Merge branch 'master' into dev

Dockerfile

@@ -11,7 +11,8 @@ ENV ODK_VERSION $ODK_VERSION
 
 # Software versions
 ENV JENA_VERSION=4.9.0
-ENV SSSOM_JAVA_VERSION=0.7.3
+ENV KGCL_JAVA_VERSION=0.3.2
+ENV SSSOM_JAVA_VERSION=0.7.5
 
 # Avoid repeated downloads of script dependencies by mounting the local coursier cache:
 # docker run -v $HOME/.coursier/cache/v1:/tools/.coursier-cache ...
@@ -108,8 +109,9 @@ RUN wget -nv https://github.com/balhoff/relation-graph/releases/download/v$RG/re
 && mv relation-graph-cli-$RG /tools/relation-graph \
 && chmod +x /tools/relation-graph
 
-# Install SSSOM-Java
+# Install ROBOT plugins
 RUN wget -nv -O /tools/sssom-cli https://github.com/gouttegd/sssom-java/releases/download/sssom-java-$SSSOM_JAVA_VERSION/sssom-cli && \
     chmod +x /tools/sssom-cli && \
     mkdir -p /tools/robot-plugins && \
-    wget -nv -O /tools/robot-plugins/sssom.jar https://github.com/gouttegd/sssom-java/releases/download/sssom-java-$SSSOM_JAVA_VERSION/sssom-robot-plugin-$SSSOM_JAVA_VERSION.jar
+    wget -nv -O /tools/robot-plugins/sssom.jar https://github.com/gouttegd/sssom-java/releases/download/sssom-java-$SSSOM_JAVA_VERSION/sssom-robot-plugin-$SSSOM_JAVA_VERSION.jar && \
+    wget -nv -O /tools/robot-plugins/kgcl.jar https://github.com/gouttegd/kgcl-java/releases/download/kgcl-java-$KGCL_JAVA_VERSION/kgcl-robot-plugin-$KGCL_JAVA_VERSION.jar

