Merge branch 'master' into fix-mirroring-pipeline

constraints.txt

@@ -2,20 +2,20 @@ airium==0.2.6
 alabaster==0.7.13
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
-anyio==4.1.0
+anyio==4.2.0
 appdirs==1.4.4
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
 asttokens==2.4.1
 async-lru==2.0.4
-attrs==23.1.0
-Babel==2.13.1
+attrs==23.2.0
+Babel==2.14.0
 bcp47==0.0.4
 beautifulsoup4==4.12.2
 bidict==0.22.1
 bleach==6.1.0
-bmt==1.1.3
+bmt==1.1.4
 cachetools==5.3.2
 cattrs==23.2.3
 certifi==2023.11.17
@@ -43,7 +43,7 @@ defusedxml==0.7.1
 Deprecated==1.2.14
 deprecation==2.1.0
 diskcache==5.6.3
-distlib==0.3.7
+distlib==0.3.8
 docker==6.1.3
 docutils==0.18.1
 dosdp==0.1.10.dev1
@@ -52,34 +52,34 @@ et-xmlfile==1.1.0
 eutils==0.6.0
 exceptiongroup==1.2.0
 executing==2.0.1
-fastjsonschema==2.19.0
+fastjsonschema==2.19.1
 fastobo==0.12.3
 filelock==3.13.1
-fonttools==4.46.0
+fonttools==4.47.0
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
-google-api-core==2.14.0
-google-api-python-client==2.109.0
-google-auth==2.25.1
-google-auth-httplib2==0.1.1
-google-auth-oauthlib==1.1.0
-googleapis-common-protos==1.61.0
+google-api-core==2.15.0
+google-api-python-client==2.111.0
+google-auth==2.25.2
+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==5.12.2
+gspread==5.12.4
 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==7.0.0
+importlib-metadata==7.0.1
 inflection==0.5.1
 iniconfig==2.0.0
-ipykernel==6.27.1
-ipython==8.18.1
+ipykernel==6.28.0
+ipython==8.19.0
 ipywidgets==8.1.1
 isodate==0.6.1
 isoduration==20.11.0
@@ -101,18 +101,18 @@ jsonpath-rw==1.4.0
 jsonpickle==3.0.2
 jsonpointer==2.4
 jsonschema==4.20.0
-jsonschema-specifications==2023.11.2
+jsonschema-specifications==2023.12.1
 jsonschema2md==1.0.0
 jsonstreams==0.6.0
 jupyter==1.0.0
 jupyter-console==6.6.3
 jupyter-events==0.9.0
 jupyter-lsp==2.2.1
 jupyter_client==8.6.0
-jupyter_core==5.5.0
-jupyter_server==2.12.0
-jupyter_server_terminals==0.4.4
-jupyterlab==4.0.9
+jupyter_core==5.5.1
+jupyter_server==2.12.1
+jupyter_server_terminals==0.5.1
+jupyterlab==4.0.10
 jupyterlab-widgets==3.0.9
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.25.2
@@ -123,11 +123,11 @@ kgx==2.2.5
 kiwisolver==1.4.5
 lark==1.1.8
 lightrdf==0.4.0
-linkml==1.6.3
+linkml==1.6.7
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
-linkml-runtime==1.6.2
-lxml==4.9.3
+linkml-runtime==1.6.3
+lxml==5.0.0
 Markdown==3.5.1
 markdown-it-py==3.0.0
 MarkupSafe==2.1.3
@@ -139,26 +139,26 @@ mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.5.3
-mkdocs-material==9.4.14
+mkdocs-material==9.5.3
 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
-mypy==1.7.1
+mypy==1.8.0
 mypy-extensions==1.0.0
 nbclient==0.9.0
-nbconvert==7.12.0
+nbconvert==7.13.1
 nbformat==5.9.2
 ndex2==3.6.0
 neo4j==4.4.11
 nest-asyncio==1.5.8
 networkx==3.2.1
-nh3==0.2.14
+nh3==0.2.15
 notebook==7.0.6
 notebook_shim==0.2.3
 numpy==1.26.2
-oaklib==0.5.24
+oaklib==0.5.25
 oauthlib==3.2.2
 ols-client==0.1.4
 ontobio==2.8.20
@@ -170,12 +170,12 @@ ordered-set==4.1.0
 overrides==7.4.0
 packaging==23.2
 paginate==0.5.6
-pandas==2.1.3
+pandas==2.1.4
 pandocfilters==1.5.0
 pansql==0.0.1
 parse==1.20.0
 parso==0.8.3
-pathspec==0.11.2
+pathspec==0.12.1
 pexpect==4.9.0
 Pillow==10.1.0
 pkginfo==1.9.6
@@ -187,32 +187,32 @@ prefixcommons==0.1.12
 prefixmaps==0.1.5
 prologterms==0.0.6
 prometheus-client==0.19.0
-prompt-toolkit==3.0.41
+prompt-toolkit==3.0.43
 pronto==2.5.5
 protobuf==4.25.1
-psutil==5.9.6
+psutil==5.9.7
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py==1.11.0
 pyasn1==0.5.1
 pyasn1-modules==0.3.0
 pycparser==2.21
-pydantic==2.5.2
-pydantic_core==2.14.5
+pydantic==2.5.3
+pydantic_core==2.14.6
 pydotplus==2.0.2
 PyGithub==2.1.1
 Pygments==2.17.2
 PyJSG==0.11.10
 PyJWT==2.8.0
-pymdown-extensions==10.5
+pymdown-extensions==10.7
 PyNaCl==1.5.0
 pyparsing==2.4.7
 PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.9.0
-pyspellchecker==0.7.2
+pyspellchecker==0.7.3
 pystow==0.5.2
-pytest==7.4.3
+pytest==7.4.4
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 python-json-logger==2.0.7
@@ -229,8 +229,8 @@ rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme-renderer==42.0
 recommonmark==0.7.1
-referencing==0.31.1
-regex==2023.10.3
+referencing==0.32.0
+regex==2023.12.25
 requests==2.31.0
 requests-cache==1.1.1
 requests-oauthlib==1.3.1
@@ -240,12 +240,12 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.7.0
-rpds-py==0.13.2
+rpds-py==0.16.2
 rsa==4.9
 ruamel.yaml==0.18.5
 ruamel.yaml.clib==0.2.8
 scipy==1.11.4
-seaborn==0.13.0
+seaborn==0.13.1
 SecretStorage==3.3.3
 semsimian==0.2.11
 semsql==0.3.3
@@ -265,9 +265,9 @@ sphinxcontrib-htmlhelp==2.0.4
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.6
 sphinxcontrib-serializinghtml==1.1.9
-SQLAlchemy==2.0.23
+SQLAlchemy==2.0.24
 SQLAlchemy-Utils==0.38.3
-sssom==0.4.0
+sssom==0.4.2
 sssom-schema==0.15.0
 stack-data==0.6.3
 stringcase==1.2.0
@@ -286,9 +286,9 @@ tsvalid==0.0.3
 twine==4.0.2
 types-python-dateutil==2.8.19.14
 typing-inspect==0.9.0
-typing_extensions==4.8.0
-tzdata==2023.3
-UpSetPlot==0.8.0
+typing_extensions==4.9.0
+tzdata==2023.4
+UpSetPlot==0.9.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3

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/)