Merge branch 'master' into add-figures-to-generated-documentation

.github/workflows/cd_publish.yml

@@ -5,9 +5,9 @@ on:
     types: [published]
 
 jobs:
-  publish:
+  build:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.7.4
+    uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.3
     if: github.repository == 'emmo-repo/EMMOntoPy' && startsWith(github.ref, 'refs/tags/v')
     with:
       git_username: EMMOntoPy Developers
@@ -21,8 +21,11 @@ jobs:
       # ontopy/__init__.py
       package_dirs: ontopy
       install_extras: "[dev]"
-      build_cmd: "python -m build"
-      publish_on_pypi: true
+      build_libs: build
+      build_cmd: "python -m build -o dists"
+      build_dir: dists
+      publish_on_pypi: false
+      upload_distribution: true
 
       # Update documentation
       update_docs: true
@@ -31,5 +34,24 @@ jobs:
       changelog_exclude_labels: dependencies
 
     secrets:
-      PyPI_token: ${{ secrets.PYPI_TOKEN }}
       PAT: ${{ secrets.RELEASE_PAT }}
+
+  publish:
+    name: Publish on PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+      url: https://pypi.org/project/EMMOntoPy
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distribution
+        uses: actions/download-artifact@v4
+        with:
+          name: dist  # The artifact will always be called 'dist'
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/ci_automerge_dependabot.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   update-dependabot-branch:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.7.4
+    uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.3
     if: github.repository_owner == 'emmo-repo' && startsWith(github.event.pull_request.head.ref, 'dependabot/') && github.actor == 'dependabot[bot]'
     secrets:
       PAT: ${{ secrets.RELEASE_PAT }}

.github/workflows/ci_cd_updated_master.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   updates-to-master:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.7.4
+    uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.3
     if: github.repository_owner == 'emmo-repo'
     with:
       git_username: EMMOntoPy Developers
@@ -29,3 +29,5 @@ jobs:
         (LICENSE.txt),(LICENSE.md)
         (tools),(../tools)
       changelog_exclude_labels: dependencies
+    secrets:
+      PAT: ${{ secrets.RELEASE_PAT }}

.github/workflows/ci_dependabot.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   create-collected-pr:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.7.4
+    uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.3
     if: github.repository_owner == 'emmo-repo'
     with:
       git_username: EMMOntoPy Developers

.github/workflows/ci_workflow.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   tests:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.7.4
+    uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.3
     with:
       # General
       install_extras: "[dev,docs]"

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-symlinks
   - id: check-xml
@@ -17,13 +17,13 @@ repos:
     args: [--markdown-linebreak-ext=md]
 
 - repo: https://github.com/ambv/black
-  rev: 24.4.2
+  rev: 24.10.0
   hooks:
   - id: black
     name: Blacken
 
 - repo: https://github.com/PyCQA/bandit
-  rev: '1.7.9'
+  rev: '1.7.10'
   hooks:
   - id: bandit
     args: [-r]
@@ -36,7 +36,7 @@ repos:
 #     exclude: ^tests/.*$
 
 - repo: https://github.com/SINTEF/ci-cd
-  rev: v2.7.4
+  rev: v2.8.3
   hooks:
   - id: docs-api-reference
     args:

ontopy/__init__.py

@@ -3,7 +3,7 @@
 # pylint: disable=wrong-import-position,wrong-import-order
 import sys
 
-__version__ = "0.7.1"
+__version__ = "0.7.2"
 
 # Ensure correct Python version
 if sys.version_info < (3, 7):

ontopy/excelparser.py

@@ -34,6 +34,7 @@ class ExcelError(EMMOntoPyException):
 
 def create_ontology_from_excel(  # pylint: disable=too-many-arguments, too-many-locals
     excelpath: str,
+    *,
     concept_sheet_name: str = "Concepts",
     metadata_sheet_name: str = "Metadata",
     imports_sheet_name: str = "ImportedOntologies",
@@ -290,7 +291,7 @@ def _relative_to_absolute_paths(path):
     )
 
