Merge pull request #446 from MannLabs/stricter_linting

add stricter linting

.pre-commit-config.yaml

@@ -13,3 +13,12 @@ repos:
     - id: ruff-format
     - id: ruff
       args: [ '--fix' ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.1 # newer version -> stricter
+  hooks:
+    - id: ruff
+      # running ruff again with rules in ruff-lint-psm-readers.toml (specific files, all rules)
+      args:
+        - "--config"
+        - "ruff-lint-strict.toml"
+        - "--fix"

pyproject.toml

@@ -78,39 +78,10 @@ select =  [
     "SIM",
     # isort
     "I",
-    #"ALL"
 ]
 
 ignore = [
-    "D",
-    "ANN",
-    "SLF001", # Private member accessed TODO this needs to be fixed in alphabase
-
     "E501",  # Line too long  (ruff wraps code, but not docstrings)
     "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
-    "B905",  # This causes problems in numba code: `zip()` without an explicit `strict=` parameter
-    "COM812", #may cause conflicts when used with the formatter
-    "ISC001", #may cause conflicts when used with the formatter
-    "D211", # no-blank-line-before-class
-    "D213", # multi-line-summary-second-line
-    "S101", # Use of `assert` detected
-    "INP001", # implicit namespace package.
-    "ERA001", # Found commented-out code
-    "D203", # 1 blank line required before class docstring
-    "TD002", "TD003", "FIX002",  # things around TO-DO
-    "PT011", #pytest.raises(ValueError) is too broad
-    "G004", "EM102", # Logging statement uses f-string
-    "TRY003", # Avoid specifying long messages outside the exception class
-    "ANN101", # Missing type annotation for `self` in method
-    "ANN102", # Missing type annotation for `cls` in classmethod
-    "ANN002", # Missing type annotation for `*args`
-    "ANN003", # Missing type annotation for `**kwargs
-    "FA102", # Missing `from __future__ import annotations
-    "EM101", # Exception must not use a string literal, assign to variable first
-    "D104", # Missing docstring in public package
-    "ANN204", # Missing return type annotation for special method `__init__`
-    "D401", # First line of docstring should be in imperative mood
-    "B023", # Function definition does not bind loop variable
-    "PD901", # Avoid using the generic variable name `df` for DataFrames"
-    "TCH003", # Move standard library import into a type-checking block
+    "B905"  # This causes problems in numba code: `zip()` without an explicit `strict=` parameter
 ]

ruff-lint-strict.toml

@@ -0,0 +1,87 @@
+# specific ruff configuraton new code (with stricter rules)
+[lint]
+select = [
+    "ALL"
+]
+
+# TODO excluding explicity is not great but it is a workaround for now
+exclude = [
+    "alphadia/fdrx/models/two_step_classifier.py",
+    "alphadia/fdrx/models/logistic_regression.py",
+    "alphadia/__*__.py",
+    "alphadia/cli.py",
+    "alphadia/exceptions.py",
+    "alphadia/fdr.py",
+    "alphadia/fdrexperimental.py",
+    "alphadia/features.py",
+    "alphadia/fragcomp.py",
+    "alphadia/grouping.py",
+    "alphadia/libtransform.py",
+    "alphadia/libtransform.py",
+    "alphadia/outputaccumulator.py",
+    "alphadia/outputtransform.py",
+    "alphadia/plexscoring.py",
+    "alphadia/quadrupole.py",
+    "alphadia/search_plan.py",
+    "alphadia/libtransform.py",
+    "alphadia/search_step.py",
+    "alphadia/utils.py",
+    "alphadia/validate.py",
+    "alphadia/test_data_downloader.py",
+    "alphadia/calibration/*.py",
+    "alphadia/consensus/*.py",
+    "alphadia/constants/*.py",
+    "alphadia/data/*.py",
+    "alphadia/fdrx/stats.py",
+    "alphadia/fdrx/plotting.py",
+    "alphadia/fdrx/base.py",
+    "alphadia/numba/*.py",
+    "alphadia/peakgroup/*.py",
+    "alphadia/plotting/*.py",
+    "alphadia/transferlearning/*.py",
+    "alphadia/utilities/*.py",
+    "alphadia/workflow/*.py",
+    "tests/*.py",
+    "release/*.py",
+    "docs/**",
+    "nbs/**/*.ipynb",
+    "misc/*.py",
+]
+
+ignore = [
+    #
+    "PD002", #pandas-use-of-inplace-argument # TODO revisit
+
+    # same as pyproject.toml
+    "E501",  # Line too long  (ruff wraps code, but not docstrings)
+    "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
+    "B006", # Do not use mutable data structures for argument defaults # TODO: fix this!
+
+    # some more sensible ignores
+    "E501",  # Line too long  (ruff wraps code, but not docstrings)
+    "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
+    "COM812", #may cause conflicts when used with the formatter
+    "ISC001", #may cause conflicts when used with the formatter
+    "D211", # no-blank-line-before-class
+    "D213", # multi-line-summary-second-line
+    "S101", # Use of `assert` detected
+    "INP001", # implicit namespace package.
+    "ERA001", # Found commented-out code
+    "D203", # 1 blank line required before class docstring
+    "TD002", "TD003", "FIX002",  # things around TO-DO
+    "PT011", #pytest.raises(ValueError) is too broad
+    "G004", "EM102", # Logging statement uses f-string
+    "TRY003", # Avoid specifying long messages outside the exception class
+    "ANN101", # Missing type annotation for `self` in method
+    "ANN102", # Missing type annotation for `cls` in classmethod
+    "ANN002", # Missing type annotation for `*args`
+    "ANN003", # Missing type annotation for `**kwargs
+    "FA102", # Missing `from __future__ import annotations
+    "EM101", # Exception must not use a string literal, assign to variable first
+    "D104", # Missing docstring in public package
+    "ANN204", # Missing return type annotation for special method `__init__`
+    "D401", # First line of docstring should be in imperative mood
+    "B023", # Function definition does not bind loop variable
+    "PD901", # Avoid using the generic variable name `df` for DataFrames"
+    "TCH003" # Move standard library import into a type-checking block
+]