Use pyproject.toml with hatch

.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 +10,134 @@ 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", "3.13"]
+        seaborn-version: ["0.11", "0.12", "0.13"]
+        exclude:
+          # exclude seaborn-version 0.11 for python >= 3.12
+          - python-version: "3.12"
+            seaborn-version: "0.11"
+          - python-version: "3.13"
+            seaborn-version: "0.11"
+          # exclude seaborn-version 0.12 for python >= 3.13
+          - python-version: "3.13"
+            seaborn-version: "0.12"
 
     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 }}-${{ matrix.seaborn-version }}
+          path: report/.coverage.*
+          if-no-files-found: error
+          include-hidden-files: true
+
+  coverage:
+    name: coverage
+    runs-on: ubuntu-22.04
+    needs: test
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Let us have colors
+        run: echo "FORCE_COLOR=true" >> "$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 +1,28 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+        exclude: '^(.*\.svg)$'
+      - id: trailing-whitespace
+        exclude: '^(.*\.svg|.*\.tsv)$'
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.27.3
+    hooks:
+      - id: typos
+
+#   - repo: https://github.com/astral-sh/ruff-pre-commit
+#     rev: v0.7.4
+#     hooks:
+#       # Run the linter.
+#       - id: ruff
+#         args: [ --fix, --unsafe-fixes ]
+#       # Run the formatter.
+#       - id: ruff-format

CHANGELOG.md

@@ -5,15 +5,15 @@
 
 ### v0.7.0
 #### Features
-- Compatibility with pandas v2+ and seaborn above v0.12+ 
+- Compatibility with pandas v2+ and seaborn above v0.12+
   (PR [#155](https://github.com/trevismd/statannotations/pull/155) by
   [getzze](https://github.com/getzze))
 
 ## v0.6
 ### v0.6.0
 #### Features
-- Add option to skip annotation of non-significant results 
-  (PR [#95](https://github.com/trevismd/statannotations/pull/95) by 
+- Add option to skip annotation of non-significant results
+  (PR [#95](https://github.com/trevismd/statannotations/pull/95) by
   [sepro](https://github.com/sepro))
 
 #### Fixes
@@ -25,42 +25,42 @@
 #### Additional testing and documentation:
   - PR [#84](https://github.com/trevismd/statannotations/pull/84) by
     [JasonMendoza2008 ](https://github.com/JasonMendoza2008)
-  - PR [#86](https://github.com/trevismd/statannotations/pull/86) by 
+  - PR [#86](https://github.com/trevismd/statannotations/pull/86) by
     [mbhall88](https://github.com/mbhall88)
   - PR [#117](https://github.com/trevismd/statannotations/pull/117) by
     [tathey1](https://github.com/tathey1)
 
 ## v0.5.0
 - Add scipy's Brunner-Munzel test
-- Fix applying statannotations for non-string group labels (Issue 
+- Fix applying statannotations for non-string group labels (Issue
   [#65](https://github.com/trevismd/statannotations/issues/65))
 - Get Zenodo DOI
 
 ### v0.4.5
 - Add MANIFEST.IN (PR [#56](https://github.com/trevismd/statannotations/pull/56)
   by [Matt Chan](https://github.com/thewchan))
 - Limit supported Seaborn version to v.0.11.x
-- Fix adding annotations with hue if data is passed as arrays 
-  (PR [#64](https://github.com/trevismd/statannotations/pull/64) by 
+- Fix adding annotations with hue if data is passed as arrays
+  (PR [#64](https://github.com/trevismd/statannotations/pull/64) by
   [getzze](https://github.com/getzze))
 
 ### v0.4.4
-- The label for Kruskal-Wallis test explicitly states that it is run pairwise 
+- The label for Kruskal-Wallis test explicitly states that it is run pairwise
   (PR [#40](https://github.com/trevismd/statannotations/pull/40) by
   [sepro](https://github.com/sepro))
 - Fix broken link in readme
   (PR [#43](https://github.com/trevismd/statannotations/pull/43) by
   [orena1](https://github.com/orena1))
-- Fix custom annotations order with respect to the given pairs (Issue 
+- Fix custom annotations order with respect to the given pairs (Issue
   [#45](https://github.com/trevismd/statannotations/issues/45))
 
 ### v0.4.3
-- The `correction_format` parameter allows changing how the multiple 
+- The `correction_format` parameter allows changing how the multiple
 comparisons correction method  adjusts the annotation when changing a result
 to non-significant.
 - Fix the `show_test_name` configuration.
-- Fix the `verbose` parameter 
- (PR [#37](https://github.com/trevismd/statannotations/pull/37) by 
+- Fix the `verbose` parameter
+ (PR [#37](https://github.com/trevismd/statannotations/pull/37) by
    [mxposed](https://github.com/mxposed))
 
