diff --git a/poetry.lock b/poetry.lock index 5776b7b..593775d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -50,17 +50,6 @@ docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib- tests = ["attrs[tests-no-zope]", "zope-interface"] tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -[[package]] -name = "autopage" -version = "0.5.1" -description = "A library to provide automatic paging for console output" -optional = false -python-versions = ">=3.6" -files = [ - {file = "autopage-0.5.1-py3-none-any.whl", hash = "sha256:0fbf5efbe78d466a26753e1dee3272423a3adc989d6a778c700e89a3f8ff0d88"}, - {file = "autopage-0.5.1.tar.gz", hash = "sha256:01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199"}, -] - [[package]] name = "babel" version = "2.12.1" @@ -264,64 +253,6 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} -[[package]] -name = "cliff" -version = "4.3.0" -description = "Command Line Interface Formulation Framework" -optional = false -python-versions = ">=3.8" -files = [ - {file = "cliff-4.3.0-py3-none-any.whl", hash = "sha256:db3dc8774f47db9aa86796921ff158d0f023630261c2746c4fff12584b75f5b2"}, - {file = "cliff-4.3.0.tar.gz", hash = "sha256:fc5b6ebc8fb815332770b2485ee36c09753937c37cce4f3227cdd4e10b33eacc"}, -] - -[package.dependencies] -autopage = ">=0.4.0" -cmd2 = ">=1.0.0" -importlib-metadata = ">=4.4" -PrettyTable = ">=0.7.2" -PyYAML = ">=3.12" -stevedore = ">=2.0.1" - -[[package]] -name = "cmaes" -version = "0.10.0" -description = "Lightweight Covariance Matrix Adaptation Evolution Strategy (CMA-ES) implementation for Python 3." -optional = false -python-versions = ">=3.7" -files = [ - {file = "cmaes-0.10.0-py3-none-any.whl", hash = "sha256:72cea747ad37b1780b0eb6f3c098cee33907fafbf6690c0c02db1e010cab72f6"}, - {file = "cmaes-0.10.0.tar.gz", hash = "sha256:48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9"}, -] - -[package.dependencies] -numpy = "*" - -[package.extras] -cmawm = ["scipy"] - -[[package]] -name = "cmd2" -version = "2.4.3" -description = "cmd2 - quickly build feature-rich and user-friendly interactive command line applications in Python" -optional = false -python-versions = ">=3.6" -files = [ - {file = "cmd2-2.4.3-py3-none-any.whl", hash = "sha256:f1988ff2fff0ed812a2d25218a081b0fa0108d45b48ba2a9272bb98091b654e6"}, - {file = "cmd2-2.4.3.tar.gz", hash = "sha256:71873c11f72bd19e2b1db578214716f0d4f7c8fa250093c601265a9a717dee52"}, -] - -[package.dependencies] -attrs = ">=16.3.0" -pyperclip = ">=1.6" -pyreadline3 = {version = "*", markers = "sys_platform == \"win32\""} -wcwidth = ">=0.1.7" - -[package.extras] -dev = ["codecov", "doc8", "flake8", "invoke", "mypy", "nox", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "sphinx", "sphinx-autobuild", "sphinx-rtd-theme", "twine (>=1.11)"] -test = ["codecov", "coverage", "gnureadline", "pytest (>=4.6)", "pytest-cov", "pytest-mock"] -validate = ["flake8", "mypy", "types-pkg-resources"] - [[package]] name = "colorama" version = "0.4.6" @@ -809,17 +740,6 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] -[[package]] -name = "joblib" -version = "1.3.2" -description = "Lightweight pipelining with Python functions" -optional = false -python-versions = ">=3.7" -files = [ - {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"}, - {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"}, -] - [[package]] name = "kallisto" version = "1.0.9" @@ -1095,37 +1015,31 @@ files = [ [[package]] name = "optuna" -version = "2.3.0" +version = "3.4.0" description = "A hyperparameter optimization framework" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "optuna-2.3.0.tar.gz", hash = "sha256:876dad2e4d9f3b368f573c0c49724ce5f3b9abfcb14dde6a5ad1b427e73e6a2e"}, + {file = "optuna-3.4.0-py3-none-any.whl", hash = "sha256:4854a6e6ec68eae3f1cbf18525abde1fcf2a22dd4f3b79912e5d43f539ba8eb1"}, + {file = "optuna-3.4.0.tar.gz", hash = "sha256:aa4a2d294ca047d7dc16292707c018cc619bdde1ec435d34721311428942d2db"}, ] [package.dependencies] -alembic = "*" -cliff = "*" -cmaes = ">=0.6.0" +alembic = ">=1.5.0" colorlog = "*" -joblib = "*" numpy = "*" packaging = ">=20.0" -scipy = "!