Merge pull request #152 from biosimulators/poetry-build

Poetry build

.flake8

@@ -4,3 +4,4 @@ exclude =
     tests/*
     docs-src/*
     build/*
+    .venv/

.github/actions/setup-poetry-env/action.yml

@@ -0,0 +1,42 @@
+name: "setup-poetry-env"
+description: "Composite action to setup the Python and poetry environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: "1.7.1"
+      run: curl -sSL https://install.python-poetry.org | python - -y
+      shell: bash
+
+    - name: Add Poetry to Path
+      run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Configure Poetry virtual environment in project
+      run: poetry config virtualenvs.in-project true
+      shell: bash
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction --with bngl,cellml,lems,neuroml,sbml,simularium,escher,containers,logging,rba,smoldyn
+      shell: bash

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ jobs:
   getVersionNumber:
     name: Get version number
     if: "startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
       version: ${{ steps.get-version-number.outputs.version }}
     steps:
@@ -21,33 +21,22 @@ jobs:
           echo "version=$version" >> $GITHUB_OUTPUT
 
   build:
-    name: Lint, test, and compile documentation
+    name: Lint, test, and compile docs (python ${{ matrix.python-version }})
     if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: [ "3.10" ]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
-      - name: Install Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.9.9' # no particular microversion of 3.9 is required; 3.9.8 behaves oddly in GitHub actions
-
-      - 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==23.0.1
-          python -m pip install --upgrade setuptools
-
       - name: Install Java # for pyNeuroML
         uses: actions/setup-java@v2
         with:
@@ -69,32 +58,21 @@ jobs:
           singularity-version: 3.7.1
 
       # install package
-      - name: Install the package
-        run: |
-          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
-          python -m pip install .[all]
-
-      # lint
-      - name: Install flake8
-        run: python -m pip install flake8
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: Lint the package
-        run: python -m flake8
-
-      # 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]
+        run: poetry run python -m flake8
 
       - name: Run the tests
         uses: GabrielBB/xvfb-action@v1
         env:
           MPLBACKEND: PDF
           # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/  # uncomment to execute tests with the dev deployment
         with:
-          run: python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
+          run: poetry run python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
 
       - name: Upload the coverage report to Codecov
         uses: codecov/codecov-action@v2
@@ -105,21 +83,21 @@ jobs:
 
       # compile documentation
       - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+        run: poetry install --with docs
 
       - name: Compile the documentation
         run: |
-          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry 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
+          poetry run sphinx-build docs-src docs
 
   release:
     name: Release a new version
     needs: [getVersionNumber, build]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           ref: dev
@@ -130,44 +108,21 @@ jobs:
           git config --local user.name "biosimulatorsdaemon"
           git config pull.rebase false
 
-      - name: Install Python
-        uses: actions/setup-python@v2
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
         with:
-          python-version: '3.9'
-
-      - 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 pip==20.3.4
-          python -m pip install --upgrade setuptools
-
-      # install package
-      - name: Install the package
-        run: python -m pip install .[all]
+          python-version: ${{ matrix.python-version }}
 
       # update Identifiers.org namespaces
       - name: Update Identifiers.org namespaces
-        run: python -c "from biosimulators_utils.utils.identifiers_org import get_identifiers_org_namespaces; get_identifiers_org_namespaces(reload=True);"
-
-      - name: Install pytest
-        run: python -m pip install pytest
-
-      - name: Install the requirements for the tests
-        run: python -m pip install .[tests]
+        run: poetry run python -c "from biosimulators_utils.utils.identifiers_org import get_identifiers_org_namespaces; get_identifiers_org_namespaces(reload=True);"
 
       - name: Test the updated Identifiers.org namespaces
         uses: GabrielBB/xvfb-action@v1
         env:
           MPLBACKEND: PDF
         with:
-          run: python -m pytest tests/utils/test_identifiers_org_utils.py
+          run: poetry run python -m pytest tests/utils/test_identifiers_org_utils.py
 
       - id: commit-identifiers-namespaces
         name: Commit the Identifiers.org namespaces
@@ -187,13 +142,13 @@ jobs:
 
       # compile and push documentation
       - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+        run: poetry install --with docs
 
       - name: Compile the documentation
         run: |
-          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry 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
+          poetry run sphinx-build docs-src docs
 
       - id: commit-docs
         name: Commit the compiled documentation
@@ -228,19 +183,12 @@ jobs:
           release_name: Release ${{ needs.getVersionNumber.outputs.version }}
 
       # Create PyPI release
-      - name: Install twine
-        run: |
-          python -m pip install wheel twine
-
       - name: Create packages to upload to PyPI
         run: |
-          python setup.py sdist
-          python setup.py bdist_wheel
+          poetry build
 
       - name: Upload packages to PyPI
         env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
         run: |
-          twine upload dist/*
-
+          poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI

.gitignore

@@ -19,3 +19,5 @@ docs/.buildinfo
 docs/.doctrees/
 docs/_raw_sources/
 docs/_sources/
+
+.python-version

biosimulators_utils/image.py

@@ -119,11 +119,20 @@ def convert_docker_image_to_singularity(docker_image_url: str, singularity_filen
     Returns:
         :obj:`str`: path where Singularity image was saved
     """
-    cmd: list[str] = ['singularity', 'build']
 
+    # We need to break the command up into two parts: a docker pull using only docker,
+    # Then a singularity build from the pulled (now local) image. This is due to docker
+    # API version error that appear to be coming from singularity's client.
+    # Unless we upgrade a major version, this is our solution.
     if ':' not in docker_image_url:
         docker_image_url += ':latest'
 
+    intermediate_archive_name = "docker_image_to_test.tar"
+    cmd1: list[str] = ['docker', 'image', 'save', docker_image_url, "-o", intermediate_archive_name]
+    subprocess.check_call(cmd1)
+
+    cmd2: list[str] = ['singularity', 'build']
+
     if not singularity_filename:
         singularity_filename: str = os.path.join(
             os.path.expanduser('~'), '.biosimulators-utils', 'singularity',
@@ -132,11 +141,11 @@ def convert_docker_image_to_singularity(docker_image_url: str, singularity_filen
     if not os.path.isdir(os.path.dirname(singularity_filename)):
         os.makedirs(os.path.dirname(singularity_filename))
 
-    cmd.append(singularity_filename)
+    cmd2.append(singularity_filename)
 
-    cmd.append('docker-daemon://' + docker_image_url)
+    cmd2.append('docker-archive:' + intermediate_archive_name)
 
     if not os.path.isfile(singularity_filename):
-        subprocess.check_call(cmd)
+        subprocess.check_call(cmd2)
 
     return singularity_filename