Merge pull request #6 from biosimulators/main

merge most recent changes

.github/workflows/buildDockerImage.yml

@@ -0,0 +1,168 @@
+name: Build and push Docker image
+
+on:
+  push:
+    paths:
+      - '.github/workflows/buildDockerImage.yml'
+      - 'Dockerfile'
+      - 'Dockerfile-base'
+      - 'Dockerfile-assets/**'
+
+jobs:
+  buildAndPushImage:
+    name: Build and push Docker image
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
+    runs-on: ubuntu-20.04
+
+    steps:
+      # Free disk space
+      # Inspiration
+      # - https://github.com/easimon/maximize-build-space/blob/master/action.yml
+      # - https://githubmemory.com/repo/ros-industrial/industrial_ci/issues/648
+      # - https://github.community/t/bigger-github-hosted-runners-disk-space/17267/11
+      - name: Maximize build space
+        run: |
+          sudo apt-get -qq purge build-essential ghc*
+          sudo apt-get clean
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /usr/local/lib/android
+          sudo rm -rf /opt/ghc
+          sudo rm -rf /usr/local/share/boost
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          docker system prune -f
+
+      # checkout repository
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+
+      # Build Docker image
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Login to GHCR
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: "${{ secrets.DOCKER_REGISTRY_USERNAME }}"
+          password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}"
+
+      - id: get-timestamp
+        name: Get timestamp
+        run: |
+          TIMESTAMP=$(date --rfc-3339=seconds | sed 's/ /T/')
+          echo "timestamp=$TIMESTAMP" >> $GITHUB_OUTPUT
+
+      - name: Copy Dockerfile to Dockerfile-assets
+        run: |
+          cp Dockerfile Dockerfile-assets/
+          cp Dockerfile-base Dockerfile-assets/
+
+      - name: Build base image
+        uses: docker/build-push-action@v2
+        with:
+          context: Dockerfile-assets
+          file: Dockerfile-base
+          pull: true
+          load: true
+          push: false
+          tags: |
+            ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}}
+          labels: |
+            org.opencontainers.image.revision=${{github.sha}}
+            org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}"
+          cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache
+          cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache,mode=max
+
+      - name: Push base Docker image
+        run: docker image push ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}}
+
+      - name: Label base Docker image
+        run: docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:latest
+
+      - name: Maximize build space
+        run: |
+          docker system prune -f
+
+      - name: Build image
+        uses: docker/build-push-action@v2
+        with:
+          context: Dockerfile-assets
+          file: Dockerfile
+          pull: false
+          load: true
+          push: false
+          tags: |
+            ghcr.io/biosimulators/biosimulators:sha-${{github.sha}}
+          labels: |
+            org.opencontainers.image.revision=${{github.sha}}
+            org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}"
+          cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache
+          cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache,mode=max
+
+      - name: Push Docker image
+        run: docker image push ghcr.io/biosimulators/biosimulators:sha-${{github.sha}}
+
+      - name: Label Docker image
+        run: docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:latest
+
+      - name: Maximize build space
+        run: |
+          docker system prune -f
+
+      # Test Docker image
+      - name: Test Docker image
+        run: |
+          cwd=$(pwd)
+          docker run \
+            --rm \
+            --entrypoint bash \
+            --mount type=bind,source=${cwd},target=/app/Biosimulators \
+            ghcr.io/biosimulators/biosimulators:latest \
+            -c "
+              pipenv install --dev --system --deploy
+              /bin/bash /xvfb-startup.sh python -m pytest --forked --verbose Biosimulators/tests/
+            "
+
+      # Get version number
+      - id: get-version-number
+        name: Get version number
+        if: startsWith(github.ref, 'refs/tags/')
+        env:
+          TAG: ${{ github.ref }}
+        run: |
+          version="${TAG/refs\/tags\//}"
+          echo "version=$version" >> $GITHUB_OUTPUT
+
+      # Create GitHub release
+      - name: Create GitHub release
+        if: startsWith(github.ref, 'refs/tags/')
+        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 }}
+
+      # Push Docker image
+      - name: Push Docker image
+        if: startsWith(github.ref, 'refs/tags/')
+        env:
+          VERSION: ${{ steps.get-version-number.outputs.version }}
+        run: |
+          docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:${VERSION}
+          docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:${VERSION}
+
+          docker push ghcr.io/biosimulators/biosimulators-base:${VERSION}
+          docker push ghcr.io/biosimulators/biosimulators-base:latest
+          docker push ghcr.io/biosimulators/biosimulators:${VERSION}
+          docker push ghcr.io/biosimulators/biosimulators:latest

