From af16331ab5acaf721c6e0272f4c910c158b4e518 Mon Sep 17 00:00:00 2001
From: David Ochoa <ochoa@ebi.ac.uk>
Date: Thu, 7 Mar 2024 09:57:55 +0000
Subject: [PATCH] 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                                      | 2 +-
 pyproject.toml                                               | 5 ++---
 tests/airflow/test_dag.py                                    | 1 +
 tests/gentropy/common/test_session.py                        | 1 +
 tests/gentropy/conftest.py                                   | 1 +
 tests/gentropy/dataset/test_colocalisation.py                | 1 +
 tests/gentropy/dataset/test_dataset.py                       | 1 +
 tests/gentropy/dataset/test_gene_index.py                    | 1 +
 tests/gentropy/dataset/test_intervals.py                     | 1 +
 tests/gentropy/dataset/test_l2g.py                           | 5 +++--
 tests/gentropy/dataset/test_ld_index.py                      | 1 +
 tests/gentropy/dataset/test_study_index.py                   | 1 +
 tests/gentropy/dataset/test_study_locus.py                   | 1 +
 tests/gentropy/dataset/test_study_locus_overlap.py           | 1 +
 tests/gentropy/dataset/test_study_locus_overlaps.py          | 1 +
 tests/gentropy/dataset/test_summary_statistics.py            | 1 +
 tests/gentropy/dataset/test_v2g.py                           | 1 +
 tests/gentropy/dataset/test_variant_annotation.py            | 1 +
 tests/gentropy/dataset/test_variant_index.py                 | 1 +
 .../gwas_catalog/test_gwas_catalog_study_splitter.py         | 1 +
 tests/gentropy/datasource/intervals/test_andersson.py        | 1 +
 tests/gentropy/datasource/intervals/test_javierre.py         | 1 +
 tests/gentropy/datasource/intervals/test_jung.py             | 1 +
 tests/gentropy/datasource/intervals/test_thurman.py          | 1 +
 .../datasource/open_targets/test_l2g_gold_standard.py        | 1 +
 tests/gentropy/datasource/open_targets/test_target.py        | 1 +
 tests/gentropy/docs/test_applying_methods.py                 | 1 +
 tests/gentropy/docs/test_create_dataset.py                   | 1 +
 tests/gentropy/docs/test_creating_spark_session.py           | 1 +
 tests/gentropy/docs/test_inspect_dataset.py                  | 1 +
 tests/gentropy/method/test_window_based_clumping.py          | 1 +
 tests/gentropy/step/test_clump_step.py                       | 1 +
 tests/gentropy/test_cli.py                                   | 1 +
 tests/gentropy/test_schemas.py                               | 1 +
 tests/gentropy/test_spark_helpers.py                         | 1 +
 35 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 45736c8af..104a97062 100644
--- a/.pre-commit-config.yaml
+++ b/.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:
diff --git a/pyproject.toml b/pyproject.toml
index 2b4150996..4ede53f24 100644
--- a/pyproject.toml
+++ b/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
diff --git a/tests/airflow/test_dag.py b/tests/airflow/test_dag.py
index 8676d70f4..49edc76ee 100644
--- a/tests/airflow/test_dag.py
+++ b/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
diff --git a/tests/gentropy/common/test_session.py b/tests/gentropy/common/test_session.py
index b7d0156d2..2ea7ccc1b 100644
--- a/tests/gentropy/common/test_session.py
+++ b/tests/gentropy/common/test_session.py
@@ -1,4 +1,5 @@
 """Tests GWAS Catalog study splitter."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/tests/gentropy/conftest.py b/tests/gentropy/conftest.py
index c7af5a589..13409ac16 100644
--- a/tests/gentropy/conftest.py
+++ b/tests/gentropy/conftest.py
@@ -1,4 +1,5 @@
 """Unit test configuration."""
+
 from __future__ import annotations
 
 from pathlib import Path
diff --git a/tests/gentropy/dataset/test_colocalisation.py b/tests/gentropy/dataset/test_colocalisation.py
index 2937efbca..1651aa2d4 100644
--- a/tests/gentropy/dataset/test_colocalisation.py
+++ b/tests/gentropy/dataset/test_colocalisation.py
@@ -1,4 +1,5 @@
 """Test colocalisation dataset."""
+
 from __future__ import annotations
 
 from gentropy.dataset.colocalisation import Colocalisation
diff --git a/tests/gentropy/dataset/test_dataset.py b/tests/gentropy/dataset/test_dataset.py
index 340906322..88f44ed5b 100644
--- a/tests/gentropy/dataset/test_dataset.py
+++ b/tests/gentropy/dataset/test_dataset.py
@@ -1,4 +1,5 @@
 """Test Dataset class."""
+
 from __future__ import annotations
 
