Merge branch 'master' into ci/update-dependencies

.github/workflows/cd_publish.yml

@@ -29,6 +29,7 @@ jobs:
       python_version_docs: "3.7"
       doc_extras: "[docs]"
       changelog_exclude_labels: dependencies
+      warnings_as_errors: false
 
     secrets:
       PyPI_token: ${{ secrets.PYPI_TOKEN }}

.github/workflows/ci_workflow.yml

@@ -67,7 +67,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repository
@@ -88,7 +88,7 @@ jobs:
         pip install -U -e .[dev]
 
     - name: Test
-      run: pytest -vvv --cov=ontopy --cov=emmopy --cov-report=xml --cov-report=term
+      run: pytest -vvv --cov=ontopy --cov=emmopy --cov-report=xml --cov-report=term --doctest-modules
 
     - name: Upload coverage to Codecov
       if: matrix.python-version == '3.7' && github.repository == 'emmo-repo/EMMOntoPy'

CHANGELOG.md

@@ -2,18 +2,63 @@
 
 ## [Unreleased](https://github.com/emmo-repo/EMMOntoPy/tree/HEAD)
 
-[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.1...HEAD)
+[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.2...HEAD)
+
+**Closed issues:**
+
+- Harmonize get\_descendants and get\_ancestors [\#406](https://github.com/emmo-repo/EMMOntoPy/issues/406)
+
+## [v0.5.2](https://github.com/emmo-repo/EMMOntoPy/tree/v0.5.2) (2023-05-12)
+
+[Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.1...v0.5.2)
 
 **Fixed bugs:**
 
-- Use custom token for GitHub changelog generator [\#545](https://github.com/emmo-repo/EMMOntoPy/issues/545)
+- Auto-merge dependabot PRs workflow invalid [\#566](https://github.com/emmo-repo/EMMOntoPy/issues/566)
+
+**Closed issues:**
+
+- Point to excelparser api from the tools-page [\#593](https://github.com/emmo-repo/EMMOntoPy/issues/593)
+- BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology [\#589](https://github.com/emmo-repo/EMMOntoPy/issues/589)
+- Owlready 0.41 support ? [\#588](https://github.com/emmo-repo/EMMOntoPy/issues/588)
+- Allow space in labels [\#583](https://github.com/emmo-repo/EMMOntoPy/issues/583)
+- is\_defined needs a better description  [\#563](https://github.com/emmo-repo/EMMOntoPy/issues/563)
+- utils line 112 in get\_iri\_name link = "{lowerlabel}" vs "{label}" [\#562](https://github.com/emmo-repo/EMMOntoPy/issues/562)
+- ontograph - update colour deafults [\#559](https://github.com/emmo-repo/EMMOntoPy/issues/559)
+- ontograph - argument leafs should be leaves [\#558](https://github.com/emmo-repo/EMMOntoPy/issues/558)
+- ontograph - write out more examples on how to use it [\#557](https://github.com/emmo-repo/EMMOntoPy/issues/557)
+- ontograph --parents not working [\#556](https://github.com/emmo-repo/EMMOntoPy/issues/556)
+- test\_graph2 is failing  [\#555](https://github.com/emmo-repo/EMMOntoPy/issues/555)
+- Add client side redirection in generated html documentation [\#552](https://github.com/emmo-repo/EMMOntoPy/issues/552)
+- Typos in PR template [\#523](https://github.com/emmo-repo/EMMOntoPy/issues/523)
+- ontograph, read format from name [\#497](https://github.com/emmo-repo/EMMOntoPy/issues/497)
+- Review default colours and style in ontopy/graph.py [\#345](https://github.com/emmo-repo/EMMOntoPy/issues/345)
+
+**Merged pull requests:**
+
+- Add links to the original FaCT++ repo, GitHub profiles, etc. [\#600](https://github.com/emmo-repo/EMMOntoPy/pull/600) ([blokhin](https://github.com/blokhin))
+- Added test update to PR template. [\#598](https://github.com/emmo-repo/EMMOntoPy/pull/598) ([jesper-friis](https://github.com/jesper-friis))
+- Changed `is_defined` into a ThingClass property and improved its documentation. [\#597](https://github.com/emmo-repo/EMMOntoPy/pull/597) ([jesper-friis](https://github.com/jesper-friis))
+- Added link to excelparser from tools for documentation of excel sheet. [\#594](https://github.com/emmo-repo/EMMOntoPy/pull/594) ([francescalb](https://github.com/francescalb))
+- Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 [\#584](https://github.com/emmo-repo/EMMOntoPy/pull/584) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Updated get\_by\_label\(\) so that it now accepts label, name and full iri [\#582](https://github.com/emmo-repo/EMMOntoPy/pull/582) ([jesper-friis](https://github.com/jesper-friis))
+- Added two additional exceptions to emmocheck [\#577](https://github.com/emmo-repo/EMMOntoPy/pull/577) ([jesper-friis](https://github.com/jesper-friis))
+- Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 [\#575](https://github.com/emmo-repo/EMMOntoPy/pull/575) ([dependabot[bot]](https://github.com/apps/dependabot))
+- get\_ancestors and get\_descendants have the same arguments. [\#572](https://github.com/emmo-repo/EMMOntoPy/pull/572) ([francescalb](https://github.com/francescalb))
+- Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 [\#571](https://github.com/emmo-repo/EMMOntoPy/pull/571) ([dependabot[bot]](https://github.com/apps/dependabot))
+- ontograph: colour updates, examples, bugfix [\#569](https://github.com/emmo-repo/EMMOntoPy/pull/569) ([francescalb](https://github.com/francescalb))
+- Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 [\#567](https://github.com/emmo-repo/EMMOntoPy/pull/567) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Changed argument leafs to leaves, with deprecation warning in ontograph [\#564](https://github.com/emmo-repo/EMMOntoPy/pull/564) ([francescalb](https://github.com/francescalb))
+- Corrected bug on getting default relation style. [\#561](https://github.com/emmo-repo/EMMOntoPy/pull/561) ([francescalb](https://github.com/francescalb))
+- Fix internal links in generated documentation generated with ontodoc [\#548](https://github.com/emmo-repo/EMMOntoPy/pull/548) ([jesper-friis](https://github.com/jesper-friis))
 
