Merge branch 'master' into dev

constraints.txt

@@ -1,5 +1,5 @@
 airium==0.2.6
-alabaster==0.7.13
+alabaster==0.7.16
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
 anyio==4.2.0
@@ -12,7 +12,7 @@ async-lru==2.0.4
 attrs==23.2.0
 Babel==2.14.0
 bcp47==0.0.4
-beautifulsoup4==4.12.2
+beautifulsoup4==4.12.3
 bidict==0.22.1
 bleach==6.1.0
 bmt==1.1.4
@@ -26,11 +26,11 @@ charset-normalizer==3.3.2
 class-resolver==0.4.2
 click==8.1.7
 colorama==0.4.6
-comm==0.2.0
+comm==0.2.1
 commonmark==0.9.1
 contourpy==1.2.0
 cryptography==41.0.7
-curies==0.7.4
+curies==0.7.6
 cycler==0.12.1
 dacite==1.8.1
 daff==1.3.46
@@ -55,14 +55,14 @@ executing==2.0.1
 fastjsonschema==2.19.1
 fastobo==0.12.3
 filelock==3.13.1
-fonttools==4.47.0
+fonttools==4.47.2
 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==2.111.0
-google-auth==2.25.2
+google-api-python-client==2.114.0
+google-auth==2.26.2
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.0
 googleapis-common-protos==1.62.0
@@ -78,16 +78,16 @@ imagesize==1.4.1
 importlib-metadata==7.0.1
 inflection==0.5.1
 iniconfig==2.0.0
-ipykernel==6.28.0
-ipython==8.19.0
+ipykernel==6.29.0
+ipython==8.20.0
 ipywidgets==8.1.1
 isodate==0.6.1
 isoduration==20.11.0
 j2cli==0.3.10
 jaraco.classes==3.3.0
 jedi==0.19.1
 jeepney==0.8.0
-Jinja2==3.1.2
+Jinja2==3.1.3
 jsbeautifier==1.14.11
 jsobject==0.10.2
 json-flattener==0.1.9
@@ -96,23 +96,23 @@ jsonasobj==1.3.1
 jsonasobj2==1.0.4
 jsonlines==3.1.0
 jsonpatch==1.33
-jsonpath-ng==1.6.0
+jsonpath-ng==1.6.1
 jsonpath-rw==1.4.0
 jsonpickle==3.0.2
 jsonpointer==2.4
-jsonschema==4.20.0
+jsonschema==4.21.1
 jsonschema-specifications==2023.12.1
-jsonschema2md==1.0.0
+jsonschema2md==1.1.0
 jsonstreams==0.6.0
 jupyter==1.0.0
 jupyter-console==6.6.3
 jupyter-events==0.9.0
-jupyter-lsp==2.2.1
+jupyter-lsp==2.2.2
 jupyter_client==8.6.0
-jupyter_core==5.5.1
-jupyter_server==2.12.1
+jupyter_core==5.7.1
+jupyter_server==2.12.5
 jupyter_server_terminals==0.5.1
-jupyterlab==4.0.10
+jupyterlab==4.0.11
 jupyterlab-widgets==3.0.9
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.25.2
@@ -121,63 +121,63 @@ kgcl-rdflib==0.5.0
 kgcl_schema==0.6.1
 kgx==2.2.5
 kiwisolver==1.4.5
-lark==1.1.8
+lark==1.1.9
 lightrdf==0.4.0
-linkml==1.6.7
+linkml==1.6.9
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
 linkml-runtime==1.6.3
-lxml==5.0.0
-Markdown==3.5.1
+lxml==5.1.0
+Markdown==3.5.2
 markdown-it-py==3.0.0
-MarkupSafe==2.1.3
-marshmallow==3.20.1
+MarkupSafe==2.1.4
+marshmallow==3.20.2
 matplotlib==3.8.2
 matplotlib-inline==0.1.6
 matplotlib-venn==0.11.9
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.5.3
-mkdocs-material==9.5.3
+mkdocs-material==9.5.4
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==0.6.0
 mkdocs-table-reader-plugin==2.0.3
 more-click==0.1.2
-more-itertools==10.1.0
+more-itertools==10.2.0
 mypy==1.8.0
 mypy-extensions==1.0.0
 nbclient==0.9.0
-nbconvert==7.13.1
+nbconvert==7.14.2
 nbformat==5.9.2
-ndex2==3.6.0
+ndex2==3.7.0
 neo4j==4.4.11
-nest-asyncio==1.5.8
+nest-asyncio==1.5.9
 networkx==3.2.1
 nh3==0.2.15
-notebook==7.0.6
+notebook==7.0.7
 notebook_shim==0.2.3
-numpy==1.26.2
+numpy==1.26.3
 oaklib==0.5.25
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.8.20
+ontobio==2.8.22
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
 openpyxl==3.1.2
 ordered-set==4.1.0
-overrides==7.4.0
+overrides==7.5.0
 packaging==23.2
 paginate==0.5.6
-pandas==2.1.4
-pandocfilters==1.5.0
+pandas==2.2.0
+pandocfilters==1.5.1
 pansql==0.0.1
 parse==1.20.0
 parso==0.8.3
 pathspec==0.12.1
 pexpect==4.9.0
-Pillow==10.1.0
+pillow==10.2.0
 pkginfo==1.9.6
 platformdirs==4.1.0
 plotly==5.18.0
@@ -189,8 +189,8 @@ prologterms==0.0.6
 prometheus-client==0.19.0
 prompt-toolkit==3.0.43
 pronto==2.5.5
-protobuf==4.25.1
-psutil==5.9.7
+protobuf==4.25.2
+psutil==5.9.8
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py==1.11.0
@@ -210,7 +210,7 @@ pyparsing==2.4.7
 PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.9.0
-pyspellchecker==0.7.3
+pyspellchecker==0.8.1
 pystow==0.5.2
 pytest==7.4.4
 pytest-logging==2015.11.4
@@ -229,7 +229,7 @@ rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme-renderer==42.0
 recommonmark==0.7.1
-referencing==0.32.0
+referencing==0.32.1
 regex==2023.12.25
 requests==2.31.0
 requests-cache==1.1.1
@@ -240,7 +240,7 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.7.0
-rpds-py==0.16.2
+rpds-py==0.17.1
 rsa==4.9
 ruamel.yaml==0.18.5
 ruamel.yaml.clib==0.2.8
@@ -259,15 +259,15 @@ soupsieve==2.5
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
 Sphinx==7.2.6
-sphinxcontrib-applehelp==1.0.7
-sphinxcontrib-devhelp==1.0.5
-sphinxcontrib-htmlhelp==2.0.4
+sphinxcontrib-applehelp==1.0.8
+sphinxcontrib-devhelp==1.0.6
+sphinxcontrib-htmlhelp==2.0.5
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.6
-sphinxcontrib-serializinghtml==1.1.9
-SQLAlchemy==2.0.24
+sphinxcontrib-qthelp==1.0.7
+sphinxcontrib-serializinghtml==1.1.10
+SQLAlchemy==2.0.25
 SQLAlchemy-Utils==0.38.3
-sssom==0.4.2
+sssom==0.4.3
 sssom-schema==0.15.0
 stack-data==0.6.3
 stringcase==1.2.0
@@ -281,10 +281,10 @@ tomli==2.0.1
 tornado==6.4
 tox==3.28.0
 tqdm==4.66.1
-traitlets==5.14.0
+traitlets==5.14.1
 tsvalid==0.0.3
 twine==4.0.2
-types-python-dateutil==2.8.19.14
+types-python-dateutil==2.8.19.20240106
 typing-inspect==0.9.0
 typing_extensions==4.9.0
 tzdata==2023.4
@@ -296,7 +296,7 @@ urllib3==2.1.0
 validators==0.20.0
 virtualenv==20.25.0
 watchdog==3.0.0
-wcwidth==0.2.12
+wcwidth==0.2.13
 webcolors==1.13
 webencodings==0.5.1
 websocket-client==1.7.0

