feat(ci,release): refactor github actions into unified ci pipeline

These revised github actions pipelines are modeled after https://github.com/copier-org/copier/blob/23f93660e7a13c521d66f2c6a1e81dd50c4d7148/.github/workflows/ci.yml. They also include changes needed to support poetry-dynamic-versioning

.github/workflows/ci.yml

@@ -0,0 +1,98 @@
+name: CI
+
+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:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - macos-latest
+          - ubuntu-latest
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Needs all tags to compute dynamic version
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Generate Cache Key PY
+        shell: bash
+        run:
+          echo "PY=$((python -VV; pip freeze) | sha256sum | cut -d' ' -f1)" >>
+          $GITHUB_ENV
+      - name: Cache venv
+        uses: actions/cache@v3
+        with:
+          path: |
+            .cache
+            .venv
+          key:
+            cache|${{ runner.os }}|${{ env.PY }}|${{ hashFiles('pyproject.toml') }}|${{
+            hashFiles('poetry.lock') }}|${{ hashFiles('.pre-commit-config.yaml') }}
+      - name: Install dependencies
+        run: |
+          python -m pip install poetry poetry-dynamic-versioning
+          poetry install --with dev,docs --all-extras -v --no-interaction
+      - name: Run pytest
+        run: poetry run pytest --cov=./ --cov-report=xml
+      - name: 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
+
+  pre-commit-ci:
+    name: Run pre-commit checks on changed files
+    strategy:
+      fail-fast: false
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo with all branches and tags
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ env.TARGET_PYTHON_VERSION }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.TARGET_PYTHON_VERSION }}
+      - name: Run pre-commit checks on any files changed between base_ref and HEAD
+        uses: pre-commit/action@v3.0.0
+        with:
+          extra_args: --from-ref origin/${{github.base_ref}} --to-ref HEAD

.github/workflows/release.yml

@@ -0,0 +1,58 @@
+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+on: [release]
+
+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
+  PYTHONIOENCODING: "UTF-8"
+  TARGET_PYTHON_VERSION: "3.10"
+
+jobs:
+  build-and-publish:
+    name: Build and publish Python 🐍 distributions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout 🛎️ repo with history
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python 🐍 ${{ env.TARGET_PYTHON_VERSION }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.TARGET_PYTHON_VERSION }}
+      - name: Generate cache key PY
+        run:
+          echo "PY=$((python -VV; pip freeze) | sha256sum | cut -d' ' -f1)" >>
+          $GITHUB_ENV
+      - name: Cache
+        uses: actions/cache@v3
+        with:
+          path: |
+            .cache
+            .venv
+          key:
+            cache|${{ runner.os }}|${{ env.PY }}|${{ hashFiles('pyproject.toml') }}|${{
+            hashFiles('poetry.lock') }}|${{ hashFiles('.pre-commit-config.yaml') }}
+      - name: Install 📦 dependencies
+        shell: bash
+        run: |
+          python -m pip install poetry poetry-dynamic-versioning
+      - 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 }}