use pyproject.toml with hatch

use hatch environments

add test_script to test plotting figures

.github/workflows/python-package.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: CI
 
 on:
   push:
@@ -10,34 +10,123 @@ on:
     branches: [ master, dev, v0.7]
 
 jobs:
-  build:
+  check:
+    name: ${{ matrix.env.name }}
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        env:
+          - {"name": "pkg", "target": "show"}
+          - {"name": "lint", "target": "run"}
+          # - {"name": "type", "target": "run"}
+          - {"name": "docs", "target": "all"}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Let us have colors
+        run: echo "FORCE_COLOR=true" >> "$GITHUB_ENV"
+      - name: Install Hatch
+        uses: pypa/hatch@install
+      - name: Setup ${{ matrix.env.name }}
+        run: |
+          hatch -v env create ${{ matrix.env.name }}
+          hatch run ${{ matrix.env.name }}:pip freeze
+      - name: Run ${{ matrix.env.name }}
+        run: hatch -v run ${{ matrix.env.name }}:${{ matrix.env.target }}
 
+  test:
+    name: test py${{ matrix.python-version }} - seaborn-${{ matrix.seaborn-version }}
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
+        # keep synchronized with hatch tests matrix
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        seaborn-version: ["0.11", "0.12", "0.13"]
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 coverage packaging
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with unittest
-      run: |
-        coverage run -m unittest discover tests
-        coverage report -m
-    - name: Upload Coverage to Codecov
-      uses: codecov/codecov-action@v4
+      - name: Setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Pick environment to run
+        run: |
+          import codecs
+          import os
+          env = "tests.py{}-{}".format("${{ matrix.python-version }}", "${{ matrix.seaborn-version }}")
+          print(f"Environment {env}")
+          with codecs.open(os.environ["GITHUB_ENV"], mode="a", encoding="utf-8") as file_handler:
+              file_handler.write("FORCE_COLOR=1\n")
+              file_handler.write(f"ENV={env}\n")
+        shell: python
+      - name: Install Hatch
+        uses: pypa/hatch@install
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup test environment
+        run: |
+          hatch -v env create ${ENV}
+          hatch run ${ENV}:pip freeze
+        shell: bash
+      - name: Run test suite
+        run: hatch -v run ${ENV}:run-cov
+        env:
+          CI_RUN: "yes"
+        shell: bash
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-${{ matrix.python-version }}-${{ matrix.seaborn-version }}
+          path: "report/.coverage.*"
+
+  coverage:
+    name: coverage
+    runs-on: ubuntu-22.04
+    needs: test
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Let us have colors
+        run: echo "FORCE_COLOR=true" >> "$GITHUB_ENV"
+      - name: Install Hatch
+        uses: pypa/hatch@install
+      - name: Setup coverage tool
+        run: |
+          hatch -v env create coverage
+          hatch run coverage:pip freeze
+      - name: Download coverage data
+        uses: actions/download-artifact@v4
+        with:
+          pattern: coverage-*
+          path: report
+          merge-multiple: true
+      - name: Combine and report coverage
+        run: hatch run coverage:run
+
+      - name: Upload HTML report
+        uses: actions/upload-artifact@v4
+        with:
+          name: html-report
+          path: report/html
+
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          directory: report
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -10,5 +10,8 @@ statannot.egg-info/requires.txt
 statannot.egg-info/SOURCES.txt
 statannot.egg-info/top_level.txt
 
+usage/figures/*
+report/
+
 # IDE files
 .idea/

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      # - id: end-of-file-fixer
+      # - id: trailing-whitespace
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.18
+    hooks:
+      - id: validate-pyproject
+#   - repo: https://github.com/astral-sh/ruff-pre-commit
+#     rev: v0.5.5
+#     hooks:
+#       # Run the linter.
+#       - id: ruff
+#         args: [ --fix, --unsafe-fixes ]
+#       # Run the formatter.
+#       - id: ruff-format

docs/source/_static/.gitignore

@@ -0,0 +1 @@
+!.gitignore

docs/source/conf.py

@@ -33,7 +33,12 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx_rtd_theme']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.doctest',
+    'sphinx_rtd_theme',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