docs/AddTermToImport.md

@@ -1,13 +1 @@
-**NOTE** This documentation is incomplete, for now you may be better consulting the [GO Editor Docs](http://wiki.geneontology.org/index.php/Ontology_Editing_Guide)
-
-### Adding Terms to the Import Files
-
-Terms are imported to GO from other ontologies, but not all terms from external ontologies are imported. Occasionally, you will find that a valid identifier exists in an external ontology, but the identifier is not available in Protege because that term is not yet imported. To import a term from an external ontology:
-
-1.	Navigate to the imports folder on GitHub, located at [https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports](https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports).
-2.	Look in the list of ontologies for the ontology that contains the term you wish to import.
-3.	Identify the ```ontology_terms.txt``` file for the target ontology. For example, for the addition of a new taxon, the file can be found at [https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/ncbitaxon_terms.txt](https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/ncbitaxon_terms.txt).
-4.	Click on the icon of a pencil in the upper right corner of the window to edit the file.
-5.	Add the new term on the next available line at the bottom of the file.
-6.	Click preview changes.
-7.	You can now either commit the file directly to master or create a branch and a pull request as described before.
+See [https://oboacademy.github.io/obook/howto/update-import/](https://oboacademy.github.io/obook/howto/update-import/)

docs/CreatingRepo.md

@@ -1 +1 @@
-Please refer to https://oboacademy.github.io/obook/howto/odk-create-repo/
+Please refer to [https://oboacademy.github.io/obook/tutorial/setting-up-project-odk/](https://oboacademy.github.io/obook/tutorial/setting-up-project-odk/)