Merge branch 'master' into flb/update_owlready2_0.45

.github/workflows/cd_publish.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   publish:
     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
@@ -31,5 +31,4 @@ jobs:
       changelog_exclude_labels: dependencies
 
     secrets:
-      PyPI_token: ${{ secrets.PYPI_TOKEN }}
       PAT: ${{ secrets.RELEASE_PAT }}

.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

.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:

CHANGELOG.md

@@ -1,12 +1,37 @@
 # Changelog
 
-## [v0.7.0.1](https://github.com/emmo-repo/EMMOntoPy/tree/v0.7.0.1) (2024-02-29)
+## [v7.0.2](https://github.com/emmo-repo/EMMOntoPy/tree/v7.0.2) (2024-10-24)
+
+[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.1...v7.0.2)
+
+**Closed issues:**
+
+- excelparser, allow for = in strings for other annotations. [\#751](https://github.com/emmo-repo/EMMOntoPy/issues/751)
+- Add options to ontoconvert for adding annotations expected by FOOPS [\#728](https://github.com/emmo-repo/EMMOntoPy/issues/728)
 
-[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.1...v0.7.0.1)
+**Merged pull requests:**
+
+- Updated to owlready2==0.44 [\#780](https://github.com/emmo-repo/EMMOntoPy/pull/780) ([francescalb](https://github.com/francescalb))
+- Added release\_pat secret to ci\_cd\_updated\_master workflow [\#777](https://github.com/emmo-repo/EMMOntoPy/pull/777) ([francescalb](https://github.com/francescalb))
+- Added test for descriptions [\#766](https://github.com/emmo-repo/EMMOntoPy/pull/766) ([jesper-friis](https://github.com/jesper-friis))
+- Fixed failing test\_save in master [\#756](https://github.com/emmo-repo/EMMOntoPy/pull/756) ([jesper-friis](https://github.com/jesper-friis))
+- Added possibility for = in extra annotations defined in excelparser [\#752](https://github.com/emmo-repo/EMMOntoPy/pull/752) ([francescalb](https://github.com/francescalb))
+- Load doamin-battery instead of battinfo which is just an extra wrapping [\#745](https://github.com/emmo-repo/EMMOntoPy/pull/745) ([francescalb](https://github.com/francescalb))
+- Rewriting ontodoc based on domain-battery [\#742](https://github.com/emmo-repo/EMMOntoPy/pull/742) ([jesper-friis](https://github.com/jesper-friis))
+- Make it possible to run HermiT on EMMO [\#740](https://github.com/emmo-repo/EMMOntoPy/pull/740) ([jesper-friis](https://github.com/jesper-friis))
+- Added minor fixes for ontoconvert [\#739](https://github.com/emmo-repo/EMMOntoPy/pull/739) ([jesper-friis](https://github.com/jesper-friis))
+- Added additional recognised prefixes [\#734](https://github.com/emmo-repo/EMMOntoPy/pull/734) ([jesper-friis](https://github.com/jesper-friis))
+- Copy EMMO annotations [\#733](https://github.com/emmo-repo/EMMOntoPy/pull/733) ([jesper-friis](https://github.com/jesper-friis))
+- Add --copy-annotation option to ontoconvert [\#732](https://github.com/emmo-repo/EMMOntoPy/pull/732) ([jesper-friis](https://github.com/jesper-friis))
+- Updated list of IRIs to ignore when checking prefLabel [\#731](https://github.com/emmo-repo/EMMOntoPy/pull/731) ([jesper-friis](https://github.com/jesper-friis))
 
 ## [v0.7.1](https://github.com/emmo-repo/EMMOntoPy/tree/v0.7.1) (2024-02-29)
 
-[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.0...v0.7.1)
+[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.0.1...v0.7.1)
+
+## [v0.7.0.1](https://github.com/emmo-repo/EMMOntoPy/tree/v0.7.0.1) (2024-02-29)
+
+[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.0...v0.7.0.1)
 
 **Closed issues:**
 

ontopy/__init__.py

@@ -3,7 +3,7 @@
 # pylint: disable=wrong-import-position,wrong-import-order
 import sys
 
-__version__ = "0.7.1"
+__version__ = "7.0.2"
 
 # 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,
@@ -584,6 +585,7 @@ 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 = ";",
@@ -902,7 +904,7 @@ 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

@@ -311,6 +311,7 @@ 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 +587,7 @@ 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 +679,7 @@ 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 +867,7 @@ def save(
         filename=None,
         format=None,
         dir=".",
+        *,
         mkdir=False,
         overwrite=False,
         recursive=False,
@@ -1162,6 +1166,7 @@ def rec_imported(onto, imported):
 
     def get_entities(  # pylint: disable=too-many-arguments
         self,
+        *,
         imported=True,
         classes=True,
         individuals=True,
@@ -1571,6 +1576,7 @@ def get_branch(  # pylint: disable=too-many-arguments
         root,
         leaves=(),
         include_leaves=True,
+        *,
         strict_leaves=False,
         exclude=None,
         sort=False,

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,

requirements_dev.txt

@@ -1,7 +1,8 @@
 pre-commit>=2.21.0,<3; python_version<"3.9"
-pre-commit~=3.7; python_version>="3.9"
+pre-commit~=4.0; python_version>="3.9"
 pylint~=2.17; python_version<"3.8"
-pylint~=3.2; python_version>="3.8"
+pylint==3.2; python_version=="3.8"
+pylint~=3.3; python_version>="3.9"
 pytest~=7.4; python_version<"3.8"
 pytest~=8.3; python_version>="3.8"
 pytest-cov~=4.1; python_version<"3.8"

requirements_docs.txt

@@ -4,5 +4,6 @@ mkdocs~=1.6; python_version>="3.8"
 mkdocs-awesome-pages-plugin~=2.9
 mkdocs-material~=9.5; python_version>="3.8"
 mkdocs-material~=9.2; python_version<"3.8"
-mkdocstrings[python-legacy]~=0.25.1; python_version>="3.8"
+mkdocstrings[python-legacy]~=0.26.2; python_version>="3.9"
+mkdocstrings[python-legacy]==0.26.1; python_version=="3.8"
 mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8"