From 8e5dd655ba3a10f57afb70ae0afac356fbb3369f Mon Sep 17 00:00:00 2001 From: Sebastian Date: Mon, 14 Oct 2024 11:40:41 +0200 Subject: [PATCH] Updating dependencies --- poetry.lock | 52 ++++++++++++++++++++++++++++++++++++++++++-------- pyproject.toml | 13 +++++++------ 2 files changed, 51 insertions(+), 14 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4b6c1108..8e42d02c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "accelerate" -version = "0.34.2" +version = "1.0.1" description = "Accelerate" optional = false python-versions = ">=3.8.0" files = [ - {file = "accelerate-0.34.2-py3-none-any.whl", hash = "sha256:d69159e2c4e4a473d14443b27d2d732929254e826b3ab4813b3785b5ac616c7c"}, - {file = "accelerate-0.34.2.tar.gz", hash = "sha256:98c1ebe1f5a45c0a3af02dc60b5bb8b7d58d60c3326a326a06ce6d956b18ca5b"}, + {file = "accelerate-1.0.1-py3-none-any.whl", hash = "sha256:c6aa0c7b8a797cb150471e90e3ca36ac41f5d4b40512cdd6f058b8bf25589467"}, + {file = "accelerate-1.0.1.tar.gz", hash = "sha256:e8f95fc2db14915dc0a9182edfcf3068e5ddb2fa310b583717ad44e5c442399c"}, ] [package.dependencies] @@ -33,8 +33,8 @@ torch = ">=1.10.0" [package.extras] deepspeed = ["deepspeed"] -dev = ["bitsandbytes", "black (>=23.1,<24.0)", "datasets", "diffusers", "evaluate", "hf-doc-builder (>=0.3.0)", "parameterized", "pytest (>=7.2.0,<=8.0.0)", "pytest-subtests", "pytest-xdist", "rich", "ruff (>=0.2.1,<0.3.0)", "scikit-learn", "scipy", "timm", "torchdata (>=0.8.0)", "torchpippy (>=0.2.0)", "tqdm", "transformers"] -quality = ["black (>=23.1,<24.0)", "hf-doc-builder (>=0.3.0)", "ruff (>=0.2.1,<0.3.0)"] +dev = ["bitsandbytes", "black (>=23.1,<24.0)", "datasets", "diffusers", "evaluate", "hf-doc-builder (>=0.3.0)", "parameterized", "pytest (>=7.2.0,<=8.0.0)", "pytest-subtests", "pytest-xdist", "rich", "ruff (>=0.6.4,<0.7.0)", "scikit-learn", "scipy", "timm", "torchdata (>=0.8.0)", "torchpippy (>=0.2.0)", "tqdm", "transformers"] +quality = ["black (>=23.1,<24.0)", "hf-doc-builder (>=0.3.0)", "ruff (>=0.6.4,<0.7.0)"] rich = ["rich"] sagemaker = ["sagemaker"] test-dev = ["bitsandbytes", "datasets", "diffusers", "evaluate", "scikit-learn", "scipy", "timm", "torchdata (>=0.8.0)", "torchpippy (>=0.2.0)", "tqdm", "transformers"] @@ -90,6 +90,31 @@ files = [ {file = "boolean.py-4.0.tar.gz", hash = "sha256:17b9a181630e43dde1851d42bef546d616d5d9b4480357514597e78b203d06e4"}, ] +[[package]] +name = "build" +version = "1.2.2.post1" +description = "A simple, correct Python build frontend" +optional = false +python-versions = ">=3.8" +files = [ + {file = "build-1.2.2.post1-py3-none-any.whl", hash = "sha256:1d61c0887fa860c01971625baae8bdd338e517b836a2f70dd1f7aa3a6b2fc5b5"}, + {file = "build-1.2.2.post1.tar.gz", hash = "sha256:b36993e92ca9375a219c99e606a122ff365a760a2d4bba0caa09bd5278b608b7"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "os_name == \"nt\""} +importlib-metadata = {version = ">=4.6", markers = "python_full_version < \"3.10.2\""} +packaging = ">=19.1" +pyproject_hooks = "*" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} + +[package.extras] +docs = ["furo (>=2023.08.17)", "sphinx (>=7.0,<8.