replaces black/flake8 formatting/linting with ruff and ensures numpy 2.0 compatibility (#446)

* replace black/flake8 config with ruff config in .toml

* run ruff linter

* run ruff formatter

* remove single unused import manually

* replace black github action with ruff github action

* enforce numpy 2.0 compatibility with ruff

* replace black with ruff in docs

* remove explicit gh output format (on by default)

Author: remrama

.github/workflows/black.yml

@@ -0,0 +1,13 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Linting"
+        uses: astral-sh/ruff-action@v1
+      - name: "Formatting"
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "format --check"

.github/workflows/ruff.yml

@@ -12,11 +12,11 @@ Code guidelines
 
 *Before starting new code*, we highly recommend opening an issue on `GitHub <https://github.com/raphaelvallat/pingouin>`_ to discuss potential changes.
 
-* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. Pingouin uses `black <https://github.com/psf/black>`_ for code formatting. Before submitting a PR, please make sure to run the following command in the root folder of Pingouin:
+* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. Pingouin uses `ruff <https://github.com/astral-sh/ruff>`_ for code formatting. Before submitting a PR, please make sure to run the following command in the root folder of Pingouin:
 
   .. code-block:: bash
 
-     $ black . --line-length=100
+     $ ruff format --line-length=100
 
 * Use `NumPy style <https://numpydoc.readthedocs.io/en/latest/format.html>`_ for docstrings. Follow existing examples for simplest guidance.
 

docs/contributing.rst

@@ -107,25 +107,19 @@ source = ["src"]
 show_missing = true
 # sort = "Cover"
 
-[tool.black]
+[tool.ruff]
 line-length = 100
-target-version = ['py311']
-include = '\.pyi?$'
-
-[tool.flake8]
-# W605 : bug when math equation in numpydoc
-# W503, W504 : line-break with math operator
-# E203: E203 whitespace before ':', not compatible with Black
-# DXXX: Docstring related
-max-line-length = 100
-ignore = ["N806", "N803", "W503", "W504", "W605", "D100", "D200", "D205", "D301", "D400", "D401", "E203"]
+target-version = "py311"
 exclude = [
-    ".git",
-    "__pycache__",
-    "docs",
-    "build",
-    "__init__.py",
-    "examples",
-    "setup.py",
+    "__init__.py",  # Skip init files bc they use star imports (breaking rules F403, F405)
+    "notebooks",  # Skip jupyter notebook examples
+]
+
+[tool.ruff.lint]
+select = [
+    "E4",  # Subset of pycodestyle rules
+    "E7",  # Subset of pycodestyle rules
+    "E9",  # Subset of pycodestyle rules
+    "F",  # All Pyflakes rules
+    "NPY201",
 ]
-statistics = true

pyproject.toml

@@ -10,7 +10,7 @@
 
 def _format_bf(bf, precision=3, trim="0"):
     """Format BF10 to floating point or scientific notation."""
-    if type(bf) == str:
+    if isinstance(bf, str):
         return bf
     if bf >= 1e4 or bf <= 1e-4:
         out = np.format_float_scientific(bf, precision=precision, trim=trim)

src/pingouin/bayesian.py

@@ -367,8 +367,7 @@ def convert_elem(elem):
             elif lower in ("y", "yes", "present", "true", "t", "positive", "p"):
                 return 1
         raise ValueError(
-            "Invalid value to build a 2x2 contingency "
-            "table on column {}: {}".format(column, elem)
+            "Invalid value to build a 2x2 contingency table on column {}: {}".format(column, elem)
         )
 
     return series.apply(convert_elem)

src/pingouin/contingency.py

@@ -1,6 +1,5 @@
 import pandas as pd
 import os.path as op
-from pingouin.utils import print_table
 
 ddir = op.dirname(op.realpath(__file__))
 dts = pd.read_csv(op.join(ddir, "datasets.csv"), sep=",")