constraints.txt

@@ -18,7 +18,7 @@ bleach==6.1.0
 bmt==1.1.4
 cachetools==5.3.2
 cattrs==23.2.3
-certifi==2023.11.17
+certifi==2024.2.2
 cffi==1.16.0
 CFGraph==0.2.1
 chardet==5.2.0
@@ -29,15 +29,15 @@ colorama==0.4.6
 comm==0.2.1
 commonmark==0.9.1
 contourpy==1.2.0
-cryptography==41.0.7
-curies==0.7.6
+cryptography==42.0.2
+curies==0.7.7
 cycler==0.12.1
 dacite==1.8.1
 daff==1.3.46
 dataclasses==0.6
-dataclasses-json==0.6.3
+dataclasses-json==0.6.4
 dataclasses-jsonschema==2.16.0
-debugpy==1.8.0
+debugpy==1.8.1
 decorator==5.1.1
 defusedxml==0.7.1
 Deprecated==1.2.14
@@ -47,44 +47,45 @@ distlib==0.3.8
 docker==6.1.3
 docutils==0.18.1
 dosdp==0.1.10.dev1
-EditorConfig==0.12.3
+EditorConfig==0.12.4
 et-xmlfile==1.1.0
 eutils==0.6.0
 exceptiongroup==1.2.0
 executing==2.0.1
 fastjsonschema==2.19.1
 fastobo==0.12.3
 filelock==3.13.1
-fonttools==4.47.2
+fonttools==4.48.1
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
-google-api-core==2.15.0
-google-api-python-client==2.114.0
-google-auth==2.26.2
+google-api-core==2.17.0
+google-api-python-client==2.117.0
+google-auth==2.27.0
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.0
 googleapis-common-protos==1.62.0
 graphviz==0.20.1
 greenlet==2.0.1
-gspread==5.12.4
+gspread==6.0.1
 gspread-formatting==1.1.2
 hbreader==0.9.1
 httplib2==0.22.0
 idna==3.6
 ijson==3.2.3
 imagesize==1.4.1
 importlib-metadata==7.0.1
+importlib-resources==6.1.1
 inflection==0.5.1
 iniconfig==2.0.0
-ipykernel==6.29.0
-ipython==8.20.0
-ipywidgets==8.1.1
+ipykernel==6.29.2
+ipython==8.21.0
+ipywidgets==8.1.2
 isodate==0.6.1
 isoduration==20.11.0
 j2cli==0.3.10
-jaraco.classes==3.3.0
+jaraco.classes==3.3.1
 jedi==0.19.1
 jeepney==0.8.0
 Jinja2==3.1.3
@@ -111,53 +112,53 @@ jupyter-lsp==2.2.2
 jupyter_client==8.6.0
 jupyter_core==5.7.1
 jupyter_server==2.12.5
-jupyter_server_terminals==0.5.1
-jupyterlab==4.0.11
-jupyterlab-widgets==3.0.9
+jupyter_server_terminals==0.5.2
+jupyterlab==4.0.12
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.25.2
+jupyterlab_widgets==3.0.10
 keyring==24.3.0
 kgcl-rdflib==0.5.0
 kgcl_schema==0.6.1
 kgx==2.2.5
 kiwisolver==1.4.5
 lark==1.1.9
 lightrdf==0.4.0
-linkml==1.6.9
+linkml==1.7.2
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
-linkml-runtime==1.6.3
+linkml-runtime==1.7.0
 lxml==5.1.0
 Markdown==3.5.2
 markdown-it-py==3.0.0
-MarkupSafe==2.1.4
+MarkupSafe==2.1.5
 marshmallow==3.20.2
 matplotlib==3.8.2
 matplotlib-inline==0.1.6
-matplotlib-venn==0.11.9
+matplotlib-venn==0.11.10
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.5.3
-mkdocs-material==9.5.4
+mkdocs-material==9.5.9
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==0.6.0
-mkdocs-table-reader-plugin==2.0.3
+mkdocs-table-reader-plugin==2.1.0
 more-click==0.1.2
 more-itertools==10.2.0
 mypy==1.8.0
 mypy-extensions==1.0.0
 nbclient==0.9.0
-nbconvert==7.14.2
+nbconvert==7.16.0
 nbformat==5.9.2
-ndex2==3.7.0
+ndex2==3.8.0
 neo4j==4.4.11
-nest-asyncio==1.5.9
+nest-asyncio==1.6.0
 networkx==3.2.1
 nh3==0.2.15
-notebook==7.0.7
+notebook==7.0.8
 notebook_shim==0.2.3
-numpy==1.26.3
+numpy==1.26.4
 oaklib==0.5.25
 oauthlib==3.2.2
 ols-client==0.1.4
@@ -167,21 +168,21 @@ ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
 openpyxl==3.1.2
 ordered-set==4.1.0
-overrides==7.5.0
+overrides==7.7.0
 packaging==23.2
 paginate==0.5.6
 pandas==2.2.0
 pandocfilters==1.5.1
 pansql==0.0.1
-parse==1.20.0
+parse==1.20.1
 parso==0.8.3
 pathspec==0.12.1
 pexpect==4.9.0
 pillow==10.2.0
 pkginfo==1.9.6
-platformdirs==4.1.0
+platformdirs==4.2.0
 plotly==5.18.0
-pluggy==1.3.0
+pluggy==1.4.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.1.5
@@ -197,10 +198,10 @@ py==1.11.0
 pyasn1==0.5.1
 pyasn1-modules==0.3.0
 pycparser==2.21
-pydantic==2.5.3
-pydantic_core==2.14.6
+pydantic==2.6.1
+pydantic_core==2.16.2
 pydotplus==2.0.2
-PyGithub==2.1.1
+PyGithub==2.2.0
 Pygments==2.17.2
 PyJSG==0.11.10
 PyJWT==2.8.0
@@ -212,12 +213,12 @@ PyShExC==0.9.1
 pysolr==3.9.0
 pyspellchecker==0.8.1
 pystow==0.5.2
-pytest==7.4.4
+pytest==8.0.0
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 python-json-logger==2.0.7
 PyTrie==0.4.0
-pytz==2023.3.post1
+pytz==2024.1
 PyYAML==6.0.1
 pyyaml_env_tag==0.1
 pyzmq==25.1.2
@@ -229,7 +230,7 @@ rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme-renderer==42.0
 recommonmark==0.7.1
-referencing==0.32.1
+referencing==0.33.0
 regex==2023.12.25
 requests==2.31.0
 requests-cache==1.1.1
@@ -242,12 +243,12 @@ rfc3987==1.3.8
 rich==13.7.0
 rpds-py==0.17.1
 rsa==4.9
-ruamel.yaml==0.18.5
+ruamel.yaml==0.18.6
 ruamel.yaml.clib==0.2.8
-scipy==1.11.4
-seaborn==0.13.1
+scipy==1.12.0
+seaborn==0.13.2
 SecretStorage==3.3.3
-semsimian==0.2.11
+semsimian==0.2.12
 semsql==0.3.3
 Send2Trash==1.8.2
 ShExJSG==0.8.2
@@ -265,11 +266,12 @@ sphinxcontrib-htmlhelp==2.0.5
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.7
 sphinxcontrib-serializinghtml==1.1.10
-SQLAlchemy==2.0.25
+SQLAlchemy==2.0.26
 SQLAlchemy-Utils==0.38.3
-sssom==0.4.3
+sssom==0.4.4
 sssom-schema==0.15.0
 stack-data==0.6.3
+StrEnum==0.4.15
 stringcase==1.2.0
 tabulate==0.9.0
 tenacity==8.2.3
@@ -280,27 +282,27 @@ tinycss2==1.2.1
 tomli==2.0.1
 tornado==6.4
 tox==3.28.0
-tqdm==4.66.1
+tqdm==4.66.2
 traitlets==5.14.1
 tsvalid==0.0.3
-twine==4.0.2
+twine==5.0.0
 types-python-dateutil==2.8.19.20240106
 typing-inspect==0.9.0
 typing_extensions==4.9.0
-tzdata==2023.4
+tzdata==2024.1
 UpSetPlot==0.9.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
-urllib3==2.1.0
+urllib3==2.2.0
 validators==0.20.0
 virtualenv==20.25.0
-watchdog==3.0.0
+watchdog==4.0.0
 wcwidth==0.2.13
 webcolors==1.13
 webencodings==0.5.1
 websocket-client==1.7.0
-widgetsnbextension==4.0.9
+widgetsnbextension==4.0.10
 wrapt==1.16.0
 yamldown==0.1.8
 zipp==3.17.0

