From 0026da078f931cea41379a7be99bbdd49ed0983a Mon Sep 17 00:00:00 2001 From: eecavanna Date: Mon, 20 Jan 2025 23:51:43 -0800 Subject: [PATCH] Bump `nmdc-schema` from `11.2.1` to `11.3.0` and sync transitive deps --- Makefile | 14 +++++--- requirements/dev.txt | 28 ++++++++-------- requirements/main.in | 2 +- requirements/main.txt | 77 ++++++++++++++++--------------------------- 4 files changed, 54 insertions(+), 67 deletions(-) diff --git a/Makefile b/Makefile index 3089f211..aafe2356 100644 --- a/Makefile +++ b/Makefile @@ -5,10 +5,16 @@ init: # Updates Python dependencies based upon the contents of the `requirements/main.in` and `requirements/dev.in` files. # -# To omit the `--upgrade` option (included by default) when running `pip-compile`: -# ``` -# $ make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT='' -# ``` +# Note: To omit the `--upgrade` option (included by default) when running `pip-compile`: +# ``` +# $ make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT='' +# ``` +# +# Note: You can run the following command on your host machine to have `$ make update-deps` run within a container: +# ```sh +# $ docker compose run --rm --no-deps fastapi sh -c 'make update-deps' +# ``` +# UPDATE_DEPS_MAIN_UPGRADE_OPT ?= --upgrade UPDATE_DEPS_DEV_UPGRADE_OPT ?= --upgrade update-deps: diff --git a/requirements/dev.txt b/requirements/dev.txt index 69a3458d..1b7a529f 100644 --- a/requirements/dev.txt +++ b/requirements/dev.txt @@ -4,7 +4,7 @@ # # pip-compile --allow-unsafe --output-file=requirements/dev.txt --strip-extras requirements/dev.in # -attrs==24.2.0 +attrs==24.3.0 # via # -c /code/requirements/main.txt # cattrs @@ -19,7 +19,7 @@ cattrs==24.1.2 # via # -c /code/requirements/main.txt # requests-cache -certifi==2024.8.30 +certifi==2024.12.14 # via # -c /code/requirements/main.txt # requests @@ -27,16 +27,16 @@ cffi==1.17.1 # via # -c /code/requirements/main.txt # cryptography -charset-normalizer==3.4.0 +charset-normalizer==3.4.1 # via # -c /code/requirements/main.txt # requests -click==8.1.7 +click==8.1.8 # via # -c /code/requirements/main.txt # black # pip-tools -coverage==7.6.8 +coverage==7.6.10 # via # -r requirements/dev.in # pytest-cov @@ -57,7 +57,7 @@ idna==3.10 # via # -c /code/requirements/main.txt # requests -importlib-metadata==8.5.0 +importlib-metadata==8.6.1 # via keyring iniconfig==2.0.0 # via @@ -75,7 +75,7 @@ jeepney==0.8.0 # via # keyring # secretstorage -keyring==25.5.0 +keyring==25.6.0 # via twine markdown-it-py==3.0.0 # via @@ -87,13 +87,13 @@ mdurl==0.1.2 # via # -c /code/requirements/main.txt # markdown-it-py -more-itertools==10.5.0 +more-itertools==10.6.0 # via # jaraco-classes # jaraco-functools mypy-extensions==1.0.0 # via black -nh3==0.2.19 +nh3==0.2.20 # via readme-renderer packaging==24.2 # via @@ -127,7 +127,7 @@ pycparser==2.22 # cffi pyflakes==3.2.0 # via flake8 -pygments==2.18.0 +pygments==2.19.1 # via # -c /code/requirements/main.txt # readme-renderer @@ -143,7 +143,7 @@ pytest==8.3.4 # pytest-asyncio # pytest-cov # pytest-mock -pytest-asyncio==0.24.0 +pytest-asyncio==0.25.2 # via -r