Fixes bug in effective mass calculation (#98) #253
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| name: Docs | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| tags: | |
| - v* | |
| pull_request: | |
| branches: | |
| - "main" | |
| jobs: | |
| build_and_deploy_docs: | |
| name: Documentation Building and Deployment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/docs_env.yaml | |
| environment-name: docs | |
| create-args: >- | |
| python=3.11 | |
| openmm>=8.1 | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| micromamba install -y -c mdtools openmm-cpp-forces | |
| python -m pip install . --no-deps | |
| micromamba list | |
| - name: Build Documentation | |
| shell: bash -l {0} | |
| run: | | |
| if [ "$GITHUB_EVENT_NAME" == "push" ] && [ "$GITHUB_REF_TYPE" == "tag" ]; then | |
| export CVPACK_VERSION=${{ github.ref_name }} | |
| else | |
| export CVPACK_VERSION=dev | |
| fi | |
| sphinx-build ./docs ./html | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest | |
| - name: Get coverage report | |
| id: coverage | |
| shell: bash -l {0} | |
| run: | | |
| COVERAGE=$(coverage report | tail -1 | awk '{print $4}') | |
| OFFSET=$(((${COVERAGE::-1}-35)/6-1)) | |
| [[ $OFFSET < 0 ]] && OFFSET=0 | |
| PALETTE="000111222333" | |
| CODE=${PALETTE:$OFFSET:3} | |
| COLOR=$(echo $CODE | sed -e "s/0/red,/g; s/1/orange,/g; s/2/yellow,/g; s/3/green,/g; s/,$//") | |
| echo "coverage=${COVERAGE}" | tee -a "${GITHUB_OUTPUT}" | |
| echo "color=${COLOR}" | tee -a "${GITHUB_OUTPUT}" | |
| - name: Generate coverage badge | |
| uses: emibcn/badge-action@v2.0.2 | |
| with: | |
| label: 'Coverage' | |
| label-color: 'black' | |
| status: ${{ steps.coverage.outputs.coverage }} | |
| color: ${{ steps.coverage.outputs.color }} | |
| path: 'htmlcov/coverage.svg' | |
| - name: Deploy documentation | |
| shell: bash -l {0} | |
| run: | | |
| if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then | |
| echo "Deployment is deactivated on pull requests" | |
| exit 0 | |
| elif [ "$GITHUB_REF_TYPE" == "tag" ]; then | |
| subdirs=(${{ github.ref_name }} latest) | |
| else | |
| subdirs=(development) | |
| fi | |
| git reset --hard HEAD | |
| set -x | |
| echo "::group::Push page to gh-pages branch" | |
| git config user.name "$(git show --format=%an -s)" | |
| git config user.email "$(git show --format=%ae -s)" | |
| git fetch origin | |
| git switch gh-pages | |
| for subdir in ${subdirs[@]}; do | |
| dir=docs/$subdir | |
| rsync -va --delete-excluded html/ $dir/ | |
| rsync -va --delete-excluded htmlcov/ $dir/coverage/ | |
| git add -f $dir/* | |
| done | |
| touch docs/.nojekyll | |
| git commit -m "Docs from $GITHUB_REF $GITHUB_SHA" || echo "Branch is up to date" | |
| git push -f origin gh-pages | |
| echo "::endgroup::" |