[REVIEW] - Adding example docstrings for cuML - PCA, TSVD, and DBSCAN algos

.gitignore

@@ -0,0 +1 @@
+*.swp

Dockerfile

@@ -0,0 +1,10 @@
+# From: https://github.com/rapidsai/pygdf/blob/master/Dockerfile
+FROM pygdf
+
+ADD ml-prims /cuML/ml-prims
+ADD cuML /cuML/cuML
+ADD python /cuML/python
+
+WORKDIR /cuML/python
+RUN source activate gdf && conda install cython
+RUN source activate gdf && python setup.py install

conda_environments/builddocs_py35.yml

@@ -0,0 +1,20 @@
+name: builddocs_py35
+channels:
+- gpuopenanalytics/label/dev
+- conda-forge
+- numba
+- defaults
+dependencies:
+- python=3.5.*
+- pytest
+- cudatoolkit=9.2
+- pygdf=0.1.0a3.*
+- numba>=0.40.0dev
+- pandas=0.20.*
+- pyarrow=0.10.*
+- cython=0.28.5
+- pip:
+  - numpydoc
+  - sphinx
+  - sphinx-rtd-theme
+  - sphinxcontrib-websupport

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = cuML
+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/README.md

@@ -0,0 +1,37 @@
+# Building Documentation
+
+A basic python environment with packages listed in `./requirement.txt` is
+enough to build the docs.
+
+## For building locally:
+```
+# From project root:
+conda create env --name docs -f conda_environments/builddocs_py35.yml
+source activate docs
+cd python
+python setup.py install
+cd ../docs
+make html
+```
+
+## For building via Docker
+
+## Start cuML container:
+```
+docker run -p 8000:8000 -it cuml bash
+```
+
+## Setup container's conda env for building docs:
+```
+sudo sh setup.sh ${cuML-container-id}
+```
+
+## Build & host docs from container:
+```
+sudo sh build.sh ${cuML-container-id}
+```
+
+## Copy docs from container to host:
+```
+docker cp ${cuML-container-id}:/docs/build/html .
+```

docs/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+CONTAINER_ID=$1
+
+cd ..
+docker cp docs $CONTAINER_ID:/
+docker exec -it $CONTAINER_ID bash -c "source activate gdf && \
+                                       cd /docs &&
+                                       make html && \
+                                       cd build/html && \
+                                       python -m http.server"

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=cuML
+
+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/requirement.txt

@@ -0,0 +1,3 @@
+sphinx
+sphinx_rtd_theme
+numpydoc

docs/setup.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+CONTAINER_ID=$1
+
+cd ..
+docker cp docs $CONTAINER_ID:/
+docker exec -it $CONTAINER_ID bash -c "source activate gdf && \
+                                       cd /docs &&
+                                       pip install -r requirement.txt"

docs/source/api.rst

@@ -0,0 +1,23 @@
+cuML API Reference
+====================
+
+.. currentmodule:: cuML.DBSCAN
+
+
+DBSCAN
+---------
+
+.. autoclass:: cuML.DBSCAN
+    :members:
+
+PCA
+---------
+
+.. autoclass:: cuML.PCA
+    :members:
+
+Truncated SVD
+-------------
+
+.. autoclass:: cuML.TruncatedSVD
+    :members:

docs/source/conf.py

@@ -0,0 +1,182 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2018, NVIDIA CORPORATION.
+#
+# pygdf documentation build configuration file, created by
+# sphinx-quickstart on Wed May  3 10:59:22 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../python'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.intersphinx',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'numpydoc',
+]
+
+# 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'
+
+# General information about the project.
+project = 'cuML'
+copyright = '2019, nvidia'
+author = 'nvidia'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.0.1-alpha'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1-alpha'
+
+# 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 patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = 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'
+
+# on_rtd is whether we are on readthedocs.org
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+if not on_rtd:
+    # only import and set the theme if we're building docs locally
+    # otherwise, readthedocs.org uses their theme by default,
+    # so no need to specify it
+    import sphinx_rtd_theme
+    html_theme = 'sphinx_rtd_theme'
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'cuMLdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'cuML.tex', 'cuML Documentation',
+     'nvidia', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'cuML', 'cuML Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'cuML', 'cuML Documentation',
+     author, 'cuML', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+
+# Config numpydoc
+numpydoc_show_inherited_class_members = False
+numpydoc_class_members_toctree = False

docs/source/index.rst

@@ -0,0 +1,15 @@
+Welcome to cuML's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api.rst
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`