hatch.toml

@@ -0,0 +1,147 @@
+# https://hatch.pypa.io/latest/config/environment/overview/
+# ---------------------------------------------------------
+[envs.default]
+description = "Development environment"
+installer = "uv pip install"
+
+# ---------------------------------------------------------
+[envs.pkg]
+description = "package information"
+[envs.pkg.scripts]
+show = [
+  "uv pip list --format=columns",
+  'python -c "import sys; print(sys.version); print(sys.executable)"',
+]
+
+
+# ---------------------------------------------------------
+[envs.lint]
+template = "lint"
+installer = "uv pip install"
+description = "lint and format"
+detached = true
+dependencies = ["pre-commit"]
+
+[envs.lint.scripts]
+run = "pre-commit run --all-files"
+
+
+# ---------------------------------------------------------
+[envs.docs]
+template = "docs"
+installer = "uv pip install"
+description = "build and check documentation"
+features = ["docs"]
+
+[envs.docs.scripts]
+build = "sphinx-build -W --keep-going -b html docs/source docs/build"
+doctest = "sphinx-build -W --keep-going -b doctest docs/source docs/build"
+linkcheck = "sphinx-build -W --keep-going -b linkcheck docs/source docs/build"
+all = ["build", "doctest", "linkcheck"]
+
+
+# ---------------------------------------------------------
+[envs.types]
+template = "types"
+installer = "uv pip install"
+description = "Run the type checker"
+dev-mode = false
+dependencies = ["mypy"]
+
+[envs.types.scripts]
+run = [
+  """
+  mypy --install-types --non-interactive --ignore-missing-imports \
+    --config-file={root}/pyproject.toml {args:statannotations tests}
+  """,
+]
+
+
+# ---------------------------------------------------------
+[envs.tests]
+template = "tests"
+installer = "uv pip install"
+description = "Run the tests suite"
+features = ["tests"]
+extra-dependencies = [
+    "matplotlib<3.9",
+    "seaborn=={matrix:seaborn_version}",
+]
+
+[[envs.tests.matrix]]
+# python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+# seaborn_version = ["0.11", "0.12", "0.13"]
+python = ["3.8", "3.9", "3.10", "3.11"]
+seaborn_version = ["0.11"]
+
+[envs.tests.overrides]
+matrix.seaborn_version.extra-dependencies = [
+    "matplotlib<3.9",
+    "seaborn=={matrix:seaborn_version}",
+    { value = "pandas<2", if = ["0.11", "0.12"]},
+    { value = "numpy<2", if = ["0.11", "0.12"]},
+]
+
+[envs.tests.env-vars]
+COVERAGE_FILE = "report/.coverage.{matrix:python}-{matrix:seaborn_version}"
+COVERAGE_PROCESS_START = "pyproject.toml"
+_COVERAGE_SRC = "statannotations"
+
+[envs.tests.scripts]
+run-cov = [
+  """
+  pytest --cov=statannotations \
+    --cov-config=pyproject.toml --cov-context=test \
+    --cov-report=term-missing:skip-covered \
+    --cov-report html:report/html{matrix:python} \
+    --cov-report xml:report/coverage{matrix:python}.xml \
+    {args:-n auto --slow}
+  """,
+]
+run = "pytest {args:-n auto}"
+
+
+# ---------------------------------------------------------
+[envs.coverage]
+template = "coverage"
+installer = "uv pip install"
+description = "combine coverage files"
+detached = true
+dependencies = [
+  "coverage[toml]>=7.3",
+]
+env-vars = { COVERAGE_FILE = "report/.coverage" }
+
+[envs.coverage.scripts]
+run = [
+  "- coverage combine --rcfile=pyproject.toml report",
+  "coverage report {args:--skip-covered --show-missing}",
+  "coverage xml -o report/coverage.xml",
+  "coverage html -d report/html",
+]
+
+
+# ---------------------------------------------------------
+[envs.examples]
+template = "examples"
+installer = "uv pip install"
+description = "Run the examples"
+python = "3.11"
+extra-dependencies = [
+    "matplotlib<3.9",
+    "seaborn=={matrix:seaborn_version}",
+]
+
+[[envs.examples.matrix]]
+seaborn_version = ["0.11", "0.12", "0.13"]
+
+[envs.examples.overrides]
+matrix.seaborn_version.extra-dependencies = [
+    "matplotlib<3.9",
+    "seaborn=={matrix:seaborn_version}",
+    { value = "pandas<2", if = ["0.11", "0.12"]},
+    { value = "numpy<2", if = ["0.11", "0.12"]},
+]
+
+[envs.examples.scripts]
+run = "- python usage/test_script.py {args}"