From 308b654b3e1b582190bfcef3fb60aba2f244d7de Mon Sep 17 00:00:00 2001 From: eecavanna <eecavanna@users.noreply.github.com> Date: Tue, 23 Jan 2024 15:41:25 -0800 Subject: [PATCH] Update `nmdc-schema` from `9.3.2` to `10.0.0` and sync deps --- requirements/dev.txt | 76 +++++++-------- requirements/main.in | 2 +- requirements/main.txt | 211 ++++++++++++++++++++---------------------- 3 files changed, 136 insertions(+), 153 deletions(-) diff --git a/requirements/dev.txt b/requirements/dev.txt index 390e5a21..fd305808 100644 --- a/requirements/dev.txt +++ b/requirements/dev.txt @@ -4,25 +4,12 @@ # # pip-compile --allow-unsafe --output-file=requirements/dev.txt --strip-extras requirements/dev.in # -aiohttp==3.9.1 +attrs==23.2.0 # via # -c requirements/main.txt - # black -aiosignal==1.3.1 - # via - # -c requirements/main.txt - # aiohttp -async-timeout==4.0.3 - # via - # -c requirements/main.txt - # aiohttp -attrs==23.1.0 - # via - # -c requirements/main.txt - # aiohttp # cattrs # requests-cache -black==23.12.0 +black==23.12.1 # via # -c requirements/main.txt # -r requirements/dev.in @@ -36,6 +23,10 @@ certifi==2023.11.17 # via # -c requirements/main.txt # requests +cffi==1.16.0 + # via + # -c requirements/main.txt + # cryptography charset-normalizer==3.3.2 # via # -c requirements/main.txt @@ -45,10 +36,14 @@ click==8.1.7 # -c requirements/main.txt # black # pip-tools -coverage==7.3.3 +coverage==7.4.0 # via # -r requirements/dev.in # pytest-cov +cryptography==42.0.0 + # via + # -c requirements/main.txt + # secretstorage docutils==0.20.1 # via # -c requirements/main.txt @@ -58,19 +53,13 @@ exceptiongroup==1.2.0 # -c requirements/main.txt # cattrs # pytest -flake8==6.1.0 +flake8==7.0.0 # via -r requirements/dev.in -frozenlist==1.4.1 - # via - # -c requirements/main.txt - # aiohttp - # aiosignal idna==3.6 # via # -c requirements/main.txt # requests - # yarl -importlib-metadata==7.0.0 +importlib-metadata==7.0.1 # via # keyring # twine @@ -82,6 +71,10 @@ invoke==2.2.0 # via -r requirements/dev.in jaraco-classes==3.3.0 # via keyring +jeepney==0.8.0 + # via + # keyring + # secretstorage keyring==24.3.0 # via twine markdown-it-py==3.0.0 @@ -94,13 +87,8 @@ mdurl==0.1.2 # via # -c requirements/main.txt # markdown-it-py -more-itertools==10.1.0 +more-itertools==10.2.0 # via jaraco-classes -multidict==6.0.4 - # via - # -c requirements/main.txt - # aiohttp - # yarl mypy-extensions==1.0.0 # via # -c requirements/main.txt @@ -132,7 +120,11 @@ pluggy==1.3.0 # pytest pycodestyle==2.11.1 # via flake8 -pyflakes==3.1.0 +pycparser==2.21 + # via + # -c requirements/main.txt + # cffi +pyflakes==3.2.0 # via # -c requirements/main.txt # flake8 @@ -143,13 +135,13 @@ pygments==2.17.2 # rich pyproject-hooks==1.0.0 # via build -pytest==7.4.3 +pytest==7.4.4 # via # -c requirements/main.txt # -r requirements/dev.in # pytest-asyncio # pytest-cov -pytest-asyncio==0.23.2 +pytest-asyncio==0.23.3 # via -r requirements/dev.in pytest-cov==4.1.0 # via -r requirements/dev.in @@ -168,14 +160,18 @@ requests-cache==1.1.1 # -r requirements/dev.in requests-mock==1.11.0 # via -r requirements/dev.in -requests-toolbelt==0.10.1 +requests-toolbelt==1.0.0 # via # -c requirements/main.txt # twine rfc3986==2.0.0 # via twine rich==13.7.0 - # via twine + # via + # -c