[Auto-generated] Update dependencies (#770)

### Update dependencies

Automatically created PR from
[`ci/dependabot-updates`](https://github.com/emmo-repo/EMMOntoPy/tree/ci/dependabot-updates).

The PR is based on the ['CI - Update dependencies PR'
workflow](https://SINTEF.github.io/ci-cd/latest/workflows/ci_update_dependencies/)
in [SINTEF/ci-cd](https://github.com/SINTEF/ci-cd).

#### To do

- [ ] Check that the diff is sensible, and that tests and builds pass
with the new dependency versions.
- [ ] Make sure that the PR is **squash** merged, with a sensible commit
message.

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com>
Co-authored-by: francescalb <francesca.l.bleken@sintef.no>
Co-authored-by: Jesper Friis <jesper-friis@users.noreply.github.com>

.github/workflows/ci_workflow.yml

@@ -26,19 +26,22 @@ jobs:
       pylint_options: "--rcfile=pyproject.toml"
       pylint_targets: "*.py tools emmopy ontopy"
 
-      # safety
-      # Ignore ID 44715 for now.
-      # See this NumPy issue for more information: https://github.com/numpy/numpy/issues/19038
-      # Also ignore IDs 44716 and 44717 as they are not deemed to be as severe as it is
-      # laid out in the CVE.
-      # Remove ignoring 48547 as soon as RDFLib/rdflib#1844 has been fixed and the fix
-      # has been released.
+
+      # safety-specific settings
       run_safety: true
+      # 48547: RDFLib vulnerability: https://pyup.io/vulnerabilities/PVE-2022-48547/48547/
+      # 44715-44717: NumPy vulnerabilities:
+      #  https://pyup.io/vulnerabilities/CVE-2021-41495/44715/
+      #  https://pyup.io/vulnerabilities/CVE-2021-41496/44716/
+      #  https://pyup.io/vulnerabilities/CVE-2021-34141/44717/
+      # 70612: Jinja2 vulnerability. Only used as subdependency for mkdocs++ in tripper.
+      #  https://data.safetycli.com/v/70612/97c/
       safety_options: |
+        --ignore=48547
         --ignore=44715
         --ignore=44716
         --ignore=44717
-        --ignore=48547
+        --ignore=70612
 
       # Build distribution
       run_build_package: true

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
     name: Blacken
 
 - repo: https://github.com/PyCQA/bandit
-  rev: '1.7.8'
+  rev: '1.7.9'
   hooks:
   - id: bandit
     args: [-r]

ontopy/excelparser.py

@@ -643,6 +643,7 @@ def _add_entities(
         if not altlabel == "nan":
             labels.update(altlabel.split(";"))
     # Find column name depending on entitytype
+    rowheader = "entity_type_not_set"
     if entitytype is owlready2.ThingClass:
         rowheader = "subClassOf"
     # If entitytype is a subclass of owlready2.PropertyClass

ontopy/ontology.py

@@ -1112,16 +1112,16 @@ def get_imported_ontologies(self, recursive=False):
         are also returned.
         """
 
-        def rec_imported(onto):
+        def rec_imported(onto, imported):
             for ontology in onto.imported_ontologies:
                 # pylint: disable=possibly-used-before-assignment
                 if ontology not in imported:
                     imported.add(ontology)
-                    rec_imported(ontology)
+                    rec_imported(ontology, imported)
 
         if recursive:
             imported = set()
-            rec_imported(self)
+            rec_imported(self, imported)
             return list(imported)
 
         return self.imported_ontologies

requirements.txt

@@ -2,7 +2,7 @@ blessings>=1.7,<2
 Cython>=0.29.21,<3.1
 defusedxml>=0.7.1,<1
 graphviz>=0.16,<0.21
-numpy>=1.19.5,<2
+numpy>=1.19.5,<3
 openpyxl>=3.0.9,<3.2
 Owlready2>=0.28,!=0.32,!=0.34,<0.44
 packaging>=21.0,<25

requirements_dev.txt

@@ -1,7 +1,7 @@
 pre-commit>=2.21.0,<3; python_version<"3.9"
 pre-commit~=3.7; python_version>="3.9"
 pylint~=2.17; python_version<"3.8"
-pylint~=3.1; python_version>="3.8"
+pylint~=3.2; python_version>="3.8"
 pytest~=7.4; python_version<"3.8"
 pytest~=8.2; python_version>="3.8"
 pytest-cov~=4.1; python_version<"3.8"

tools/excel2onto

@@ -71,6 +71,7 @@ def main(argv: list = None):
     except SystemExit as exc:
         sys.exit(exc.code)  # Exit without traceback on invalid arguments
 
+    input_ontology = None
     if args.update:
         try:
             if args.input_ontology:
@@ -83,7 +84,6 @@ def main(argv: list = None):
                     "Did not find the output ontology to be updated, "
                     "will fully generate a new one."
                 )
-                input_ontology = None
             else:
                 raise FileNotFoundError(
                     "The output ontology to be updated "