Merge pull request #98 from jjmccollum/97-positive-proportionsproport… #245
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| name: beast | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-package: 'jdk+fx' | |
| distribution: 'zulu' | |
| java-version: '17.0.6+10' | |
| - name: Install poetry | |
| run: pipx install poetry | |
| - name: Install dependencies for Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'poetry' | |
| - run: poetry install | |
| - name: Testing | |
| run: | | |
| poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock strict --seed 1337 example/ubs_ephesians.xml beast_strict_example.xml | |
| poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock uncorrelated --seed 1337 example/ubs_ephesians.xml beast_uncorrelated_example.xml | |
| poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock local --seed 1337 example/ubs_ephesians.xml beast_local_example.xml | |
| - name: Install Phylogenetics Package | |
| run: | | |
| export JAVA_HOME=/opt/hostedtoolcache/Java_Zulu_jdk+fx/17.0.6-10/x64 | |
| export PATH=${JAVA_HOME}/bin:${PATH} | |
| git clone https://github.com/CompEvol/beast2.git | |
| git clone https://github.com/CompEvol/BeastFX.git | |
| cd BeastFX | |
| ant -DopenjreLnx=$JAVA_HOME linux | |
| cd ~ | |
| mkdir .beast | |
| cd .beast | |
| cp /home/runner/work/teiphy/teiphy/beast2/release/Linux/*.tgz . | |
| tar zxvf *.tgz | |
| ~/.beast/beast/bin/packagemanager -add BEAST_CLASSIC | |
| ~/.beast/beast/bin/packagemanager -add BEASTLabs | |
| ~/.beast/beast/bin/packagemanager -add BDSKY | |
| - name: Phylogenetics Run | |
| run: | | |
| ~/.beast/beast/bin/beast -overwrite beast_strict_example.xml | |
| ~/.beast/beast/bin/beast -overwrite beast_uncorrelated_example.xml | |
| ~/.beast/beast/bin/beast -overwrite beast_local_example.xml | |