Export to R phylo format #694
Workflow file for this run
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| name: Windows | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| tags-ignore: | |
| - '*' | |
| pull_request: | |
| env: | |
| PERL5LIB: c:\cx\lib\perl5 | |
| PERL_LOCAL_LIB_ROOT: c:/cx | |
| PERL_MB_OPT: --install_base C:/cx | |
| PERL_MM_OPT: INSTALL_BASE=C:/cx | |
| #ALIEN_BUILD_PRELOAD: Fetch::Cache | |
| AUTOMATED_TESTING: 1 | |
| jobs: | |
| perl: | |
| runs-on: windows-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Perl | |
| run: | | |
| choco install strawberryperl | |
| echo "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append | |
| ##echo $env:PATH | |
| #- name: Check path | |
| # run: | | |
| # echo $env:PATH | |
| # echo "glargglarg" | |
| # echo $GITHUB_PATH | |
| # echo "zogzogzog" | |
| # $env:PATH = "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH" | |
| # echo $env:PATH | |
| # echo "zigzig" | |
| # echo "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH" > $GITHUB_PATH | |
| # echo $GITHUB_PATH | |
| - name: perl -V | |
| run: perl -V | |
| - name: Prepare for CPAN cache | |
| run: | | |
| perl -V > perlversion.txt | |
| echo "20220920" >> perlversion.txt | |
| dir perlversion.txt | |
| - name: Cache CPAN modules | |
| uses: actions/cache@v3 | |
| with: | |
| path: c:\cx | |
| key: ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }} | |
| - name: Prepare for Alien cache | |
| run: | | |
| perl -V > aliencache.txt | |
| echo 'aliens' >> aliencache.txt | |
| dir aliencache.txt | |
| - name: Cache Alien downloads | |
| uses: actions/cache@v3 | |
| with: | |
| path: $HOMEPATH\.alienbuild | |
| key: ${{ runner.os }}-build-${{ hashFiles('aliencache.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-${{ hashFiles('aliencache.txt') }} | |
| #- name: Install Dependencies | |
| # run: curl -sL https://git.io/cpm | perl - install -g --show-build-log-on-failure | |
| #- name: Install dependencies 1 | |
| # run: | | |
| # #cpanm --notest local::lib | |
| # #eval "$(perl -Mlocal::lib=${PWD}/perl_modules)" | |
| # cpanm --quiet --notest Alien::Build | |
| # cpanm --quiet --notest Alien::Build::MM | |
| # cpanm --quiet --notest Sort::Versions | |
| # cpanm --quiet --notest PkgConfig | |
| # cpanm --quiet --notest Alien::Build::Plugin::Cleanse::BuildDir | |
| # cpanm --quiet --notest File::Find::Rule | |
| # cpanm --quiet --notest Alien::Build::Plugin::Fetch::Cache | |
| # cpanm --quiet --notest Env::ShellWords | |
| # cpanm --quiet --notest Test2::Suite | |
| - name: Install dependencies Alien::MSYS | |
| run: | | |
| cpanm Alien::Build::Plugin::Fetch::Cache | |
| cpanm --notest Alien::MSYS | |
| - name: Install dependencies Alien::sqlite | |
| run: | | |
| echo $env:PATH | |
| cpanm --notest --installdeps Alien::sqlite | |
| cpanm -v Alien::sqlite~1.05 | |
| - name: Install dependencies Alien::proj | |
| run: | | |
| #cpanm -v --notest https://github.com/shawnlaffan/perl-alien-proj.git | |
| cpanm --notest --installdeps Alien::proj | |
| cpanm -v --notest Alien::proj | |
| - name: Install dependencies Alien::geos::af | |
| run: | | |
| cpanm --notest --installdeps Alien::geos::af | |
| cpanm -v Alien::geos::af | |
| - name: Install dependencies Alien::gdal | |
| run: | | |
| cpanm --notest --installdeps Alien::gdal | |
| echo "ALIEN_GDAL_CONFIG_ARGS=--with-hide_internal_symbols" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append | |
| # qhull issues on gdal 3.5, maybe fixed in 3.6 | |
| $env:ALIEN_GDAL_CONFIG_ARGS = "--with-hide-internal-symbols=yes --without-gnm --without-qhull" | |
| Get-PSDrive C | Select-Object Used,Free | |
| # clunky path override | |
| # $env:PATH = "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH" | |
| cpanm -v Alien::gdal | |
| Get-PSDrive C | Select-Object Used,Free | |
| - name: Install task deps | |
| run: | | |
| #cpanm --notest Task::Biodiverse::NoGUI | |
| cpanm --notest --no-man-pages PDL | |
| cpanm --notest --installdeps . | |
| cpanm --installdeps . | |
| # Runs a set of commands using the runners shell | |
| - name: Run tests | |
| run: | | |
| prove | |