.github/workflows/buildImage.yaml

@@ -0,0 +1,165 @@
+name: Validate and/or commit simulator
+
+on:
+  deployment 
+
+jobs:
+  validateCommit:
+    name: Validate and/or commit simulator
+    runs-on: ubuntu-20.04 # includes Docker
+    if: |
+      github.event.issue.state == 'open'
+      && contains(github.event.issue.labels.*.name, 'Validate/submit simulator')
+      && (
+        github.event.action == 'edited'
+        || (
+            github.event.action == 'labeled'
+            && github.event.label.name == 'Validate/submit simulator'
+           )
+        || (
+            github.event.action == 'labeled'
+            && github.event.label.name == 'Approved'
+            && github.event.sender.login != 'biosimulators-daemon'
+           )
+      )
+    steps:
+      - name: Install Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      #- name: Setup pip cache
+      #  uses: actions/cache@v2
+      #  with:
+      #    path: /opt/hostedtoolcache/Python
+      #    key: ${{ runner.os }}-pip-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.txt') }}-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.optional.txt') }}
+      #    restore-keys: |
+      #      ${{ runner.os }}-pip-
+
+      - name: Install pip and setuptools
+        run: |
+          wget https://bootstrap.pypa.io/get-pip.py
+          python get-pip.py pip>=21.0.0
+          python -m pip install --upgrade setuptools
+
+      - name: Install Java # for pyNeuroML
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'adopt'
+          java-version: '15'
+
+      - name: Install Perl # for BioNetGen
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y --no-install-recommends perl
+
+      - name: Install XPP
+        run: |
+          sudo apt-get install -y --no-install-recommends xppaut
+
+      - name: Install Go (for Singularity)
+        uses: actions/setup-go@v3
+        with:
+          go-version: '^1.13.1' # The Go version to download (if necessary) and use.
+
+      - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
+        env:
+          GO_VERSION: 1.17.2
+          SINGULARITY_VERSION: 3.9.5
+          OS: linux
+          ARCH: amd64
+        run: |
+          sudo apt-get install -y --no-install-recommends \
+            build-essential \
+            libseccomp-dev \
+            pkg-config \
+            squashfs-tools \
+            cryptsetup
+
+          wget https://dl.google.com/go/go$GO_VERSION.$OS-$ARCH.tar.gz
+          sudo tar -C /usr/local -xzvf go$GO_VERSION.$OS-$ARCH.tar.gz
+          rm go$GO_VERSION.$OS-$ARCH.tar.gz
+
+          echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc
+          source ~/.bashrc
+          echo "/usr/local/go/bin" >> $GITHUB_PATH
+
+          wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
+          tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz
+          cd singularity-ce-${SINGULARITY_VERSION}
+
+          ./mconfig
+          make -C builddir
+          sudo make -C builddir install
+
+      - name: Checkout BioSimulators test suite
+        uses: actions/checkout@v3
+        with:
+          repository: biosimulators/biosimulators_test_suite
+          fetch-depth: 1
+          ref: depFixes
+
+      - name: Install simulator validation utilities
+        working-directory: ${{ github.workspace }}
+        run: |
+          python -m pip cache purge
+          python -m pip install --no-cache-dir "biosimulators_utils @ git+https://github.com/biosimulators/Biosimulators_utils@depFixes#egg=biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn]"