odk/odk.py

@@ -586,7 +586,7 @@ class OntologyProject(JsonSchemaMixin):
     ci : Optional[List[str]] = field(default_factory=lambda: ['github_actions'])
     """continuous integration defaults; currently available: travis, github_actions, gitlab-ci"""
 
-    workflows : Optional[List[str]] = field(default_factory=lambda: ['docs'])
+    workflows : Optional[List[str]] = field(default_factory=lambda: ['docs', 'qc'])
     """Workflows that are synced when updating the repo. Currently available: docs, diff, qc, release-diff."""
 
     import_pattern_ontology : bool = False

template/_dynamic_files.jinja2

@@ -737,7 +737,7 @@ branches:
 notifications:
   email:
     - [email protected]
-{% endif -%}{% if 'github_actions' in project.ci %}
+{% endif -%}{% if (('github_actions' in project.ci) and ('qc' in project.workflows)) %}
 ^^^ .github/workflows/qc.yml
 # Basic ODK workflow
 

template/src/ontology/run.sh.jinja2

@@ -74,7 +74,7 @@ if [ x$ODK_DEBUG = xyes ]; then
     # If you wish to change the format string, take care of using
     # non-breaking spaces (U+00A0) instead of normal spaces, to
     # prevent the shell from tokenizing the format string.
-    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
 rm -f tmp/debug.log

template/src/scripts/update_repo.sh.jinja2

@@ -30,7 +30,7 @@ cp -n target/$OID/.travis.yml $ROOTDIR/
 {%- endif -%}{% if 'github_actions' in project.ci %}
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp {% if 'qc' not in project.workflows %}-n {% endif %}target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+{% if 'qc' in project.workflows %}cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml{% endif %}
 {% if 'diff' in project.workflows %}cp target/$OID/.github/workflows/diff.yml $ROOTDIR/.github/workflows/diff.yml{% endif %}
 {% if 'release-diff' in project.workflows %}cp target/$OID/.github/workflows/release-diff.yml $ROOTDIR/.github/workflows/release-diff.yml{% endif %}
 {% if project.documentation is not none %}