From 98383ef8676c221b9f96d34d4b1de0a7a824ec99 Mon Sep 17 00:00:00 2001 From: eecavanna Date: Thu, 13 Feb 2025 23:48:26 -0800 Subject: [PATCH 1/3] Bump `nmdc-schema` from `11.3.0` to `11.4.0` and sync transitive deps --- requirements/dev.txt | 21 +++---- requirements/main.in | 2 +- requirements/main.txt | 134 ++++++++++++++++++++++-------------------- 3 files changed, 82 insertions(+), 75 deletions(-) diff --git a/requirements/dev.txt b/requirements/dev.txt index 1b7a529f..3d9bbe8e 100644 --- a/requirements/dev.txt +++ b/requirements/dev.txt @@ -4,14 +4,14 @@ # # pip-compile --allow-unsafe --output-file=requirements/dev.txt --strip-extras requirements/dev.in # -attrs==24.3.0 +attrs==25.1.0 # via # -c /code/requirements/main.txt # cattrs # requests-cache backports-tarfile==1.2.0 # via jaraco-context -black==24.10.0 +black==25.1.0 # via -r requirements/dev.in build==1.2.2.post1 # via pip-tools @@ -19,7 +19,7 @@ cattrs==24.1.2 # via # -c /code/requirements/main.txt # requests-cache -certifi==2024.12.14 +certifi==2025.1.31 # via # -c /code/requirements/main.txt # requests @@ -36,11 +36,11 @@ click==8.1.8 # -c /code/requirements/main.txt # black # pip-tools -coverage==7.6.10 +coverage==7.6.12 # via # -r requirements/dev.in # pytest-cov -cryptography==44.0.0 +cryptography==44.0.1 # via # -c /code/requirements/main.txt # secretstorage @@ -53,6 +53,8 @@ exceptiongroup==1.2.2 # pytest flake8==7.1.1 # via -r requirements/dev.in +id==1.5.0 + # via twine idna==3.10 # via # -c /code/requirements/main.txt @@ -108,8 +110,6 @@ pathspec==0.12.1 # black pip-tools==7.4.1 # via -r requirements/dev.in -pkginfo==1.12.0 - # via twine platformdirs==4.3.6 # via # -c /code/requirements/main.txt @@ -143,7 +143,7 @@ pytest==8.3.4 # pytest-asyncio # pytest-cov # pytest-mock -pytest-asyncio==0.25.2 +pytest-asyncio==0.25.3 # via -r requirements/dev.in pytest-cov==6.0.0 # via -r requirements/dev.in @@ -154,6 +154,7 @@ readme-renderer==44.0 requests==2.32.3 # via # -c /code/requirements/main.txt + # id # requests-cache # requests-mock # requests-toolbelt @@ -188,7 +189,7 @@ tomli==2.2.1 # coverage # pip-tools # pytest -twine==6.0.1 +twine==6.1.0 # via -r requirements/dev.in typing-extensions==4.12.2 # via @@ -212,7 +213,7 @@ zipp==3.21.0 # via importlib-metadata # The following packages are considered to be unsafe in a requirements file: -pip==24.3.1 +pip==25.0.1 # via # -r requirements/dev.in # pip-tools diff --git a/requirements/main.in b/requirements/main.in index 25755143..92156bc0 100644 --- a/requirements/main.in +++ b/requirements/main.in @@ -25,7 +25,7 @@ mkdocs-jupyter mkdocs-material mkdocs-mermaid2-plugin motor -nmdc-schema==11.3.0 +nmdc-schema==11.4.0 openpyxl pandas passlib[bcrypt] diff --git a/requirements/main.txt b/requirements/main.txt index 44145d2b..54ca952e 100644 --- a/requirements/main.txt +++ b/requirements/main.txt @@ -31,13 +31,13 @@ asttokens==3.0.0 # via stack-data async-lru==2.0.4 # via jupyterlab -attrs==24.3.0 +attrs==25.1.0 # via # cattrs # jsonschema # referencing # requests-cache -babel==2.16.0 +babel==2.17.0 # via # jupyterlab-server # mkdocs-material @@ -49,22 +49,22 @@ bcrypt==4.2.1 # via passlib beanie==1.29.0 # via -r requirements/main.in -beautifulsoup4==4.12.3 +beautifulsoup4==4.13.3 # via # -r requirements/main.in # mkdocs-mermaid2-plugin # nbconvert bleach==6.2.0 # via nbconvert -boto3==1.36.2 +boto3==1.36.20 # via -r requirements/main.in -botocore==1.36.2 +botocore==1.36.20 # via # boto3 # s3transfer cattrs==24.1.2 # via requests-cache -certifi==2024.12.14 +certifi==2025.1.31 # via # httpcore # httpx @@ -85,15 +85,19 @@ click==8.1.8 # via # -r requirements/main.in # beanie + # click-log # dagster # dagster-webserver # json-flattener # linkml # linkml-runtime # mkdocs + # nmdc-schema # prefixcommons # typer # uvicorn +click-log==0.4.0 + # via nmdc-schema colorama==0.4.6 # via mkdocs-material coloredlogs==14.0 @@ -102,29 +106,30 @@ comm==0.2.2 # via # ipykernel # ipywidgets -cryptography==44.0.0 +cryptography==44.0.1 # via python-jose -curies==0.10.2 +curies==0.9.2 # via # linkml-runtime + # nmdc-schema # prefixmaps -dagit==1.9.9 +dagit==1.10.0 # via -r requirements/main.in -dagster==1.9.9 +dagster==1.10.0 # via # -r requirements/main.in # dagster-graphql # dagster-postgres # dagster-webserver -dagster-graphql==1.9.9 +dagster-graphql==1.10.0 # via # -r requirements/main.in # dagster-webserver -dagster-pipes==1.9.9 +dagster-pipes==1.10.0 # via dagster -dagster-postgres==0.25.9 +dagster-postgres==0.26.0 # via -r requirements/main.in -dagster-webserver==1.9.9 +dagster-webserver==1.10.0 # via dagit debugpy==1.8.12 # via ipykernel @@ -134,8 +139,10 @@ defusedxml==0.7.1 # via nbconvert dependency-injector==4.45.0 # via -r requirements/main.in -deprecated==1.2.15 - # via linkml-runtime +deprecated==1.2.18 + # via + # linkml-runtime + # nmdc-schema dnspython==2.7.0 # via # email-validator @@ -158,15 +165,15 @@ exceptiongroup==1.2.2 # cattrs # ipython # pytest -executing==2.1.0 +executing==2.2.0 # via stack-data -fastapi==0.115.6 +fastapi==0.115.8 # via -r requirements/main.in fastjsonschema==2.21.1 # via # -r requirements/main.in # nbformat -filelock==3.16.1 +filelock==3.17.0 # via dagster fnc==0.5.3 # via -r requirements/main.in @@ -174,7 +181,7 @@ fqdn==1.5.1 # via jsonschema frozendict==2.4.6 # via -r requirements/main.in -fsspec==2024.12.0 +fsspec==2025.2.0 # via universal-pathlib ghp-import==2.1.0 # via mkdocs @@ -184,7 +191,7 @@ gql==3.5.0 # via dagster-graphql graphene==3.4.3 # via dagster-graphql -graphql-core==3.2.5 +graphql-core==3.2.6 # via # gql # graphene @@ -195,11 +202,11 @@ graphviz==0.20.3 # via linkml greenlet==3.1.1 # via sqlalchemy -grpcio==1.69.0 +grpcio==1.70.0 # via # dagster # grpcio-health-checking -grpcio-health-checking==1.69.0 +grpcio-health-checking==1.70.0 # via dagster h11==0.14.0 # via @@ -234,14 +241,14 @@ ipykernel==6.29.5 # jupyter-console # jupyterlab # mkdocs-jupyter -ipython==8.31.0 +ipython==8.32.0 # via # ipykernel # ipywidgets # jupyter-console ipywidgets==8.1.5 # via jupyter -isodate==0.7.2 +isodate==0.6.1 # via # linkml # rdflib @@ -266,7 +273,7 @@ jmespath==1.0.1 # botocore jq==1.8.0 # via -r requirements/main.in -jsbeautifier==1.15.1 +jsbeautifier==1.15.3 # via mkdocs-mermaid2-plugin json-flattener==0.1.9 # via linkml-runtime @@ -281,6 +288,7 @@ jsonasobj2==1.0.4 # -r requirements/main.in # linkml # linkml-runtime + # nmdc-schema jsonpatch==1.33 # via linkml-dataops jsonpath-ng==1.7.0 @@ -296,6 +304,7 @@ jsonschema==4.23.0 # linkml # linkml-runtime # nbformat + # nmdc-schema jsonschema-specifications==2024.10.1 # via jsonschema jupyter==1.1.1 @@ -318,7 +327,7 @@ jupyter-core==5.7.2 # nbclient # nbconvert # nbformat -jupyter-events==0.11.0 +jupyter-events==0.12.0 # via jupyter-server jupyter-lsp==2.2.5 # via jupyterlab @@ -331,7 +340,7 @@ jupyter-server==2.15.0 # notebook-shim jupyter-server-terminals==0.5.3 # via jupyter-server -jupyterlab==4.3.4 +jupyterlab==4.3.5 # via # -r requirements/main.in # jupyter @@ -344,7 +353,7 @@ jupyterlab-server==2.27.3 # notebook jupyterlab-widgets==3.0.13 # via ipywidgets -jupytext==1.16.6 +jupytext==1.16.7 # via mkdocs-jupyter lazy-model==0.2.0 # via beanie @@ -361,9 +370,9 @@ linkml-runtime==1.8.3 # linkml-dataops # nmdc-schema # refscan -lxml==5.3.0 +lxml==5.3.1 # via -r requirements/main.in -mako==1.3.8 +mako==1.3.9 # via alembic markdown==3.7 # via @@ -393,33 +402,26 @@ mergedeep==1.3.4 # via # mkdocs # mkdocs-get-deps -mistune==3.1.0 +mistune==3.1.1 # via nbconvert mkdocs==1.6.1 # via # mkdocs-jupyter # mkdocs-material # mkdocs-mermaid2-plugin - # mkdocs-redirects - # nmdc-schema mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-jupyter==0.25.1 # via -r requirements/main.in -mkdocs-material==9.5.50 +mkdocs-material==9.6.4 # via # -r requirements/main.in # mkdocs-jupyter - # mkdocs-mermaid2-plugin mkdocs-material-extensions==1.3.1 # via mkdocs-material -mkdocs-mermaid2-plugin==0.6.0 - # via - # -r requirements/main.in - # nmdc-schema -mkdocs-redirects==1.2.2 - # via nmdc-schema -motor==3.6.1 +mkdocs-mermaid2-plugin==1.2.1 + # via -r requirements/main.in +motor==3.7.0 # via # -r requirements/main.in # beanie @@ -427,7 +429,7 @@ multidict==6.1.0 # via yarl nbclient==0.10.2 # via nbconvert -nbconvert==7.16.5 +nbconvert==7.16.6 # via # jupyter # jupyter-server @@ -440,7 +442,7 @@ nbformat==5.10.4 # nbconvert nest-asyncio==1.6.0 # via ipykernel -nmdc-schema==11.3.0 +nmdc-schema==11.4.0 # via -r requirements/main.in notebook==7.3.2 # via jupyter @@ -448,7 +450,7 @@ notebook-shim==0.2.4 # via # jupyterlab # notebook -numpy==2.2.2 +numpy==2.2.3 # via pandas openpyxl==3.1.5 # via @@ -460,6 +462,7 @@ packaging==24.2 # via # dagster # ipykernel + # jupyter-events # jupyter-server # jupyterlab # jupyterlab-server @@ -513,7 +516,7 @@ protobuf==5.29.3 # via # dagster # grpcio-health-checking -psutil==6.1.1 +psutil==7.0.0 # via ipykernel psycopg2-binary==2.9.10 # via dagster-postgres @@ -529,7 +532,7 @@ pyasn1==0.6.1 # rsa pycparser==2.22 # via cffi -pydantic==2.10.5 +pydantic==2.10.6 # via # -r requirements/main.in # beanie @@ -554,11 +557,11 @@ pyjsg==0.11.10 # linkml # pyshexc # shexjsg -pymdown-extensions==10.14 +pymdown-extensions==10.14.3 # via # mkdocs-material # mkdocs-mermaid2-plugin -pymongo==4.9.2 +pymongo==4.11.1 # via # -r requirements/main.in # motor @@ -589,6 +592,7 @@ python-dotenv==1.0.1 # via # -r requirements/main.in # dagster + # nmdc-schema # uvicorn python-jose==3.3.0 # via -r requirements/main.in @@ -598,7 +602,7 @@ python-multipart==0.0.20 # via -r requirements/main.in pytrie==0.4.0 # via curies -pytz==2024.2 +pytz==2025.1 # via # dagster # pandas @@ -613,7 +617,7 @@ pyyaml==6.0.2 # linkml-runtime # mkdocs # mkdocs-get-deps - # mkdocs-mermaid2-plugin + # nmdc-schema # prefixcommons # prefixmaps # pymdown-extensions @@ -621,17 +625,18 @@ pyyaml==6.0.2 # uvicorn pyyaml-env-tag==0.1 # via mkdocs -pyzmq==26.2.0 +pyzmq==26.2.1 # via # ipykernel # jupyter-client # jupyter-console # jupyter-server -rdflib==7.1.3 +rdflib==6.3.2 # via # cfgraph # linkml # linkml-runtime + # nmdc-schema # rdflib-jsonld # rdflib-shim # sparqlslurper @@ -643,7 +648,7 @@ rdflib-shim==1.0.3 # pyshex # pyshexc # sparqlslurper -referencing==0.36.1 +referencing==0.36.2 # via # jsonschema # jsonschema-specifications @@ -663,6 +668,7 @@ requests==2.32.3 # linkml-runtime # mkdocs-material # mkdocs-mermaid2-plugin + # nmdc-schema # prefixcommons # pyshex # requests-cache @@ -693,14 +699,12 @@ rpds-py==0.22.3 rsa==4.9 # via python-jose ruamel-yaml==0.18.10 - # via - # linkml-dataops - # nmdc-schema + # via linkml-dataops ruamel-yaml-clib==0.2.12 # via ruamel-yaml -s3transfer==0.11.1 +s3transfer==0.11.2 # via boto3 -semver==3.0.2 +semver==3.0.4 # via -r