 ## [v0.5.1](https://github.com/emmo-repo/EMMOntoPy/tree/v0.5.1) (2023-02-07)
 
 [Full Changelog](https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.0...v0.5.1)
 
 **Fixed bugs:**
 
+- Use custom token for GitHub changelog generator [\#545](https://github.com/emmo-repo/EMMOntoPy/issues/545)
 - Avoid using Azure mirror for APT packages [\#541](https://github.com/emmo-repo/EMMOntoPy/issues/541)
 
 **Merged pull requests:**

README.md

@@ -7,6 +7,7 @@
 
 ![CI tests](https://github.com/emmo-repo/EMMOntoPy/workflows/CI%20Tests/badge.svg)
 [![PyPI version](https://badge.fury.io/py/EMMOntoPy.svg)](https://badge.fury.io/py/EMMOntoPy)
+[![DOI](https://zenodo.org/badge/190286064.svg)](https://zenodo.org/badge/latestdoi/190286064)
 
 > ***Note**: EMMOntoPy is a continuation of the EMMO-python project and the associated `emmo` Python package.
 > To see the legacy versions go to [PyPI](https://pypi.org/project/EMMO/).*

docs/index.md

@@ -7,6 +7,7 @@
 
 ![CI tests](https://github.com/emmo-repo/EMMOntoPy/workflows/CI%20Tests/badge.svg)
 [![PyPI version](https://badge.fury.io/py/EMMOntoPy.svg)](https://badge.fury.io/py/EMMOntoPy)
+[![DOI](https://zenodo.org/badge/190286064.svg)](https://zenodo.org/badge/latestdoi/190286064)
 
 > ***Note**: EMMOntoPy is a continuation of the EMMO-python project and the associated `emmo` Python package.
 > To see the legacy versions go to [PyPI](https://pypi.org/project/EMMO/).*

examples/ontology-from-excel/make_microstructure_onto.py

@@ -1,11 +1,15 @@
 """
 python example for creating ontology from excel
 """
+from pathlib import Path
+
 from ontopy.excelparser import create_ontology_from_excel
 from ontopy.utils import write_catalog
 
+
+thisdir = Path(__file__).resolve().parent
 ontology, catalog, errdict = create_ontology_from_excel(
-    "tool/microstructure.xlsx"
+    thisdir / "tool/microstructure.xlsx"
 )
 
 ontology.save("microstructure_ontology.ttl", format="turtle", overwrite=True)

ontopy/__init__.py

@@ -2,7 +2,7 @@
 # pylint: disable=wrong-import-position,wrong-import-order
 import sys
 
-__version__ = "0.5.1"
+__version__ = "0.5.2"
 
 # Ensure correct Python version
 if sys.version_info < (3, 7):