Merge remote-tracking branch 'origin/main' into rdf

.bumpversion.cfg

@@ -1,7 +1,10 @@
 [bumpversion]
-current_version = 0.5.17
+current_version = 0.5.40
 commit = True
 tag = True
-files = pyproject.toml
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
 serialize = {major}.{minor}.{patch}
+
+[bumpversion:file:pyproject.toml]
+
+[bumpversion:file:biocypher/_metadata.py]

.github/actions/build_docs/action.yaml

@@ -0,0 +1,12 @@
+name: 'Build docs'
+description: 'Build docs and run doc tests'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Test code snippets in documentation
+      run: poetry run make doctest --directory docs/
+      shell: bash
+    - name: Build documentation
+      run: poetry run make html --directory docs/
+      shell: bash

.github/actions/install/action.yaml

@@ -0,0 +1,29 @@
+name: 'Install'
+description: 'Install dependencies'
+inputs:
+  PYTHON_VERSION:
+    description: 'Python version'
+    default: 3.9
+
+runs:
+  using: "composite"
+  steps:
+    #----------------------------------------------
+    #       load cached venv if cache exists
+    #----------------------------------------------
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v3
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.PYTHON_VERSION }}-${{ hashFiles('**/poetry.lock') }}
+    #----------------------------------------------
+    # install dependencies if cache does not exist
+    #----------------------------------------------
+    - name: Install Dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction --no-root
+      shell: bash
+    - name: Install library
+      run: poetry install --no-interaction
+      shell: bash

.github/actions/setup/action.yaml

@@ -0,0 +1,34 @@
+name: 'Setup'
+description: 'Setup Python and Poetry'
+inputs:
+  PYTHON_VERSION:
+    description: 'Python version'
+    default: 3.9
+  POETRY_VERSION:
+    description: 'Poetry version'
+    default: 1.5.1
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python ${{inputs.PYTHON_VERSION}}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{inputs.PYTHON_VERSION}}
+    - name: Load cached Poetry installation
+      if: runner.os == 'Linux' # TODO: add support for other OS
+      id: cached-poetry
+      uses: actions/cache@v3
+      with:
+        path: ~/.local
+        key: poetry-cache-${{ runner.os }}-${{ inputs.PYTHON_VERSION }}-${{ inputs.POETRY_VERSION }}
+    - name: Install and configure Poetry
+      if: steps.cached-poetry.outputs.cache-hit != 'true'
+      uses: snok/install-poetry@v1
+      with:
+        version: 1.5.1
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+    - name: Check Poetry installation
+      run: poetry --version
+      shell: bash

.github/actions/test/action.yaml

@@ -0,0 +1,40 @@
+name: 'Test and code quality'
+description: 'Run tests and code quality checks'
+
+runs:
+  using: "composite"
+  steps:
+    #----------------------------------------------
+    #    setup docker containers for testing
+    #----------------------------------------------
+    # currently only available for ubuntu and macos
+    - name: Install Docker
+      uses: douglascamata/setup-docker-macos-action@v1-alpha
+      if: ${{ runner.os == 'macOS' }}
+    - name: Start Neo4j Docker
+      run: docker run --restart always --publish=7474:7474 --publish=7687:7687 --env NEO4J_AUTH=neo4j/your_password_here --env NEO4J_PLUGINS='["apoc"]' --env=NEO4J_ACCEPT_LICENSE_AGREEMENT=yes -d neo4j:4.4-enterprise
+      shell: bash
+      if: ${{ runner.os != 'Windows' }}
+    - name: Start Postgres Docker
+      run: docker run --restart always --publish=5432:5432 --env POSTGRES_PASSWORD=postgres -d postgres:11.21-bullseye
+      shell: bash
+      if: ${{ runner.os != 'Windows' }}
+    #----------------------------------------------
+    #     run tests and code quality checks
+    #----------------------------------------------
+    - name: Run Tests (Windows)
+      run: |
+        source .venv/scripts/activate
+        pytest --version
+        pytest --password=your_password_here
+      shell: bash
+      if: runner.os == 'Windows'
+    - name: Run tests (Linux and MacOS)
+      run: |
+        source .venv/bin/activate
+        pytest --version
+        pytest --password=your_password_here
+      shell: bash
+      if: runner.os != 'Windows'
+    - name: Check code quality
+      uses: pre-commit/[email protected]

.github/actions/test_coverage/action.yaml

@@ -0,0 +1,24 @@
+name: 'Test coverage'
+description: 'Check test coverage'
+
+inputs:
+  token:
+    description: 'A Github PAT'
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Generate coverage report
+      run: poetry run coverage run -m pytest --password=your_password_here
+      shell: bash
+    - name: Generate coverage badge
+      run: poetry run coverage-badge -f -o docs/coverage/coverage.svg
+      shell: bash
+    - name: Commit changes
+      uses: s0/git-publish-subdir-action@develop
+      env:
+        REPO: self
+        BRANCH: coverage
+        FOLDER: docs/coverage
+        GITHUB_TOKEN: ${{ inputs.token }}

