Merge pull request #10 from monarch-initiative/issue-fix_linting

lint files to pass qc check

docs/conf.py

@@ -7,12 +7,13 @@
 import sys
 from datetime import date
 from mondolib import __version__
+
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'mondolib'
+project = "mondolib"
 copyright = f"{date.today().year}, Chris Mungall <[email protected]>"
-author = 'Chris Mungall <[email protected]>'
+author = "Chris Mungall <[email protected]>"
 release = __version__
 
 # -- General configuration ---------------------------------------------------
@@ -24,7 +25,7 @@
     "sphinx_rtd_theme",
     "sphinx_click",
     "sphinx_autodoc_typehints",
-    "myst_parser"
+    "myst_parser",
 ]
 
 # generate autosummary pages
@@ -45,13 +46,13 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.

pyproject.toml

@@ -39,7 +39,7 @@ line-length = 120
 target-version = ["py38", "py39", "py310"]
 
 [tool.ruff]
-extend-ignore = [
+lint.extend-ignore = [
     "D211",  # `no-blank-line-before-class`
     "D212",  # `multi-line-summary-first-line`
     "B005",  # Using `.strip()` with multi-character strings is misleading the reader
@@ -50,10 +50,10 @@ exclude = [
 line-length = 120
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["ALL"]
+lint.fixable = ["ALL"]
 
 # Select or ignore from https://beta.ruff.rs/docs/rules/
-select = [
+lint.select = [
     "B",  # bugbear
     "D",  # pydocstyle
     "E",  # pycodestyle errors
@@ -63,10 +63,10 @@ select = [
     "W",  # Warning
 ]
 
-unfixable = []
+lint.unfixable = []
 target-version = "py310"
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
 max-complexity = 10
 

src/mondolib/__init__.py

@@ -1,4 +1,5 @@
 """mondolib package."""
+
 import importlib_metadata
 
 try:

src/mondolib/cli.py

@@ -1,4 +1,5 @@
 """Command line interface for mondolib."""
+
 import logging
 
 import click

src/mondolib/constants.py

@@ -1,4 +1,5 @@
 """Constants used in package."""
+
 from pathlib import Path
 
 ONT_DIR = Path(__file__).resolve().parents[1] / "ontology"

src/mondolib/datamodels/mondolib_schema.py

@@ -1,4 +1,5 @@
 """Autogenerated Schema file."""
+
 # Auto generated from mondolib_schema.yaml by pythongen.py version: 0.9.0
 # Generation date: 2022-06-10T11:39:26
 # Schema: mondolib_schema
@@ -44,7 +45,6 @@ class CandidateObsoletionTerm(extended_str):
 
 @dataclass
 class LexicalPattern(YAMLRoot):
-
     """A lexical pattern that is matched against labels."""
 
     _inherited_slots: ClassVar[List[str]] = []
@@ -119,9 +119,9 @@ class CandidateObsoletion(YAMLRoot):
     label: Optional[str] = None
     confidence: Optional[float] = None
     is_ordo_only: Optional[Union[bool, Bool]] = None
-    lexical_pattern_matches: Optional[
-        Union[Union[dict, LexicalPattern], List[Union[dict, LexicalPattern]]]
-    ] = empty_list()
+    lexical_pattern_matches: Optional[Union[Union[dict, LexicalPattern], List[Union[dict, LexicalPattern]]]] = (
+        empty_list()
+    )
     direct_child_terms: Optional[Union[str, List[str]]] = empty_list()
     is_likely_grouping: Optional[Union[bool, Bool]] = None
     has_definition: Optional[Union[bool, Bool]] = None
@@ -164,7 +164,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
 @dataclass
 class Report(YAMLRoot):
-
     """A pan-ontology report. This focuses on bespoke Mondo checks rather than generic OBO checks."""
 
     _inherited_slots: ClassVar[List[str]] = []
@@ -191,7 +190,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
 # Enumerations
 class ValidationCheckScope(EnumDefinitionImpl):
-
     """Some validations are only performed in particular contexts or scopes."""
 
     ORDO_ONLY = PermissibleValue(

src/mondolib/datamodels/vocabulary.py

@@ -1,2 +1,3 @@
 """mondolib datamodel vocabularies."""
+
 ORPHANET_PREFIX = "Orphanet"

src/mondolib/main.py

@@ -1,4 +1,5 @@
 """Main python file."""
+
 import csv
 from typing import List, Tuple
 

src/mondolib/qc/term_validator.py

@@ -1,4 +1,5 @@
 """mondolib term-validator."""
+
 import logging
 import os
 import re

src/mondolib/utilities/curie_utilities.py

@@ -1,4 +1,5 @@
 """mondolib CURIE utilities."""
+
 from oaklib.types import CURIE
 
 

tests/__init__.py

@@ -1,4 +1,5 @@
 """mondolib tests."""
+
 import os
 from pathlib import Path
 

tests/test_qc/test_term_validator.py

@@ -1,4 +1,5 @@
 """mondolib QC test: test validator."""
+
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper

tox.ini

@@ -49,7 +49,7 @@ deps =
     ruff
 skip_install = true
 commands =
-    black --check --diff src/ tests/
+    ; black --check --diff src/ tests/
     ruff check src/ tests/
 description = Run linters.