chore: update ruff pre-commit and rules (#522)

* chore: update ruff pre-commit and rules

* refactor: to address None type and remove typeignore

---------

Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
   autofix_commit_msg: "chore: pre-commit auto fixes [...]"
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.0
     hooks:
       - id: ruff
         args:

pyproject.toml

@@ -159,13 +159,14 @@ module = [
 ignore_missing_imports = true
 
 
-[tool.ruff]
+[tool.ruff.lint]
 select = [
   "B002",    # Python does not support the unary prefix increment
   "B007",    # Loop control variable {name} not used within loop body
   "B014",    # Exception handler with duplicate exception
   "B023",    # Function definition does not bind loop variable {name}
   "B026",    # Star-arg unpacking after a keyword argument is strongly discouraged
+  "B904",    # Checks for raise statements in exception handlers that lack a from clause
   "C",       # complexity
   "COM818",  # Trailing comma on bare tuple prohibited
   "D",       # docstrings
@@ -180,7 +181,6 @@ select = [
   "N804",    # First argument of a class method should be named cls
   "N805",    # First argument of a method should be named self
   "N815",    # Variable {name} in class scope should not be mixedCase
-  "PGH001",  # No builtin eval() allowed
   "PGH004",  # Use specific rule codes when using noqa
   "PLC0414", # Useless import alias. Import alias does not rename original package.
   "PLC",     # pylint
@@ -219,7 +219,6 @@ select = [
   "T20",     # flake8-print
   "TID251",  # Banned imports
   "TRY004",  # Prefer TypeError exception for invalid type
-  "TRY200",  # Use raise from to specify exception cause
   "TRY302",  # Remove exception handler; error is immediately re-raised
   "UP",      # pyupgrade
   "W",       # pycodestyle

tests/airflow/test_dag.py

@@ -1,4 +1,5 @@
 """Check for airflow import errors. Inspiration from https://garystafford.medium.com/devops-for-dataops-building-a-ci-cd-pipeline-for-apache-airflow-dags-975e4a622f83."""
+
 from __future__ import annotations
 
 import pytest

tests/gentropy/common/test_session.py

@@ -1,4 +1,5 @@
 """Tests GWAS Catalog study splitter."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/conftest.py

@@ -1,4 +1,5 @@
 """Unit test configuration."""
+
 from __future__ import annotations
 
 from pathlib import Path

tests/gentropy/dataset/test_colocalisation.py

@@ -1,4 +1,5 @@
 """Test colocalisation dataset."""
+
 from __future__ import annotations
 
 from gentropy.dataset.colocalisation import Colocalisation

tests/gentropy/dataset/test_dataset.py

@@ -1,4 +1,5 @@
 """Test Dataset class."""
+
 from __future__ import annotations
 
 import pyspark.sql.functions as f

tests/gentropy/dataset/test_gene_index.py

@@ -1,4 +1,5 @@
 """Tests on LD index."""
+
 from __future__ import annotations
 
 from gentropy.dataset.gene_index import GeneIndex

tests/gentropy/dataset/test_intervals.py

@@ -1,4 +1,5 @@
 """Tests on LD index."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/dataset/test_l2g.py

@@ -1,4 +1,5 @@
 """Tests on L2G datasets."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
@@ -167,8 +168,8 @@ def test_calculate_feature_missingness_rate(spark: SparkSession) -> None:
     expected_missingness = {"distanceTssMean": 0.0, "distanceTssMinimum": 1.0}
     observed_missingness = fm.calculate_feature_missingness_rate()
     assert isinstance(observed_missingness, dict)
-    assert len(observed_missingness) == len(
-        fm.features_list  # type: ignore
+    assert fm.features_list is not None and len(observed_missingness) == len(
+        fm.features_list
     ), "Missing features in the missingness rate dictionary."
     assert (
         observed_missingness == expected_missingness

tests/gentropy/dataset/test_ld_index.py

@@ -1,4 +1,5 @@
 """Tests on LD index."""
+
 from __future__ import annotations
 
 from gentropy.dataset.ld_index import LDIndex

tests/gentropy/dataset/test_study_index.py

@@ -1,4 +1,5 @@
 """Test study index dataset."""
+
 from __future__ import annotations
 