requirements/main.in send2trash==1.8.3 # via jupyter-server @@ -717,6 +721,7 @@ six==1.17.0 # base32-lib # dagster # ecdsa + # isodate # jsbeautifier # python-dateutil # rfc3339-validator @@ -733,14 +738,14 @@ sparqlwrapper==2.0.0 # via # pyshex # sparqlslurper -sqlalchemy==2.0.37 +sqlalchemy==2.0.38 # via # alembic # dagster # linkml stack-data==0.6.3 # via ipython -starlette==0.41.3 +starlette==0.45.3 # via # dagster-graphql # dagster-webserver @@ -808,6 +813,7 @@ typing-extensions==4.12.2 # anyio # async-lru # beanie + # beautifulsoup4 # cattrs # curies # dagster @@ -825,7 +831,7 @@ typing-extensions==4.12.2 # structlog # typer # uvicorn -tzdata==2024.2 +tzdata==2025.1 # via pandas universal-pathlib==0.2.6 # via dagster @@ -870,7 +876,7 @@ wrapt==1.17.2 # via deprecated xlrd==2.0.1 # via -r requirements/main.in -xlsxwriter==3.2.0 +xlsxwriter==3.2.2 # via -r requirements/main.in yarl==1.18.3 # via gql From 497fccb07e497b86a1aecf82a1c84703a529e985 Mon Sep 17 00:00:00 2001 From: eecavanna Date: Fri, 14 Feb 2025 00:04:37 -0800 Subject: [PATCH 2/3] Revert "Bump `nmdc-schema` from `11.3.0` to `11.4.0` and sync transitive deps" This reverts commit 98383ef8676c221b9f96d34d4b1de0a7a824ec99. --- requirements/dev.txt | 21 ++++--- requirements/main.in | 2 +- requirements/main.txt | 134 ++++++++++++++++++++---------------------- 3 files changed, 75 insertions(+), 82 deletions(-) diff --git a/requirements/dev.txt b/requirements/dev.txt index 3d9bbe8e..1b7a529f 100644 --- a/requirements/dev.txt +++ b/requirements/dev.txt @@ -4,14 +4,14 @@ # # pip-compile --allow-unsafe --output-file=requirements/dev.txt --strip-extras requirements/dev.in # -attrs==25.1.0 +attrs==24.3.0 # via # -c /code/requirements/main.txt # cattrs # requests-cache backports-tarfile==1.2.0 # via jaraco-context -black==25.1.0 +black==24.10.0 # via -r requirements/dev.in build==1.2.2.post1 # via pip-tools @@ -19,7 +19,7 @@ cattrs==24.1.2 # via # -c /code/requirements/main.txt # requests-cache -certifi==2025.1.31 +certifi==2024.12.14 # via # -c /code/requirements/main.txt # requests @@ -36,11 +36,11 @@ click==8.1.8 # -c /code/requirements/main.txt # black # pip-tools -coverage==7.6.12 +coverage==7.6.10 # via # -r requirements/dev.in # pytest-cov -cryptography==44.0.1 +cryptography==44.0.0 # via # -c /code/requirements/main.txt # secretstorage @@ -53,8 +53,6 @@ exceptiongroup==1.2.2 # pytest flake8==7.1.1 # via -r requirements/dev.in -id==1.5.0 - # via twine idna==3.10 # via # -c /code/requirements/main.txt @@ -110,6 +108,8 @@ pathspec==0.12.1 # black pip-tools==7.4.1 # via -r requirements/dev.in +pkginfo==1.12.0 + # via twine platformdirs==4.3.6 # via # -c /code/requirements/main.txt @@ -143,7 +143,7 @@ pytest==8.3.4 # pytest-asyncio # pytest-cov # pytest-mock -pytest-asyncio==0.25.3 +pytest-asyncio==0.25.2 # via -r requirements/dev.in pytest-cov==6.0.0 # via -r requirements/dev.in @@ -154,7 +154,6 @@ readme-renderer==44.0 requests==2.32.3 # via # -c /code/requirements/main.txt - # id # requests-cache # requests-mock # requests-toolbelt @@ -189,7 +188,7 @@ tomli==2.2.1 # coverage # pip-tools # pytest -twine==6.1.0 +twine==6.0.1 # via -r requirements/dev.in typing-extensions==4.12.2 # via @@ -213,7 +212,7 @@ zipp==3.21.0 # via importlib-metadata # The following packages are considered to be unsafe in a requirements file: -pip==25.0.1 +pip==24.3.1 # via # -r requirements/dev.in # pip-tools diff --git a/requirements/main.in b/requirements/main.in index 92156bc0..25755143 100644 --- a/requirements/main.in +++ b/requirements/main.in @@ -25,7 +25,7 @@ mkdocs-jupyter