Some ruff

notebooks/Bioregistry Taxonomy Curation via Wikidata.ipynb

@@ -9,13 +9,14 @@
    "source": [
     "# Get wikidata taxonomy properties\n",
     "\n",
-    "import bioregistry\n",
-    "import bioregistry.version\n",
-    "import requests\n",
     "import pandas as pd\n",
-    "from bioregistry.utils import norm, query_wikidata\n",
+    "import requests\n",
     "from bs4 import BeautifulSoup\n",
     "\n",
+    "import bioregistry\n",
+    "import bioregistry.version\n",
+    "from bioregistry.utils import query_wikidata\n",
+    "\n",
     "pd.set_option(\"display.max_rows\", None)"
    ]
   },

notebooks/Preparing the GO Annotation Database for Integration.ipynb

@@ -107,9 +107,10 @@
     }
    ],
    "source": [
-    "import bioregistry.pandas as brpd\n",
     "import pandas as pd\n",
     "\n",
+    "import bioregistry.pandas as brpd\n",
+    "\n",
     "# Focus on these columns when displaying the data\n",
     "columns = [0, 1, 4, 5, 7, 12]\n",
     "\n",

src/bioregistry/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Extract registry information."""
 
 from .collection_api import get_collection, get_context  # noqa:F401

src/bioregistry/__main__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Command line interface for the bioregistry."""
 
 from .cli import main  # type:ignore

src/bioregistry/analysis/__init__.py

@@ -1,3 +1 @@
-# -*- coding: utf-8 -*-
-
 """Analyses build on the Bioregistry."""

src/bioregistry/app/__init__.py

@@ -1,3 +1 @@
-# -*- coding: utf-8 -*-
-
 """Web application for the Bioregistry."""

src/bioregistry/app/api.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """FastAPI blueprint and routes."""
 
 from __future__ import annotations
 
-from typing import Any, List, Mapping, Optional, Set
+from collections.abc import Mapping
+from typing import Any, List, Optional, Set
 
 import yaml
 from curies import Reference

src/bioregistry/app/cli.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Web command for running the app."""
 
 from pathlib import Path

src/bioregistry/app/constants.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*
-
 """Large data chunks for the web app."""
 
 from bioregistry import version

src/bioregistry/app/impl.py

@@ -1,9 +1,10 @@
 """App builder interface."""
 
 import json
+from collections.abc import Mapping
 from pathlib import Path
 from textwrap import dedent
-from typing import TYPE_CHECKING, Any, Mapping, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional, Union
 
 from a2wsgi import WSGIMiddleware
 from curies.mapping_service import MappingServiceGraph, MappingServiceSPARQLProcessor

src/bioregistry/app/test.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Test the resolution API."""
 
 import sys

src/bioregistry/app/ui.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """User blueprint for the bioregistry web application."""
 
 from __future__ import annotations

src/bioregistry/app/utils.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """Utility functions for the Bioregistry :mod:`flask` app."""
 
 import json
+from collections.abc import Mapping, Sequence
 from functools import partial
-from typing import Any, Callable, Dict, List, Mapping, Optional, Sequence, Tuple
+from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import yaml
 from flask import (
@@ -87,22 +86,22 @@ def _autocomplete(manager_: Manager, q: str, url_prefix: Optional[str] = None) -
     Before completion is of prefix:
 
     >>> from bioregistry import manager
-    >>> _autocomplete(manager, 'cheb')
+    >>> _autocomplete(manager, "cheb")
     {'query': 'cheb', 'results': [('chebi', ''), ('chebi', 'chebiid'), ('goche', 'gochebi')], 'success': True, 'reason': 'searched prefix', 'url': None}
 
     If only prefix is complete:
 
-    >>> _autocomplete(manager, 'chebi')
+    >>> _autocomplete(manager, "chebi")
     {'query': 'chebi', 'results': [('chebi', ''), ('chebi', 'chebiid'), ('goche', 'gochebi')], 'success': True, 'reason': 'matched prefix', 'url': '/chebi'}
 