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)", "sphinx-issues (>=3.0.0)"] +test = ["build[uv,virtualenv]", "filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "setuptools (>=56.0.0)", "setuptools (>=56.0.0)", "setuptools (>=67.8.0)", "wheel (>=0.36.0)"] +typing = ["build[uv]", "importlib-metadata (>=5.1)", "mypy (>=1.9.0,<1.10.0)", "tomli", "typing-extensions (>=3.7.4.3)"] +uv = ["uv (>=0.1.18)"] +virtualenv = ["virtualenv (>=20.0.35)"] + [[package]] name = "cachecontrol" version = "0.14.0" @@ -1200,9 +1225,9 @@ files = [ [package.dependencies] numpy = [ - {version = ">=1.23.3", markers = "python_version >= \"3.11\""}, {version = ">=1.21.2", markers = "python_version >= \"3.10\" and python_version < \"3.11\""}, {version = ">=1.21", markers = "python_version < \"3.10\""}, + {version = ">=1.23.3", markers = "python_version >= \"3.11\""}, ] [package.extras] @@ -1688,8 +1713,8 @@ files = [ [package.dependencies] numpy = [ - {version = ">=1.23.2", markers = "python_version == \"3.11\""}, {version = ">=1.22.4", markers = "python_version < \"3.11\""}, + {version = ">=1.23.2", markers = "python_version == \"3.11\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -2010,6 +2035,17 @@ files = [ [package.extras] diagrams = ["jinja2", "railroad-diagrams"] +[[package]] +name = "pyproject-hooks" +version = "1.2.0" +description = "Wrappers to call pyproject.toml-based build backend hooks." +optional = false +python-versions = ">=3.7" +files = [ + {file = "pyproject_hooks-1.2.0-py3-none-any.whl", hash = "sha256:9e5c6bfa8dcc30091c74b0cf803c81fdd29d94f01992a7707bc97babb1141913"}, + {file = "pyproject_hooks-1.2.0.tar.gz", hash = "sha256:1e859bd5c40fae9448642dd871adf459e5e2084186e8d2c2a79a824c970da1f8"}, +] + [[package]] name = "pyreadline3" version = "3.5.4" @@ -3174,4 +3210,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.12" -content-hash = "cbe39b83a3b5bc7a78cc1185a453ab7ad632a59bc4b02c82f0fd4699511944d0" +content-hash = "e1f4fedb50146aa63019e3bb2b2cd35ff54d38b7dd08931f445704991435be65" diff --git a/pyproject.toml b/pyproject.toml index 2f9b02cf..e1ff2246 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,32 +33,33 @@ repository = "https://github.com/sacdallago/biotrainer" [tool.poetry.dependencies] python = ">=3.9,<3.12" -accelerate = "^0.34.2" +accelerate = "^1.0.1" biopython = ">=1.83,<2.0" matplotlib = ">=3.7.2,<4.0.0" h5py = ">=3.8.0,<4.0.0" numpy = ">=1.26.4,<2.0.0" pip-audit = "^2.7.3" plotly = ">=5.16.1,<6.0.0" -protobuf = "^5.27.3" +protobuf = "^5.28.2" pyyaml = "6.0.2" "ruamel.yaml" = ">=0.17.40,<0.18.0" sentencepiece = "^0.2.0" scipy = ">=1.13.1,<2.0.0" # Latest version 1.14.1 requires python >= 3.10 scikit-learn = "^1.5.1" -tensorboard = "^2.17.1" +tensorboard = "^2.18.0" torch = "2.4.1" tqdm = "^4.66.5" -transformers = "^4.44.2" -torchmetrics = "^1.4.2" +transformers = "^4.45.2" +torchmetrics = "^1.4.3" safetensors = "^0.4.4" onnx = "1.16.2" onnxscript = "^0.1.0.dev20240806" onnxruntime = "^1.19.0" -pandas = "^2.2.2" +pandas = "^2.2.3" [tool.poetry.dev-dependencies] pytest = "^8.3.3" +build = "^1.2.2" [build-system] requires = ["poetry-core>=1.0.0"]