mkdocs-material mkdocs-mermaid2-plugin motor -nmdc-schema==11.4.0 +nmdc-schema==11.3.0 openpyxl pandas passlib[bcrypt] diff --git a/requirements/main.txt b/requirements/main.txt index 54ca952e..44145d2b 100644 --- a/requirements/main.txt +++ b/requirements/main.txt @@ -31,13 +31,13 @@ asttokens==3.0.0 # via stack-data async-lru==2.0.4 # via jupyterlab -attrs==25.1.0 +attrs==24.3.0 # via # cattrs # jsonschema # referencing # requests-cache -babel==2.17.0 +babel==2.16.0 # via # jupyterlab-server # mkdocs-material @@ -49,22 +49,22 @@ bcrypt==4.2.1 # via passlib beanie==1.29.0 # via -r requirements/main.in -beautifulsoup4==4.13.3 +beautifulsoup4==4.12.3 # via # -r requirements/main.in # mkdocs-mermaid2-plugin # nbconvert bleach==6.2.0 # via nbconvert -boto3==1.36.20 +boto3==1.36.2 # via -r requirements/main.in -botocore==1.36.20 +botocore==1.36.2 # via # boto3 # s3transfer cattrs==24.1.2 # via requests-cache -certifi==2025.1.31 +certifi==2024.12.14 # via # httpcore # httpx @@ -85,19 +85,15 @@ click==8.1.8 # via # -r requirements/main.in # beanie - # click-log # dagster # dagster-webserver # json-flattener # linkml # linkml-runtime # mkdocs - # nmdc-schema # prefixcommons # typer # uvicorn -click-log==0.4.0 - # via nmdc-schema colorama==0.4.6 # via mkdocs-material coloredlogs==14.0 @@ -106,30 +102,29 @@ comm==0.2.2 # via # ipykernel # ipywidgets -cryptography==44.0.1 +cryptography==44.0.0 # via python-jose -curies==0.9.2 +curies==0.10.2 # via # linkml-runtime - # nmdc-schema # prefixmaps -dagit==1.10.0 +dagit==1.9.9 # via -r requirements/main.in -dagster==1.10.0 +dagster==1.9.9 # via # -r requirements/main.in # dagster-graphql # dagster-postgres # dagster-webserver -dagster-graphql==1.10.0 +dagster-graphql==1.9.9 # via # -r requirements/main.in # dagster-webserver -dagster-pipes==1.10.0 +dagster-pipes==1.9.9 # via dagster -dagster-postgres==0.26.0 +dagster-postgres==0.25.9 # via -r requirements/main.in -dagster-webserver==1.10.0 +dagster-webserver==1.9.9 # via dagit debugpy==1.8.12 # via ipykernel @@ -139,10 +134,8 @@ defusedxml==0.7.1 # via nbconvert dependency-injector==4.45.0 # via -r requirements/main.in -deprecated==1.2.18 - # via - # linkml-runtime - # nmdc-schema +deprecated==1.2.15 + # via linkml-runtime dnspython==2.7.0 # via # email-validator @@ -165,15 +158,15 @@ exceptiongroup==1.2.2 # cattrs # ipython # pytest -executing==2.2.0 +executing==2.1.0 # via stack-data -fastapi==0.115.8 +fastapi==0.115.6 # via -r requirements/main.in fastjsonschema==2.21.1 # via # -r requirements/main.in # nbformat -filelock==3.17.0 +filelock==3.16.1 # via dagster fnc==0.5.3 # via -r requirements/main.in @@ -181,7 +174,7 @@ fqdn==1.5.1 # via jsonschema frozendict==2.4.6 # via -r requirements/main.in -fsspec==2025.2.0 +fsspec==2024.12.0 # via universal-pathlib ghp-import==2.1.0 # via mkdocs @@ -191,7 +184,7 @@ gql==3.5.0 # via dagster-graphql graphene==3.4.3 # via dagster-graphql -graphql-core==3.2.6 +graphql-core==3.2.5 # via # gql # graphene @@ -202,11 +195,11 @@ graphviz==0.20.3 # via linkml greenlet==3.1.1 # via sqlalchemy -grpcio==1.70.0 +grpcio==1.69.0 # via # dagster # grpcio-health-checking -grpcio-health-checking==1.70.0 +grpcio-health-checking==1.69.0 # via dagster h11==0.14.0 # via @@ -241,14 +234,14 @@ ipykernel==6.29.5 # jupyter-console # jupyterlab # mkdocs-jupyter -ipython==8.32.0 +ipython==8.31.0 # via # ipykernel # ipywidgets # jupyter-console ipywidgets==8.1.5 # via jupyter -isodate==0.6.1 +isodate==0.7.2 # via # linkml # rdflib @@ -273,7 +266,7 @@ jmespath==1.0.1 # botocore jq==1.8.0 # via -r requirements/main.in -jsbeautifier==1.15.3 +jsbeautifier==1.15.1 # via mkdocs-mermaid2-plugin json-flattener==0.1.9 # via linkml-runtime @@ -288,7 +281,6 @@ jsonasobj2==1.0.4 # -r requirements/main.in # linkml # linkml-runtime - # nmdc-schema jsonpatch==1.33 # via linkml-dataops jsonpath-ng==1.7.0 @@ -304,7 +296,6 @@ jsonschema==4.23.0 # linkml # linkml-runtime # nbformat - # nmdc-schema jsonschema-specifications==2024.10.1 # via jsonschema jupyter==1.1.1 @@ -327,7 +318,7 @@ jupyter-core==5.7.2 # nbclient # nbconvert # nbformat -jupyter-events==0.12.0 +jupyter-events==0.11.0 # via jupyter-server jupyter-lsp==2.2.5 # via jupyterlab @@ -340,7 +331,7 @@ jupyter-server==2.15.0 # notebook-shim jupyter-server-terminals==0.5.3 # via jupyter-server -jupyterlab==4.3.5 +jupyterlab==4.3.4 # via # -r requirements/main.in # jupyter @@ -353,7 +344,7 @@ jupyterlab-server==2.27.3 # notebook jupyterlab-widgets==3.0.13 # via ipywidgets -jupytext==1.16.7 +jupytext==1.16.6 # via mkdocs-jupyter lazy-model==0.2.0 # via beanie @@ -370,9 +361,9 @@ linkml-runtime==1.8.3 # linkml-dataops # nmdc-schema # refscan -lxml==5.3.1 +lxml==5.3.0 # via -r requirements/main.in -mako==1.3.9 +mako==1.3.8 # via alembic markdown==3.7 # via @@ -402,26 +393,33 @@ mergedeep==1.3.4 # via # mkdocs # mkdocs-get-deps -mistune==3.1.1 +mistune==3.1.0 # via nbconvert mkdocs==1.6.1 # via # mkdocs-jupyter # mkdocs-material # mkdocs-mermaid2-plugin + # mkdocs-redirects + # nmdc-schema mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-jupyter==0.25.1 # via -r requirements/main.in -mkdocs-material==9.6.4 +mkdocs-material==9.5.50 # via # -r requirements/main.in # mkdocs-jupyter + # mkdocs-mermaid2-plugin mkdocs-material-extensions==1.3.1 # via mkdocs-material -mkdocs-mermaid2-plugin==1.2.1 - # via -r requirements/main.in -motor==3.7.0 +mkdocs-mermaid2-plugin==0.6.0 + # via + # -r requirements/main.in + # nmdc-schema +mkdocs-redirects==1.2.2 + # via nmdc-schema +motor==3.6.1 # via # -r requirements/main.in # beanie @@ -429,7 +427,7 @@ multidict==6.1.0 # via yarl nbclient==0.10.2 # via nbconvert -nbconvert==7.16.6 +nbconvert==7.16.5 # via # jupyter # jupyter-server @@ -442,7 +440,7 @@ nbformat==5.10.4 # nbconvert nest-asyncio==1.6.0 # via ipykernel -nmdc-schema==11.4.0 +nmdc-schema==11.3.0 # via -r requirements/main.in notebook==7.3.2 # via jupyter @@ -450,7 +448,7 @@ notebook-shim==0.2.4 # via # jupyterlab # notebook -numpy==2.2.3 +numpy==2.2.2 # via pandas openpyxl==3.1.5 # via @@ -462,7 +460,6 @@ packaging==24.2 # via # dagster # ipykernel - # jupyter-events # jupyter-server # jupyterlab # jupyterlab-server @@ -516,7 +513,7 @@ protobuf==5.29.3 # via # dagster # grpcio-health-checking -psutil==7.0.0 +psutil==6.1.1 # via ipykernel psycopg2-binary==2.9.10 # via dagster-postgres @@ -532,7 +529,7 @@ pyasn1==0.6.1 # rsa pycparser==2.22 # via cffi -pydantic==2.10.6 +pydantic==2.10.5 # via # -r requirements/main.in # beanie @@ -557,11 +554,11 @@ pyjsg==0.11.10 # linkml # pyshexc # shexjsg -pymdown-extensions==10.14.3 +pymdown-extensions==10.14 # via # mkdocs-material # mkdocs-mermaid2-plugin -pymongo==4.11.1 +pymongo==4.9.2 # via # -r requirements/main.in # motor @@ -592,7 +589,6 @@ python-dotenv==1.0.1 # via # -r requirements/main.in # dagster - # nmdc-schema # uvicorn python-jose==3.3.0 # via -r requirements/main.in @@ -602,7 +598,7 @@ python-multipart==0.0.20 # via -r requirements/main.in pytrie==0.4.0 # via curies -pytz==2025.1 +pytz==2024.2 # via # dagster # pandas @@ -617,7 +613,7 @@ pyyaml==6.0.2 # linkml-runtime # mkdocs # mkdocs-get-deps - # nmdc-schema + # mkdocs-mermaid2-plugin # prefixcommons # prefixmaps # pymdown-extensions @@ -625,18 +621,17 @@ pyyaml==6.0.2 # uvicorn pyyaml-env-tag==0.1 # via mkdocs -pyzmq==26.2.1 +pyzmq==26.2.0 # via # ipykernel # jupyter-client # jupyter-console # jupyter-server -rdflib==6.3.2 +rdflib==7.1.3 # via # cfgraph # linkml # linkml-runtime - # nmdc-schema # rdflib-jsonld # rdflib-shim # sparqlslurper @@ -648,7 +643,7 @@ rdflib-shim==1.0.3 # pyshex # pyshexc # sparqlslurper -referencing==0.36.2 +referencing==0.36.1 # via # jsonschema # jsonschema-specifications @@ -668,7 +663,6 @@ requests==2.32.3 # linkml-runtime # mkdocs-material # mkdocs-mermaid2-plugin - # nmdc-schema # prefixcommons # pyshex # requests-cache @@ -699,12 +693,14 @@ rpds-py==0.22.3 rsa==4.9 # via python-jose ruamel-yaml==0.18.10 - # via linkml-dataops + # via + # linkml-dataops + # nmdc-schema ruamel-yaml-clib==0.2.12 # via ruamel-yaml -s3transfer==0.11.2 +s3transfer==0.11.1 # via boto3 -semver==3.0.4 +semver==3.0.2 # via -r requirements/main.in send2trash==1.8.3 # via jupyter-server @@ -721,7 +717,6 @@ six==1.17.0 # base32-lib # dagster # ecdsa - # isodate # jsbeautifier # python-dateutil # rfc3339-validator @@ -738,14 +733,14 @@ sparqlwrapper==2.0.0 # via # pyshex # sparqlslurper -sqlalchemy==2.0.38 +sqlalchemy==2.0.37 # via # alembic # dagster # linkml stack-data==0.6.3 # via ipython -starlette==0.45.3 +starlette==0.41.3 # via # dagster-graphql # dagster-webserver @@ -813,7 +808,6 @@ typing-extensions==4.12.2 # anyio # async-lru # beanie - # beautifulsoup4 # cattrs # curies # dagster @@ -831,7 +825,7 @@ typing-extensions==4.12.2 # structlog # typer # uvicorn -tzdata==2025.1 +tzdata==2024.2 # via pandas universal-pathlib==0.2.6 # via dagster @@ -876,7 +870,7 @@ wrapt==1.17.2 # via deprecated xlrd==2.0.1 # via -r requirements/main.in -xlsxwriter==3.2.2 +xlsxwriter==3.2.0 # via -r requirements/main.in yarl==1.18.3 # via gql From 85942d977e136c49492201401ef5ad3e1e30e26f Mon Sep 17 00:00:00 2001 From: eecavanna Date: Fri, 14 Feb 2025 00:18:08 -0800 Subject: [PATCH 3/3] Bump `nmdc-schema` from `11.3.0` to `11.4.0` without updating Dagster In this commit, I bumped `nmdc-schema` in `main.in`, then ran: ``` make update-deps \ UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT='' ``` When those two options are included, the underlying `pip-compile` command does not include the `--upgrade` option. As a result, `pip-compile` does not try to upgrade all dependencies to their latest versions. I did this because, when the `--upgrade` option was being passed to `pip-compile`, the automated test suite in GitHub Actions was failing due to something related to Dagster, which did get updated in a way that has breaking changes documented in its changelog. This is my attempt to avoid that for now (kick the can down the road). --- Makefile | 6 +++++- requirements/main.in | 2 +- requirements/main.txt | 34 ++++++++++++++++++++-------------- 3 files changed, 26 insertions(+), 16 deletions(-) diff --git a/Makefile b/Makefile index aafe2356..41904027 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ init: # Updates Python dependencies based upon the contents of the `requirements/main.in` and `requirements/dev.in` files. # -# Note: To omit the `--upgrade` option (included by default) when running `pip-compile`: +# Note: To omit the `--upgrade` option (included by default) from the constituent `pip-compile` commands: # ``` # $ make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT='' # ``` @@ -14,6 +14,10 @@ init: # ```sh # $ docker compose run --rm --no-deps fastapi sh -c 'make update-deps' # ``` +# To omit the `--upgrade` option (included by default) from the constituent `pip-compile` commands: +# ```sh +# $ docker compose run --rm --no-deps fastapi sh -c 'make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT="" UPDATE_DEPS_DEV_UPGRADE_OPT=""' +# ``` # UPDATE_DEPS_MAIN_UPGRADE_OPT ?