diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0cb7485..c412c20 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,11 +1,11 @@ repos: - repo: https://github.com/asottile/pyupgrade - rev: v2.37.3 + rev: "v2.37.3" hooks: - id: pyupgrade - repo: https://github.com/pre-commit/pre-commit-hooks - rev: "v4.1.0" + rev: "v4.3.0" hooks: # - id: check-added-large-files - id: check-executables-have-shebangs diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 0000000..0542ac2 --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,9 @@ +{ + "recommendations": [ + "ms-vscode-remote.remote-containers", + "ms-azuretools.vscode-docker", + "editorconfig.editorconfig", + "njpwerner.autodocstring", + "ms-python.python" + ] +} diff --git a/.vscode/settings.json b/.vscode/settings.json index 446f92c..4c6dc73 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,7 +4,9 @@ "editor.formatOnSave": true, "python.linting.enabled": true, "python.linting.lintOnSave": true, + "python.linting.flake8Enabled": true, "python.linting.mypyEnabled": true, + "python.linting.banditEnabled": true, "jupyter.debugJustMyCode": false, "[python]": { "editor.codeActionsOnSave": { diff --git a/poetry.lock b/poetry.lock index 582faca..c991e3c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -110,6 +110,25 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "bandit" +version = "1.7.4" +description = "Security oriented static analyser for python code." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = ">=0.3.9", markers = "platform_system == \"Windows\""} +GitPython = ">=1.0.1" +PyYAML = ">=5.3.1" +stevedore = ">=1.20.0" + +[package.extras] +test = ["beautifulsoup4 (>=4.8.0)", "coverage (>=4.5.4)", "fixtures (>=3.0.0)", "flake8 (>=4.0.0)", "pylint (==1.9.4)", "stestr (>=2.5.0)", "testscenarios (>=0.5.0)", "testtools (>=2.3.0)", "toml"] +toml = ["toml"] +yaml = ["PyYAML"] + [[package]] name = "black" version = "22.8.0" @@ -142,20 +161,9 @@ category = "main" optional = false python-versions = "~=3.7" -[[package]] -name = "Cerberus" -version = "1.3.4" -description = "Lightweight, extensible schema and data validation tool for Python dictionaries." -category = "main" -optional = false -python-versions = ">=2.7" - -[package.dependencies] -setuptools = "*" - [[package]] name = "certifi" -version = "2022.6.15" +version = "2022.6.15.1" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -306,11 +314,51 @@ python-versions = ">=3.7" docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"] testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"] +[[package]] +name = "flake8" +version = "5.0.4" +description = "the modular source code checker: pep8 pyflakes and co" +category = "dev" +optional = false +python-versions = ">=3.6.1" + +[package.dependencies] +mccabe = ">=0.7.0,<0.8.0" +pycodestyle = ">=2.9.0,<2.10.0" +pyflakes = ">=2.5.0,<2.6.0" + +[[package]] +name = "flake8-docstrings" +version = "1.6.0" +description = "Extension for flake8 which uses pydocstyle to check docstrings" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +flake8 = ">=3" +pydocstyle = ">=2.1" + +[[package]] +name = "Flake8-pyproject" +version = "1.1.0.post0" +description = "Flake8 plug-in loading the configuration from pyproject.toml" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +Flake8 = ">=5,<6" +TOMLi = {version = "*", markers = "python_version < \"3.11\""} + +[package.extras] +test = ["pyTest", "pyTest-cov"] + [[package]] name = "flatbuffers" version = "2.0.7" description = "The FlatBuffers serialization format for Python" -category = "main" +category = "dev" optional = false python-versions = "*" @@ -450,17 +498,6 @@ six = ">=1.5.2" [package.extras] protobuf = ["grpcio-tools (>=1.48.1)"] -[[package]] -name = "h5py" -version = "3.7.0" -description = "Read and write HDF5 files from