 ### v0.4.2
@@ -72,50 +72,50 @@ to non-significant.
  - Support for horizontal orientation
 
 ### v0.4.0
- - Major refactoring, change to an Annotator `class` to prepare and add 
+ - Major refactoring, change to an Annotator `class` to prepare and add
    annotations in separate function (now method) calls.
  - Support for `violinplot`
- - Fixes in rendering of non-significant tests results after multiple 
+ - Fixes in rendering of non-significant tests results after multiple
    comparisons correction
- - Fix the printout of the star annotation legend 
- - Fix the failure when providing a dataframe with categories as different 
+ - Fix the printout of the star annotation legend
+ - Fix the failure when providing a dataframe with categories as different
    columns.
- - Fix a bug where an incorrect xunits calculation resulted in wrong 
-   association of points within a box, leading to erroneous max y position for 
+ - Fix a bug where an incorrect xunits calculation resulted in wrong
+   association of points within a box, leading to erroneous max y position for
    that box.
  - Reduced code complexity, more SOLID.
  - Many unit and integration tests
 
 ## v0.3
 ### v0.3.2
  - Fix `simple` format outputs
- - Fix `ImportError` when applying a multiple comparison correction without 
+ - Fix `ImportError` when applying a multiple comparison correction without
    statsmodels.
- - Multiple comparison correction is `None` by default, as `statsmodels` is an 
+ - Multiple comparison correction is `None` by default, as `statsmodels` is an
    additional dependency.
 
 ### v0.3.1
- - Added support of functions returning more than the two expected values when 
+ - Added support of functions returning more than the two expected values when
    used in `StatTest`
  - Fix version numbers in CHANGELOG
 
 ### v0.3.0
 (Explicitly Requires Python 3.6)
 
  - Refactoring with implementation of `StatTest`
-   ([#7](https://github.com/trevismd/statannotations/pull/5)), removing the 
+   ([#7](https://github.com/trevismd/statannotations/pull/5)), removing the
    `stat_func` parameter, and `test_long_name`.
- - Annotations y-positions based on plot coordinates instead of data 
-   coordinates 
-   (PR [#5](https://github.com/trevismd/statannotations/pull/5) by 
-   [JosephLalli](https://github.com/JosephLalli), 
+ - Annotations y-positions based on plot coordinates instead of data
+   coordinates
+   (PR [#5](https://github.com/trevismd/statannotations/pull/5) by
+   [JosephLalli](https://github.com/JosephLalli),
    fixes https://github.com/webermarcolivier/statannot/issues/21).
  - Add this CHANGELOG
 
 ## v0.2
 ### v0.2.8
- - Fix bug on group/box named 0, fixes 
+ - Fix bug on group/box named 0, fixes
    https://github.com/trevismd/statannotations/issues/10, originally in
-   https://github.com/webermarcolivier/statannot/issues/78. Independently 
-   fixed in https://github.com/webermarcolivier/statannot/pull/73 before this 
+   https://github.com/webermarcolivier/statannot/issues/78. Independently
+   fixed in https://github.com/webermarcolivier/statannot/pull/73 before this
    issue.

CONTRIBUTING.md

@@ -1,21 +1,21 @@
 ## Contributing to statannotations
-Thank you for your interest! This package is truly the work of multiple 
+Thank you for your interest! This package is truly the work of multiple
 developers and participating users and this mustn't change.
 
-Contributions are appreciated in all their forms, such as the opening of new 
-issues when discovering a (possible) bug, suggestion/upvote new features, 
+Contributions are appreciated in all their forms, such as the opening of new
+issues when discovering a (possible) bug, suggestion/upvote new features,
 participation to discussions, improvements of the documentation, etc.
 
-If you wish specifically to submit code changes, please use the following 
+If you wish specifically to submit code changes, please use the following
 guide:
-- [ ] If it is not an answer to an open issue, please consider opening one 
+- [ ] If it is not an answer to an open issue, please consider opening one
   first, even more if the changes are major and/or possibly controversial
-- [ ] Make sure to have the dev dependencies installed: `packaging` and 
+- [ ] Make sure to have the dev dependencies installed: `packaging` and
   `statsmodels`
 - Fork the repository and make a new branch from the latest `dev` commit
-- [ ] Make your code modifications, including unit testing if possible. 
+- [ ] Make your code modifications, including unit testing if possible.
   Please follow PEP8 guidelines.
 - [ ] Run the test suite and make sure previous (and new) tests pass
 - [ ] Update CHANGELOG.md to describe your changes
-- [ ] Open a PR to the `dev` branch, containing at least what was added to the 
+- [ ] Open a PR to the `dev` branch, containing at least what was added to the
   changelog, as well as a reference to the issue if any