Run tox -e lint

_data/operations.yml

@@ -115,6 +115,16 @@ members:
   name: James Stevenson
   orcid: 0000-0002-2568-6163
   wikidata: Q125208044
+- affiliation:
+    name: Rancho Biosciences
+    ror: 0114vcr39
+  country: UK
+  github: janelomax
+  groups:
+  - outreach
+  name: Jane Lomax
+  orcid: 0000-0001-8865-4321
+  wikidata: Q20746117
 - affiliation:
     name: University of Michigan, Ann Arbor, MI
     ror: 00jmfr291
@@ -218,13 +228,3 @@ members:
   name: Shawn Tan
   orcid: 0000-0001-7258-9596
   wikidata: Q57023310
-- affiliation:
-    name: Rancho Biosciences
-    ror: 0114vcr39
-  country: UK
-  github: janelomax
-  groups:
-  - outreach
-  name: Jane Lomax
-  orcid: 0000-0001-8865-4321
-  wikidata: Q20746117

tests/test_integrity.py

@@ -217,16 +217,18 @@ def test_has_purl_config(self):
         """Tests that OBO PURL configuration is available."""
         existing_purl_configs = set()
         missing = set()
-        res = requests.get('https://api.github.com/repos/OBOFoundry/purl.obolibrary.org/git/trees/master?recursive=1')
+        res = requests.get(
+            "https://api.github.com/repos/OBOFoundry/purl.obolibrary.org/git/trees/master?recursive=1"
+        )
         self.assertEqual(
             200,
             res.status_code,
-            "Error while fetching Git tree for OBOFoundry/purl.obolibrary.org"
+            "Error while fetching Git tree for OBOFoundry/purl.obolibrary.org",
         )
         data = res.json()
-        for entry in data['tree']:
-            if entry['path'].startswith('config/'):
-                existing_purl_configs.add(entry['path'])
+        for entry in data["tree"]:
+            if entry["path"].startswith("config/"):
+                existing_purl_configs.add(entry["path"])
         for prefix, record in self.ontologies.items():
             if self.skip_inactive(record):
                 continue
@@ -235,9 +237,7 @@ def test_has_purl_config(self):
                 if filename not in existing_purl_configs:
                     missing.add(prefix)
         self.assertEqual(
-            set(),
-            missing,
-            msg=f"PURL configuration missing for {', '.join(missing)}"
+            set(), missing, msg=f"PURL configuration missing for {', '.join(missing)}"
         )
 
 

tox.ini

@@ -24,7 +24,7 @@ description = Run the new-style tests
 [testenv:flake8]
 skip_install = true
 deps =
-    flake8<5.0.0
+    flake8
     flake8-docstrings
     black==24.8.0
     flake8-black
@@ -37,7 +37,7 @@ description = Run the flake8 code quality checks
 [testenv:lint]
 usedevelop = true
 deps =
-    black
+    black==24.8.0
     isort
     pyyaml
 commands =

util/extract-metadata.py

@@ -143,7 +143,7 @@ def validate_structure(obj):
                 errs.append(f"%s: {p}" % (fn))
             elif p.level == "warning":
                 warn.append(f"%s: {p}" % (fn))
-        (obj, md) = load_md(fn)
+        obj, md = load_md(fn)
         errs += validate_structure(obj)
     if len(warn) > 0:
         print("WARNINGS:", file=sys.stderr)
@@ -255,7 +255,7 @@ def concat_principles_yaml(args):
         with open(args.include, "r") as f:
             cfg = yaml.load(f.read(), Loader=yaml.SafeLoader)
     for fn in args.files:
-        (obj, md) = load_md(fn)
+        obj, md = load_md(fn)
         objs.append(obj)
     objs.sort(key=lambda x: x["id"])
     cfg["principles"] = objs

util/make-shacl-prefixes.py

@@ -34,8 +34,7 @@ def main():
 
     """
     parser = ArgumentParser(
-        description="""
-  Takes ontologies.yml file and makes a triple file with shacl prefixes"""
+        description="Takes ontologies.yml file and makes a triple file with shacl prefixes"
     )
     parser.add_argument("input")
     args = parser.parse_args()