Python" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -numpy = ">=1.14.5" - [[package]] name = "humanfriendly" version = "10.0" @@ -493,7 +530,7 @@ python-versions = ">=3.5" [[package]] name = "imageio" -version = "2.21.2" +version = "2.21.3" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." category = "main" optional = false @@ -749,11 +786,19 @@ python-versions = ">=3.5" [package.dependencies] traitlets = "*" +[[package]] +name = "mccabe" +version = "0.7.0" +description = "McCabe checker, plugin for flake8" +category = "dev" +optional = false +python-versions = ">=3.6" + [[package]] name = "mpmath" version = "1.2.1" description = "Python library for arbitrary-precision floating-point arithmetic" -category = "main" +category = "dev" optional = false python-versions = "*" @@ -831,7 +876,7 @@ setuptools = "*" [[package]] name = "numpy" -version = "1.23.2" +version = "1.23.3" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -839,7 +884,7 @@ python-versions = ">=3.8" [[package]] name = "oauthlib" -version = "3.2.0" +version = "3.2.1" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" category = "main" optional = false @@ -854,7 +899,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] name = "onnx" version = "1.12.0" description = "Open Neural Network Exchange" -category = "main" +category = "dev" optional = false python-versions = "*" @@ -898,25 +943,6 @@ packaging = "*" protobuf = "*" sympy = "*" -[[package]] -name = "onnxruntime-training" -version = "1.12.0" -description = "ONNX Runtime is a runtime accelerator for Machine Learning models" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -cerberus = "*" -flatbuffers = "*" -h5py = "*" -numpy = ">=1.16.6" -onnx = "*" -packaging = "*" -protobuf = ">=3.12.2,<=3.20.1" -setuptools = ">=41.4.0" -sympy = "*" - [[package]] name = "opencv-python-headless" version = "4.6.0.66" @@ -972,6 +998,14 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "pbr" +version = "5.10.0" +description = "Python Build Reasonableness" +category = "dev" +optional = false +python-versions = ">=2.6" + [[package]] name = "pexpect" version = "4.8.0" @@ -1133,6 +1167,14 @@ python-versions = ">=3.5" matplotlib = ">=2.1.0" numpy = "*" +[[package]] +name = "pycodestyle" +version = "2.9.1" +description = "Python style guide checker" +category = "dev" +optional = false +python-versions = ">=3.6" + [[package]] name = "pycparser" version = "2.21" @@ -1149,6 +1191,28 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "pydocstyle" +version = "6.1.1" +description = "Python docstring style checker" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +snowballstemmer = "*" + +[package.extras] +toml = ["toml"] + +[[package]] +name = "pyflakes" +version = "2.5.0" +description = "passive checker of Python programs" +category = "dev" +optional = false +python-versions = ">=3.6" + [[package]] name = "Pygments" version = "2.13.0" @@ -1192,7 +1256,7 @@ six = ">=1.5" [[package]] name = "pytorch-lightning" -version = "1.7.4" +version = "1.7.5" description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. Scale your models. Write less boilerplate." category = "main" optional = false @@ -1211,15 +1275,15 @@ tqdm = ">=4.57.0" typing-extensions = ">=4.0.0" [package.extras] -all = ["cloudpickle (>=1.3)", "codecov (>=2.1)", "comet-ml (>=3.1.12)", "coverage (>=6.4)", "deepspeed (>=0.6.0)", "fairscale (>=0.4.5)", "fastapi", "gcsfs (>=2021.5.0)", "gym[classic_control] (>=0.17.0)", "hivemind (>=1.0.1)", "horovod (>=0.21.2,!=0.24.0)", "hydra-core (>=1.0.5)", "ipython[all]", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "mlflow (>=1.0.0)", "mypy (==0.971)", "neptune-client (>=0.10.0)", "omegaconf (>=2.0.5)", "onnxruntime", "pandas (>1.0)", "pre-commit (>=1.0)", "psutil", "pytest (>=7.0)", "pytest-cov", "pytest-forked", "pytest-rerunfailures (>=10.2)", "rich (>=10.14.0,!