fix(docs/update_readme.py,pyproject.toml-,+7): fix linter warnings

populationgenomics · Dec 18, 2024 · 97acdb8 · 97acdb8
1 parent d3f6b6b
commit 97acdb8
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Showing 9 changed files with 177 additions and 201 deletions.
diff --git a/docs/update_readme.py b/docs/update_readme.py
@@ -11,7 +11,7 @@
 
 
 def load_descriptions(description_file):
-    with open(description_file, 'r') as f:
+    with open(description_file) as f:
         descriptions = yaml.safe_load(f)
         return descriptions
 
@@ -22,7 +22,7 @@ def parse_workflows(directory, description_file):
     for filename in os.listdir(directory):
         if filename.endswith('.yaml') or filename.endswith('.yml'):
             filepath = os.path.join(directory, filename)
-            with open(filepath, 'r') as file:
+            with open(filepath) as file:
                 try:
                     data = yaml.load(file, Loader=yaml.BaseLoader)
                     workflow_name = data.get('name', 'Unnamed Workflow')
@@ -57,9 +57,9 @@ def parse_triggers(on_field):
             else:
                 triggers.append(f'`{trigger}`')
         return ' and '.join(triggers)
-    elif isinstance(on_field, list):  # Handle `on: [event1, event2]`
+    if isinstance(on_field, list):  # Handle `on: [event1, event2]`
         return ', '.join([f'`{event}`' for event in on_field])
-    elif isinstance(on_field, str):  # Handle `on: event`
+    if isinstance(on_field, str):  # Handle `on: event`
         return f'`{on_field}`'
     return '`manual`'  # Default if `on` is missing
 
@@ -77,7 +77,7 @@ def generate_markdown(workflows):
 
 
 def update_readme(markdown, readme_file):
-    with open(readme_file, 'r') as file:
+    with open(readme_file) as file:
         content = file.read()
 
     start_marker = '### 🎢 Workflows'

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,6 @@ dependencies = [
     "grpcio-status>=1.48,<1.50",
     "metamist>=6.9.0",
     "networkx>=3.4.2",
-    "coloredlogs>=15.0.1",
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -144,146 +143,140 @@ fixable = [
 ]
 