     Not matching the pattern:
 
-    >>> _autocomplete(manager, 'chebi:NOPE')
+    >>> _autocomplete(manager, "chebi:NOPE")
     {'query': 'chebi:NOPE', 'prefix': 'chebi', 'pattern': '^\\d+$', 'identifier': 'NOPE', 'success': False, 'reason': 'failed validation', 'url': None}
 
     Matching the pattern:
 
-    >>> _autocomplete(manager, 'chebi:1234')
+    >>> _autocomplete(manager, "chebi:1234")
     {'query': 'chebi:1234', 'prefix': 'chebi', 'pattern': '^\\d+$', 'identifier': '1234', 'success': True, 'reason': 'passed validation', 'url': '/chebi:1234'}
     """  # noqa: E501
     if url_prefix is None:

src/bioregistry/app/wsgi.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Web application for the Bioregistry."""
 
 from bioregistry.app.impl import get_app

src/bioregistry/benchmarks/__main__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Run the benchmarks CLI."""
 
 from .cli import main

src/bioregistry/benchmarks/cli.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Run all benchmarks."""
 
 import click

src/bioregistry/benchmarks/curie_parsing.py

@@ -3,8 +3,9 @@
 import itertools as itt
 import random
 import time
+from collections.abc import Iterable
 from statistics import mean
-from typing import Iterable, Tuple
+from typing import Tuple
 
 import click
 import matplotlib.pyplot as plt

src/bioregistry/benchmarks/curie_validation.py

@@ -2,7 +2,8 @@
 
 import random
 import time
-from typing import Iterable, Tuple
+from collections.abc import Iterable
+from typing import Tuple
 
 import click
 import matplotlib.pyplot as plt

src/bioregistry/benchmarks/uri_parsing.py

@@ -1,8 +1,9 @@
 """A benchmark for Bioregistry's URI parser."""
 
 import time
+from collections.abc import Iterable
 from statistics import mean
-from typing import Iterable, Tuple
+from typing import Tuple
 
 import click
 import matplotlib.pyplot as plt

src/bioregistry/bibliometrics.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """Utilities for publications."""
 
 import typing
 from collections import Counter
-from typing import TYPE_CHECKING, Iterable, List
+from collections.abc import Iterable
+from typing import TYPE_CHECKING, List
 
 from .resource_manager import manager
 from .schema.struct import Publication, deduplicate_publications

src/bioregistry/cli.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Command line interface for the bioregistry."""
 
 import sys
@@ -87,7 +85,7 @@ def align(
         secho(f"Aligning {aligner_cls.key}")
         try:
             aligner_cls.align(force_download=not no_force)
-        except (IOError, OLSBroken) as e:
+        except (OSError, OLSBroken) as e:
             secho(f"Failed to align {aligner_cls.key}: {e}", fg="red")
 
     if pre_digests != get_hexdigests():

src/bioregistry/collection_api.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """API for collections."""
 
 from typing import Optional

src/bioregistry/compare.py

@@ -94,7 +94,7 @@ def _get_has_present(func: Callable[[str], X | None]) -> Counter[X]:
 
 
 def _save(
-    fig: "matplotlib.figure.Figure",
+    fig: matplotlib.figure.Figure,
     name: str,
     *,
     svg: bool = True,
@@ -733,8 +733,7 @@ def plot_xrefs(registry_infos, watermark: bool) -> FigAxPair:
     ax.text(
         x1,
         h + 1,
-        f"No identifier resources are\navailable in more than\n"
-        f"{max_mapped} external registries",
+        f"No identifier resources are\navailable in more than\n{max_mapped} external registries",
         horizontalalignment="center",
         verticalalignment="bottom",
         fontdict=dict(fontsize=12),
@@ -766,7 +765,9 @@ def _get_licenses_mapped_counter(threshold: int = 30) -> List[str]:
         (
             "None"
             if license_ is None
-            else license_ if licenses_counter[license_] > threshold else "Other"
+            else license_
+            if licenses_counter[license_] > threshold
+            else "Other"
         )
         for license_ in licenses
     ]

src/bioregistry/constants.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Constants and utilities for registries."""
 
