:${{ github.repository }} is:pr sha:${{ github.event.workflow_run.head_sha }}', | ||
| per_page: 1, | ||
| }) | ||
| const items = response.data.items | ||
| if (items.length < 1) { | ||
| console.error('No PRs found') | ||
| return | ||
| } | ||
| const pullRequestNumber = items[0].number | ||
| console.info("Pull request number is", pullRequestNumber) | ||
| return pullRequestNumber | ||
| - uses: codecov/codecov-action@v4 | ||
| name: Upload coverage report | ||
| with: | ||
| files: ./coverage.xml | ||
| fail_ci_if_error: true | ||
| override_pr: ${{ steps.pr.outputs.result }} | ||
| env: | ||
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |
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