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"sacrebleu (>=1.4.12,<2.0.0)", "sacremoses", "scikit-learn", "sentencepiece (>=0.1.91,!=0.1.92)", "sigopt", "sudachidict-core (>=20220729)", "sudachipy (>=0.6.6)", "tensorboard", "timeout-decorator", "timm", "tokenizers (>=0.19,<0.20)", "torch", "torchaudio", "torchvision", "unidic (>=1.0.2)", "unidic-lite (>=1.0.7)", "urllib3 (<2.0.0)"] +flax = ["flax (>=0.4.1,<=0.7.0)", "jax (>=0.4.1,<=0.4.13)", "jaxlib (>=0.4.1,<=0.4.13)", "optax (>=0.0.8,<=0.1.4)", "scipy (<1.13.0)"] flax-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)"] ftfy = ["ftfy"] integrations = ["optuna", "ray[tune] (>=2.7.0)", "sigopt"] @@ -3940,7 +4286,7 @@ natten = ["natten (>=0.14.6,<0.15.0)"] onnx = ["onnxconverter-common", "onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)", "tf2onnx"] onnxruntime = ["onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)"] optuna = ["optuna"] -quality = ["GitPython (<3.1.19)", "datasets (!=2.5.0)", "hf-doc-builder (>=0.3.0)", "isort (>=5.5.4)", "ruff (==0.1.5)", "urllib3 (<2.0.0)"] +quality = ["GitPython (<3.1.19)", "datasets (!=2.5.0)", "isort (>=5.5.4)", "ruff (==0.1.5)", "urllib3 (<2.0.0)"] ray = ["ray[tune] (>=2.7.0)"] retrieval = ["datasets (!=2.5.0)", "faiss-cpu"] sagemaker = ["sagemaker (>=2.31.0)"] @@ -3949,16 +4295,16 @@ serving = ["fastapi", "pydantic", "starlette", "uvicorn"] sigopt = ["sigopt"] sklearn = ["scikit-learn"] speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"] -testing = ["GitPython (<3.1.19)", "beautifulsoup4", "cookiecutter (==1.7.3)", "datasets (!=2.5.0)", "dill (<0.3.5)", "evaluate (>=0.2.0)", "faiss-cpu", "hf-doc-builder (>=0.3.0)", "nltk", "parameterized", "protobuf", "psutil", "pydantic", "pytest (>=7.2.0,<8.0.0)", "pytest-timeout", "pytest-xdist", "rjieba", "rouge-score (!=0.0.7,!=0.0.8,!=0.1,!=0.1.1)", "ruff (==0.1.5)", "sacrebleu (>=1.4.12,<2.0.0)", "sacremoses", "sentencepiece (>=0.1.91,!=0.1.92)", "tensorboard", "timeout-decorator"] -tf = ["keras-nlp (>=0.3.1)", 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["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)"] timm = ["timm"] tokenizers = ["tokenizers (>=0.19,<0.20)"] torch = ["accelerate (>=0.21.0)", "torch"] torch-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"] torch-vision = ["Pillow (>=10.0.1,<=15.0)", "torchvision"] -torchhub = ["filelock", "huggingface-hub (>=0.19.3,<1.0)", "importlib-metadata", "numpy (>=1.17)", "packaging (>=20.0)", "protobuf", "regex (!=2019.12.17)", "requests", "sentencepiece (>=0.1.91,!=0.1.92)", "tokenizers (>=0.19,<0.20)", "torch", "tqdm (>=4.27)"] +torchhub = ["filelock", "huggingface-hub (>=0.23.0,<1.0)", "importlib-metadata", "numpy (>=1.17)", "packaging (>=20.0)", "protobuf", "regex (!=2019.12.17)", "requests", "sentencepiece (>=0.1.91,!=0.1.92)", "tokenizers (>=0.19,<0.20)", "torch", "tqdm (>=4.27)"] video = ["av (==9.2.0)", "decord (==0.6.0)"] vision = ["Pillow (>=10.0.1,<=15.0)"] @@ -3998,13 +4344,13 @@ files = [ [[package]] name = "typing-extensions" -version = "4.11.0" +version = "4.12.1" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, - {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.1-py3-none-any.whl", hash = "sha256:6024b58b69089e5a89c347397254e35f1bf02a907728ec7fee9bf0fe837d203a"}, + {file = "typing_extensions-4.12.1.tar.gz", hash = "sha256:915f5e35ff76f56588223f15fdd5938f9a1cf9195c0de25130c627e4d597f6d1"}, ] [[package]] @@ -4068,7 +4414,7 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -optional = true +optional = false python-versions = "*" files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, @@ -4093,13 +4439,13 @@ test = ["websockets"] [[package]] name = "werkzeug" -version = "3.0.2" +version = "3.0.3" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.8" files = [ - {file = "werkzeug-3.0.2-py3-none-any.whl", hash = "sha256:3aac3f5da756f93030740bc235d3e09449efcf65f2f55e3602e1d851b8f48795"}, - {file = "werkzeug-3.0.2.tar.gz", hash = "sha256:e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d"}, + {file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"}, + {file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"}, ] [package.dependencies] @@ -4110,29 +4456,29 @@ watchdog = ["watchdog (>=2.3)"] [[package]] name = "widgetsnbextension" -version = "4.0.10" +version = "4.0.11" description = "Jupyter interactive widgets for Jupyter Notebook" optional = true python-versions = ">=3.7" files = [ - {file = "widgetsnbextension-4.0.10-py3-none-any.whl", hash = "sha256:d37c3724ec32d8c48400a435ecfa7d3e259995201fbefa37163124a9fcb393cc"}, - {file = "widgetsnbextension-4.0.10.tar.gz", hash = "sha256:64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f"}, + {file = "widgetsnbextension-4.0.11-py3-none-any.whl", hash = "sha256:55d4d6949d100e0d08b94948a42efc3ed6dfdc0e9468b2c4b128c9a2ce3a7a36"}, + {file = "widgetsnbextension-4.0.11.tar.gz", hash = "sha256:8b22a8f1910bfd188e596fe7fc05dcbd87e810c8a4ba010bdb3da86637398474"}, ] [[package]] name = "zipp" -version = "3.18.1" +version = "3.19.1" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, + {file = "zipp-3.19.1-py3-none-any.whl", hash = "sha256:2828e64edb5386ea6a52e7ba7cdb17bb30a73a858f5eb6eb93d8d36f5ea26091"}, + {file = "zipp-3.19.1.tar.gz", hash = "sha256:35427f6d5594f4acf82d25541438348c26736fa9b3afa2754bcd63cdb99d8e8f"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] jupyter = ["jupyter"] @@ -4140,4 +4486,4 @@ jupyter = ["jupyter"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.11" -content-hash = "e99d01b8c09a5b97f429a4316febee78ebbb8b6d3bc7b0a4ab56795bc0de0c55" +content-hash = "5b189c03a9764f66ad2f27ba6cae9635a21e9da34e1f033726e6d0330ee394ef" diff --git a/pyproject.toml b/pyproject.toml index 6c9f8e1d..e85ec103 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "biotrainer" -version = "0.8.3" +version = "0.8.4" description = "Biotrainers for embeddings" authors = [ "Christian Dallago ", @@ -33,29 +33,30 @@ repository = "https://github.com/sacdallago/biotrainer" [tool.poetry.dependencies] python = ">=3.9,<3.11" -accelerate = "^0.29.3" +accelerate = "^0.30.1" biopython = ">=1.83,<2.0" matplotlib = ">=3.7.2,<4.0.0" h5py = ">=3.8.0,<4.0.0" numpy = "1.26.4" +pip-audit = "^2.7.3" plotly = ">=5.16.1,<6.0.0" -protobuf = "^5.26.1" +protobuf = "^5.27.0" pyyaml = "6.0.1" "ruamel.yaml" = ">=0.17.40,<0.18.0" sentencepiece = "^0.2.0" scipy = ">=1.11.2,<2.0.0" -scikit-learn = "^1.4.2" +scikit-learn = "^1.5.0" tensorboard = "^2.14.1" # Latest version 2.15.1 conflicts with latest version of protobuf torch = "2.3.0" -tqdm = ">=4.66.1,<5.0.0" -transformers = "^4.40.1" +tqdm = "^4.66.4" +transformers = "^4.41.2" torchmetrics = "^1.3.2" # Optional jupyter = { version = "^1.0.0", optional = true } [tool.poetry.dev-dependencies] -pytest = "7.4.4" +pytest = "8.2.1" [tool.poetry.extras] jupyter = ["jupyter"]