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Several bug fixes realted to documentation
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| Original file line number | Diff line number | Diff line change |
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| name: tests | ||
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| on: | ||
| # workflow_dispatch | ||
| push: | ||
| branches: [ main ] | ||
| paths-ignore: | ||
| - '.gitignore' | ||
| - '.readthedocs.yaml' | ||
| - 'LICENSE' | ||
| - 'setup.py' | ||
| - 'README.md' | ||
| - 'CITATION.cff' | ||
| - 'references.jsonld' | ||
| - '**/docs/**' | ||
| - '**/json_schemas/**' | ||
|
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| jobs: | ||
| # Name of the Job | ||
| lint_and_test: | ||
| strategy: | ||
| matrix: | ||
| os: [self-hosted] | ||
| python-version: ["3.8", "3.9", "3.10"] | ||
| runs-on: ${{ matrix.os }} | ||
| steps: | ||
| - name: Check out repository code | ||
| uses: actions/checkout@v4 | ||
|
|
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| - run: echo "Repository -> ${{ github.repository }}" | ||
| - run: echo "Branch -> ${{ github.ref }}" | ||
| - run: echo "Trigger event -> ${{ github.event_name }}" | ||
| - run: echo "Runner OS -> ${{ runner.os }}" | ||
|
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||
| - name: List files in the repository | ||
| run: | | ||
| ls ${{ github.workspace }} | ||
| - name: Remove all micromamba installations | ||
| run: | | ||
| rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null | ||
| touch /home/user/.bash_profile | ||
| - name: provision-with-micromamba | ||
| uses: mamba-org/setup-micromamba@v1 | ||
| with: | ||
| generate-run-shell: true | ||
| post-cleanup: all | ||
| environment-file: .github/env.yaml | ||
| create-args: >- | ||
| python=${{ matrix.python-version }} | ||
| pytest | ||
| pytest-cov | ||
| pytest-html | ||
| flake8 | ||
| pip | ||
| - name: Install genbadge from pip | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: pip install genbadge[all] | ||
|
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||
| - name: List installed package versions | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: micromamba list | ||
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| - name: Lint with flake8 | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: | | ||
| # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html | ||
| # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes | ||
| # Workflow fails: Stop the build if there are Python syntax errors or undefined names | ||
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
| # Create directory for flake8 reports | ||
| mkdir -p ./reports/flake8 | ||
| # Exit-zero treats all errors as warnings, workflow will not fail: | ||
| flake8 . --exclude=docs --ignore=C901,E226,W605 --count --exit-zero --max-complexity=10 --max-line-length=9999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt | ||
| - name: Generate Flake8 badge | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: | | ||
| genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt --output-file ./reports/flake8/flake8badge.svg | ||
| - name: Checkout biobb_common | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| repository: bioexcel/biobb_common | ||
| path: './biobb_common' | ||
|
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| - name: Run tests | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: | | ||
| # Ignoring docker and singularity tests | ||
| export PYTHONPATH=.:./biobb_common:$PYTHONPATH | ||
| # Create directory for tests reports | ||
| mkdir -p ./reports/junit | ||
| # Producction one | ||
| pytest biobb_haddock/test/unitests/ --cov=biobb_haddock/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html | ||
| - name: Generate Tests badge | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: | | ||
| genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml --output-file ./reports/junit/testsbadge.svg | ||
| - name: Generate Coverage badge | ||
| shell: micromamba-shell {0} # necessary for conda env to be active | ||
| run: | | ||
