Repo setup

.gitignore

@@ -8,6 +8,7 @@
 *.so
 *.pyc
 .classpath
+*build
 
 # Packages #
 ############
@@ -54,5 +55,4 @@ Thumbs.db
 /data
 example_scripts/example_output/
 */tmp/*
-venv
-docs
+venv

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)

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

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),
+}

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

docs/source/installation.rst

@@ -0,0 +1,7 @@
+============
+Installation
+============
+
+At the command line::
+
+    $ pip install constrainedmf

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
+<https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.

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 <https://arxiv.org/abs/2104.00864>`_,
+with the peer reviewed version accepted for publication in Applied Physics Reviews.

docs/source/usage.rst

@@ -0,0 +1,9 @@
+=====
+Usage
+=====
+
+Start by importing constrained-matrix-factorization.
+
+.. code-block:: python
+
+    import constrainedmf

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={