 ignore = [
+    "A001",
+    "A002",
+    "ANN001",
+    "ANN002",
+    "ANN003",
     "ANN101",  # Missing type annotation for self in method
     "ANN102",  # Missing type annotation for `cls` in classmethod
     "ANN201",  # Missing return type annotation for public function
+    "ANN202",
     "ANN204",  # Missing type annotation for special method `__init__`
+    "ANN205",
     "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
+    "ARG001",  # Unused function argument
+    "ARG002",  # Unused method argument
+    "ARG005",
+    "B006",
+    "B007",
+    "B008",
+    "B023",
+    "B904",
+    "BLE001",
+    "C400",
+    "C401",
+    "C403",
+    "C405",
+    "C408",
+    "C416",
+    "C417",
+    "C419",
+    "C901",
+    "COM819",
+    "DTZ002",
+    "DTZ005",
+    "DTZ011",
+    "E401",
+    "E402",
     "E501",    # Line length too long
+    "E712",
+    "E713",
     "E731",    # Do not assign a lambda expression, use a def
     "E741",    # Ambiguous variable name
-    "G004",    # Logging statement uses f-string
-    "PLR0911", # Too many return statements
-    "PLR0912", # Too many branches
-    "PLR0913", # Too many arguments to function call
-    "PLR0915", # Too many statements
-    "PLW0603", # Using the global statement to update `<VAR>` is discouraged
-    "PT018",   # Assertion should be broken down into multiple parts
-    "Q000",    # Single quotes found but double quotes preferred
-    "S101",    # Use of assert detected
-    "SLF001",  # Private member accessed: `_preemptible`
-
-    "ARG001", # Unused function argument
-    "ARG002", # Unused method argument
-
-    "PLR2004", # Magic value used
-
-    "ANN001",
-    "ANN202",
-    "C408",
-    "TID252",
-    "RET504",
-    "ERA001",
-    "UP032",
-    "RUF100",
-    "ISC001",
-    "PIE804",
-    "F401",
-    "C901",
-    "W605",
-    "RET505",
-    "ANN003",
-    "RUF013",
-    "UP031",
-    "RUF010",
-    "B006",
-    "ANN002",
-    "B023",
+    "ERA001",  # Found commented-out code
     "EXE001",
+    "F401",
+    "F403",
+    "F821",
+    "F841",
     "G001",
-    "SIM108",
-    "RUF005",
     "G002",
-    "PD901",
-    "N999",
-    "SIM118",
-    "SIM102",
-    "PLW2901",
-    "S603",
-    "ARG005",
-    "PGH003",
-    "B904",
-    "N802",
+    "G003",
+    "G004",    # Logging statement uses f-string
+    "ISC001",
+    "ISC002",
     "ISC003",
-    "ANN205",
-    "S607",
-    "RUF015",
-    "E701",
-    "N818",
-    "PIE790",
+    "N802",
     "N803",
-    "A002",
-    "RUF012",
-    "W291",
-    "S113",
-    "S311",
+    "N805",
     "N806",
-    "PLR5501",
-    "F403",
-    "SIM115",
-    "B007",
-    "F841",
-    "C405",
-    "C419",
-    "SIM300",
+    "N818",
+    "N999",
+    "PD003",
+    "PD010",
     "PD011",
-    "UP015",
-    "S602",
-    "Q002",
-    "ISC002",
-    "COM819",
-    "C416",
-    "DTZ005",
-    "G003",
-    "S608",
+    "PD901",
+    "PGH003",
+    "PIE790",
+    "PIE804",
     "PIE808",
-    "B008",
-    "S108",
-    "E402",
-    "S605",
-    "F821",
-    "RET507",
-    "RET503",
-    "UP030",
-    "UP026",
-    "PLR1714",
-    "C403",
-    "PLR1711",
     "PIE810",
-    "DTZ011",
-    "S105",
-    "BLE001",
-    "C401",
-    "C400",
     "PLR0402",
-    "SIM201",
-    "RET506",
-    "C417",
-    "PD010",
+    "PLR0911", # Too many return statements
+    "PLR0912", # Too many branches
+    "PLR0913", # Too many arguments to function call
+    "PLR0915", # Too many statements
+    "PLR1711",
+    "PLR1714",
+    "PLR2004", # Magic value used
+    "PLR5501",
+    "PLW0603", # Using the global statement to update `<VAR>` is discouraged
     "PLW1510",
-    "A001",
-    "W292",
-    "PYI024",
+    "PLW2901",
+    "Q000",    # Single quotes found but double quotes preferred
+    "Q001",
+    "Q002",
     "Q003",
-    "S301",
     "RET501",
-    "PD003",
-    "SIM117",
+    "RET503",
+    "RET504",
+    "RET505",
+    "RET506",
+    "RET507",
     "RUF002",
-    "UP027",
-    "SIM105",
-    "E713",
-    "S324",
+    "RUF005",
+    "RUF010",
+    "RUF012",
+    "RUF013",
+    "RUF015",
+    "RUF100",
+    "S101",    # Use of assert detected
+    "S105",
+    "S108",
+    "S113",
+    "S301",
     "S310",
-    "Q001",
-    "UP020",
+    "S311",
+    "S324",
     "S506",
-    "N805",
-    "E712",
-    "E401",
+    "S602",
+    "S603",
+    "S605",
+    "S607",
+    "S608",
+    "SIM102",
+    "SIM105",
+    "SIM108",
+    "SIM115",
+    "SIM117",
+    "SIM118",
+    "SIM201",
     "SIM212",
-    "DTZ002",
+    "SIM300",
+    "SLF001",  # Private member accessed: `_preemptible`
+    "TID252",
     "UP007",
+    "UP015",
+    "UP020",
+    "UP026",
+    "UP027",
+    "UP030",
+    "UP031",
+    "UP032",
+    "W291",
+    "W292",
+    "W605",
 ]
 
 [tool.ruff.lint.isort]

diff --git a/src/cpg_flow/inputs.py b/src/cpg_flow/inputs.py
@@ -173,7 +173,6 @@ def _populate_alignment_inputs(
             f'No reads found for sequencing group {sequencing_group.id} of type {entry["type"]}',
         )
 
-    return None
 
 
 def _populate_analysis(dataset: Dataset) -> None:
-Original file line number
+Diff line change
@@ Expand Up / @@ -173,7 +173,6 @@ def _populate_alignment_inputs( @@
                 f'No reads found for sequencing group {sequencing_group.id} of type {entry["type"]}',
             )
-        return None
     def _populate_analysis(dataset: Dataset) -> None:
@@ Expand Down @@