Merge branch 'master' into undo-owltools-update

constraints.txt

@@ -17,7 +17,7 @@ bcp47==0.1.0
 beautifulsoup4==4.12.3
 bidict==0.23.1
 bleach==6.1.0
-bmt==1.4.2
+bmt==1.4.3
 cachetools==5.3.3
 cattrs==23.2.3
 certifi==2024.6.2
@@ -56,24 +56,24 @@ et-xmlfile==1.1.0
 eutils==0.6.0
 exceptiongroup==1.2.1
 executing==2.0.1
-fastjsonschema==2.19.1
+fastjsonschema==2.20.0
 fastobo==0.12.3
-filelock==3.14.0
+filelock==3.15.4
 fonttools==4.53.0
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
 google-api-core==2.19.0
-google-api-python-client==2.132.0
+google-api-python-client==2.134.0
 google-auth==2.30.0
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.0
 googleapis-common-protos==1.63.1
 graphviz==0.20.3
 greenlet==3.0.3
 gspread==6.1.2
-gspread-formatting==1.1.2
+gspread-formatting==1.2.0
 h11==0.14.0
 hbreader==0.9.1
 httpcore==1.0.5
@@ -82,7 +82,7 @@ httpx==0.27.0
 idna==3.7
 ijson==3.3.0
 imagesize==1.4.1
-importlib_metadata==7.1.0
+importlib_metadata==7.2.1
 importlib_resources==6.4.0
 inflection==0.5.1
 iniconfig==2.0.0
@@ -108,8 +108,8 @@ jsonlines==4.0.0
 jsonpatch==1.33
 jsonpath-ng==1.6.1
 jsonpath-rw==1.4.0
-jsonpickle==3.2.1
-jsonpointer==2.4
+jsonpickle==3.2.2
+jsonpointer==3.0.0
 jsonschema==4.22.0
 jsonschema-specifications==2023.12.1
 jsonschema2md==1.1.0
@@ -136,7 +136,7 @@ lightrdf==0.4.0
 linkml==1.7.10
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
-linkml-runtime==1.7.6
+linkml-runtime==1.7.7
 llm==0.13.1
 lxml==5.2.2
 Markdown==3.6
@@ -151,42 +151,42 @@ mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.6.0
 mkdocs-get-deps==0.2.0
-mkdocs-material==9.5.26
+mkdocs-material==9.5.27
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==1.1.1
 mkdocs-table-reader-plugin==2.2.2
 more-click==0.1.2
-more-itertools==10.2.0
+more-itertools==10.3.0
 mypy==1.10.0
 mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==7.16.4
 nbformat==5.10.4
-ndex2==3.8.0
+ndex2==3.9.0
 neo4j==4.4.12
 nest-asyncio==1.6.0
 networkx==3.3
 nh3==0.2.17
 notebook==7.2.1
 notebook_shim==0.2.4
 numpy==1.26.4
-oaklib==0.6.9
+oaklib==0.6.10
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.9.0
+ontobio==2.9.1
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.33.0
-openpyxl==3.1.3
+openai==1.35.3
+openpyxl==3.1.4
 ordered-set==4.1.0
 overrides==7.7.0
 packaging==24.1
 paginate==0.5.6
 pandas==2.2.2
 pandocfilters==1.5.1
 pansql==0.0.1
-parse==1.20.1
+parse==1.20.2
 parso==0.8.4
 pathspec==0.12.1
 pexpect==4.9.0
@@ -202,16 +202,16 @@ prologterms==0.0.6
 prometheus_client==0.20.0
 prompt_toolkit==3.0.47
 pronto==2.5.7
-proto-plus==1.23.0
+proto-plus==1.24.0
 protobuf==4.25.3
-psutil==5.9.8
+psutil==6.0.0
 ptyprocess==0.7.0
 pure-eval==0.2.2
 pyarrow==15.0.2
 pyasn1==0.6.0
 pyasn1_modules==0.4.0
 pycparser==2.22
-pydantic==2.7.3
+pydantic==2.7.4
 pydantic_core==2.18.4
 pydotplus==2.0.2
 PyGithub==2.3.0
@@ -221,7 +221,7 @@ PyJWT==2.8.0
 pymdown-extensions==10.8.1
 PyNaCl==1.5.0
 pyparsing==2.4.7
-pyproject-api==1.6.1
+pyproject-api==1.7.1
 PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.9.0
@@ -232,7 +232,7 @@ pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
 python-json-logger==2.0.7
-python-ulid==2.6.0
+python-ulid==2.7.0
 PyTrie==0.4.0
 pytz==2024.1
 PyYAML==6.0.1
@@ -249,7 +249,7 @@ recommonmark==0.7.1
 referencing==0.35.1
 regex==2024.5.15
 requests==2.32.3
-requests-cache==1.2.0
+requests-cache==1.2.1
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 rfc3339-validator==0.1.4
@@ -282,7 +282,7 @@ sphinxcontrib-htmlhelp==2.0.5
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.7
 sphinxcontrib-serializinghtml==1.1.10
-SQLAlchemy==2.0.30
+SQLAlchemy==2.0.31
 SQLAlchemy-Utils==0.38.3
 sqlite-fts4==1.0.3
 sqlite-migrate==0.1b0
@@ -292,7 +292,7 @@ sssom-schema==0.15.2
 stack-data==0.6.3
 stringcase==1.2.0
 tabulate==0.9.0
-tenacity==8.3.0
+tenacity==8.4.1
 termcolor==2.4.0
 terminado==0.18.1
 terminaltables==3.1.10
@@ -312,9 +312,9 @@ UpSetPlot==0.9.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
-urllib3==2.2.1
+urllib3==2.2.2
 validators==0.20.0
-virtualenv==20.26.2
+virtualenv==20.26.3
 watchdog==4.0.1
 wcwidth==0.2.13
 webcolors==24.6.0