 
-def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-branches,too-many-statements,too-many-arguments
+def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-branches,too-many-statements,too-many-arguments, too-many-positional-arguments
     data: pd.DataFrame,
     objectproperties: pd.DataFrame,
     annotationproperties: pd.DataFrame,
@@ -312,6 +313,15 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     if input_ontology:
         onto = input_ontology
         catalog = {}
+        # Since we will remove newly created python_name added
+        # by owlready2 in the triples, we keep track of those
+        # that come from the input ontology
+        pyname_triples_to_keep = list(
+            onto.get_unabbreviated_triples(
+                predicate="http://www.lesfleursdunormal.fr/static/_downloads/"
+                "owlready_ontology.owl#python_name"
+            )
+        )
     else:  # Create new ontology
         onto, catalog = get_metadata_from_dataframe(
             metadata, base_iri, imports=imports
@@ -455,6 +465,22 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     entities_with_errors = {
         key: set(value) for key, value in entities_with_errors.items()
     }
+
+    # Remove triples with predicate 'python_name' added by owlready2
+    onto._del_data_triple_spod(  # pylint: disable=protected-access
+        p=onto._abbreviate(  # pylint: disable=protected-access
+            "http://www.lesfleursdunormal.fr/static/_downloads/"
+            "owlready_ontology.owl#python_name"
+        )
+    )
+
+    # Add back the triples python name triples that were in the input_ontology.
+    if input_ontology:
+        for triple in pyname_triples_to_keep:
+            onto._add_data_triple_spod(  # pylint: disable=protected-access
+                s=triple[0], p=triple[1], o=triple[2]
+            )
+
     return onto, catalog, entities_with_errors
 
 
@@ -585,6 +611,7 @@ def _add_literal(  # pylint: disable=too-many-arguments
     data: Union[pd.DataFrame, pd.Series],
     destination: owlready2.prop.IndividualValueList,  #
     name: str,
+    *,
     metadata: bool = False,
     only_one: bool = False,
     sep: str = ";",
@@ -903,7 +930,7 @@ def _add_range_domain(
     return onto, properties_with_errors
 
 
-def _make_entity_list(  # pylint: disable=too-many-arguments
+def _make_entity_list(  # pylint: disable=too-many-arguments, too-many-positional-arguments
     onto: owlready2.Ontology,
     row: pd.Series,
     rowheader: str,

ontopy/graph.py

@@ -239,6 +239,7 @@ def __init__(  # pylint: disable=too-many-arguments,too-many-locals
         self,
         ontology,
         root=None,
+        *,
         leaves=None,
         entities=None,
         relations="isA",
@@ -296,7 +297,7 @@ def __init__(  # pylint: disable=too-many-arguments,too-many-locals
         elif root:
             self.add_branch(
                 root,
-                leaves,
+                leaves=leaves,
                 relations=relations,
                 edgelabels=edgelabels,
                 addnodes=addnodes,
@@ -326,6 +327,7 @@ def __init__(  # pylint: disable=too-many-arguments,too-many-locals
     def add_entities(  # pylint: disable=too-many-arguments
         self,
         entities=None,
+        *,
         relations="isA",
         edgelabels=None,
         addnodes=False,
@@ -353,6 +355,7 @@ def add_entities(  # pylint: disable=too-many-arguments
     def add_branch(  # pylint: disable=too-many-arguments,too-many-locals
         self,
         root,
+        *,
         leaves=None,
         include_leaves=True,
         strict_leaves=False,
@@ -427,6 +430,7 @@ def add_branch(  # pylint: disable=too-many-arguments,too-many-locals
     def add_parents(  # pylint: disable=too-many-arguments
         self,
         name,
+        *,
         levels=1,
         relations="isA",
         edgelabels=None,
@@ -522,6 +526,7 @@ def add_edge(self, subject, predicate, obj, edgelabel=None, **attrs):
     def add_source_edges(  # pylint: disable=too-many-arguments,too-many-branches
         self,
         source,
+        *,
         relations=None,
         edgelabels=None,
         addnodes=None,
@@ -607,6 +612,7 @@ def add_source_edges(  # pylint: disable=too-many-arguments,too-many-branches
 
     def add_edges(  # pylint: disable=too-many-arguments
         self,
+        *,
         sources=None,
         relations=None,
         edgelabels=None,
@@ -998,6 +1004,7 @@ def setmodules(onto):
 def plot_modules(  # pylint: disable=too-many-arguments
     src,
     filename=None,
+    *,
     fmt=None,
     show=False,
     strip_base=None,

ontopy/ontodoc.py

@@ -597,6 +597,7 @@ def __init__(  # pylint: disable=too-many-arguments
         template,
         ontodoc,
         basedir=".",
+        *,
         figdir="genfigs",
         figformat="png",
         figscale=1.0,
@@ -756,7 +757,7 @@ def process_branches(self):
                     branch, int(opts.header_level)  # pylint: disable=no-member
                 ).split("\n")
 