 import pyspark.sql.functions as f
diff --git a/tests/gentropy/dataset/test_gene_index.py b/tests/gentropy/dataset/test_gene_index.py
index 68c279cab..999f089b3 100644
--- a/tests/gentropy/dataset/test_gene_index.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_intervals.py b/tests/gentropy/dataset/test_intervals.py
index bfa12ad69..26d79acd1 100644
--- a/tests/gentropy/dataset/test_intervals.py
+++ b/tests/gentropy/dataset/test_intervals.py
@@ -1,4 +1,5 @@
 """Tests on LD index."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/tests/gentropy/dataset/test_l2g.py b/tests/gentropy/dataset/test_l2g.py
index 045b98d62..a6a14c346 100644
--- a/tests/gentropy/dataset/test_l2g.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_ld_index.py b/tests/gentropy/dataset/test_ld_index.py
index c3eff6a4d..dc2b49c09 100644
--- a/tests/gentropy/dataset/test_ld_index.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_study_index.py b/tests/gentropy/dataset/test_study_index.py
index 1d43b3b07..6e327c086 100644
--- a/tests/gentropy/dataset/test_study_index.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_study_locus.py b/tests/gentropy/dataset/test_study_locus.py
index 037ede068..c12597d54 100644
--- a/tests/gentropy/dataset/test_study_locus.py
+++ b/tests/gentropy/dataset/test_study_locus.py
@@ -1,4 +1,5 @@
 """Test study locus dataset."""
+
 from __future__ import annotations
 
 from typing import Any
diff --git a/tests/gentropy/dataset/test_study_locus_overlap.py b/tests/gentropy/dataset/test_study_locus_overlap.py
index ca49fc067..53d87226c 100644
--- a/tests/gentropy/dataset/test_study_locus_overlap.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_study_locus_overlaps.py b/tests/gentropy/dataset/test_study_locus_overlaps.py
index 6a812fb39..ee89eec84 100644
--- a/tests/gentropy/dataset/test_study_locus_overlaps.py
+++ b/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
diff --git a/tests/gentropy/dataset/test_summary_statistics.py b/tests/gentropy/dataset/test_summary_statistics.py
index b148994b6..9885181a8 100644
--- a/tests/gentropy/dataset/test_summary_statistics.py
+++ b/tests/gentropy/dataset/test_summary_statistics.py
@@ -1,4 +1,5 @@
 """Test study index dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/tests/gentropy/dataset/test_v2g.py b/tests/gentropy/dataset/test_v2g.py
index e53395fe4..24a917508 100644
--- a/tests/gentropy/dataset/test_v2g.py
+++ b/tests/gentropy/dataset/test_v2g.py
@@ -1,4 +1,5 @@
 """Tests V2G dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/tests/gentropy/dataset/test_variant_annotation.py b/tests/gentropy/dataset/test_variant_annotation.py
index 563d3c05c..05fa0cd60 100644
--- a/tests/gentropy/dataset/test_variant_annotation.py
+++ b/tests/gentropy/dataset/test_variant_annotation.py
@@ -1,4 +1,5 @@
 """Tests variant annotation dataset."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/tests/gentropy/dataset/test_variant_index.py b/tests/gentropy/dataset/test_variant_index.py
index c79a04092..a41db3031 100644
--- a/tests/gentropy/dataset/test_variant_index.py
+++ b/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
diff --git a/tests/gentropy/datasource/gwas_catalog/test_gwas_catalog_study_splitter.py b/tests/gentropy/datasource/gwas_catalog/test_gwas_catalog_study_splitter.py
index 2955cee91..58bcb53c8 100644
--- a/tests/gentropy/datasource/gwas_catalog/test_gwas_catalog_study_splitter.py
+++ b/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
diff --git a/tests/gentropy/datasource/intervals/test_andersson.py b/tests/gentropy/datasource/intervals/test_andersson.py
index b7283597b..09204967d 100644
--- a/tests/gentropy/datasource/intervals/test_andersson.py
+++ b/tests/gentropy/datasource/intervals/test_andersson.py
@@ -1,4 +1,5 @@
 """Test Andersson Intervals."""
+
 from __future__ import annotations
 
 import pytest
diff --git a/tests/gentropy/datasource/intervals/test_javierre.py b/tests/gentropy/datasource/intervals/test_javierre.py
index be8c528e2..a6a74e94e 100644
--- a/tests/gentropy/datasource/intervals/test_javierre.py
+++ b/tests/gentropy/datasource/intervals/test_javierre.py
@@ -1,4 +1,5 @@
 """Test JavierreIntervals."""
+
 from __future__ import annotations
 