= --upgrade UPDATE_DEPS_DEV_UPGRADE_OPT ?= --upgrade diff --git a/requirements/main.in b/requirements/main.in index 25755143..92156bc0 100644 --- a/requirements/main.in +++ b/requirements/main.in @@ -25,7 +25,7 @@ mkdocs-jupyter mkdocs-material mkdocs-mermaid2-plugin motor -nmdc-schema==11.3.0 +nmdc-schema==11.4.0 openpyxl pandas passlib[bcrypt] diff --git a/requirements/main.txt b/requirements/main.txt index 44145d2b..a50760b6 100644 --- a/requirements/main.txt +++ b/requirements/main.txt @@ -85,15 +85,19 @@ click==8.1.8 # via # -r requirements/main.in # beanie + # click-log # dagster # dagster-webserver # json-flattener # linkml # linkml-runtime # mkdocs + # nmdc-schema # prefixcommons # typer # uvicorn +click-log==0.4.0 + # via nmdc-schema colorama==0.4.6 # via mkdocs-material coloredlogs==14.0 @@ -104,9 +108,10 @@ comm==0.2.2 # ipywidgets cryptography==44.0.0 # via python-jose -curies==0.10.2 +curies==0.9.2 # via # linkml-runtime + # nmdc-schema # prefixmaps dagit==1.9.9 # via -r requirements/main.in @@ -135,7 +140,9 @@ defusedxml==0.7.1 dependency-injector==4.45.0 # via -r requirements/main.in deprecated==1.2.15 - # via linkml-runtime + # via + # linkml-runtime + # nmdc-schema dnspython==2.7.0 # via # email-validator @@ -281,6 +288,7 @@ jsonasobj2==1.0.4 # -r requirements/main.in # linkml # linkml-runtime + # nmdc-schema jsonpatch==1.33 # via linkml-dataops jsonpath-ng==1.7.0 @@ -296,6 +304,7 @@ jsonschema==4.23.0 # linkml # linkml-runtime # nbformat + # nmdc-schema jsonschema-specifications==2024.10.1 # via jsonschema jupyter==1.1.1 @@ -400,8 +409,6 @@ mkdocs==1.6.1 # mkdocs-jupyter # mkdocs-material # mkdocs-mermaid2-plugin - # mkdocs-redirects - # nmdc-schema mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-jupyter==0.25.1 @@ -414,11 +421,7 @@ mkdocs-material==9.5.50 mkdocs-material-extensions==1.3.1 # via mkdocs-material mkdocs-mermaid2-plugin==0.6.0 - # via - # -r requirements/main.in - # nmdc-schema -mkdocs-redirects==1.2.2 - # via nmdc-schema + # via -r requirements/main.in motor==3.6.1 # via # -r requirements/main.in @@ -440,7 +443,7 @@ nbformat==5.10.4 # nbconvert nest-asyncio==1.6.0 # via ipykernel -nmdc-schema==11.3.0 +nmdc-schema==11.4.0 # via -r requirements/main.in notebook==7.3.2 # via jupyter @@ -589,6 +592,7 @@ python-dotenv==1.0.1 # via # -r requirements/main.in # dagster + # nmdc-schema # uvicorn python-jose==3.3.0 # via -r requirements/main.in @@ -614,6 +618,7 @@ pyyaml==6.0.2 # mkdocs # mkdocs-get-deps # mkdocs-mermaid2-plugin + # nmdc-schema # prefixcommons # prefixmaps # pymdown-extensions @@ -627,11 +632,12 @@ pyzmq==26.2.0 # jupyter-client # jupyter-console # jupyter-server -rdflib==7.1.3 +rdflib==6.2.0 # via # cfgraph # linkml # linkml-runtime + # nmdc-schema # rdflib-jsonld # rdflib-shim # sparqlslurper @@ -663,6 +669,7 @@ requests==2.32.3 # linkml-runtime # mkdocs-material # mkdocs-mermaid2-plugin + # nmdc-schema # prefixcommons # pyshex # requests-cache @@ -693,9 +700,7 @@ rpds-py==0.22.3 rsa==4.9 # via python-jose ruamel-yaml==0.18.10 - # via - # linkml-dataops - # nmdc-schema + # via linkml-dataops ruamel-yaml-clib==0.2.12 # via ruamel-yaml s3transfer==0.11.1 @@ -881,4 +886,5 @@ setuptools==75.8.0 # dagster # jupyterlab # mkdocs-mermaid2-plugin + # rdflib # setuptools-scm