-    def _make_branchfig(  # pylint: disable=too-many-arguments,too-many-locals
+    def _make_branchfig(  # pylint: disable=too-many-arguments,too-many-locals, too-many-positional-arguments
         self,
         name: str,
         path: "Union[Path, str]",
@@ -1142,6 +1143,7 @@ def process(self):
     def write(  # pylint: disable=too-many-arguments
         self,
         outfile,
+        *,
         fmt=None,
         pandoc_option_files=(),
         pandoc_options=(),
@@ -1288,6 +1290,7 @@ def run_pandoc(  # pylint: disable=too-many-arguments
     genfile,
     outfile,
     fmt,
+    *,
     pandoc_option_files=(),
     pandoc_options=(),
     verbose=True,
@@ -1444,6 +1447,7 @@ def get_maxwidth(fmt):
 def get_docpp(  # pylint: disable=too-many-arguments
     ontodoc,
     infile,
+    *,
     figdir="genfigs",
     figformat="png",
     maxwidth=None,

ontopy/ontology.py

@@ -156,6 +156,7 @@ def get_unabbreviated_triples(
     ):
         # pylint: disable=invalid-name
         """Returns all triples unabbreviated.
+        Imported ontologies not included.
 
         If any of the `subject`, `predicate` or `obj` arguments are given,
         only matching triples will be returned.
@@ -311,6 +312,7 @@ def set_default_label_annotations(self):
     def get_by_label(
         self,
         label: str,
+        *,
         label_annotations: str = None,
         prefix: str = None,
         imported: bool = True,
@@ -586,6 +588,7 @@ def set_common_prefix(
 
     def load(  # pylint: disable=too-many-arguments,arguments-renamed
         self,
+        *,
         only_local=False,
         filename=None,
         format=None,  # pylint: disable=redefined-builtin
@@ -677,6 +680,7 @@ def load(  # pylint: disable=too-many-arguments,arguments-renamed
 
     def _load(  # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
         self,
+        *,
         only_local=False,
         filename=None,
         format=None,  # pylint: disable=redefined-builtin
@@ -864,6 +868,7 @@ def save(
         filename=None,
         format=None,
         dir=".",
+        *,
         mkdir=False,
         overwrite=False,
         recursive=False,
@@ -1128,6 +1133,7 @@ def rec_imported(onto, imported):
 
     def get_entities(  # pylint: disable=too-many-arguments
         self,
+        *,
         imported=True,
         classes=True,
         individuals=True,
@@ -1537,6 +1543,7 @@ def get_branch(  # pylint: disable=too-many-arguments
         root,
         leaves=(),
         include_leaves=True,
+        *,
         strict_leaves=False,
         exclude=None,
         sort=False,
@@ -2151,6 +2158,7 @@ def _get_unabbreviated_triples(
     onto, subject=None, predicate=None, obj=None, blank=None
 ):
     """Help function returning all matching triples unabbreviated.
+    Does not include imported ontologies.
 
     If `blank` is given, it will be used to represent blank nodes.
     """

ontopy/utils.py

@@ -342,6 +342,7 @@ class ReadCatalogError(IOError):
 
 def read_catalog(  # pylint: disable=too-many-locals,too-many-statements,too-many-arguments
     uri,
+    *,
     catalog_file="catalog-v001.xml",
     baseuri=None,
     recursive=False,
@@ -602,6 +603,7 @@ def _validate_installed_version(
 def convert_imported(  # pylint: disable=too-many-arguments,too-many-locals
     input_ontology: "Union[Path, str]",
     output_ontology: "Union[Path, str]",
+    *,
     input_format: "Optional[str]" = None,
     output_format: str = "xml",
     url_from_catalog: "Optional[bool]" = None,