From e56f554c02693fae12faa9d70c48ca956085c757 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Fri, 11 Oct 2024 13:31:44 +0200 Subject: [PATCH] ci: install instanovo with --no-deps --- .github/workflows/docs.yml | 2 +- requirements/requirements-docs.in | 3 - requirements/requirements-docs.txt | 403 ++--------------------------- 3 files changed, 16 insertions(+), 392 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ccc5d97..abb26ea 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -18,4 +18,4 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} CONFIG_FILE: mkdocs.yml EXTRA_PACKAGES: build-base - REQUIREMENTS: requirements/requirements-docs.txt + REQUIREMENTS: --no-deps instanovo -r requirements/requirements-docs.txt diff --git a/requirements/requirements-docs.in b/requirements/requirements-docs.in index 39f3b99..59c2a1a 100644 --- a/requirements/requirements-docs.in +++ b/requirements/requirements-docs.in @@ -1,6 +1,3 @@ -torch==2.4.0+cpu ---extra-index-url https://download.pytorch.org/whl/cpu -instanovo mkdocs mkdocs-gen-files mkdocs-git-revision-date-plugin diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt index ff72c23..4615cad 100644 --- a/requirements/requirements-docs.txt +++ b/requirements/requirements-docs.txt @@ -1,168 +1,37 @@ # This file was autogenerated by uv via the following command: # uv pip compile requirements/requirements-docs.in --output-file=requirements/requirements-docs.txt -absl-py==2.1.0 - # via tensorboard -aiobotocore==2.15.2 - # via s3fs -aiohappyeyeballs==2.4.3 - # via aiohttp -aiohttp==3.10.10 - # via - # aiobotocore - # datasets - # fsspec - # s3fs -aioitertools==0.12.0 - # via aiobotocore -aiosignal==1.3.1 - # via aiohttp -antlr4-python3-runtime==4.9.3 - # via - # hydra-core - # omegaconf -appdirs==1.4.4 - # via spectrum-utils -arrow==1.3.0 - # via isoduration -async-timeout==4.0.3 - # via aiohttp -attrs==24.2.0 - # via - # aiohttp - # jsonschema - # referencing babel==2.16.0 # via mkdocs-material -boto3==1.35.36 - # via neptune -botocore==1.35.36 - # via - # aiobotocore - # boto3 - # s3transfer bracex==2.5.post1 # via wcmatch -bravado==11.0.3 - # via neptune -bravado-core==6.1.1 - # via bravado -certifi==2022.12.7 +certifi==2024.8.30 # via requests -charset-normalizer==2.1.1 +charset-normalizer==3.4.0 # via requests click==8.1.7 # via - # instanovo - # jiwer # mkdocs # mkdocstrings - # neptune colorama==0.4.6 # via # griffe # mkdocs-material -contourpy==1.3.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -datasets==2.19.1 - # via instanovo -deprecated==1.2.14 - # via matchms -dill==0.3.8 - # via - # datasets - # multiprocess -fastobo==0.12.3 - # via spectrum-utils -filelock==3.13.1 - # via - # datasets - # huggingface-hub - # torch -fonttools==4.54.1 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -frozenlist==1.4.1 - # via - # aiohttp - # aiosignal -fsspec==2024.2.0 - # via - # datasets - # huggingface-hub - # pytorch-lightning - # s3fs - # torch -future==1.0.0 - # via neptune ghp-import==2.1.0 # via mkdocs gitdb==4.0.11 # via gitpython gitpython==3.1.43 - # via - # mkdocs-git-revision-date-plugin - # neptune + # via mkdocs-git-revision-date-plugin griffe==1.3.2 # via mkdocstrings-python -grpcio==1.66.2 - # via tensorboard -huggingface-hub==0.25.2 - # via datasets -hydra-core==1.3.2 - # via instanovo -idna==3.4 - # via - # jsonschema - # requests - # yarl -importlib-resources==6.4.5 - # via swagger-spec-validator -instanovo==1.0.0 - # via -r requirements/requirements-docs.in -isoduration==20.11.0 - # via jsonschema -jaxtyping==0.2.34 - # via instanovo -jinja2==3.1.3 +idna==3.10 + # via requests +jinja2==3.1.4 # via # mkdocs # mkdocs-git-revision-date-plugin # mkdocs-material # mkdocstrings - # torch -jiwer==3.0.4 - # via instanovo -jmespath==1.0.1 - # via - # boto3 - # botocore -joblib==1.4.2 - # via scikit-learn -jsonpointer==3.0.0 - # via jsonschema -jsonref==1.1.0 - # via bravado-core -jsonschema==4.23.0 - # via - # bravado-core - # swagger-spec-validator -jsonschema-specifications==2024.10.1 - # via jsonschema -kiwisolver==1.4.7 - # via matplotlib -lark==1.2.2 - # via spectrum-utils -lightning-utilities==0.11.7 - # via - # pytorch-lightning - # torchmetrics -llvmlite==0.43.0 - # via numba -lxml==5.3.0 - # via matchms markdown==3.7 # via # mkdocs @@ -170,21 +39,12 @@ markdown==3.7 # mkdocs-material # mkdocstrings # pymdown-extensions - # tensorboard -markupsafe==2.1.5 +markupsafe==3.0.1 # via # jinja2 # mkdocs # mkdocs-autorefs # mkdocstrings - # werkzeug -matchms==0.21.1 - # via instanovo -matplotlib==3.9.2 - # via - # matchms - # pyopenms - # spectrum-utils mergedeep==1.3.4 # via # mkdocs @@ -224,277 +84,44 @@ mkdocstrings==0.26.1 # mkdocstrings-python mkdocstrings-python==1.11.1 # via -r requirements/requirements-docs.in -monotonic==1.6 - # via bravado -mpmath==1.3.0 - # via sympy -msgpack==1.1.0 - # via - # bravado - # bravado-core -multidict==6.1.0 - # via - # aiohttp - # yarl -multiprocess==0.70.16 - # via datasets -neptune==1.12.0 - # via instanovo -networkx==3.2.1 - # via - # matchms - # torch -numba==0.60.0 - # via - # matchms - # sparsestack - # spectrum-utils -numpy==1.26.3 - # via - # contourpy - # datasets - # instanovo - # matchms - # matplotlib - # numba - # pandas - # pyarrow - # pyopenms - # scikit-learn - # scipy - # sparsestack - # spectrum-utils - # tensorboard - # torchmetrics -oauthlib==3.2.2 - # via - # neptune - # requests-oauthlib -omegaconf==2.3.0 - # via - # hydra-core - # instanovo -packaging==22.0 - # via - # datasets - # huggingface-hub - # hydra-core - # lightning-utilities - # matplotlib - # mkdocs - # neptune - # pytorch-lightning - # tensorboard - # torchmetrics +packaging==24.1 + # via mkdocs paginate==0.5.7 # via mkdocs-material -pandas==2.2.3 - # via - # datasets - # instanovo - # matchms - # neptune - # pyopenms pathspec==0.12.1 # via mkdocs -pickydict==0.5.0 - # via matchms -pillow==10.2.0 - # via - # matchms - # matplotlib - # neptune platformdirs==4.3.6 # via # mkdocs-get-deps # mkdocstrings -# polars==1.9.0 - # via instanovo -propcache==0.2.0 - # via yarl -protobuf==5.28.2 - # via tensorboard -psutil==6.0.0 - # via neptune -pyarrow==17.0.0 - # via datasets -pyarrow-hotfix==0.6 - # via datasets pygments==2.18.0 # via mkdocs-material -pyjwt==2.9.0 - # via neptune pymdown-extensions==10.11.2 # via # -r requirements/requirements-docs.in # mkdocs-material # mkdocstrings -# pyopenms==3.2.0 - # via instanovo -pyparsing==3.1.4 - # via matplotlib -pyteomics==4.7.4 - # via - # matchms - # spectrum-utils python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # bravado - # bravado-core - # ghp-import - # matplotlib - # pandas -python-dotenv==1.0.1 - # via instanovo -pytorch-lightning==2.4.0 - # via instanovo -pytz==2024.2 - # via - # bravado-core - # pandas + # via ghp-import pyyaml==6.0.2 # via - # bravado - # bravado-core - # datasets - # huggingface-hub # mkdocs # mkdocs-get-deps - # omegaconf # pymdown-extensions - # pytorch-lightning # pyyaml-env-tag - # swagger-spec-validator pyyaml-env-tag==0.1 # via mkdocs -rapidfuzz==3.10.0 - # via jiwer -referencing==0.35.1 - # via - # jsonschema - # jsonschema-specifications regex==2024.9.11 # via mkdocs-material -requests==2.28.1 - # via - # bravado - # bravado-core - # datasets - # huggingface-hub - # matchms - # mkdocs-material - # neptune - # requests-oauthlib -requests-oauthlib==2.0.0 - # via neptune -rfc3339-validator==0.1.4 - # via jsonschema -rfc3986-validator==0.1.1 - # via jsonschema -rpds-py==0.20.0 - # via - # jsonschema - # referencing -s3fs==2024.2.0 - # via instanovo -s3transfer==0.10.3 - # via boto3 -scikit-learn==1.5.2 - # via instanovo -scipy==1.14.1 - # via - # matchms - # scikit-learn - # sparsestack -setuptools==70.0.0 - # via - # lightning-utilities - # tensorboard -simplejson==3.19.3 - # via - # bravado - # bravado-core +requests==2.32.3 + # via mkdocs-material six==1.16.0 - # via - # bravado - # bravado-core - # neptune - # python-dateutil - # rfc3339-validator - # tensorboard + # via python-dateutil smmap==5.0.1 # via gitdb -sparsestack==0.5.0 - # via matchms -spectrum-utils==0.4.2 - # via instanovo -swagger-spec-validator==3.0.4 - # via - # bravado-core - # neptune -sympy==1.12 - # via torch -tensorboard==2.18.0 - # via instanovo -tensorboard-data-server==0.7.2 - # via tensorboard -threadpoolctl==3.5.0 - # via scikit-learn -torch==2.4.0+cpu - # via - # -r requirements/requirements-docs.in - # instanovo - # pytorch-lightning - # torchmetrics -torchmetrics==1.0.3 - # via pytorch-lightning -tqdm==4.64.1 - # via - # datasets - # huggingface-hub - # instanovo - # matchms - # pytorch-lightning -typeguard==2.13.3 - # via jaxtyping -types-python-dateutil==2.9.0.20241003 - # via arrow -typing-extensions==4.9.0 - # via - # bravado - # huggingface-hub - # lightning-utilities - # multidict - # neptune - # pytorch-lightning - # swagger-spec-validator - # torch -tzdata==2024.2 - # via pandas -uri-template==1.3.0 - # via jsonschema -urllib3==1.26.13 - # via - # botocore - # neptune - # requests +urllib3==2.2.3 + # via requests watchdog==5.0.3 # via mkdocs wcmatch==10.0 # via mkdocs-include-markdown-plugin -webcolors==24.8.0 - # via jsonschema -websocket-client==1.8.0 - # via neptune -werkzeug==3.0.4 - # via tensorboard -wrapt==1.16.0 - # via - # aiobotocore - # deprecated -xxhash==3.5.0 - # via datasets -yarl==1.14.0 - # via aiohttp