requirements/main.txt + # twine +secretstorage==3.3.3 + # via keyring six==1.16.0 # via # -c requirements/main.txt @@ -201,7 +197,7 @@ url-normalize==1.4.3 # via # -c requirements/main.txt # requests-cache -urllib3==1.26.18 +urllib3==2.0.7 # via # -c requirements/main.txt # requests @@ -209,19 +205,15 @@ urllib3==1.26.18 # twine wheel==0.42.0 # via pip-tools -yarl==1.9.4 - # via - # -c requirements/main.txt - # aiohttp zipp==3.17.0 # via importlib-metadata # The following packages are considered to be unsafe in a requirements file: -pip==23.3.1 +pip==23.3.2 # via # -r requirements/dev.in # pip-tools -setuptools==69.0.2 +setuptools==69.0.3 # via # -c requirements/main.txt # -r requirements/dev.in diff --git a/requirements/main.in b/requirements/main.in index 4509db70..7b892bce 100644 --- a/requirements/main.in +++ b/requirements/main.in @@ -24,7 +24,7 @@ mkdocs-jupyter mkdocs-material mkdocs-mermaid2-plugin motor -nmdc-schema==9.3.2 +nmdc-schema==10.0.0 openpyxl pandas passlib[bcrypt] diff --git a/requirements/main.txt b/requirements/main.txt index 0bec54d1..36914c61 100644 --- a/requirements/main.txt +++ b/requirements/main.txt @@ -4,13 +4,9 @@ # # pip-compile --allow-unsafe --output-file=requirements/main.txt --strip-extras requirements/main.in # -aiohttp==3.9.1 - # via black -aiosignal==1.3.1 - # via aiohttp -alabaster==0.7.13 +alabaster==0.7.16 # via sphinx -alembic==1.13.0 +alembic==1.13.1 # via dagster aniso8601==9.0.1 # via graphene @@ -21,14 +17,12 @@ antlr4-python3-runtime==4.9.3 # linkml # pyjsg # pyshexc -anyio==3.7.1 +anyio==4.2.0 # via - # fastapi + # gql # jupyter-server # starlette # watchfiles -appnope==0.1.3 - # via ipykernel argon2-cffi==23.1.0 # via jupyter-server argon2-cffi-bindings==21.2.0 @@ -39,11 +33,8 @@ asttokens==2.4.1 # via stack-data async-lru==2.0.4 # via jupyterlab -async-timeout==4.0.3 - # via aiohttp -attrs==23.1.0 +attrs==23.2.0 # via - # aiohttp # cattrs # jsonschema # referencing @@ -61,20 +52,20 @@ base32-lib==1.0.2 # via -r requirements/main.in bcrypt==4.1.2 # via passlib -beanie==1.23.6 +beanie==1.24.0 # via -r requirements/main.in -beautifulsoup4==4.12.2 +beautifulsoup4==4.12.3 # via # -r requirements/main.in # mkdocs-mermaid2-plugin # nbconvert -black==23.12.0 +black==23.12.1 # via shed bleach==6.1.0 # via nbconvert -boto3==1.34.2 +boto3==1.34.26 # via -r requirements/main.in -botocore==1.34.2 +botocore==1.34.26 # via # boto3 # s3transfer @@ -102,7 +93,6 @@ click==8.1.7 # -r requirements/main.in # beanie # black - # click-log # dagster # dagster-webserver # json-flattener @@ -113,8 +103,6 @@ click==8.1.7 # prefixmaps # terminusdb-client # uvicorn -click-log==0.4.0 - # via nmdc-schema colorama==0.4.6 # via # mkdocs-material @@ -123,35 +111,35 @@ coloredlogs==14.0 # via dagster com2ann==0.3.0 # via shed -comm==0.2.0 +comm==0.2.1 # via # ipykernel # ipywidgets croniter==2.0.1 # via dagster -cryptography==41.0.7 +cryptography==42.0.0 # via python-jose -curies==0.7.4 +curies==0.7.6 # via # linkml-runtime # prefixmaps -dagit==1.5.13 +dagit==1.6.1 # via -r requirements/main.in -dagster==1.5.13 +dagster==1.6.1 # via # -r requirements/main.in # dagster-graphql # dagster-postgres # dagster-webserver -dagster-graphql==1.5.13 +dagster-graphql==1.6.1 # via # -r