| # Create directory for flake8 reports | ||
| mkdir -p ./reports/coverage | ||
| coverage xml -o ./reports/coverage/coverage.xml | ||
| coverage html -d ./reports/coverage/ | ||
| genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml --output-file ./reports/coverage/coveragebadge.svg | ||
| - name: Publish coverage report to GitHub Pages | ||
| uses: JamesIves/github-pages-deploy-action@v4 | ||
| with: | ||
| folder: ./reports | ||
|
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| # - name: Restore .bash_profile | ||
| # run: cp ~/.bash_profile_orig ~/.bash_profile | ||
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| # YAML 1.2 | ||
| --- | ||
| abstract: "BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments." | ||
| authors: | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Andrio" | ||
| given-names: "Pau" | ||
| orcid: "https://orcid.org/0000-0003-2116-3880" | ||
| - | ||
| affiliation: "Institute for Research in Biomedicine (IRB Barcelona)" | ||
| family-names: "Hospital" | ||
| given-names: "Adam" | ||
| orcid: "https://orcid.org/0000-0002-8291-8071" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Conejero" | ||
| given-names: "Javier" | ||
| orcid: "https://orcid.org/0000-0001-6401-6229" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Jordà" | ||
| given-names: "Luis" | ||
| orcid: "https://orcid.org/0000-0002-9407-9703" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Del Pino" | ||
| given-names: "Marc" | ||
| orcid: "https://orcid.org/0000-0001-5565-7577" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Laia" | ||
| given-names: "Codó" | ||
| orcid: "https://orcid.org/0000-0002-6797-8746" | ||
| - | ||
| affiliation: "School of computer Science, the University of Manchester" | ||
| family-names: Werkhoven | ||
| given-names: Ben | ||
| name-particle: van | ||
| orcid: "https://orcid.org/0000-0002-7508-3272" | ||
| - | ||
| affiliation: "University of Manchester (UOM)" | ||
| family-names: "Soiland-Reyes" | ||
| given-names: "Stian" | ||
| orcid: "https://orcid.org/0000-0001-9842-9718" | ||
| - | ||
| affiliation: "University of Manchester (UOM)" | ||
| family-names: "Goble" | ||
| given-names: "Carole" | ||
| orcid: "https://orcid.org/0000-0003-1219-2137" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Lezzi" | ||
| given-names: "Daniele" | ||
| orcid: "https://orcid.org/0000-0001-5081-7244" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC)" | ||
| family-names: "Rosa M" | ||
| given-names: "Badia" | ||
| orcid: "https://orcid.org/0000-0003-2941-5499" | ||
| - | ||
| affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)" | ||
| family-names: "Orozco" | ||
| given-names: "Modesto" | ||
| orcid: "https://orcid.org/0000-0002-8608-3278" | ||
| - | ||
| affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)" | ||
| family-names: "Gelpí" | ||
| given-names: "Josep Ll." | ||
| orcid: "https://orcid.org/0000-0002-0566-7723" | ||
| email: "[email protected]" | ||
|
|
||
| cff-version: "1.2.0" | ||
| date-released: "2019-09-10" | ||
| keywords: | ||
| - "BioExcel" | ||
| - "BioBB" | ||
| - "Bioinformatics" | ||
| - "Computational Biology" | ||
| - "Biomolecular Workflows" | ||
| license: "Apache-2.0" | ||
| message: "If you use this software, please cite it using these metadata." | ||
| repository-code: "https://github.com/bioexcel/biobb" | ||
| title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| $(document).ready(function() { | ||
| var path = ''; | ||
|
|
||
| if($('.icon.icon-home').attr('href') == '../index.html') path = '../'; | ||
| else if($('.icon.icon-home').attr('href') == '../../index.html') path = '../../'; | ||
| if($('.wy-side-nav-search .icon.icon-home').attr('href') == '../index.html') path = '../'; | ||
| else if($('.wy-side-nav-search .icon.icon-home').attr('href') == '../../index.html') path = '../../'; | ||
|
|
||
| $('.icon.icon-home').html('<img src="' + path + '_static/logo.png" class="logo" alt="Logo">'); | ||
| $('.wy-side-nav-search .icon.icon-home').html('<img src="' + path + '_static/logo.png" class="logo" alt="Logo">'); | ||
| }); |
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