From 0d67578a8a7198e246163f87318f756c98095bee Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:07:50 -0400 Subject: [PATCH 01/14] Remove files not needed --- .travis.yml | 35 ----------------------------------- AUTHORS.txt | 2 -- LICENSE.txt | 33 --------------------------------- rever.xsh | 13 ------------- setup.py | 39 --------------------------------------- 5 files changed, 122 deletions(-) delete mode 100644 .travis.yml delete mode 100644 AUTHORS.txt delete mode 100644 LICENSE.txt delete mode 100644 rever.xsh delete mode 100644 setup.py diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index df9531b..0000000 --- a/.travis.yml +++ /dev/null @@ -1,35 +0,0 @@ -sudo: False - -language: python -python: - - "3.7" -cache: - directories: - - $HOME/.cache/pip - -matrix: - include: - - python: 3.7 - - -install: - # Install conda - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh - - bash miniconda.sh -b -p $HOME/miniconda - - export PATH="$HOME/miniconda/bin:$PATH" - - conda config --set always_yes yes --set changeps1 no - - conda config --add channels conda-forge - - conda config --add channels diffpy - - conda update conda - # Install dependencies - - conda create -n test --file requirements/run.txt python=3.7 - - source activate test - - python setup.py install - -script: - - set -e - - conda install --file requirements/test.txt - - python -m pytest - -notifications: - email: false diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index f05c34d..0000000 --- a/AUTHORS.txt +++ /dev/null @@ -1,2 +0,0 @@ -Simon J. L. Billinge -Zachary A. Thatcher diff --git a/LICENSE.txt b/LICENSE.txt deleted file mode 100644 index 77e7af7..0000000 --- a/LICENSE.txt +++ /dev/null @@ -1,33 +0,0 @@ -This program is part of the DiffPy open-source project at Columbia -University and is available subject to the conditions and terms laid out below. - -Copyright © 2009-2019, Trustees of Columbia University in the City of New York, -all rights reserved. - -For more information please visit the diffpy web-page at http://diffpy.org or -email Prof. Simon Billinge at sb2896@columbia.edu. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - - * Neither the names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the - names of their contributors may be used to endorse or promote products - derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/rever.xsh b/rever.xsh deleted file mode 100644 index 60880c9..0000000 --- a/rever.xsh +++ /dev/null @@ -1,13 +0,0 @@ -$PROJECT = 'diffpy.nmf_mapping' -$ACTIVITIES = ['version_bump', 'changelog', 'tag', 'push_tag', 'ghrelease'] - -$VERSION_BUMP_PATTERNS = [ - ('diffpy/nmf_mapping/__init__.py', '__version__\s*=.*', "__version__ = '$VERSION'"), - ('setup.py', 'version\s*=.*,', "version='$VERSION',") - ] -$CHANGELOG_FILENAME = 'CHANGELOG.rst' -$CHANGELOG_IGNORE = ['TEMPLATE.rst'] -$PUSH_TAG_REMOTE = 'git@github.com:diffpy/diffpy.nmf_mapping.git' - -$GITHUB_ORG = 'diffpy' -$GITHUB_REPO = 'diffpy.nmf_mapping' diff --git a/setup.py b/setup.py deleted file mode 100644 index 05f92d9..0000000 --- a/setup.py +++ /dev/null @@ -1,39 +0,0 @@ -#!/usr/bin/env python - -# Installation script for diffpy.nmf_mapping - -"""nmf_mapping - tools for performing NMF on PDF and XRD data. -Packages: diffpy.nmf_mapping -""" - -from setuptools import find_packages, setup - -with open("README.md", "r") as fh: - long_description = fh.read() - - -setup( - name="diffpy.nmf_mapping", - version="1.0.0", - author="Simon J.L. Billinge", - author_email="sb2896@columbia.edu", - description="Run NMF analysis on PDF and XRD data", - long_description=long_description, - test_suite="tests", - long_description_content_type="text/markdown", - packages=find_packages(exclude=["tests", "applications", "examples"]), - classifiers=[ - "Programming Language :: Python :: 3", - "Operating System :: OS Independent", - ], - entry_points={ - "console_scripts": ["nmf_mapping = diffpy.nmf_mapping.nmf_mapping.main:main"], - }, - data_files=[("", ["LICENSE.txt"])], - url="http://www.diffpy.org/", - download_url="http://www.diffpy.org/packages/", - license="BSD", - keywords="diffpy PDF NMF", - python_requires=">=3.6", - zip_safe=False, -) From 9cf05f64f41ecf9b618bdb7af81a144e4ead0ac0 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:21:01 -0400 Subject: [PATCH 02/14] Rename and use cookiecutter doc setup --- doc/Makefile | 194 ++++++++++++ {docs => doc}/examples/NMFBatching.ipynb | 0 {docs => doc}/examples/data/edited.INP | 0 {docs => doc}/examples/data/example.INP | 0 .../examples/data/example_phases/LiO2.cif | 0 .../data/example_phases/RuO2_tetragonal.cif | 0 .../Ru_mp-8639_conventional_standard.cif | 0 .../synthetic_r_vs_gr/batch_0/synthetic0.gr | 0 .../synthetic_r_vs_gr/batch_0/synthetic1.gr | 0 .../synthetic_r_vs_gr/batch_0/synthetic2.gr | 0 .../synthetic_r_vs_gr/batch_0/synthetic3.gr | 0 .../synthetic_r_vs_gr/batch_0/synthetic4.