Update the dependencies

requirements-freeze.txt

@@ -1,24 +1,32 @@
+airium==0.2.6
 annotated-types==0.7.0
 antlr4-python3-runtime==4.9.3
+appdirs==1.4.4
 argcomplete==3.3.0
 arrow==1.3.0
 attrs==23.2.0
 bcp47==0.1.0
 CacheControl==0.14.0
+cattrs==24.1.0
 certifi==2024.6.2
 CFGraph==0.2.1
 chardet==5.2.0
 charset-normalizer==3.3.2
 check-jsonschema==0.28.4
+class_resolver==0.5.0
 click==8.1.7
 coloredlogs==15.0.1
 curies==0.7.9
 cwl-upgrader==1.2.11
 cwl-utils==0.33
 cwltool==3.1.20240508115724
+defusedxml==0.7.1
 Deprecated==1.2.14
+deprecation==2.1.0
 et-xmlfile==1.1.0
+eutils==0.6.0
 exceptiongroup==1.2.1
+fastobo==0.12.3
 filelock==3.14.0
 fqdn==1.5.1
 funowl==0.2.3
@@ -27,63 +35,88 @@ greenlet==3.0.3
 hbreader==0.9.1
 humanfriendly==10.0
 idna==3.7
+ijson==3.3.0
+importlib_resources==6.4.5
 iniconfig==2.0.0
 isodate==0.6.1
 isoduration==20.11.0
 Jinja2==3.1.4
 json-flattener==0.1.9
 jsonasobj==1.3.1
 jsonasobj2==1.0.4
+jsonlines==4.0.0
 jsonpatch==1.33
 jsonpath-ng==1.6.1
 jsonpointer==2.4
 jsonschema==4.22.0
 jsonschema-specifications==2023.12.1
+kgcl-rdflib==0.5.0
+kgcl_schema==0.6.9
+lark==1.2.2
 linkml==1.7.10
 linkml-dataops==0.1.0
+linkml-renderer==0.3.1
 linkml-runtime==1.7.6
 linkml_owl==0.4.2
 lxml==5.2.2
 MarkupSafe==2.1.5
 mistune==3.0.2
+more-click==0.1.2
 msgpack==1.0.8
 mypy-extensions==1.0.0
+ndex2==3.9.0
 networkx==3.3
 nodeenv==1.9.1
+numpy==2.1.1
+oaklib==0.6.16
+ols-client==0.1.4
+ontoportal-client==0.0.4
 openpyxl==3.1.3
 packaging==24.0
+pandas==2.2.2
+pansql==0.0.1
 parse==1.20.1
+platformdirs==4.3.2
 pluggy==1.5.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.2.4
+pronto==2.5.7
 prov==1.5.1
-psutil==5.9.8
-pydantic==2.7.3
+psutil==6.0.0
+pydantic==2.7.4
 pydantic_core==2.18.4
 pydot==2.0.0
 PyJSG==0.11.10
 pyparsing==3.1.2
 PyShEx==0.8.1
 PyShExC==0.9.1
+pysolr==3.9.0
+pystow==0.5.5
 pytest==8.2.2
 pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 PyTrie==0.4.0
+pytz==2024.1
 PyYAML==6.0.1
+ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 referencing==0.35.1
 regress==0.4.5
 requests==2.32.3
+requests-cache==1.2.1
+requests-toolbelt==1.0.0
 rfc3339-validator==0.1.4
 rfc3987==1.3.8
 rpds-py==0.18.1
 ruamel.yaml==0.18.6
 ruamel.yaml.clib==0.2.8
 schema-salad==8.5.20240503091721
+scipy==1.14.1
 semsql==0.3.3
+setuptools==74.1.2
 shellescape==3.8.1
 ShExJSG==0.8.2
 six==1.16.0
@@ -93,11 +126,18 @@ SPARQLWrapper==2.0.0
 spython==0.3.13
 SQLAlchemy==2.0.30
 SQLAlchemy-Utils==0.38.3
+sssom==0.4.11
+sssom-schema==0.15.2
+tenacity==9.0.0
 tomli==2.0.1
+tqdm==4.66.5
 types-python-dateutil==2.9.0.20240316
 typing_extensions==4.12.1
+tzdata==2024.1
 uri-template==1.3.0
+url-normalize==1.4.3
 urllib3==2.2.1
+validators==0.34.0
 watchdog==4.0.1
 webcolors==24.6.0
 wrapt==1.16.0