pyproject.toml.rej

diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
@@ -2,7 +2,6 @@
 build-backend = "hatchling.build"
 requires = ["hatchling"]
 
-
 [project]
 name = "cellcharter"
 version = "0.0.1"
@@ -61,32 +60,62 @@ addopts = [
     "--import-mode=importlib",  # allow using test files with same name
 ]
 
-[tool.isort]
-include_trailing_comma = true
-multi_line_output = 3
-profile = "black"
-skip_glob = ["docs/*"]
-
 [tool.black]
 line-length = 120
-target-version = ['py38']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-)
-'''
+target-version = ["py38"]
+
+[tool.ruff]
+src = ["src"]
+line-length = 120
+target-version = "py38"
+select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "I",  # isort
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+    "TID",  # flake8-tidy-imports
+    "C4",  # flake8-comprehensions
+    "BLE",  # flake8-blind-except
+    "UP",  # pyupgrade
+    "RUF100",  # Report unused noqa directives
+]
+ignore = [
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix
+    "E741",
+    # Missing docstring in public package
+    "D104",
+    # Missing docstring in public module
+    "D100",
+    # Missing docstring in __init__
+    "D107",
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
+    "B008",
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    "D400",
+    # First line should be in imperative mood; try rephrasing
+    "D401",
+    ## Disable one in each pair of mutually incompatible rules
+    # We don’t want a blank line before a class docstring
+    "D203",
+    # We want docstrings to start immediately after the opening triple quote
+    "D213",
+]
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.per-file-ignores]
+"docs/*" = ["I"]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
 
 [tool.jupytext]
 formats = "ipynb,md"