feat(ci): refactor actions and add linting

- refactor: revise testing into unified integration pipeline
- refactor: create re-usable setup-env action
- feat: add pipeline support for poetry dynamic versioning
- feat: add actionlint to pre-commit hooks.

.github/actions/setup-env/action.yaml

@@ -0,0 +1,81 @@
+name: Setup Environment and Cache
+description: |
+  A reusable composite action to setup the environment for a job.
+  This action will:
+  - Setup Python
+  - Cache the pre-commit installation
+  - Cache the virtual environment
+  - Setup poetry
+  - Install dependencies
+inputs:
+  python-version:
+    description: The version of Python to use (passed to actions/setup-python)
+    required: true
+  cache-pre-commit:
+    description: Whether to cache the pre-commit installation
+    required: false
+    default: "true"
+  cache-venv:
+    description: Whether to cache the virtual environment
+    required: false
+    default: "true"
+  setup-poetry:
+    description: Whether to setup poetry
+    required: false
+    default: "true"
+  install-deps:
+    description: Whether to install dependencies
+    required: false
+    default: "true"
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+    - name: Generate Cache Key PY
+      # The cache key PY is a hash of the Python version and the
+      # output of `pip freeze` (the installed packages).
+      # This ensures that the cache is invalidated when the Python
+      # version or the default packages change. Both of the remaining
+      # cache keys depend on PY.
+      shell: bash
+      run: echo "PY=$((python -VV; pip freeze) | sha256sum | cut -d' ' -f1)" >>
+        $GITHUB_ENV
+    - name: Cache pre-commit installation
+      # The cache key for the pre-commit installation is a hash of the
+      # operating system, PY (see above), and the pre-commit config.
+      # This allows for caching the pre-commit hook installation across
+      # jobs and workflows.
+      if: ${{ inputs.cache-pre-commit == 'true' }}
+      uses: actions/cache@v3
+      with:
+        path: |
+          .cache
+          pre-commit
+        key: cache|${{ runner.os }}|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
+    - name: Cache venv
+      # The cache key for the virtual environment is a hash of the
+      # operating system, PY (see above), the pyproject.toml and
+      # the poetry.lock file. This allows for caching the virtual
+      # environment with all the dependencies.
+      if: ${{ inputs.cache-venv == 'true' }}
+      uses: actions/cache@v3
+      with:
+        path: |
+          .cache
+          .venv
+        key:
+          cache|${{ runner.os }}|${{ env.PY }}|${{ hashFiles('pyproject.toml') }}|${{
+          hashFiles('poetry.lock') }}
+    - name: Setup poetry and poetry-dynamic-versioning
+      shell: bash
+      if: ${{ inputs.setup-poetry == 'true' }}
+      run: |
+        python -m pip install poetry poetry-dynamic-versioning
+    - name: Install dependencies with poetry
+      shell: bash
+      if: ${{ inputs.install-deps == 'true' }}
+      run: |
+        poetry install --with dev,docs --all-extras -v --no-interaction

