diff --git a/.gitignore b/.gitignore index 99c9143..fe02382 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,7 @@ *.so *.pyc .classpath +*build # Packages # ############ @@ -54,5 +55,4 @@ Thumbs.db /data example_scripts/example_output/ */tmp/* -venv -docs \ No newline at end of file +venv \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..b4a5893 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = "-W" # This flag turns warnings into errors. +SPHINXBUILD = sphinx-build +SPHINXPROJ = PackagingScientificPython +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) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..2be8306 --- /dev/null +++ b/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=PackagingScientificPython + +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 diff --git a/docs/source/_static/.placeholder b/docs/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..aba3808 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,215 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# constrained-matrix-factorization documentation build configuration file, created by +# sphinx-quickstart on Thu Jun 28 12:35:56 2018. +# +# 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('.')) + + +# -- 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.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.githubpages", + "sphinx.ext.intersphinx", + "sphinx.ext.mathjax", + "sphinx.ext.viewcode", + "IPython.sphinxext.ipython_directive", + "IPython.sphinxext.ipython_console_highlighting", + "matplotlib.sphinxext.plot_directive", + "numpydoc", + "sphinx_copybutton", +] + +# Configuration options for plot_directive. See: +# https://github.com/matplotlib/matplotlib/blob/f3ed922d935751e08494e5fb5311d3050a3b637b/lib/matplotlib/sphinxext/plot_directive.py#L81 +plot_html_show_source_link = False +plot_html_show_formats = False + +# Generate the API documentation when building +autosummary_generate = True +numpydoc_show_class_members = 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" + +# General information about the project. +project = "constrained-matrix-factorization" +copyright = "2021, Phil Maffettone" +author = "Phil Maffettone" + +# 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. +# +import constrainedmf + +# The short X.Y version. +version = constrainedmf.__version__ +# The full version, including alpha/beta/rc tags. +release = constrainedmf.__version__ + +# 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" +import 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"] + +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# This is required for the alabaster theme +# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars +html_sidebars = { + "**": [ + "relations.html", # needs 'show_related': True theme option to display + "searchbox.html", + ] +} + + +# -- Options for HTMLHelp output ------------------------------------------ + +# Output file base name for HTML help builder. +htmlhelp_basename = "constrainedmf" + + +# -- 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, + "constrainedmf.tex", + "constrained-matrix-factorization Documentation", + "Contributors", + "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, + "constrainedmf", + "constrained-matrix-factorization 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, + "constrainedmf", + "constrained-matrix-factorization Documentation", + author, + "constrainedmf", + "Advancements on non-negative matrix factorization in PyTorch, with crystallography as a primary use case.", + "Miscellaneous", + ), +] + + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None), + "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None), + "matplotlib": ("https://matplotlib.org/stable", None), +} diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..3621fc4 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,15 @@ +.. Packaging Scientific Python documentation master file, created by + sphinx-quickstart on Thu Jun 28 12:35:56 2018. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +constrained-matrix-factorization Documentation +============================================== + +.. toctree:: + :maxdepth: 2 + + installation + usage + release-history + min_versions diff --git a/docs/source/installation.rst b/docs/source/installation.rst new file mode 100644 index 0000000..5bc20fe --- /dev/null +++ b/docs/source/installation.rst @@ -0,0 +1,7 @@ +============ +Installation +============ + +At the command line:: + + $ pip install constrainedmf diff --git a/docs/source/min_versions.rst b/docs/source/min_versions.rst new file mode 100644 index 0000000..d28e747 --- /dev/null +++ b/docs/source/min_versions.rst @@ -0,0 +1,28 @@ +=================================== +Minimum Version of Python and NumPy +=================================== + + +- This project supports at least the minor versions of Python + initially released 42 months prior to a planned project release + date. +- The project will always support at least the 2 latest minor + versions of Python. +- The project will support minor versions of ``numpy`` initially + released in the 24 months prior to a planned project release date or + the oldest version that supports the minimum Python version + (whichever is higher). +- The project will always support at least the 3 latest minor + versions of NumPy. + +The minimum supported version of Python will be set to +``python_requires`` in ``setup``. All supported minor versions of +Python will be in the test matrix and have binary artifacts built +for releases. + +The project should adjust upward the minimum Python and NumPy +version support on every minor and major release, but never on a +patch release. + +This is consistent with NumPy `NEP 29 +`__. diff --git a/docs/source/release-history.rst b/docs/source/release-history.rst new file mode 100644 index 0000000..16ff130 --- /dev/null +++ b/docs/source/release-history.rst @@ -0,0 +1,9 @@ +=============== +Release History +=============== + +v0.1.0 (2021-11-01) +---------------------------- +This initial release marks the transfer of this repository to the NSLS-II organization. +Initial publication details can be found on `the arXiv `_, +with the peer reviewed version accepted for publication in Applied Physics Reviews. \ No newline at end of file diff --git a/docs/source/usage.rst b/docs/source/usage.rst new file mode 100644 index 0000000..37c34b6 --- /dev/null +++ b/docs/source/usage.rst @@ -0,0 +1,9 @@ +===== +Usage +===== + +Start by importing constrained-matrix-factorization. + +.. code-block:: python + + import constrainedmf diff --git a/setup.py b/setup.py index 7c7947b..3420400 100644 --- a/setup.py +++ b/setup.py @@ -39,14 +39,14 @@ setup( - name="constrainedmf", + name="constrained-matrix-factorization", version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), description="Advancements on non-negative matrix factorization in PyTorch, with crystallography as a primary use case.", long_description=readme, author="Phil Maffettone", author_email="pmaffettone@bnl.gov", - url="https://github.com/maffettone/constrained-matrix-factorization", + url="https://github.com/NSLS-II/constrained-matrix-factorization", python_requires=">={}".format(".".join(str(n) for n in min_version)), packages=find_packages(exclude=["docs", "tests"]), entry_points={