.github/workflows/docs.yaml

@@ -0,0 +1,75 @@
+name: Docs
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  build_docs:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+    #----------------------------------------------
+    # check-out repo and set-up python and poetry
+    #----------------------------------------------
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+    - name: Setup Python and Poetry
+      uses: ./.github/actions/setup
+    #----------------------------------------------
+    #            install dependencies
+    #----------------------------------------------
+    - name: Install dependencies
+      uses: ./.github/actions/install
+    - name: Install pandoc
+      run: sudo apt-get -y install pandoc
+    #----------------------------------------------
+    #                  build docs
+    #----------------------------------------------
+    - name: Build docs
+      uses: ./.github/actions/build_docs
+
+  build_and_deploy_docs:
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+    #----------------------------------------------
+    # check-out repo and set-up python and poetry
+    #----------------------------------------------
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+    - name: Setup Python and Poetry
+      uses: ./.github/actions/setup
+    #----------------------------------------------
+    #            install dependencies
+    #----------------------------------------------
+    - name: Install dependencies
+      uses: ./.github/actions/install
+    - name: Install pandoc
+      run: sudo apt-get -y install pandoc
+    #----------------------------------------------
+    #                  build docs
+    #----------------------------------------------
+    - name: Install dependencies
+      uses: ./.github/actions/build_docs
+    - name: Commit files
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        touch docs/_build/html/.nojekyll
+        echo 'biocypher.org' > docs/_build/html/CNAME
+        git add -f docs/_build/
+        git commit -m "Update autodoc" -a
+    #----------------------------------------------
+    #                  deploy docs
+    #----------------------------------------------
+    - name: Deploy
+      uses: s0/git-publish-subdir-action@develop
+      env:
+        REPO: self
+        BRANCH: gh-pages
+        FOLDER: docs/_build/html
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pr.yaml

@@ -0,0 +1,41 @@
+name: Tests and code quality checks for pull requests
+
+on: [pull_request]
+
+jobs:
+  tests_and_code_quality:
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
+    runs-on: ${{ matrix.os }}
+    env:
+      POETRY_VERSION: 1.5.1
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    #----------------------------------------------
+    #  checkout repo and set-up python and poetry
+    #----------------------------------------------
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+    - name: Setup Python and Poetry
+      uses: ./.github/actions/setup
+      with:
+        PYTHON_VERSION: ${{ matrix.python-version }}
+        POETRY_VERSION: ${{ env.POETRY_VERSION }}
+    #----------------------------------------------
+    #       install dependencies
+    #----------------------------------------------
+    - name: Install dependencies
+      uses: ./.github/actions/install
+      with:
+        PYTHON_VERSION: ${{ matrix.python-version }}
+    #----------------------------------------------
+    #      run tests and code quality checks
+    #----------------------------------------------
+    - name: Run tests
+      uses: ./.github/actions/test

.github/workflows/publish.yaml

@@ -0,0 +1,64 @@
+name: Publish
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+    # TODO: ensure semver style - "[0-9]+.[0-9]+.[0-9]+(-[a-z]+)?(.[0-9]+)?"
+
+jobs:
+  call-tests_and_code_quality:
+    if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+    uses: "./.github/workflows/tests_and_code_quality.yaml"
+
+  build_and_deploy_artifact:
+    if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+    needs: call-tests_and_code_quality
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: 3.9
+    environment:
+      name: release
+      url: https://upload.pypi.org/legacy/
+    permissions:
+      id-token: write
+      contents: write
+    steps:
+    #----------------------------------------------
+    # check-out repo and set-up python and poetry
+    #----------------------------------------------
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+    - name: Setup Python and Poetry
+      uses: ./.github/actions/setup
+    #----------------------------------------------
+    #            install dependencies
+    #----------------------------------------------
+    - name: Install dependencies
+      uses: ./.github/actions/install
+    #----------------------------------------------
+    #             build artifact
+    #----------------------------------------------
+    - name: Build artifact
+      run: poetry build
+    #----------------------------------------------
+    #             upload to PyPi
+    #----------------------------------------------
+    - name: Publish artifact to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://upload.pypi.org/legacy/
+    #----------------------------------------------
+    #           create Github release
+    #----------------------------------------------
+    - name: Create Github release
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        tag: ${{ github.ref_name }}
+      run: |
+        gh release create "$tag" \
+            --repo="$GITHUB_REPOSITORY" \
+            --title="$tag" \
+            --generate-notes