Bio::Tools::CodonTable: add codon table 15 (#389) #27
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 . |