 import pytest
diff --git a/tests/gentropy/datasource/intervals/test_jung.py b/tests/gentropy/datasource/intervals/test_jung.py
index 81506ae55..44062f680 100644
--- a/tests/gentropy/datasource/intervals/test_jung.py
+++ b/tests/gentropy/datasource/intervals/test_jung.py
@@ -1,4 +1,5 @@
 """Test Jung Intervals."""
+
 from __future__ import annotations
 
 import pytest
diff --git a/tests/gentropy/datasource/intervals/test_thurman.py b/tests/gentropy/datasource/intervals/test_thurman.py
index f89c9d3da..853adb380 100644
--- a/tests/gentropy/datasource/intervals/test_thurman.py
+++ b/tests/gentropy/datasource/intervals/test_thurman.py
@@ -1,4 +1,5 @@
 """Test Thurman."""
+
 from __future__ import annotations
 
 import pytest
diff --git a/tests/gentropy/datasource/open_targets/test_l2g_gold_standard.py b/tests/gentropy/datasource/open_targets/test_l2g_gold_standard.py
index 448e2a50c..0690781f5 100644
--- a/tests/gentropy/datasource/open_targets/test_l2g_gold_standard.py
+++ b/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
diff --git a/tests/gentropy/datasource/open_targets/test_target.py b/tests/gentropy/datasource/open_targets/test_target.py
index 33bb6ddc9..c0a92fcd7 100644
--- a/tests/gentropy/datasource/open_targets/test_target.py
+++ b/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
diff --git a/tests/gentropy/docs/test_applying_methods.py b/tests/gentropy/docs/test_applying_methods.py
index 255752f46..cbfdb9155 100644
--- a/tests/gentropy/docs/test_applying_methods.py
+++ b/tests/gentropy/docs/test_applying_methods.py
@@ -1,4 +1,5 @@
 """Testing applying methods docs."""
+
 from typing import Any
 
 import pytest
diff --git a/tests/gentropy/docs/test_create_dataset.py b/tests/gentropy/docs/test_create_dataset.py
index 663254753..2daae0c6a 100644
--- a/tests/gentropy/docs/test_create_dataset.py
+++ b/tests/gentropy/docs/test_create_dataset.py
@@ -1,4 +1,5 @@
 """Testing creating dataset docs."""
+
 from typing import Any
 
 import pytest
diff --git a/tests/gentropy/docs/test_creating_spark_session.py b/tests/gentropy/docs/test_creating_spark_session.py
index 6e1cf1ca5..197d22d56 100644
--- a/tests/gentropy/docs/test_creating_spark_session.py
+++ b/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 (
diff --git a/tests/gentropy/docs/test_inspect_dataset.py b/tests/gentropy/docs/test_inspect_dataset.py
index daefa9793..38e258158 100644
--- a/tests/gentropy/docs/test_inspect_dataset.py
+++ b/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
 
diff --git a/tests/gentropy/method/test_window_based_clumping.py b/tests/gentropy/method/test_window_based_clumping.py
index 59bf0277a..03546df9d 100644
--- a/tests/gentropy/method/test_window_based_clumping.py
+++ b/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
diff --git a/tests/gentropy/step/test_clump_step.py b/tests/gentropy/step/test_clump_step.py
index 701afc950..ab40de901 100644
--- a/tests/gentropy/step/test_clump_step.py
+++ b/tests/gentropy/step/test_clump_step.py
@@ -1,4 +1,5 @@
 """Test clump step."""
+
 from __future__ import annotations
 
 import tempfile
diff --git a/tests/gentropy/test_cli.py b/tests/gentropy/test_cli.py
index 92effa840..5675713ce 100644
--- a/tests/gentropy/test_cli.py
+++ b/tests/gentropy/test_cli.py
@@ -1,4 +1,5 @@
 """Test the command-line interface (CLI)."""
+
 from unittest.mock import patch
 
 import pytest
diff --git a/tests/gentropy/test_schemas.py b/tests/gentropy/test_schemas.py
index 768a3d4df..417eb4657 100644
--- a/tests/gentropy/test_schemas.py
+++ b/tests/gentropy/test_schemas.py
@@ -1,4 +1,5 @@
 """Tests on spark schemas."""
+
 from __future__ import annotations
 
 import json
diff --git a/tests/gentropy/test_spark_helpers.py b/tests/gentropy/test_spark_helpers.py
index 76abcbe56..a3790c62e 100644
--- a/tests/gentropy/test_spark_helpers.py
+++ b/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