=1.4.0" -sqlalchemy = ">=1.1.0" +PyYAML = "*" +sqlalchemy = ">=1.3.0" tqdm = "*" [package.extras] -checking = ["black", "blackdoc", "hacking", "isort", "mypy (==0.782)"] -codecov = ["codecov", "pytest-cov"] -doctest = ["cma", "matplotlib (>=3.0.0)", "mlflow", "pandas", "plotly (>=4.0.0)", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize"] -document = ["matplotlib", "pillow", "scikit-learn", "sphinx (==3.0.4)", "sphinx-gallery", "sphinx_rtd_theme (<0.5.0)"] -example = ["allennlp (==1.0.0)", "catalyst", "catboost", "chainer", "dask-ml", "dask[dataframe]", "fastai (<2)", "keras", "lightgbm", "mlflow", "mpi4py", "mxnet", "nbval", "pytorch-ignite", "pytorch-lightning (>=0.8.1)", "scikit-image", "scikit-learn (>=0.19.0,<0.23.0)", "skorch", "stable-baselines3 (>=0.7.0)", "tensorflow (>=2.0.0)", "tensorflow-datasets", "thop", "torch (==1.6.0+cpu)", "torchvision (==0.7.0+cpu)", "xgboost"] -experimental = ["redis"] -integration = ["allennlp (==1.0.0)", "catalyst", "chainer (>=5.0.0)", "cma", "fastai (<2)", "keras", "lightgbm", "mlflow", "mpi4py", "mxnet", "pandas", "pytorch-ignite", "pytorch-lightning (>=0.8.1)", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize", "skorch", "tensorflow", "tensorflow-datasets", "torch (==1.6.0+cpu)", "torchvision (==0.7.0+cpu)", "xgboost"] -optional = ["bokeh (<2.0.0)", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "redis", "scikit-learn (>=0.19.0,<0.23.0)"] -testing = ["allennlp (==1.0.0)", "bokeh (<2.0.0)", "catalyst", "chainer (>=5.0.0)", "cma", "fakeredis", "fastai (<2)", "keras", "lightgbm", "matplotlib (>=3.0.0)", "mlflow", "mpi4py", "mxnet", "pandas", "plotly (>=4.0.0)", "pytest", "pytorch-ignite", "pytorch-lightning (>=0.8.1)", "scikit-learn (>=0.19.0,<0.23.0)", "scikit-optimize", "skorch", "tensorflow", "tensorflow-datasets", "torch (==1.6.0+cpu)", "torchvision (==0.7.0+cpu)", "xgboost"] -tests = ["fakeredis", "pytest"] +benchmark = ["asv (>=0.5.0)", "botorch", "cma", "scikit-optimize", "virtualenv"] +checking = ["black", "blackdoc", "flake8", "isort", "mypy", "mypy-boto3-s3", "types-PyYAML", "types-redis", "types-setuptools", "types-tqdm", "typing-extensions (>=3.10.0.0)"] +document = ["ase", "botorch", "cma", "cmaes (>=0.10.0)", "distributed", "fvcore", "lightgbm", "matplotlib (!=3.6.0)", "mlflow", "pandas", "pillow", "plotly (>=4.9.0)", "scikit-learn", "scikit-optimize", "sphinx", "sphinx-copybutton", "sphinx-gallery", "sphinx-plotly-directive", "sphinx-rtd-theme (>=1.2.0)", "torch", "torchaudio", "torchvision"] +integration = ["botorch (>=0.4.0)", "catboost (>=0.26)", "catboost (>=0.26,<1.2)", "cma", "distributed", "fastai", "lightgbm", "mlflow", "pandas", "pytorch-ignite", "pytorch-lightning (>=1.6.0)", "scikit-learn (>=0.24.2)", "scikit-optimize", "shap", "tensorflow", "torch", "torchaudio", "torchvision", "wandb", "xgboost"] +optional = ["boto3", "botorch", "cmaes (>=0.10.0)", "google-cloud-storage", "matplotlib (!=3.6.0)", "pandas", "plotly (>=4.9.0)", "redis", "scikit-learn (>=0.24.2)"] +test = ["coverage", "fakeredis[lua]", "kaleido", "moto", "pytest", "scipy (>=1.9.2)"] [[package]] name = "packaging" @@ -1307,23 +1221,6 @@ files = [ "ruamel.yaml" = ">=0.15" tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} -[[package]] -name = "prettytable" -version = "3.9.0" -description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" -optional = false -python-versions = ">=3.8" -files = [ - {file = "prettytable-3.9.0-py3-none-any.whl", hash = "sha256:a71292ab7769a5de274b146b276ce938786f56c31cf7cea88b6f3775d82fe8c8"}, - {file = "prettytable-3.9.0.tar.gz", hash = "sha256:f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34"}, -] - -[package.dependencies] -wcwidth = "*" - -[package.extras] -tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"] - [[package]] name = "pycodestyle" version = "2.8.0" @@ -1391,27 +1288,6 @@ files = [ [package.extras] diagrams = ["jinja2", "railroad-diagrams"] -[[package]] -name = "pyperclip" -version = "1.8.2" -description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" -optional = false -python-versions = "*" -files = [ - {file = "pyperclip-1.8.2.tar.gz", hash = "sha256:105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57"}, -] - -[[package]] -name = "pyreadline3" -version = "3.4.1" -description = "A python implementation of GNU readline." -optional = false -python-versions = "*" -files = [ - {file = "pyreadline3-3.4.1-py3-none-any.whl", hash = "sha256:b0efb6516fd4fb07b45949053826a62fa4cb353db5be2bbb4a7aa1fdd1e345fb"}, - {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"}, -] - [[package]] name = "pytest" version = "7.4.2" @@ -2176,17 +2052,6 @@ platformdirs = ">=3.9.1,<4" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] -[[package]] -name = "wcwidth" -version = "0.2.6" -description = "Measures the displayed width of unicode strings in a terminal" -optional = false -python-versions = "*" -files = [ - {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"}, - {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"}, -] - [[package]] name = "xdoctest" version = "1.1.1" diff --git a/pyproject.toml b/pyproject.toml index 7f831dc..5b30c1d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ kallisto = "^1.0.9" optional = true [tool.poetry.group.optuna.dependencies] -optuna = {version = "2.3.0"} +optuna = {version = "3.4.0"} [tool.poetry.dev-dependencies] pytest = "^7.4.0"