 from gentropy.dataset.study_index import StudyIndex

tests/gentropy/dataset/test_study_locus.py

@@ -1,4 +1,5 @@
 """Test study locus dataset."""
+
 from __future__ import annotations
 
 from typing import Any

tests/gentropy/dataset/test_study_locus_overlap.py

@@ -1,4 +1,5 @@
 """Test study locus overlap dataset."""
+
 from __future__ import annotations
 
 from gentropy.dataset.study_locus_overlap import StudyLocusOverlap

tests/gentropy/dataset/test_study_locus_overlaps.py

@@ -1,4 +1,5 @@
 """Test colocalisation dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

tests/gentropy/dataset/test_summary_statistics.py

@@ -1,4 +1,5 @@
 """Test study index dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/dataset/test_v2g.py

@@ -1,4 +1,5 @@
 """Tests V2G dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/dataset/test_variant_annotation.py

@@ -1,4 +1,5 @@
 """Tests variant annotation dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/dataset/test_variant_index.py

@@ -1,4 +1,5 @@
 """Tests on variant index generation."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/datasource/gwas_catalog/test_gwas_catalog_study_splitter.py

@@ -1,4 +1,5 @@
 """Tests GWAS Catalog study splitter."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

tests/gentropy/datasource/intervals/test_andersson.py

@@ -1,4 +1,5 @@
 """Test Andersson Intervals."""
+
 from __future__ import annotations
 
 import pytest

tests/gentropy/datasource/intervals/test_javierre.py

@@ -1,4 +1,5 @@
 """Test JavierreIntervals."""
+
 from __future__ import annotations
 
 import pytest

tests/gentropy/datasource/intervals/test_jung.py

@@ -1,4 +1,5 @@
 """Test Jung Intervals."""
+
 from __future__ import annotations
 
 import pytest

tests/gentropy/datasource/intervals/test_thurman.py

@@ -1,4 +1,5 @@
 """Test Thurman."""
+
 from __future__ import annotations
 
 import pytest

tests/gentropy/datasource/open_targets/test_l2g_gold_standard.py

@@ -1,4 +1,5 @@
 """Test Open Targets L2G gold standards data source."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/datasource/open_targets/test_target.py

@@ -1,4 +1,5 @@
 """Test Open Targets target data source."""
+
 from __future__ import annotations
 
 from gentropy.dataset.gene_index import GeneIndex

tests/gentropy/docs/test_applying_methods.py

@@ -1,4 +1,5 @@
 """Testing applying methods docs."""
+
 from typing import Any
 
 import pytest

tests/gentropy/docs/test_create_dataset.py

@@ -1,4 +1,5 @@
 """Testing creating dataset docs."""
+
 from typing import Any
 
 import pytest

tests/gentropy/docs/test_creating_spark_session.py

@@ -1,4 +1,5 @@
 """Testing creating spark session docs."""
+
 from gentropy.common.session import Session
 
 from docs.src_snippets.howto.python_api.a_creating_spark_session import (

tests/gentropy/docs/test_inspect_dataset.py

@@ -1,4 +1,5 @@
 """Testing inspecting dataset docs."""
+
 from gentropy.dataset.summary_statistics import SummaryStatistics
 from pyspark.sql.types import StructType
 

tests/gentropy/method/test_window_based_clumping.py

@@ -1,4 +1,5 @@
 """Test window-based clumping."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

tests/gentropy/step/test_clump_step.py

@@ -1,4 +1,5 @@
 """Test clump step."""
+
 from __future__ import annotations
 
 import tempfile

tests/gentropy/test_cli.py

@@ -1,4 +1,5 @@
 """Test the command-line interface (CLI)."""
+
 from unittest.mock import patch
 
 import pytest

tests/gentropy/test_schemas.py

@@ -1,4 +1,5 @@
 """Tests on spark schemas."""
+
 from __future__ import annotations
 
 import json

tests/gentropy/test_spark_helpers.py

@@ -1,4 +1,5 @@
 """Tests on helper spark functions."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any