Merge pull request #1197 from INCATools/create-pull-request/patch

Update constraints.txt

Author: matentzn

constraints.txt

@@ -9,17 +9,18 @@ argon2-cffi-bindings==21.2.0
 arrow==1.3.0
 asttokens==3.0.0
 async-lru==2.0.4
-attrs==24.3.0
-babel==2.16.0
+attrs==25.1.0
+babel==2.17.0
 babelon==0.3.4
+backrefs==5.8
 bcp47==0.1.0
-beautifulsoup4==4.12.3
+beautifulsoup4==4.13.3
 bidict==0.23.1
 bleach==6.2.0
 bmt==1.4.4
-cachetools==5.5.0
+cachetools==5.5.2
 cattrs==24.1.2
-certifi==2024.12.14
+certifi==2025.1.31
 cffi==1.17.1
 CFGraph==0.2.1
 chardet==5.2.0
@@ -31,19 +32,19 @@ colorama==0.4.6
 comm==0.2.2
 commonmark==0.9.1
 contourpy==1.3.1
-cryptography==44.0.0
-curies==0.10.2
+cryptography==44.0.2
+curies==0.10.6
 cycler==0.12.1
-dacite==1.8.1
+dacite==1.9.2
 daff==1.3.46
 dataclasses==0.6
 dataclasses-json==0.6.7
 dataclasses-jsonschema==2.16.0
-debugpy==1.8.12
-decorator==5.1.1
+debugpy==1.8.13
+decorator==5.2.1
 deepl==1.21.0
 defusedxml==0.7.1
-Deprecated==1.2.15
+Deprecated==1.2.18
 deprecation==2.1.0
 diskcache==5.6.3
 distlib==0.3.9
@@ -54,52 +55,54 @@ dosdp==0.1.10.dev1
 EditorConfig==0.17.0
 et_xmlfile==2.0.0
 eutils==0.6.0
-executing==2.1.0
+executing==2.2.0
 fastjsonschema==2.21.1
-fastobo==0.12.3
-filelock==3.16.1
-fonttools==4.55.3
+fastobo==0.13.0
+filelock==3.17.0
+fonttools==4.56.0
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
-google-api-core==2.24.0
-google-api-python-client==2.159.0
-google-auth==2.37.0
+google-api-core==2.24.1
+google-api-python-client==2.163.0
+google-auth==2.38.0
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.1
-googleapis-common-protos==1.66.0
+googleapis-common-protos==1.69.1
 graphviz==0.20.3
 greenlet==3.1.1
-gspread==6.1.4
-gspread-formatting==1.2.0
+gspread==6.2.0
+gspread-formatting==1.2.1
 h11==0.14.0
 hbreader==0.9.1
 httpcore==1.0.7
 httplib2==0.22.0
 httpx==0.28.1
+id==1.5.0
 idna==3.10
 ijson==3.3.0
 imagesize==1.4.1
-importlib_metadata==8.5.0
+importlib_metadata==8.6.1
 importlib_resources==6.5.2
 inflection==0.5.1
 iniconfig==2.0.0
 ipykernel==6.29.5
-ipython==8.31.0
+ipython==9.0.2
+ipython_pygments_lexers==1.1.1
 ipywidgets==8.1.5
 isodate==0.7.2
 isoduration==20.11.0
 jaraco.classes==3.4.0
 jaraco.context==6.0.1
 jaraco.functools==4.1.0
 jedi==0.19.2
-jeepney==0.8.0
-Jinja2==3.1.5
-jinjanator==24.4.0
+jeepney==0.9.0
+Jinja2==3.1.6
+jinjanator==25.1.0
 jinjanator-plugins==24.2.0
 jiter==0.8.2
-jsbeautifier==1.15.1
+jsbeautifier==1.15.4
 jsobject==0.10.2
 json-flattener==0.1.9
 json5==0.10.0
@@ -109,21 +112,21 @@ jsonlines==4.0.0
 jsonpatch==1.33
 jsonpath-ng==1.7.0
 jsonpath-rw==1.4.0
-jsonpickle==4.0.1
+jsonpickle==4.0.2
 jsonpointer==3.0.0
 jsonschema==4.23.0
 jsonschema-specifications==2024.10.1
 jsonschema2md==1.3.0
 jsonstreams==0.6.0
 jupyter==1.1.1
 jupyter-console==6.6.3
-jupyter-events==0.11.0
+jupyter-events==0.12.0
 jupyter-lsp==2.2.5
 jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyter_server==2.15.0
 jupyter_server_terminals==0.5.3
-jupyterlab==4.3.4
+jupyterlab==4.3.5
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.27.3
 jupyterlab_widgets==3.0.13
@@ -134,51 +137,52 @@ kgx==2.4.2
 kiwisolver==1.4.8
 lark==1.2.2
 lightrdf==0.4.0
-linkml==1.8.6
+linkml==1.8.7
 linkml-dataops==0.1.0
 linkml-renderer==0.3.1
 linkml-runtime==1.8.3
-llm==0.19.1
-lxml==5.3.0
+llm==0.23
+lxml==5.3.1
 Markdown==3.7
 markdown-it-py==3.0.0
 MarkupSafe==3.0.2
-marshmallow==3.25.1
-matplotlib==3.10.0
+marshmallow==3.26.1
+matplotlib==3.10.1
 matplotlib-inline==0.1.7
-matplotlib-venn==1.1.1
