update finemap recipe with latest bioconda standards #114
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| name: Tests | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| # Publish semver tags as releases. | |
| tags: [ 'v*.*.*' ] | |
| paths-ignore: | |
| - 'README.md' | |
| pull_request: | |
| branches: [ "main" ] | |
| paths-ignore: | |
| - 'README.md' | |
| jobs: | |
| # adapted from https://docs.github.com/en/actions/learn-github-actions/expressions#example-returning-a-json-object | |
| get_dirs: | |
| name: List changed recipes | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: read | |
| strategy: | |
| fail-fast: false | |
| outputs: | |
| matrix: ${{ steps.output-dirs.outputs.matrix }} # contains a list of the module names encoded as a json array | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: List changed packages | |
| id: filter | |
| uses: dorny/paths-filter@v3 | |
| with: | |
| list-files: shell | |
| filters: | | |
| changed: | |
| - added|modified: 'recipes/**' | |
| - name: get directory names | |
| id: output-dirs | |
| # adapted from https://stackoverflow.com/a/71687652 | |
| run: | | |
| matrix=$(for i in ${{ steps.filter.outputs.changed_files }}; do sed 's\recipes/\\;s\/.*$\\' <<< $i; done | sort -u | jq --raw-input --slurp --compact-output 'split("\n")[:-1]') | |
| echo "$matrix" | |
| echo "matrix=$matrix" >> $GITHUB_OUTPUT | |
| build: | |
| name: Build on ${{ matrix.os }} | |
| needs: get_dirs | |
| runs-on: ${{ matrix.os }} | |
| permissions: | |
| contents: read | |
| packages: write | |
| if: ${{ needs.get_dirs.outputs.matrix != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-13, macos-latest] | |
| packagename: ${{ fromJson(needs.get_dirs.outputs.matrix) }} | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: biobuild | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache Conda env | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if needed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Install biobuild environment | |
| shell: bash -el {0} | |
| run: | |
| mamba create -y -n biobuild -c conda-forge -c bioconda -c nodefaults bioconda-utils anaconda-client | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Run test | |
| shell: bash -el {0} | |
| run: | | |
| bioconda-utils build ${{ (startsWith(matrix.os, 'ubuntu') && '--docker --mulled-test') || '' }} --packages ${{ matrix.packagename }} | |
| - name: Upload built package as GitHub artifact | |
| uses: "actions/upload-artifact@v4" | |
| with: | |
| name: ${{ matrix.packagename }}-${{ matrix.os }} | |
| path: ${{ env.CONDA }}/envs/biobuild/conda-bld/ | |
| # - name: Upload built package to Anaconda | |
| # shell: bash -el {0} | |
| # env: | |
| # ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }} | |
| # if: ${{ env.ANACONDA_API_TOKEN == '' }} | |
| # run: | | |
| # anaconda upload ${{ env.CONDA }}/envs/biobuild/conda-bld/linux-64/*.tar.bz2 |