From f7e4844fcb19c25ad267a14a1fd83d7625077b2a Mon Sep 17 00:00:00 2001 From: Brent Yi Date: Tue, 20 Sep 2022 18:40:24 -0700 Subject: [PATCH] Add example, tests for initializing Flax modules --- docs/source/examples/17_flax_modules.rst | 76 +++ examples/17_flax_modules.py | 52 ++ poetry.lock | 690 ++++++++++++++++++++++- pyproject.toml | 6 +- tests/test_flax.py | 60 ++ 5 files changed, 853 insertions(+), 31 deletions(-) create mode 100644 docs/source/examples/17_flax_modules.rst create mode 100644 examples/17_flax_modules.py create mode 100644 tests/test_flax.py diff --git a/docs/source/examples/17_flax_modules.rst b/docs/source/examples/17_flax_modules.rst new file mode 100644 index 00000000..64b6ef71 --- /dev/null +++ b/docs/source/examples/17_flax_modules.rst @@ -0,0 +1,76 @@ +.. Comment: this file is automatically generated by `update_example_docs.py`. + It should not be modified manually. + +17. Flax Modules +========================================== + + +If you use `Flax `_\ , modules can be instantiated +directly from ``dcargs.cli``. + + + +.. code-block:: python + :linenos: + + + from flax import linen as nn + from jax import numpy as jnp + + import dcargs + + + class Classifier(nn.Module): + layers: int + """Layers in our network.""" + units: int = 32 + """Hidden unit count.""" + output_dim: int = 10 + """Number of classes.""" + + @nn.compact + def __call__(self, x: jnp.ndarray) -> jnp.ndarray: # type: ignore + for i in range(self.layers - 1): + x = nn.Dense( + self.units, + kernel_init=nn.initializers.kaiming_normal(), + )(x) + x = nn.relu(x) + + x = nn.Dense( + self.output_dim, + kernel_init=nn.initializers.xavier_normal(), + )(x) + x = nn.sigmoid(x) + return x + + + def train(model: Classifier, num_iterations: int = 1000) -> None: + """Train a model. + + Args: + model: Model to train. + num_iterations: Number of training iterations. + """ + print(f"{model=}") + print(f"{num_iterations=}") + + + if __name__ == "__main__": + dcargs.cli(train) + +------------ + +.. raw:: html + + python 17_flax_modules.py --help + +.. program-output:: python ../../examples/17_flax_modules.py --help + +------------ + +.. raw:: html + + python 17_flax_modules.py --model.layers 4 + +.. program-output:: python ../../examples/17_flax_modules.py --model.layers 4 diff --git a/examples/17_flax_modules.py b/examples/17_flax_modules.py new file mode 100644 index 00000000..37ebb3d1 --- /dev/null +++ b/examples/17_flax_modules.py @@ -0,0 +1,52 @@ +"""If you use [Flax](https://github.com/google/flax), modules can be instantiated +directly from `dcargs.cli`. + +Usage: +`python ./17_flax_modules.py --help` +`python ./17_flax_modules.py --model.layers 4` +""" + +from flax import linen as nn +from jax import numpy as jnp + +import dcargs + + +class Classifier(nn.Module): + layers: int + """Layers in our network.""" + units: int = 32 + """Hidden unit count.""" + output_dim: int = 10 + """Number of classes.""" + + @nn.compact + def __call__(self, x: jnp.ndarray) -> jnp.ndarray: # type: ignore + for i in range(self.layers - 1): + x = nn.Dense( + self.units, + kernel_init=nn.initializers.kaiming_normal(), + )(x) + x = nn.relu(x) + + x = nn.Dense( + self.output_dim, + kernel_init=nn.initializers.xavier_normal(), + )(x) + x = nn.sigmoid(x) + return x + + +def train(model: Classifier, num_iterations: int = 1000) -> None: + """Train a model. + + Args: + model: Model to train. + num_iterations: Number of training iterations. + """ + print(f"{model=}") + print(f"{num_iterations=}") + + +if __name__ == "__main__": + dcargs.cli(train) diff --git a/poetry.lock b/poetry.lock index 6c208604..2d40220f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,18 +1,18 @@ [[package]] -name = "antlr4-python3-runtime" -version = "4.9.3" -description = "ANTLR 4.9.3 runtime for Python 3.7" +name = "absl-py" +version = "1.2.0" +description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] -name = "atomicwrites" -version = "1.4.1" -description = "Atomic file writes." +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = "*" [[package]] name = "attrs" @@ -36,6 +36,22 @@ category = "main" optional = false python-versions = ">=3.6.0" +[[package]] +name = "chex" +version = "0.1.5" +description = "Chex: Testing made fun, in JAX!" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +absl-py = ">=0.9.0" +dm-tree = ">=0.1.5" +jax = ">=0.1.55" +jaxlib = ">=0.1.37" +numpy = ">=1.18.0" +toolz = ">=0.9.0" + [[package]] name = "colorama" version = "0.4.5" @@ -69,6 +85,22 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1 [package.extras] toml = ["tomli"] +[[package]] +name = "cycler" +version = "0.11.0" +description = "Composable style cycles" +category = "dev" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "dm-tree" +version = "0.1.7" +description = "Tree is a library for working with nested data structures." +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "docstring-parser" version = "0.14.1" @@ -77,6 +109,78 @@ category = "main" optional = false python-versions = ">=3.6,<4.0" +[[package]] +name = "etils" +version = "0.8.0" +description = "Collection of common python utils" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +importlib_resources = {version = "*", optional = true, markers = "extra == \"epath\""} +typing_extensions = {version = "*", optional = true, markers = "extra == \"epath\""} +zipp = {version = "*", optional = true, markers = "extra == \"epath\""} + +[package.extras] +all = ["etils[array-types]", "etils[ecolab]", "etils[edc]", "etils[enp]", "etils[epath]", "etils[epy]", "etils[etqdm]", "etils[etree-dm]", "etils[etree-jax]", "etils[etree-tf]", "etils[etree]"] +array-types = ["etils[enp]"] +dev = ["chex", "pylint (>=2.6.0)", "pytest", "pytest-subtests", "pytest-xdist", "yapf"] +ecolab = ["etils[enp]", "etils[epy]", "jupyter", "mediapy", "numpy"] +edc = ["etils[epy]"] +enp = ["etils[epy]", "numpy"] +epath = ["etils[epy]", "importlib_resources", "typing_extensions", "zipp"] +epy = ["typing_extensions"] +etqdm = ["absl-py", "etils[epy]", "tqdm"] +etree = ["etils[array_types]", "etils[enp]", "etils[epy]", "etils[etqdm]"] +etree-dm = ["dm-tree", "etils[etree]"] +etree-jax = ["etils[etree]", "jax[cpu]"] +etree-tf = ["etils[etree]", "tf-nightly"] +lazy-imports = ["etils[ecolab]"] + +[[package]] +name = "flax" +version = "0.6.0" +description = "Flax: A neural network library for JAX designed for flexibility" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +jax = ">=0.3.16" +matplotlib = "*" +msgpack = "*" +numpy = ">=1.12" +optax = "*" +PyYAML = ">=5.4.1" +rich = ">=11.1,<12.0" +typing-extensions = ">=4.1.1" + +[package.extras] +testing = ["atari-py (==0.2.5)", "clu", "gym (==0.18.3)", "jaxlib", "jraph (>=0.0.6dev0)", "ml-collections", "opencv-python", "pytest", "pytest-cov", "pytest-custom-exit-code", "pytest-xdist (==1.34.0)", "pytype", "sentencepiece", "svn", "tensorflow", "tensorflow-datasets", "tensorflow-text (>=2.4.0)", "torch"] + +[[package]] +name = "fonttools" +version = "4.37.3" +description = "Tools to manipulate font files" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] +graphite = ["lz4 (>=1.7.4.2)"] +interpolatable = ["munkres", "scipy"] +lxml = ["lxml (>=4.0,<5)"] +pathops = ["skia-pathops (>=0.5.0)"] +plot = ["matplotlib"] +repacker = ["uharfbuzz (>=0.23.0)"] +symfont = ["sympy"] +type1 = ["xattr"] +ufo = ["fs (>=2.2.0,<3)"] +unicode = ["unicodedata2 (>=14.0.0)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] + [[package]] name = "frozendict" version = "2.3.4" @@ -102,6 +206,21 @@ docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] perf = ["ipython"] testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] +[[package]] +name = "importlib-resources" +version = "5.9.0" +description = "Read resources from Python packages" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + [[package]] name = "iniconfig" version = "1.1.1" @@ -110,6 +229,83 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "jax" +version = "0.3.17" +description = "Differentiate, compile, and transform Numpy code." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +absl-py = "*" +etils = {version = "*", extras = ["epath"]} +numpy = ">=1.20" +opt_einsum = "*" +scipy = ">=1.5" +typing_extensions = "*" + +[package.extras] +australis = ["protobuf (>=3.13,<4)"] +ci = ["jaxlib (==0.3.15)"] +cpu = ["jaxlib (==0.3.15)"] +cuda = ["jaxlib (==0.3.15+cuda11.cudnn82)"] +cuda11_cudnn805 = ["jaxlib (==0.3.15+cuda11.cudnn805)"] +cuda11_cudnn82 = ["jaxlib (==0.3.15+cuda11.cudnn82)"] +minimum-jaxlib = ["jaxlib (==0.3.14)"] +tpu = ["jaxlib (==0.3.15)", "libtpu-nightly (==0.1.dev20220723)", "requests"] + +[[package]] +name = "jaxlib" +version = "0.3.15" +description = "XLA library for JAX" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +absl-py = "*" +numpy = ">=1.19" +scipy = ">=1.5" + +[[package]] +name = "kiwisolver" +version = "1.4.4" +description = "A fast implementation of the Cassowary constraint solver" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} + +[[package]] +name = "matplotlib" +version = "3.5.3" +description = "Python plotting package" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +cycler = ">=0.10" +fonttools = ">=4.22.0" +kiwisolver = ">=1.0.1" +numpy = ">=1.17" +packaging = ">=20.0" +pillow = ">=6.2.0" +pyparsing = ">=2.2.1" +python-dateutil = ">=2.7" +setuptools_scm = ">=4,<7" + +[[package]] +name = "msgpack" +version = "1.0.4" +description = "MessagePack serializer" +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "mypy" version = "0.971" @@ -158,7 +354,7 @@ python-versions = ">=3.7" [[package]] name = "omegaconf" -version = "2.2.2" +version = "2.2.3" description = "A flexible configuration library" category = "dev" optional = false @@ -168,6 +364,37 @@ python-versions = ">=3.6" antlr4-python3-runtime = ">=4.9.0,<4.10.0" PyYAML = ">=5.1.0" +[[package]] +name = "opt-einsum" +version = "3.3.0" +description = "Optimizing numpys einsum function" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +numpy = ">=1.7" + +[package.extras] +docs = ["numpydoc", "sphinx (==1.2.3)", "sphinx-rtd-theme", "sphinxcontrib-napoleon"] +tests = ["pytest", "pytest-cov", "pytest-pep8"] + +[[package]] +name = "optax" +version = "0.1.3" +description = "A gradient processing and optimisation library in JAX." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +absl-py = ">=0.7.1" +chex = ">=0.0.4" +jax = ">=0.1.55" +jaxlib = ">=0.1.37" +numpy = ">=1.18.0" +typing-extensions = ">=3.10.0" + [[package]] name = "packaging" version = "21.3" @@ -179,6 +406,18 @@ python-versions = ">=3.6" [package.dependencies] pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +[[package]] +name = "Pillow" +version = "9.2.0" +description = "Python Imaging Library (Fork)" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] + [[package]] name = "pluggy" version = "1.0.0" @@ -226,7 +465,7 @@ diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyright" -version = "1.1.266" +version = "1.1.271" description = "Command line wrapper for pyright" category = "dev" optional = false @@ -242,14 +481,13 @@ dev = ["twine (>=3.4.1)"] [[package]] name = "pytest" -version = "7.1.2" +version = "7.1.3" description = "pytest: simple powerful testing with Python" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} @@ -278,7 +516,18 @@ pytest = ">=4.6" testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] [[package]] -name = "pyyaml" +name = "python-dateutil" +version = "2.8.2" +description = "Extensions to the standard Python datetime module" +category = "dev" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" + +[package.dependencies] +six = ">=1.5" + +[[package]] +name = "PyYAML" version = "6.0" description = "YAML parser and emitter for Python" category = "main" @@ -287,20 +536,32 @@ python-versions = ">=3.6" [[package]] name = "rich" -version = "12.5.1" +version = "11.2.0" description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" category = "main" optional = false -python-versions = ">=3.6.3,<4.0.0" +python-versions = ">=3.6.2,<4.0.0" [package.dependencies] +colorama = ">=0.4.0,<0.5.0" commonmark = ">=0.9.0,<0.10.0" pygments = ">=2.6.0,<3.0.0" -typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""} +typing-extensions = {version = ">=3.7.4,<5.0", markers = "python_version < \"3.8\""} [package.extras] jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"] +[[package]] +name = "scipy" +version = "1.6.1" +description = "SciPy: Scientific Library for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = ">=1.16.5" + [[package]] name = "setuptools" version = "65.3.0" @@ -314,6 +575,31 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-g testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] +[[package]] +name = "setuptools-scm" +version = "6.4.2" +description = "the blessed package to manage your versions by scm tags" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +packaging = ">=20.0" +setuptools = "*" +tomli = ">=1.0.0" + +[package.extras] +test = ["pytest (>=6.2)", "virtualenv (>20)"] +toml = ["setuptools (>=42)"] + +[[package]] +name = "six" +version = "1.16.0" +description = "Python 2 and 3 compatibility utilities" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" + [[package]] name = "tomli" version = "2.0.1" @@ -322,6 +608,14 @@ category = "dev" optional = false python-versions = ">=3.7" +[[package]] +name = "toolz" +version = "0.12.0" +description = "List processing tools and functional utilities" +category = "dev" +optional = false +python-versions = ">=3.5" + [[package]] name = "torch" version = "1.12.1" @@ -364,15 +658,16 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>= [metadata] lock-version = "1.1" python-versions = "^3.7" 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--git a/pyproject.toml b/pyproject.toml index 80a484af..65f5aa06 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,8 +17,7 @@ PyYAML = "^6.0" "backports.cached-property" = { version = "^1.0.2", python = "~3.7" } colorama = {version = "^0.4.0", platform = "win32"} frozendict = "^2.3.4" -# shtab = "^1.5.5" -rich = "^12.5.1" +rich = ">=11.1.0" [tool.poetry.dev-dependencies] pytest = "^7.1.2" @@ -31,6 +30,9 @@ pyright = "^1.1.264" coverage = {extras = ["toml"], version = "^6.4.2"} numpy = ">=1.20.0" +[tool.poetry.group.dev.dependencies] +flax = "^0.6.0" + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" diff --git a/tests/test_flax.py b/tests/test_flax.py new file mode 100644 index 00000000..fa2cb027 --- /dev/null +++ b/tests/test_flax.py @@ -0,0 +1,60 @@ +"""Tests initializing flax modules directly via dcargs.""" +import jax +import pytest +from flax import linen as nn +from jax import numpy as jnp + +import dcargs + + +class Classifier(nn.Module): + layers: int + units: int + output_dim: int + + @nn.compact + def __call__(self, x: jnp.ndarray) -> jnp.ndarray: # type: ignore + for i in range(self.layers - 1): + x = nn.Dense( + self.units, + kernel_init=nn.initializers.kaiming_normal(), + )(x) + x = nn.relu(x) + + x = nn.Dense( + self.output_dim, + kernel_init=nn.initializers.xavier_normal(), + )(x) + x = nn.sigmoid(x) + return x + + +def test_ok(): + network = dcargs.cli( + Classifier, + args=[ + "--layers", + "3", + "--units", + "8", + "--output-dim", + "3", + ], + ) + + x = jnp.zeros((10, 4)) + params = network.init(jax.random.PRNGKey(0), x) + assert network.apply(params, x).shape == (10, 3) + + +def test_missing(): + with pytest.raises(SystemExit): + dcargs.cli( + Classifier, + args=[ + "--layers", + "3", + "--units", + "8", + ], + )