 import importlib.metadata
@@ -11,13 +9,13 @@
 import pystow
 
 __all__ = [
-    "HERE",
-    "DATA_DIRECTORY",
+    "BIOREGISTRY_MODULE",
     "BIOREGISTRY_PATH",
-    "METAREGISTRY_PATH",
     "COLLECTIONS_PATH",
+    "DATA_DIRECTORY",
+    "HERE",
+    "METAREGISTRY_PATH",
     "MISMATCH_PATH",
-    "BIOREGISTRY_MODULE",
     "RAW_DIRECTORY",
 ]
 

src/bioregistry/curation/__init__.py

@@ -1,3 +1 @@
-# -*- coding: utf-8 -*-
-
 """Curation tools."""

src/bioregistry/curation/add_co_providers.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Add providers for Crop Ontology entries."""
 
 import click

src/bioregistry/curation/add_descriptions_from_gs.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Add descriptions from a google curation sheet."""
 
 import click

src/bioregistry/curation/add_examples.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Script for adding examples automatically."""
 
 import random

src/bioregistry/curation/add_examples_from_javert.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Script for adding examples automatically."""
 
 import gzip

src/bioregistry/curation/add_examples_from_ols.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Add examples from OLS."""
 
 import random
-from typing import Mapping
+from collections.abc import Mapping
 
 import requests
 from tqdm import tqdm

src/bioregistry/curation/add_ontology_regexes.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Assert regular expression patterns for common identifier styles."""
 
 import re

src/bioregistry/curation/bulk_import.py

@@ -17,7 +17,8 @@
 
 import sys
 from collections import defaultdict
-from typing import Any, DefaultDict, Dict, Mapping, Optional
+from collections.abc import Mapping
+from typing import Any, DefaultDict, Dict, Optional
 
 import click
 import pandas as pd

src/bioregistry/curation/deprecation_diff.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Show discrepancies between Bioregistry and OBO Foundry deprecation status."""
 
 import click

src/bioregistry/curation/import_pc_semiautomatic.py

@@ -97,7 +97,7 @@ def main():
 def _works(url: str) -> bool:
     try:
         homepage_res = requests.head(url, timeout=3, allow_redirects=True)
-    except IOError:
+    except OSError:
         return False
     else:
         return homepage_res.status_code == 200

src/bioregistry/curation/literature.py

@@ -3,8 +3,8 @@
 import enum
 
 __all__ = [
-    "CurationRelevance",
     "COLUMNS",
+    "CurationRelevance",
 ]
 
 COLUMNS = [

src/bioregistry/curation/make_description_curation_sheet.py

@@ -1,6 +1,5 @@
-# -*- coding: utf-8 -*-
-
 """Make a curation sheet for the bioregistry."""
+
 import click
 import pandas as pd
 

src/bioregistry/data/__init__.py

@@ -1,3 +1 @@
-# -*- coding: utf-8 -*-
-
 """Data in the bioregistry."""

src/bioregistry/export/__init__.py

@@ -1,3 +1 @@
-# -*- coding: utf-8 -*-
-
 """Exports for the Bioregistry."""

src/bioregistry/export/__main__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Export the Bioregistry."""
 
 from .cli import export

src/bioregistry/export/cli.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Export the Bioregistry."""
 
 import click

src/bioregistry/export/prefix_maps.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Export extended prefix maps (EPMs), JSON-LD contexts, and SHACL RDF documents.
 
 .. seealso:: https://github.com/biopragmatics/bioregistry/pull/972

src/bioregistry/export/rdf_export.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Export the Bioregistry to RDF."""
 
 import logging