+matplotlib-venn==1.1.2
 mdurl==0.1.2
 mergedeep==1.3.4
-mistune==3.1.0
+mistune==3.1.2
 mkdocs==1.6.1
 mkdocs-get-deps==0.2.0
-mkdocs-material==9.5.50
+mkdocs-material==9.6.7
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==1.2.1
 mkdocs-table-reader-plugin==3.1.0
 more-click==0.1.2
 more-itertools==10.6.0
-mypy==1.14.1
+mypy==1.15.0
 mypy-extensions==1.0.0
+narwhals==1.30.0
 nbclient==0.10.2
-nbconvert==7.16.5
+nbconvert==7.16.6
 nbformat==5.10.4
 ndex2==3.10.0
-neo4j==5.27.0
+neo4j==5.28.1
 nest-asyncio==1.6.0
 networkx==3.4.2
-nh3==0.2.20
+nh3==0.2.21
 notebook==7.3.2
 notebook_shim==0.2.4
 numpy==1.26.4
-oaklib==0.6.18
+oaklib==0.6.21
 oauthlib==3.2.2
 ols-client==0.1.4
 ontobio==2.9.12
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.59.8
+openai==1.65.5
 openpyxl==3.1.5
 ordered-set==4.1.0
 overrides==7.7.0
@@ -192,62 +196,60 @@ parso==0.8.4
 pathspec==0.12.1
 pexpect==4.9.0
 pillow==11.1.0
-pkginfo==1.12.0
 platformdirs==4.3.6
-plotly==5.24.1
+plotly==6.0.0
 pluggy==1.5.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.2.6
 prologterms==0.0.6
 prometheus_client==0.21.1
-prompt_toolkit==3.0.49
-pronto==2.5.8
-proto-plus==1.25.0
+prompt_toolkit==3.0.50
+pronto==2.7.0
+proto-plus==1.26.0
 protobuf==5.29.3
-psutil==6.1.1
+psutil==7.0.0
 ptyprocess==0.7.0
 pure_eval==0.2.3
 puremagic==1.28
 pyarrow==15.0.2
 pyasn1==0.6.1
 pyasn1_modules==0.4.1
 pycparser==2.22
-pydantic==2.10.5
+pydantic==2.10.6
 pydantic_core==2.27.2
 pydotplus==2.0.2
-PyGithub==2.5.0
+PyGithub==2.6.1
 Pygments==2.19.1
 PyJSG==0.11.10
 PyJWT==2.10.1
-pymdown-extensions==10.14
+pymdown-extensions==10.14.3
 PyNaCl==1.5.0
 pyparsing==2.4.7
-pyproject-api==1.8.0
+pyproject-api==1.9.0
 PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.10.0
 pyspellchecker==0.8.2
 pystow==0.7.0
-pytest==8.3.4
+pytest==8.3.5
 pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
-python-json-logger==3.2.1
+python-json-logger==3.3.0
 python-ulid==3.0.0
 PyTrie==0.4.0
-pytz==2024.2
+pytz==2025.1
 PyYAML==6.0.2
 pyyaml_env_tag==0.1
-pyzmq==26.2.0
+pyzmq==26.2.1
 ratelimit==2.2.1
 rdflib==7.1.3
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme_renderer==44.0
 recommonmark==0.7.1
-referencing==0.36.1
-regex==2024.11.6
+referencing==0.36.2
 requests==2.32.3
 requests-cache==1.2.1
 requests-oauthlib==2.0.0
@@ -257,15 +259,16 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.9.4
-rpds-py==0.22.3
+roman-numerals-py==3.1.0
+rpds-py==0.23.1
 rsa==4.9
 ruamel.yaml==0.18.10
 ruamel.yaml.clib==0.2.12
-scipy==1.15.1
+scipy==1.15.2
 seaborn==0.13.2
 SecretStorage==3.3.3
 semsimian==0.2.19
-semsql==0.3.3
+semsql==0.4.0
 Send2Trash==1.8.3
 setuptools==68.1.2
 ShExJSG==0.8.2
@@ -276,14 +279,14 @@ sortedcontainers==2.4.0
 soupsieve==2.6
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
-Sphinx==8.1.3
+Sphinx==8.2.3
 sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
-SQLAlchemy==2.0.37
+SQLAlchemy==2.0.38
 SQLAlchemy-Utils==0.38.3
 sqlite-fts4==1.0.3
 sqlite-migrate==0.1b0
@@ -299,22 +302,22 @@ terminado==0.18.1
 terminaltables==3.1.10
 tinycss2==1.4.0
 tornado==6.4.2
-tox==4.23.2
+tox==4.24.2
 tqdm==4.67.1
 traitlets==5.14.3
 tsvalid==0.0.5
-twine==6.0.1
+twine==6.1.0
 types-python-dateutil==2.9.0.20241206
 typing-inspect==0.9.0
 typing_extensions==4.12.2
-tzdata==2024.2
+tzdata==2025.1
 UpSetPlot==0.9.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
 urllib3==2.3.0
 validators==0.20.0
-virtualenv==20.29.1
+virtualenv==20.29.3
 watchdog==6.0.0
 wcwidth==0.2.13
 webcolors==24.11.1