=10.15.0.a)", "scikit-learn (>0.22.1)", "test-tube (>=0.7.5)", "torchtext (>=0.10)", "torchvision (>=0.10)", "uvicorn", "wandb (>=0.10.22)"] +all = ["cloudpickle (>=1.3)", "codecov (>=2.1)", "comet-ml (>=3.1.12)", "coverage (>=6.4)", "deepspeed (>=0.6.0)", "fairscale (>=0.4.5)", "fastapi", "gcsfs (>=2021.5.0)", "gym[classic_control] (>=0.17.0)", "hivemind (>=1.0.1)", "horovod (>=0.21.2,!=0.24.0)", "hydra-core (>=1.0.5)", "ipython[all]", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "mlflow (>=1.0.0)", "mypy (==0.971)", "neptune-client (>=0.10.0)", "omegaconf (>=2.0.5)", "onnxruntime", "pandas (>1.0)", "pre-commit (>=1.0)", "protobuf (<=3.20.1)", "psutil", "pytest (>=7.0)", "pytest-cov", "pytest-forked", "pytest-rerunfailures (>=10.2)", "rich (>=10.14.0,!=10.15.0.a)", "scikit-learn (>0.22.1)", "torchtext (>=0.10)", "torchvision (>=0.10)", "uvicorn", "wandb (>=0.10.22)"] deepspeed = ["deepspeed (>=0.6.0)"] -dev = ["cloudpickle (>=1.3)", "codecov (>=2.1)", "comet-ml (>=3.1.12)", "coverage (>=6.4)", "fastapi", "gcsfs (>=2021.5.0)", "hydra-core (>=1.0.5)", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "mlflow (>=1.0.0)", "mypy (==0.971)", "neptune-client (>=0.10.0)", "omegaconf (>=2.0.5)", "onnxruntime", "pandas (>1.0)", "pre-commit (>=1.0)", "psutil", "pytest (>=7.0)", "pytest-cov", "pytest-forked", "pytest-rerunfailures (>=10.2)", "rich (>=10.14.0,!=10.15.0.a)", "scikit-learn (>0.22.1)", "test-tube (>=0.7.5)", "torchtext (>=0.10)", "uvicorn", "wandb (>=0.10.22)"] +dev = ["cloudpickle (>=1.3)", "codecov (>=2.1)", "comet-ml (>=3.1.12)", "coverage (>=6.4)", "fastapi", "gcsfs (>=2021.5.0)", "hydra-core (>=1.0.5)", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "mlflow (>=1.0.0)", "mypy (==0.971)", "neptune-client (>=0.10.0)", "omegaconf (>=2.0.5)", "onnxruntime", "pandas (>1.0)", "pre-commit (>=1.0)", "protobuf (<=3.20.1)", "psutil", "pytest (>=7.0)", "pytest-cov", "pytest-forked", "pytest-rerunfailures (>=10.2)", "rich (>=10.14.0,!=10.15.0.a)", "scikit-learn (>0.22.1)", "torchtext (>=0.10)", "uvicorn", "wandb (>=0.10.22)"] examples = ["gym[classic_control] (>=0.17.0)", "ipython[all]", "torchvision (>=0.10)"] -extra = ["gcsfs (>=2021.5.0)", "hydra-core (>=1.0.5)", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "omegaconf (>=2.0.5)", "rich (>=10.14.0,!=10.15.0.a)", "torchtext (>=0.10)"] +extra = ["gcsfs (>=2021.5.0)", "hydra-core (>=1.0.5)", "jsonargparse[signatures] (>=4.12.0)", "matplotlib (>3.1)", "omegaconf (>=2.0.5)", "protobuf (<=3.20.1)", "rich (>=10.14.0,!=10.15.0.a)", "torchtext (>=0.10)"] fairscale = ["fairscale (>=0.4.5)"] hivemind = ["hivemind (>=1.0.1)"] horovod = ["horovod (>=0.21.2,!=0.24.0)"] -loggers = ["comet-ml (>=3.1.12)", "mlflow (>=1.0.0)", "neptune-client (>=0.10.0)", "test-tube (>=0.7.5)", "wandb (>=0.10.22)"] +loggers = ["comet-ml (>=3.1.12)", "mlflow (>=1.0.0)", "neptune-client (>=0.10.0)", "wandb (>=0.10.22)"] strategies = ["deepspeed (>=0.6.0)", "fairscale (>=0.4.5)", "hivemind (>=1.0.1)", "horovod (>=0.21.2,!=0.24.0)"] test = ["cloudpickle (>=1.3)", "codecov (>=2.1)", "coverage (>=6.4)", "fastapi", "mypy (==0.971)", "onnxruntime", "pandas (>1.0)", "pre-commit (>=1.0)", "psutil", "pytest (>=7.0)", "pytest-cov", "pytest-forked", "pytest-rerunfailures (>=10.2)", "scikit-learn (>0.22.1)", "uvicorn"] @@ -1488,6 +1552,14 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "snowballstemmer" +version = "2.2.0" +description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "stack-data" version = "0.5.0" @@ -1504,11 +1576,22 @@ pure-eval = "*" [package.extras] tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] +[[package]] +name = "stevedore" +version = "4.0.0" +description = "Manage dynamic plugins for Python applications" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +pbr = ">=2.0.0,<2.1.0 || >2.1.0" + [[package]] name = "sympy" version = "1.11.1" description = "Computer algebra system (CAS) in Python" -category = "main" +category = "dev" optional = false python-versions = ">=3.8" @@ -1688,6 +1771,14 @@ python-versions = ">=3.7" [package.extras] test = ["pre-commit", "pytest"] +[[package]] +name = "types-PyYAML" +version = "6.0.11" +description = "Typing stubs for PyYAML" +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "typing-extensions" version = "4.3.0" @@ -1711,7 +1802,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.16.4" +version = "20.16.5" description = "Virtual Python Environment builder" category = "dev" optional = false @@ -1728,7 +1819,7 @@ testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7 [[package]] name = "wandb" -version = "0.13.2" +version = "0.13.3" description = "A CLI and library for interacting with the Weights and Biases API." category = "main" optional = false @@ -1759,7 +1850,7 @@ kubeflow = ["google-cloud-storage", "kubernetes", "minio", "sh"] launch = ["boto3", "botocore", "chardet", "google-cloud-storage", "iso8601", "kubernetes", "nbconvert", "nbformat", "typing-extensions"] media = ["bokeh", "moviepy", "numpy", "pillow", "plotly", "rdkit-pypi", "soundfile"] models = ["cloudpickle"] -sweeps = ["sweeps (>=0.1.0)"] +sweeps = ["sweeps (>=0.2.0)"] [[package]] name = "wcwidth" @@ -1821,7 +1912,7 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>= [metadata] lock-version = "1.1" python-versions = ">=3.8,<3.11" -content-hash = "7bfd78b5b905b80524e0e85692f28b29f7b5a0fa6ad395ab31dc5d0d2d61f60d" +content-hash = "29a47327e618883870cd556a7d1c7a886eed762f0392fefceff26e2ddd743d7b" [metadata.files] absl-py = [ @@ -1930,6 +2021,10 @@ backcall = [ {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"}, {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"}, ] +bandit = [ + {file = "bandit-1.7.4-py3-none-any.whl", hash = "sha256:412d3f259dab4077d0e7f0c11f50f650cc7d10db905d98f6520a95a18049658a"}, + {file = "bandit-1.7.4.tar.gz", hash = "sha256:2d63a8c573417bae338962d4b9b06fbc6080f74ecd955a092849e1e65c717bd2"}, +] black = [ {file = "black-22.8.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ce957f1d6b78a8a231b18e0dd2d94a33d2ba738cd88a7fe64f53f659eea49fdd"}, {file = "black-22.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5107ea36b2b61917956d018bd25129baf9ad1125e39324a9b18248d362156a27"}, @@ -1959,12 +2054,9 @@ cachetools = [ {file = "cachetools-5.2.0-py3-none-any.whl", hash = "sha256:f9f17d2aec496a9aa6b76f53e3b614c965223c061982d434d160f930c698a9db"}, {file = "cachetools-5.2.0.tar.gz", hash = "sha256:6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757"}, ] -Cerberus = [ - {file = "Cerberus-1.3.4.tar.gz", hash = "sha256:d1b21b3954b2498d9a79edf16b3170a3ac1021df88d197dc2ce5928ba519237c"}, -] certifi = [ - {file = "certifi-2022.6.15-py3-none-any.whl", hash = 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true + +[tool.poetry.group.notebooks.dependencies] ipykernel = "^6.15.2" -isort = "^5.10.1" matplotlib = "^3.5.3" -mypy = "^0.971" +onnx = "^1.12.0" onnxruntime = "^1.12.1" onnxruntime-gpu = "^1.12.1" + +[tool.poetry.group.dev.dependencies] +Flake8-pyproject = "^1.1.0" +bandit = "^1.7.4" +black = {extras = ["jupyter"], version = "^22.8.0"} +flake8 = "^5.0.4" +flake8-docstrings = "^1.6.0" +isort = "^5.10.1" +mypy = "^0.971" pre-commit = "^2.20.0" [build-system] build-backend = "poetry.core.masonry.api" requires = ["poetry-core>=1.0.0"] +[tool.flake8] +# rules ignored +extend-ignore = ["W503", "D401", "D403"] +per-file-ignores = ["__init__.py:F401", "__init__.py:D104"] +# black +ignore = "E203" +max-line-length = 120 + [tool.black] exclude = ''' /( @@ -47,3 +65,8 @@ target-version = ["py310"] [tool.isort] multi_line_output = 3 profile = "black" + +[tool.mypy] +python_version = "3.10" +warn_return_any = true +warn_unused_configs = true