Bio::Tools::CodonTable: update data from versino 4.2 to 4.9 (#391) #28
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| name: Run Tests | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| env: | |
| PKG_DEPS_UBUNTU: >- | |
| libdb-dev | |
| PKG_DEPS_DEBIAN: >- | |
| libdb-dev | |
| PERL_MIN_VERSION: '5.12' | |
| jobs: | |
| dist: | |
| name: Make distribution using Dist::Zilla | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Build the dist using Dist::Zilla. | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Cache ~/perl5 | |
| uses: actions/cache@v3 | |
| with: | |
| key: ${{ runner.os }}-dist-locallib | |
| path: ~/perl5 | |
| - name: Perl version | |
| run: | | |
| perl -v | |
| - name: Install cpanm | |
| run: | | |
| curl -L https://cpanmin.us | perl - --sudo App::cpanminus | |
| - name: Install local::lib | |
| run: | | |
| cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) | |
| - name: Install Dist::Zilla | |
| shell: bash | |
| run: | | |
| eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) | |
| cpanm -n Dist::Zilla | |
| dzil authordeps --missing | cpanm -n | |
| - name: Make distribution | |
| shell: bash | |
| run: | | |
| eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) | |
| dzil build --in build-dir | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: ./build-dir | |
| # Get Perl versions to test. | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| - id: set-perl-versions | |
| name: Get Perl versions to test (minimum and median) | |
| shell: perl {0} | |
| run: | | |
| use Actions::Core; | |
| use List::Util qw(uniqstr first); | |
| die 'Minimum version not specified as major version 5.xyz' unless $ENV{PERL_MIN_VERSION} =~ /^5\.[0-9]+$/; | |
| my $min_perl = $ENV{PERL_MIN_VERSION}; | |
| info("Minimum Perl version is $min_perl"); | |
| set_output(min => $min_perl); | |
| my @non_patch_versions = uniqstr map { /^(\d+\.\d+)/ } perl_versions( platform => 'linux' ); | |
| my $min_idx = first { $non_patch_versions[$_] eq $min_perl } 0..$#non_patch_versions; | |
| my $median_perl = $non_patch_versions[int($min_idx/2)]; | |
| info("Median Perl version is $median_perl"); | |
| set_output(med => $median_perl ); | |
| outputs: | |
| min-perl-version: ${{ steps.set-perl-versions.outputs.min }} | |
| med-perl-version: ${{ steps.set-perl-versions.outputs.med }} | |
| test: | |
| needs: dist | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macos-latest, windows-latest, ubuntu-latest] | |
| perl: ['5'] | |
| author-testing: [false] | |
| include: | |
| - { os: 'ubuntu-latest', perl: "5" , author-testing: true , coverage: true } | |
| - { os: 'ubuntu-latest', perl: "${{ needs.dist.outputs.med-perl-version }}" } | |
| - { os: 'ubuntu-latest', perl: "${{ needs.dist.outputs.min-perl-version }}" } | |
| name: Perl ${{ matrix.perl }} on ${{ matrix.os }}, author (${{ matrix.author-testing || 'false' }}), coverage (${{ matrix.coverage }}) | |
| steps: | |
| - name: Get dist artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| # Setup system deps | |
| - name: Setup system deps (apt) | |
| if: runner.os == 'Linux' && env.PKG_DEPS_UBUNTU | |
| run: | | |
| sudo apt-get -y update && sudo apt-get install -y --no-install-recommends ${{ env.PKG_DEPS_UBUNTU }} | |
| - name: Set up perl | |
| uses: shogo82148/actions-setup-perl@v1 | |
| if: matrix.os != 'windows-latest' | |
| with: | |
| perl-version: ${{ matrix.perl }} | |
| - name: Set up perl (Strawberry) | |
| uses: shogo82148/actions-setup-perl@v1 | |
| if: matrix.os == 'windows-latest' | |
| with: | |
| distribution: 'strawberry' | |
| - run: perl -V | |
| - name: Install Perl deps | |
| run: | | |
| cpanm --notest --installdeps . | |
| - name: Install Perl develop deps | |
| if: matrix.author-testing | |
| run: | | |
| cpanm --notest --installdeps --with-develop . | |
| - name: Install Perl coverage deps | |
| if: matrix.coverage | |
| run: | | |
| cpanm --notest Devel::Cover::Report::Coveralls | |
| - name: Set AUTHOR_TESTING | |
| if: matrix.author-testing | |
| shell: bash | |
| run: | | |
| echo "AUTHOR_TESTING=1" >> $GITHUB_ENV | |
| - name: Run tests (no coverage) | |
| if: ${{ ! matrix.coverage }} | |
| run: | | |
| cpanm --verbose --test-only . | |
| - name: Run tests (with coverage) | |
| if: matrix.coverage | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| HARNESS_PERL_SWITCHES: -MDevel::Cover | |
| run: | | |
| cpanm --verbose --test-only . | |
| cover -report Coveralls | |
| containers: | |
| needs: dist | |
| runs-on: ubuntu-latest | |
| container: ${{ matrix.container }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| container: ['debian:bullseye', 'debian:bookworm'] | |
| steps: | |
| - name: Get dist artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| - name: Setup system deps (apt) | |
| if: ${{ startsWith(matrix.container, 'debian:') }} | |
| run: | | |
| apt-get -y update && apt-get install -y --no-install-recommends perl cpanminus make apt-file | |
| apt-file update | |
| apt-get install -y --no-install-recommends \ | |
| ${{ env.PKG_DEPS_DEBIAN }} \ | |
| $( cpanm -q --showdeps . | perl -MConfig -MCwd=abs_path '-M5;@prefixes = map abs_path($_), @Config{qw(vendorlibexp vendorarchexp)}' -lpe 's,~.*$,,; s,::,/,g; $mod = $_; $_ = join qq{\n}, map { qq{$_/${mod}.pm} } @prefixes' | apt-file search -lFf - ) | |
| - name: Run tests | |
| run: | | |
| cpanm --verbose --test-only . |