+          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
+          python -m pip install -e .[all]
+          python --version
+          python -m pip freeze
+
+      - name: Login into Docker registries
+        run: |
+          # Docker Hub
+          docker login \
+            --username ${{ secrets.DOCKER_HUB_USERNAME }} \
+            --password ${{ secrets.DOCKER_HUB_TOKEN }}
+
+          # BioSimulators Docker registry (GHCR)
+          docker login ${{ secrets.DOCKER_REGISTRY_URL }} \
+            --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
+            --password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
+
+      - id: validateCommitSimulator
+        name: Validate and commit simulator
+        uses: GabrielBB/xvfb-action@v1
+        env:
+          GH_REPO: ${{ github.repository }}
+          GH_ACTION_RUN_ID: ${{ github.run_id }}
+          GH_ISSUE_NUMBER: ${{ github.event.issue.number }}
+          GH_ISSUES_USER: ${{ secrets.GH_ISSUES_USER }}
+          GH_ISSUES_ACCESS_TOKEN: ${{ secrets.GH_ISSUES_ACCESS_TOKEN }}
+
+          DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
+          DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
+
+          DOCKER_REGISTRY_URL: ${{ secrets.DOCKER_REGISTRY_URL }}
+          DOCKER_REGISTRY_USERNAME: ${{ secrets.DOCKER_REGISTRY_USERNAME }}
+          DOCKER_REGISTRY_TOKEN: ${{ secrets.DOCKER_REGISTRY_TOKEN }}
+
+          BIOSIMULATORS_API_CLIENT_ID: ${{ secrets.BIOSIMULATORS_API_CLIENT_ID }}
+          BIOSIMULATORS_API_CLIENT_SECRET: ${{ secrets.BIOSIMULATORS_API_CLIENT_SECRET }}
+          # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to use the dev deployment of the BioSimulators API
+
+          RUNBIOSIMULATIONS_API_CLIENT_ID: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_ID }}
+          RUNBIOSIMULATIONS_API_CLIENT_SECRET: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_SECRET }}
+          # RUNBIOSIMULATIONS_API_ENDPOINT: https://api.biosimulations.dev/ # uncomment to use the dev deployment of the BioSimulators API
+        with:
+          working-directory: ${{ github.workspace }}
+          run: |
+            python -m pip install --upgrade biosimulators_utils
+            python -c "from biosimulators_test_suite.exec_gh_action import ValidateCommitSimulatorGitHubAction; ValidateCommitSimulatorGitHubAction().run(); exit();"
+
+      - name: Setup tmate session 3 (if failed)
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
+        timeout-minutes: 40
+
+      - name: Save test results
+        uses: actions/upload-artifact@v2
+        if: success() || failure()
+        with:
+          name: Validation test results
+          path: ${{ github.workspace }}/.biosimulators-test-suite-results.json
+          if-no-files-found: warn

.github/workflows/pytest.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/checkout@main
       with:
         ref: main
-        fetch-depth: 0
+        # fetch-depth: 0
 
     - name: Set up Python
       uses: actions/setup-python@main
@@ -37,4 +37,4 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest --cov=biosimulator_processes
+        pytest

.gitignore

@@ -1,24 +1 @@
-.python-version
-__pycache__/
-.idea/
-*.ipynb_checkpoints/
-dist/
-.DS_Store
-*.egg-info/
-refresh-env.sh
-smoldyn-2.72-mac/
-build/
-commit.sh
-install.sh
-push-image.sh
-release.sh
-run.sh
-ray_job.sh
-__pycache__
 .pytest_cache
-submit-biosimulators-container.sh
-.vagrant
-._vagrant
-.THIS-IS-FOR-CONTAINER-DEV-ONLY
-buildDockerImage.yml
-.env