.github/workflows/integration-test.yml

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+name: Integration Workflow
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    tags: ["*"]
+  workflow_dispatch:
+    inputs:
+      pytest_addopts:
+        description: Extra options for pytest; use -vv for full details; see
+          https://docs.pytest.org/en/latest/example/simple.html#how-to-change-command-line-options-defaults
+        required: false
+        default: ""
+
+env:
+  LANG: "en_US.utf-8"
+  LC_ALL: "en_US.utf-8"
+  PIP_CACHE_DIR: ${{ github.workspace }}/.cache/pip
+  POETRY_CACHE_DIR: ${{ github.workspace }}/.cache/pypoetry
+  POETRY_VIRTUALENVS_IN_PROJECT: "true"
+  PRE_COMMIT_HOME: ${{ github.workspace }}/.cache/pre-commit
+  PYTEST_ADDOPTS: ${{ github.event.inputs.pytest_addopts }}
+  PYTHONIOENCODING: "UTF-8"
+  TARGET_PYTHON_VERSION: "3.9"
+
+jobs:
+  quality-test:
+    # This job is used to run pre-commit checks to ensure that all files are
+    # are formatted correctly.
+    name: Pre-commit checks
+    # Runs pre-commit checks on all files
+    # This job doesn't fail fast to ensure that feedback on function is still provided
+    strategy:
+      fail-fast: false
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          # Full history likely required for planned commitizen checks
+          # See #345
+          fetch-depth: 0
+      - name: Setup python, and check pre-commit cache
+        uses: ./.github/actions/setup-env
+        with:
+          python-version: ${{ env.TARGET_PYTHON_VERSION }}
+          cache-pre-commit: true
+          cache-venv: false
+          setup-poetry: false
+      - name: Run pre-commit checks on all files
+        uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files
+  integration-test:
+    name: Pytest (Python ${{ matrix.python-version }} on ${{ matrix.os }})
+    # Runs pytest on all tested versions of python and OSes
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - macos-latest
+          - ubuntu-latest
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    runs-on: ${{ matrix.os }}
+    env:
+      OS: ${{ matrix.os }}
+      # This is needed to avoid a warning from SQLAlchemy
+      # https://sqlalche.me/e/b8d9
+      # We can remove this once we upgrade to SQLAlchemy >= 2.0
+      SQLALCHEMY_SILENCE_UBER_WARNING: "1"
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Setup python, and load cache
+        uses: ./.github/actions/setup-env
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-pre-commit: false
+          cache-venv: true
+          setup-poetry: true
+          install-deps: true
+      - name: Run pytest and generate coverage report
+        # For the target version and ubuntu, run pytest and generate coverage report
+        if: (matrix.os == 'ubuntu-latest')  && (matrix.python-version == env.TARGET_PYTHON_VERSION)
+        run: poetry run pytest --cov=./ --cov-report=xml ${{ github.event.inputs.pytest_addopts }}
+      - name: Upload coverage to Codecov
+        # For the target version and ubuntu, upload coverage to Codecov
+        continue-on-error: true
+        if: (matrix.os == 'ubuntu-latest') && (matrix.python-version == env.TARGET_PYTHON_VERSION )
+        uses: codecov/codecov-action@v3
+        env:
+          OS: ${{ matrix.os }}
+          PYTHON: ${{ matrix.python-version }}
+        with:
+          file: ./coverage.xml
+          files: ./coverage1.xml,./coverage2.xml
+          directory: ./coverage/reports/
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          flags: unittests
+          name: pycytominer
+      - name: Run pytest
+        # For every other version and/or OS, run pytest without coverage
+        if: (matrix.os != 'ubuntu-latest') || (matrix.python-version != env.TARGET_PYTHON_VERSION )
+        run: poetry run pytest ${{ github.event.inputs.pytest_addopts }}

.github/workflows/pypi-release.yml

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+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+on: [release]
+
+env:
+  LANG: "en_US.utf-8"
+  LC_ALL: "en_US.utf-8"
+  PYTHONIOENCODING: "UTF-8"
+  TARGET_PYTHON_VERSION: "3.9"
+
+jobs:
+  build-and-publish:
+    name: Build and publish Python 🐍 distributions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          # We do not need to fetch all the history of the repository
+          # as commit being released is guaranteed to have a tag.
+          # poetry-dynamic-versioning will use that tag use to set the
+          # build version of the package.
+          fetch-depth: 1
+      - name: Setup base environment
+        uses: ./.github/actions/setup-env
+        with:
+          python-version: ${{ env.TARGET_PYTHON_VERSION }}
+          cache-pre-commit: false
+          cache-venv: false
+          setup-poetry: true
+          install-deps: false
+      - name: Build 📦 distributions
+        run: |
+          poetry build
+      - name: Publish any distribution 📦 to Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          repository-url: https://test.pypi.org/legacy/
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      - name: Publish tagged distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: startsWith(github.ref, 'refs/tags')
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}