requirements/dev.in pytest-cov==6.0.0 # via -r requirements/dev.in @@ -176,7 +176,7 @@ rich==13.9.4 # twine secretstorage==3.3.3 # via keyring -six==1.16.0 +six==1.17.0 # via # -c /code/requirements/main.txt # url-normalize @@ -200,7 +200,7 @@ url-normalize==1.4.3 # via # -c /code/requirements/main.txt # requests-cache -urllib3==2.2.3 +urllib3==2.3.0 # via # -c /code/requirements/main.txt # requests @@ -216,7 +216,7 @@ pip==24.3.1 # via # -r requirements/dev.in # pip-tools -setuptools==75.6.0 +setuptools==75.8.0 # via # -c /code/requirements/main.txt # -r requirements/dev.in diff --git a/requirements/main.in b/requirements/main.in index 35078e3f..25755143 100644 --- a/requirements/main.in +++ b/requirements/main.in @@ -25,7 +25,7 @@ mkdocs-jupyter mkdocs-material mkdocs-mermaid2-plugin motor -nmdc-schema==11.2.1 +nmdc-schema==11.3.0 openpyxl pandas passlib[bcrypt] diff --git a/requirements/main.txt b/requirements/main.txt index 5e9e9b83..44145d2b 100644 --- a/requirements/main.txt +++ b/requirements/main.txt @@ -1,10 +1,10 @@ # -# This file is autogenerated by pip-compile with Python 3.9 +# This file is autogenerated by pip-compile with Python 3.10 # by the following command: # # pip-compile --allow-unsafe --output-file=requirements/main.txt --strip-extras requirements/main.in # -alembic==1.14.0 +alembic==1.14.1 # via dagster annotated-types==0.7.0 # via pydantic @@ -21,8 +21,6 @@ anyio==4.8.0 # jupyter-server # starlette # watchfiles -appnope==0.1.4 - # via ipykernel argon2-cffi==23.1.0 # via jupyter-server argon2-cffi-bindings==21.2.0 @@ -58,9 +56,9 @@ beautifulsoup4==4.12.3 # nbconvert bleach==6.2.0 # via nbconvert -boto3==1.35.98 +boto3==1.36.2 # via -r requirements/main.in -botocore==1.35.98 +botocore==1.36.2 # via # boto3 # s3transfer @@ -104,33 +102,31 @@ comm==0.2.2 # via # ipykernel # ipywidgets -croniter==5.0.1 - # via dagster cryptography==44.0.0 # via python-jose curies==0.10.2 # via # linkml-runtime # prefixmaps -dagit==1.9.8 +dagit==1.9.9 # via -r requirements/main.in -dagster==1.9.8 +dagster==1.9.9 # via # -r requirements/main.in # dagster-graphql # dagster-postgres # dagster-webserver -dagster-graphql==1.9.8 +dagster-graphql==1.9.9 # via # -r requirements/main.in # dagster-webserver -dagster-pipes==1.9.8 +dagster-pipes==1.9.9 # via dagster -dagster-postgres==0.25.8 +dagster-postgres==0.25.9 # via -r requirements/main.in -dagster-webserver==1.9.8 +dagster-webserver==1.9.9 # via dagit -debugpy==1.8.11 +debugpy==1.8.12 # via ipykernel decorator==5.1.1 # via ipython @@ -156,8 +152,6 @@ email-validator==2.2.0 # via pydantic et-xmlfile==2.0.0 # via openpyxl -eval-type-backport==0.2.2 - # via curies exceptiongroup==1.2.2 # via # anyio @@ -199,6 +193,8 @@ graphql-relay==3.2.0 # via graphene graphviz==0.20.3 # via linkml +greenlet==3.1.1 + # via sqlalchemy grpcio==1.69.0 # via # dagster @@ -230,16 +226,6 @@ idna==3.10 # jsonschema # requests # yarl -importlib-metadata==8.5.0 - # via - # jupyter-client - # jupyter-lsp - # jupyterlab - # jupyterlab-server - # markdown - # mkdocs - # mkdocs-get-deps - # nbconvert iniconfig==2.0.0 # via pytest ipykernel==6.29.5 @@ -248,7 +234,7 @@ ipykernel==6.29.5 # jupyter-console # jupyterlab # mkdocs-jupyter -ipython==8.18.1 +ipython==8.31.0 # via # ipykernel # ipywidgets @@ -420,7 +406,7 @@ mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-jupyter==0.25.1 # via -r requirements/main.in -mkdocs-material==9.5.49 +mkdocs-material==9.5.50 # via # -r requirements/main.in # mkdocs-jupyter @@ -433,7 +419,7 @@ mkdocs-mermaid2-plugin==0.6.0 # nmdc-schema mkdocs-redirects==1.2.2 # via nmdc-schema -motor==3.6.0 +motor==3.6.1 # via # -r requirements/main.in # beanie @@ -454,7 +440,7 @@ nbformat==5.10.4 # nbconvert nest-asyncio==1.6.0 # via ipykernel -nmdc-schema==11.2.1 +nmdc-schema==11.3.0 # via -r requirements/main.in notebook==7.3.2 # via jupyter @@ -462,7 +448,7 @@ notebook-shim==0.2.4 # via # jupyterlab # notebook -numpy==2.0.2 +numpy==2.2.2 # via pandas openpyxl==3.1.5 # via @@ -517,7 +503,7 @@ prefixmaps==0.2.6 # linkml-runtime prometheus-client==0.21.1 # via jupyter-server -prompt-toolkit==3.0.48 +prompt-toolkit==3.0.50 # via # ipython # jupyter-console @@ -594,7 +580,6 @@ python-dateutil==2.9.0.post0 # via # arrow # botocore - # croniter # ghp-import # graphene # jupyter-client @@ -615,7 +600,6 @@ pytrie==0.4.0 # via curies pytz==2024.2 # via - # croniter # dagster # pandas pyyaml==6.0.2 @@ -643,7 +627,7 @@ pyzmq==26.2.0 # jupyter-client # jupyter-console # jupyter-server -rdflib==7.1.2 +rdflib==7.1.3 # via # cfgraph # linkml @@ -659,7 +643,7 @@ rdflib-shim==1.0.3 # pyshex # pyshexc # sparqlslurper -referencing==0.35.1 +referencing==0.36.1 # via # jsonschema # jsonschema-specifications @@ -714,7 +698,7 @@ ruamel-yaml==0.18.10 # nmdc-schema ruamel-yaml-clib==0.2.12 # via ruamel-yaml -s3transfer==0.10.4 +s3transfer==0.11.1 # via boto3 semver==3.0.2 # via -r requirements/main.in @@ -731,6 +715,7 @@ shexjsg==0.8.2 six==1.17.0 # via # base32-lib + # dagster # ecdsa # jsbeautifier # python-dateutil @@ -760,7 +745,7 @@ starlette==0.41.3 # dagster-graphql # dagster-webserver # fastapi -structlog==24.4.0 +structlog==25.1.0 # via dagster tabulate==0.9.0 # via dagster @@ -828,18 +813,16 @@ typing-extensions==4.12.2 # dagster # fastapi # graphene - # graphql-core # ipython # linkml # mistune # multidict # pydantic # pydantic-core - # python-json-logger + # referencing # rich - # setuptools-scm # sqlalchemy - # starlette + # structlog # typer # uvicorn tzdata==2024.2 @@ -850,7 +833,7 @@ uri-template==1.3.0 # via jsonschema url-normalize==1.4.3 # via requests-cache -urllib3==1.26.20 +urllib3==2.3.0 # via # botocore # pyshex @@ -879,11 +862,11 @@ webencodings==0.5.1 # tinycss2 websocket-client==1.8.0 # via jupyter-server -websockets==14.1 +websockets==14.2 # via uvicorn widgetsnbextension==4.0.13 # via ipywidgets -wrapt==1.17.1 +wrapt==1.17.2 # via deprecated xlrd==2.0.1 # via -r requirements/main.in @@ -891,8 +874,6 @@ xlsxwriter==3.2.0 # via -r requirements/main.in yarl==1.18.3 # via gql -zipp==3.21.0 - # via importlib-metadata # The following packages are considered to be unsafe in a requirements file: setuptools==75.8.0