Add sphinx docs (#10)

Author: fritzo

Makefile

@@ -0,0 +1,20 @@
+.PHONY: all install docs lint  test clean FORCE
+
+all: docs test
+
+install:
+	pip install -e .[dev,test]
+
+docs: FORCE
+	make -C docs html
+
+lint: FORCE
+	flake8
+
+test: lint FORCE
+	pytest -vx test
+
+clean: FORCE
+	git clean -dfx -e pyroapi-egg.info
+
+FORCE:

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,90 @@
+import os
+import sys
+
+import sphinx_rtd_theme
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- Project information -----------------------------------------------------
+
+project = u'Pyro API'
+copyright = u'2019, Uber Technologies, Inc'
+author = u'Uber AI Labs'
+
+# The full version, including alpha/beta/rc tags
+release = u'0.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+]
+
+# Disable documentation inheritance so as to avoid inheriting
+# docstrings in a different format, e.g. when the parent class
+# is a PyTorch class.
+
+autodoc_inherit_docstrings = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# do not prepend module name to functions
+add_module_names = False
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/dispatch.rst

@@ -0,0 +1,43 @@
+Dispatch
+========
+
+It's easiest to see how to use pyroapi by example:
+
+.. code-block:: python
+
+    from pyroapi import distributions as dist
+    from pyroapi import infer, ops, optim, pyro, pyro_backend
+
+    # These model and guide are backend-agnostic.
+    def model():
+        locs = pyro.param("locs", ops.tensor([0.2, 0.3, 0.5]))
+        p = ops.tensor([0.2, 0.3, 0.5])
+        with pyro.plate("plate", len(data), dim=-1):
+            x = pyro.sample("x", dist.Categorical(p))
+            pyro.sample("obs", dist.Normal(locs[x], 1.), obs=data)
+
+    def guide():
+        p = pyro.param("p", ops.tensor([0.5, 0.3, 0.2]))
+        with pyro.plate("plate", len(data), dim=-1):
+            pyro.sample("x", dist.Categorical(p))
+
+    # We can now set a backend at inference time.
+    with pyro_backend("numpyro"):
+        elbo = infer.Trace_ELBO(ignore_jit_warnings=True)
+        adam = optim.Adam({"lr": 1e-6})
+        inference = infer.SVI(model, guide, adam, elbo)
+        for step in range(10):
+            loss = inference.step(*args, **kwargs)
+            print(f"step {step} loss = {loss}")
+
+.. automodule:: pyroapi.dispatch
+.. autofunction:: pyroapi.dispatch.pyro_backend
+
+Generic Modules
+---------------
+- pyro - The main pyro module.
+- distributions - Includes distributions.transforms and distributions.constraints.
+- handlers - Generalizing the original pyro.poutine.
+- infer - Inference algorithms.
+- optim - Optimization utilities.
+- ops - Basic tensor operations (like numpy or torch).

docs/source/index.rst

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+.. pyroapi documentation master file, created by
+   sphinx-quickstart on Fri Oct 18 13:54:39 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Pyro API
+========
+
+The ``pyroapi`` package dynamically dispatches among multiple Pyro backends, including standard Pyro_, NumPyro_, Funsor_, and custom user-defined backends.
+This package includes both **dispatch** mechanisms for use in model and inference code, and **testing** utilities to help develop and test new Pyro backends.
+
+.. _Pyro: https://pyro.ai
+.. _NumPyro: https://num.pyro.ai
+.. _Funsor: https://funsor.pyro.ai
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   dispatch
+   testing
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/testing.rst

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+Testing
+=======
+
+The pyroapi package includes tests to ensure new backends conform to the standard API, indeed these tests serve as the formal API description.
+To add tests to your new backend say in ``project/test/`` follow these steps (or see the example_ in funsor):
+
+.. _example: https://github.com/pyro-ppl/funsor/tree/master/test/pyroapi
+
+1. Create a new directory ``project/test/pyroapi/``.
+
+2. Create a file ``project/test/pyroapi/conftest.py`` and a hook to treat missing features as xfail:
+
+.. code-block:: python
+
+    import pytest
+
+
+    def pytest_runtest_call(item):
+        try:
+            item.runtest()
+        except NotImplementedError as e:
+            pytest.xfail(str(e))
+
+3. Create a file ``project/test/pyroapi/test_pyroapi.py`` and define a ``backend`` fixture:
+
+.. code-block:: python
+
+    import pytest
+    from pyroapi import pyro_backend
+    from pyroapi.tests import *  # noqa F401
+
+    @pytest.yield_fixture
+    def backend():
+        with pyro_backend("my_backend"):
+            yield
+
+4. Test your backend with pytest
+
+.. code-block:: bash
+
+    pytest -vx test/pyroapi

setup.py

@@ -37,7 +37,11 @@
             'numpyro@https://api.github.com/repos/pyro-ppl/numpyro/tarball/master',
             'funsor@https://api.github.com/repos/pyro-ppl/funsor/tarball/master',
         ],
-        'dev': ['ipython'],
+        'dev': [
+            'sphinx>=2.0',
+            'sphinx_rtd_theme',
+            'ipython',
+        ],
     },
     long_description=long_description,
     long_description_content_type='text/markdown',