requirements/main.in # dagster-webserver -dagster-pipes==1.5.13 +dagster-pipes==1.6.1 # via dagster -dagster-postgres==0.21.13 +dagster-postgres==0.22.1 # via -r requirements/main.in -dagster-webserver==1.5.13 +dagster-webserver==1.6.1 # via dagit debugpy==1.8.0 # via ipykernel @@ -165,7 +153,7 @@ deprecated==1.2.14 # via linkml-runtime distlib==0.3.8 # via virtualenv -dnspython==2.4.2 +dnspython==2.5.0 # via # email-validator # pymongo @@ -191,9 +179,9 @@ exceptiongroup==1.2.0 # pytest executing==2.0.1 # via stack-data -fastapi==0.105.0 +fastapi==0.109.0 # via -r requirements/main.in -fastjsonschema==2.19.0 +fastjsonschema==2.19.1 # via # -r requirements/main.in # nbformat @@ -205,19 +193,15 @@ fnc==0.5.3 # via -r requirements/main.in fqdn==1.5.1 # via jsonschema -frozendict==2.3.10 +frozendict==2.4.0 # via -r requirements/main.in -frozenlist==1.4.1 - # via - # aiohttp - # aiosignal fsspec==2023.12.2 # via universal-pathlib ghp-import==2.1.0 # via mkdocs git-root==0.1 # via -r requirements/main.in -gql==3.4.1 +gql==3.5.0 # via # dagster-graphql # gql @@ -232,6 +216,8 @@ graphql-relay==3.2.0 # via graphene graphviz==0.20.1 # via linkml +greenlet==3.0.3 + # via sqlalchemy grpcio==1.60.0 # via # dagster @@ -260,14 +246,14 @@ imagesize==1.4.1 # via sphinx iniconfig==2.0.0 # via pytest -ipykernel==6.27.1 +ipykernel==6.29.0 # via # jupyter # jupyter-console # jupyterlab # mkdocs-jupyter # qtconsole -ipython==8.18.1 +ipython==8.20.0 # via # ipykernel # ipywidgets @@ -284,7 +270,7 @@ isort==5.13.2 # via shed jedi==0.19.1 # via ipython -jinja2==3.1.2 +jinja2==3.1.3 # via # dagster # jupyter-server @@ -320,13 +306,13 @@ jsonasobj2==1.0.4 # linkml-runtime jsonpatch==1.33 # via linkml-dataops -jsonpath-ng==1.6.0 +jsonpath-ng==1.6.1 # via linkml-dataops jsonpointer==2.4 # via # jsonpatch # jsonschema -jsonschema==4.20.0 +jsonschema==4.21.1 # via # jsonschema # jupyter-events @@ -334,7 +320,7 @@ jsonschema==4.20.0 # linkml # linkml-runtime # nbformat -jsonschema-specifications==2023.11.2 +jsonschema-specifications==2023.12.1 # via jsonschema jupyter==1.0.0 # via -r requirements/main.in @@ -347,7 +333,7 @@ jupyter-client==8.6.0 # qtconsole jupyter-console==6.6.3 # via jupyter -jupyter-core==5.5.0 +jupyter-core==5.7.1 # via # ipykernel # jupyter-client @@ -360,18 +346,18 @@ jupyter-core==5.5.0 # qtconsole jupyter-events==0.9.0 # via jupyter-server -jupyter-lsp==2.2.1 +jupyter-lsp==2.2.2 # via jupyterlab -jupyter-server==2.12.1 +jupyter-server==2.12.5 # via # jupyter-lsp # jupyterlab # jupyterlab-server # notebook # notebook-shim -jupyter-server-terminals==0.5.0 +jupyter-server-terminals==0.5.2 # via jupyter-server -jupyterlab==4.0.9 +jupyterlab==4.0.11 # via # -r requirements/main.in # notebook @@ -383,13 +369,13 @@ jupyterlab-server==2.25.2 # notebook jupyterlab-widgets==3.0.9 # via ipywidgets -jupytext==1.16.0 +jupytext==1.16.1 # via mkdocs-jupyter lazy-model==0.2.0 # via beanie libcst==1.1.0 # via shed -linkml==1.6.6 +linkml==1.6.9 # via # -r requirements/main.in # nmdc-schema @@ -401,9 +387,9 @@ linkml-runtime==1.6.3 # linkml # linkml-dataops # nmdc-schema -mako==1.3.0 +mako==1.3.1 # via alembic -markdown==3.5.1 +markdown==3.5.2 # via # mkdocs # mkdocs-material @@ -412,7 +398,8 @@ markdown-it-py==3.0.0 # via # jupytext # mdit-py-plugins -markupsafe==2.1.3 + # rich +markupsafe==2.1.4 # via # jinja2 # mako @@ -435,31 +422,36 @@ mkdocs==1.5.3 # mkdocs-jupyter # mkdocs-material # mkdocs-mermaid2-plugin + # mkdocs-redirects + # nmdc-schema mkdocs-jupyter==0.24.6 # via -r requirements/main.in -mkdocs-material==9.5.2 +mkdocs-material==9.5.4 # via # -r requirements/main.in # mkdocs-jupyter + # mkdocs-mermaid2-plugin mkdocs-material-extensions==1.3.1 # via mkdocs-material -mkdocs-mermaid2-plugin==1.1.1 - # via -r requirements/main.in +mkdocs-mermaid2-plugin==0.6.0 + # via + # -r requirements/main.in + # nmdc-schema +mkdocs-redirects==1.2.1 + # via nmdc-schema motor==3.3.2 # via # -r requirements/main.in # beanie multidict==6.0.4 - # via - # aiohttp - # yarl + # via yarl mypy-extensions==1.0.0 # via # black # typing-inspect nbclient==0.9.0 # via nbconvert -nbconvert==7.12.0 +nbconvert==7.14.2 # via # jupyter # jupyter-server @@ -470,17 +462,17 @@ nbformat==5.9.2 # jupytext # nbclient # nbconvert -nest-asyncio==1.5.8 +nest-asyncio==1.6.0 # via ipykernel -nmdc-schema==9.3.2 +nmdc-schema==10.0.0 # via -r requirements/main.in -notebook==7.0.6 +notebook==7.0.7 # via jupyter notebook-shim==0.2.3 # via # jupyterlab # notebook -numpy==1.26.2 +numpy==1.26.3 # via # pandas # terminusdb-client @@ -490,7 +482,7 @@ openpyxl==3.1.2 # via # -r requirements/main.in # linkml -overrides==7.4.0 +overrides==7.6.0 # via jupyter-server packaging==23.2 # via @@ -512,11 +504,11 @@ packaging==23.2 # tox paginate==0.5.6 # via mkdocs-material -pandas==2.1.4 +pandas==2.2.0 # via # -r requirements/main.in # terminusdb-client -pandocfilters==1.5.0 +pandocfilters==1.5.1 # via nbconvert parse==1.20.0 # via linkml @@ -550,7 +542,7 @@ prefixcommons==0.1.12 # via # linkml # linkml-runtime -prefixmaps==0.2.0 +prefixmaps==0.2.1 # via # linkml # linkml-runtime @@ -560,11 +552,11 @@ prompt-toolkit==3.0.43 # via # ipython # jupyter-console -protobuf==4.25.1 +protobuf==4.25.2 # via # dagster # grpcio-health-checking -psutil==5.9.6 +psutil==5.9.8 # via ipykernel psycopg2-binary==2.9.9 # via dagster-postgres @@ -580,7 +572,7 @@ pyasn1==0.5.1 # rsa pycparser==2.21 # via cffi -pydantic==2.5.2 +pydantic==2.5.3 # via # -r requirements/main.in # beanie @@ -592,9 +584,9 @@ pydantic==2.5.2 # linkml-runtime # prefixmaps # pydantic -pydantic-core==2.14.5 +pydantic-core==2.14.6 # via pydantic -pyflakes==3.1.0 +pyflakes==3.2.0 # via autoflake pygments==2.17.2 # via @@ -604,13 +596,14 @@ pygments==2.17.2 # mkdocs-material # nbconvert # qtconsole + # rich # sphinx pyjsg==0.11.10 # via # linkml # pyshexc # shexjsg -pymdown-extensions==10.5 +pymdown-extensions==10.7 # via # mkdocs-material # mkdocs-mermaid2-plugin @@ -618,6 +611,7 @@ pymongo==4.6.1 # via # -r requirements/main.in # motor + # nmdc-schema pyparsing==3.1.1 # via rdflib pyproject-api==1.6.1 @@ -628,7 +622,7 @@ pyshexc==0.9.1 # via # linkml # pyshex -pytest==7.4.3 +pytest==7.4.4 # via pytest-logging pytest-logging==2015.11.4 # via prefixcommons @@ -643,7 +637,7 @@ python-dateutil==2.8.2 # linkml # pandas # pendulum -python-dotenv==1.0.0 +python-dotenv==1.0.1 # via # -r requirements/main.in # dagster @@ -676,6 +670,7 @@ pyyaml==6.0.1 # linkml # linkml-runtime # mkdocs + # mkdocs-mermaid2-plugin # prefixcommons # prefixmaps # pymdown-extensions @@ -710,12 +705,12 @@ rdflib-shim==1.0.3 # pyshex # pyshexc # sparqlslurper -referencing==0.32.0 +referencing==0.32.1 # via # jsonschema # jsonschema-specifications # jupyter-events -regex==2023.10.3 +regex==2023.12.25 # via mkdocs-material requests==2.31.0 # via @@ -737,7 +732,7 @@ requests==2.31.0 # terminusdb-client requests-cache==1.1.1 # via -r requirements/main.in -requests-toolbelt==0.10.1 +requests-toolbelt==1.0.0 # via gql rfc3339-validator==0.1.4 # via @@ -749,7 +744,9 @@ rfc3986-validator==0.1.1 # jupyter-events rfc3987==1.3.8 # via jsonschema -rpds-py==0.13.2 +rich==13.7.0 + # via dagster +rpds-py==0.17.1 # via # jsonschema # referencing @@ -759,7 +756,7 @@ ruamel-yaml==0.18.5 # via linkml-dataops ruamel-yaml-clib==0.2.8 # via ruamel-yaml -s3transfer==0.9.0 +s3transfer==0.10.0 # via boto3 semver==3.0.2 # via -r requirements/main.in @@ -800,37 +797,33 @@ sparqlwrapper==2.0.0 # pyshex # sparqlslurper sphinx==7.2.6 - # via - # numpydoc - # sphinxcontrib-applehelp - # sphinxcontrib-devhelp - # sphinxcontrib-htmlhelp - # sphinxcontrib-qthelp - # sphinxcontrib-serializinghtml -sphinxcontrib-applehelp==1.0.7 + # via numpydoc +sphinxcontrib-applehelp==1.0.8 # via sphinx -sphinxcontrib-devhelp==1.0.5 +sphinxcontrib-devhelp==1.0.6 # via sphinx -sphinxcontrib-htmlhelp==2.0.4 +sphinxcontrib-htmlhelp==2.0.5 # via sphinx sphinxcontrib-jsmath==1.0.1 # via sphinx -sphinxcontrib-qthelp==1.0.6 +sphinxcontrib-qthelp==1.0.7 # via sphinx -sphinxcontrib-serializinghtml==1.1.9 +sphinxcontrib-serializinghtml==1.1.10 # via sphinx -sqlalchemy==2.0.23 +sqlalchemy==2.0.25 # via # alembic # dagster # linkml stack-data==0.6.3 # via ipython -starlette==0.27.0 +starlette==0.35.1 # via # dagster-graphql # dagster-webserver # fastapi +structlog==24.1.0 + # via dagster tabulate==0.9.0 # via # dagster @@ -874,14 +867,14 @@ tornado==6.4 # jupyterlab # notebook # terminado -tox==4.11.4 +tox==4.12.1 # via prefixmaps tqdm==4.66.1 # via # -r requirements/main.in # dagster # terminusdb-client -traitlets==5.14.0 +traitlets==5.14.1 # via # comm # ipykernel @@ -900,11 +893,12 @@ traitlets==5.14.0 # qtconsole typeguard==2.13.3 # via terminusdb-client -types-python-dateutil==2.8.19.14 +types-python-dateutil==2.8.19.20240106 # via arrow typing-extensions==4.9.0 # via # alembic + # anyio # async-lru # beanie # black @@ -920,7 +914,7 @@ typing-extensions==4.9.0 # uvicorn typing-inspect==0.9.0 # via libcst -tzdata==2023.3 +tzdata==2023.4 # via pandas universal-pathlib==0.1.4 # via dagster @@ -928,14 +922,13 @@ uri-template==1.3.0 # via jsonschema url-normalize==1.4.3 # via requests-cache -urllib3==1.26.18 +urllib3==2.0.7 # via # botocore - # gql # pyshex # requests # requests-cache -uvicorn==0.24.0.post1 +uvicorn==0.27.0 # via # -r requirements/main.in # dagster-webserver @@ -950,7 +943,7 @@ watchdog==3.0.0 # mkdocs watchfiles==0.21.0 # via uvicorn -wcwidth==0.2.12 +wcwidth==0.2.13 # via prompt-toolkit webcolors==1.13 # via jsonschema @@ -971,12 +964,10 @@ xlrd==2.0.1 xlsxwriter==3.1.9 # via -r requirements/main.in yarl==1.9.4 - # via - # aiohttp - # gql + # via gql # The following packages are considered to be unsafe in a requirements file: -setuptools==69.0.2 +setuptools==69.0.3 # via # dagster # mkdocs-mermaid2-plugin