getting tellurium working again, updating to tellurium 2.2.0, startin…

…g to modularize code
biosimulators · Jan 5, 2021 · ce6a7fb · ce6a7fb
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,333 @@
+name: Continuous integration
+
+on:
+  push:
+  workflow_dispatch:
+    inputs:
+      simulatorVersion:
+        description: New version of the underlying simulation tool (e.g., '1.5.6')
+        required: true
+      simulatorVersionLatest:
+        description: Is this version the latest version of the underlying simulation tool ("true" or "false")?
+        required: false
+
+jobs:
+  continuousIntegration:
+    name: Update simulator version, lint, test, compile documentation, and release
+    runs-on: ubuntu-latest
+    outputs:
+      mainBranch: ${{ steps.get-main-branch.outputs.mainBranch }}
+      mainBranchRef: ${{ steps.get-main-branch.outputs.mainBranchRef }}
+      mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
+      version: ${{ steps.get-version-number.outputs.version }}
+      simulatorId: ${{ steps.get-docker-image-tag.outputs.simulatorId }}
+      simulatorVersion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
+      simulatorName: ${{ steps.get-docker-image-tag.outputs.simulatorName }}
+      dockerImageBaseUrl: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}
+      dockerRegistry: ${{ steps.get-docker-image-tag.outputs.dockerRegistry }}
+      release: ${{ steps.determine-if-release-needed.outputs.release }}
+      docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
+    steps:
+      - name: Clone repository
+        run: |
+          git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} .
+
+      - id: get-main-branch
+        name: Determine main branch
+        run: |
+          mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4)
+          mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
+          echo "::set-output name=mainBranch::$mainBranch"
+          echo "::set-output name=mainBranchRef::refs/heads/$mainBranch"
+          echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision"
+
+      - name: Checkout ref
+        run: |
+          if [[ "${{ github.ref }}" =~ ^refs/heads/ ]]; then
+            branch=$(echo "${{ github.ref }}" | cut -d'/' -f 3-)
+            git checkout ${branch}
+          else
+            git checkout ${{ github.ref }}
+          fi
+
+      #############################################
+      ## Update the version of the simulator
+      #############################################
+      - name: Update the version of the simulator
+        if: github.event.inputs.simulatorVersion
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y --no-install-recommends jq moreutils
+
+          IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
+          jq ".version = \"${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json
+          jq ".image.url = \"${IMAGE_BASE_URL}:${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json
+
+          sed -i -E \
+            "s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${{ github.event.inputs.simulatorVersion }}\"/" \
+            Dockerfile
+
+      #############################################
+      ## Install package and its dependencies
+      #############################################
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+
+      - name: Setup pip cache
+        uses: actions/cache@v2
+        with:
+          path: /opt/hostedtoolcache/Python
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install pip and setuptools
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools
+
+      - name: Install libXML2
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y -no-install-recommends libxml2
+
+      # install package
+      - name: Install the package
+        run: python -m pip install .[all]
+
+      #############################################
+      ## Lint
+      #############################################
+      - name: Install flake8
+        run: python -m pip install flake8
+
+      - name: Lint the package
+        run: python -m flake8
+
+      #############################################
+      ## Build Docker image
+      #############################################
+      - id: get-version-number
+        name: Get version number
+        env:
+          TAG: ${{ github.ref }}
+        run: |
+          if [[ "${TAG}" =~ ^refs/tags/ ]]; then
+            version="${TAG/refs\/tags\//}"
+          else
+            versionFileDir=$(find -name _version.py | rev | cut -d / -f 2- | rev)
+            version=$(PYTHONPATH=$versionFileDir python -c "import _version; print(_version.__version__)")
+          fi
+
+          echo "::set-output name=version::$version"
+
+      - id: get-docker-image-tag
+        name: Determine Docker image tag
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y --no-install-recommends jq
+
+          SIMULATOR_ID=$(jq -r '.id' biosimulators.json)
+          SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json)
+          SIMULATOR_NAME=$(jq -r '.name' biosimulators.json)
+          IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
+          DOCKER_REGISTRY=$(echo $IMAGE_BASE_URL | cut -d / -f 1)
+
+          echo "::set-output name=simulatorId::${SIMULATOR_ID}"
+          echo "::set-output name=simulatorVersion::${SIMULATOR_VERSION}"
+          echo "::set-output name=simulatorName::${SIMULATOR_NAME}"
+          echo "::set-output name=dockerImageBaseUrl::${IMAGE_BASE_URL}"
+          echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}"
+
+      - name: Build Docker image
+        run: |
+          REVISION=$(git rev-parse HEAD)
+          CREATED=$(date --rfc-3339=seconds | sed 's/ /T/')
+          docker build \
+            --label org.opencontainers.image.source=https://github.com/${{ github.repository }} \
+            --label org.opencontainers.image.revision=${REVISION} \
+            --label org.opencontainers.image.created=${CREATED} \
+            --build-arg VERSION=${{ steps.get-version-number.outputs.version }} \
+            --build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
+            --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
+            --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \
+            .
+
+      #############################################
+      ## Test and upload coverage report to Codecov
+      #############################################
+      - name: Install pytest
+        run: python -m pip install pytest pytest-cov
+
+      - name: Install the requirements for the tests
+        run: python -m pip install .[tests]
+
+      - name: Run the tests
+        run: python -m pytest tests/ --cov=./ --cov-report=xml
+
+      - name: Upload the coverage report to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests
+          file: ./coverage.xml
+
+      #############################################
+      ## Compile documentation
+      #############################################
+      - name: Install the requirements for compiling the documentation
+        run: python -m pip install -r docs-src/requirements.txt
+
+      - name: Compile the documentation
+        run: |
+          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          mkdir -p docs-src/_static
+          sphinx-build docs-src docs
+
+      #############################################
+      ## Commit and push new version of simulator
+      #############################################
+      # If new version of simulator, commit and push the new version
+      - name: Commit the revised version of the simulator
+        if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "biosimulatorsdaemon"
+          git config pull.rebase false
+          git stash -- biosimulators.json Dockerfile
+          git clean -f -d
+          git checkout .
