diff --git a/_data/operations.yml b/_data/operations.yml index db4b61254..80274f476 100644 --- a/_data/operations.yml +++ b/_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 diff --git a/tests/test_integrity.py b/tests/test_integrity.py index 49148a278..73733c233 100644 --- a/tests/test_integrity.py +++ b/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)}" ) diff --git a/tox.ini b/tox.ini index 6fc814e46..7c7b577f1 100644 --- a/tox.ini +++ b/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 = diff --git a/util/extract-metadata.py b/util/extract-metadata.py index 33890389e..1ce752ae5 100755 --- a/util/extract-metadata.py +++ b/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 diff --git a/util/make-shacl-prefixes.py b/util/make-shacl-prefixes.py index 10045358a..22e2a8326 100755 --- a/util/make-shacl-prefixes.py +++ b/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()