+          git pull
+          git stash pop
+          git add biosimulators.json Dockerfile
+          git commit -m "Updating version of simulator"
+
+      - name: Push the revised version of the simulator
+        if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
+
+      #############################################
+      ## Release
+      #############################################
+
+      - id: determine-if-release-needed
+        name: Determine if a release should be made
+        run: |
+          release="0"
+
+          if [ ! -z "${{ github.event.inputs.simulatorVersion }}" ]; then
+            if [ "${{ github.ref }}" == "${{ steps.get-main-branch.outputs.mainBranchRef }}" ]; then
+              release="1"
+            fi
+          fi
+
+          if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
+            tag_hash=$(git rev-parse "${{ github.ref }}")
+            if [ "$tag_hash" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then
+              release="1"
+            fi
+          fi
+
+          echo "::set-output name=release::$release"
+
+      # If new tag, commit and push documentation
+      - id: commit-docs
+        name: Commit the compiled documentation
+        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "biosimulatorsdaemon"
+          git config pull.rebase false
+          git stash
+          git checkout ${{ steps.get-main-branch.outputs.mainBranch }}
+          git pull
+          set +e
+          git stash pop
+          git add docs
+          git commit -m "Updating compiled documentation"
+          git checkout .
+          git clean -f -d
+          if [[ $? = 0 ]]; then
+            docsChanged=1
+          else
+            docsChanged=0
+          fi
+          echo "::set-output name=docsChanged::$docsChanged"
+
+      - name: Push the compiled documentation
+        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1' && steps.commit-docs.outputs.docsChanged == '1'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ steps.get-main-branch.outputs.mainBranch }}
+
+      # Create GitHub release
+      - name: Create GitHub release
+        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.get-version-number.outputs.version }}
+          release_name: Release ${{ steps.get-version-number.outputs.version }}
+
+      # Create PyPI release
+      - name: Create PyPI release
+        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          # Install pandoc
+          sudo apt-get update -y
+          sudo apt-get install -y --no-install-recommends wget
+
+          wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
+          urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
+          wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
+          sudo dpkg -i /tmp/pandoc.deb
+          rm /tmp/pandocVersions.html
+          rm /tmp/pandoc.deb
+
+          # Convert README to .rst format
+          pandoc --from=gfm --output=README.rst --to=rst README.md
+
+          # Install twine
+          python -m pip install wheel twine
+
+          # Create packages to upload to PyPI
+          python setup.py sdist
+          python setup.py bdist_wheel
+
+          # Upload packages to PyPI
+          twine upload dist/*
+
+      # build Docker image and push to GitHub Container Registry
+      - name: Push Docker image
+        if: steps.determine-if-release-needed.outputs.release == '1'
+        run: |
+          docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \
+            --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
+            --password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
+          docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
+
+          if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ github.event.inputs.simulatorVersionLatest }}" == "true" ]; then
+            docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
+          fi
+
+      # Submit to BioSimulators registry
+      - name: Submit to BioSimulators registry
+        if: steps.determine-if-release-needed.outputs.release == '1'
+        run: |
+          REVISION=$(git rev-parse HEAD)
+          curl \
+            -X POST \
+            -u ${{ secrets.GH_ISSUE_USERNAME }}:${{ secrets.GH_ISSUE_TOKEN }} \
+            -H "Accept: application/vnd.github.v3+json" \
+            https://api.github.com/repos/biosimulators/Biosimulators/issues \
+            -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit ${{ steps.get-docker-image-tag.outputs.simulatorName }} ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\", \"body\": \"---\nid: ${{ steps.get-docker-image-tag.outputs.simulatorId }}\nversion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n  version: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n  image:\n    url: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -59,7 +59,7 @@ sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --n
 sphinx-build docs-src docs
 ```
 
-## Submitting changes   
+## Submitting changes
 
 Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.
 
@@ -88,7 +88,7 @@ Below are instructions for releasing a new version:
 ## Reporting issues
 
 Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_tellurium/issues) to report any issues to the development community.
-    
+
 ## Getting help
 
 Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_tellurium/issues) to post questions or contact the lead developers at [[email protected]](mailto:[email protected]).
diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@
 FROM python:3.7.9-slim-buster
 
 ARG VERSION="0.0.1"
-ARG SIMULATOR_VERSION="2.1.6"
+ARG SIMULATOR_VERSION="2.2.0"
 
 # metadata
 LABEL \
@@ -30,7 +30,7 @@ LABEL \
     org.opencontainers.image.licenses="Apache-2.0" \
     \
     base_image="python:3.7.9-slim-buster" \
-    version="${VERSION}" \ 
+    version="${VERSION}" \
     software="tellurium" \
     software.version="${SIMULATOR_VERSION}" \
     about.summary="Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology" \
@@ -45,12 +45,17 @@ LABEL \
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
         libxml2 \
+        libncurses5 \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
 
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_tellurium
 RUN pip install /root/Biosimulators_tellurium \
+    && mkdir -p /.cache/matplotlib \
+    && mkdir -p /.config/matplotlib \
+    && chmod ugo+rw /.config/matplotlib \
+    && chmod ugo+rw /.cache/matplotlib \
     && rm -rf /root/Biosimulators_tellurium
 RUN pip install tellurium==${SIMULATOR_VERSION}