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic10.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic11.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic12.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic5.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic6.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic7.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic8.gr | 0 .../synthetic_r_vs_gr/batch_1/synthetic9.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic13.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic14.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic15.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic16.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic17.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic18.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic19.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic20.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic21.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic22.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic23.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic24.gr | 0 .../synthetic_r_vs_gr/batch_2/synthetic25.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic26.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic27.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic28.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic29.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic30.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic31.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic32.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic33.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic34.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic35.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic36.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic37.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic38.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic39.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic40.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic41.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic42.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic43.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic44.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic45.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic46.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic47.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic48.gr | 0 .../synthetic_r_vs_gr/batch_3/synthetic49.gr | 0 .../data/synthetic_r_vs_gr/synthetic0.gr | 0 .../data/synthetic_r_vs_gr/synthetic1.gr | 0 .../data/synthetic_r_vs_gr/synthetic10.gr | 0 .../data/synthetic_r_vs_gr/synthetic11.gr | 0 .../data/synthetic_r_vs_gr/synthetic12.gr | 0 .../data/synthetic_r_vs_gr/synthetic13.gr | 0 .../data/synthetic_r_vs_gr/synthetic14.gr | 0 .../data/synthetic_r_vs_gr/synthetic15.gr | 0 .../data/synthetic_r_vs_gr/synthetic16.gr | 0 .../data/synthetic_r_vs_gr/synthetic17.gr | 0 .../data/synthetic_r_vs_gr/synthetic18.gr | 0 .../data/synthetic_r_vs_gr/synthetic19.gr | 0 .../data/synthetic_r_vs_gr/synthetic2.gr | 0 .../data/synthetic_r_vs_gr/synthetic20.gr | 0 .../data/synthetic_r_vs_gr/synthetic21.gr | 0 .../data/synthetic_r_vs_gr/synthetic22.gr | 0 .../data/synthetic_r_vs_gr/synthetic23.gr | 0 .../data/synthetic_r_vs_gr/synthetic24.gr | 0 .../data/synthetic_r_vs_gr/synthetic25.gr | 0 .../data/synthetic_r_vs_gr/synthetic26.gr | 0 .../data/synthetic_r_vs_gr/synthetic27.gr | 0 .../data/synthetic_r_vs_gr/synthetic28.gr | 0 .../data/synthetic_r_vs_gr/synthetic29.gr | 0 .../data/synthetic_r_vs_gr/synthetic3.gr | 0 .../data/synthetic_r_vs_gr/synthetic30.gr | 0 .../data/synthetic_r_vs_gr/synthetic31.gr | 0 .../data/synthetic_r_vs_gr/synthetic32.gr | 0 .../data/synthetic_r_vs_gr/synthetic33.gr | 0 .../data/synthetic_r_vs_gr/synthetic34.gr | 0 .../data/synthetic_r_vs_gr/synthetic35.gr | 0 .../data/synthetic_r_vs_gr/synthetic36.gr | 0 .../data/synthetic_r_vs_gr/synthetic37.gr | 0 .../data/synthetic_r_vs_gr/synthetic38.gr | 0 .../data/synthetic_r_vs_gr/synthetic39.gr | 0 .../data/synthetic_r_vs_gr/synthetic4.gr | 0 .../data/synthetic_r_vs_gr/synthetic40.gr | 0 .../data/synthetic_r_vs_gr/synthetic41.gr | 0 .../data/synthetic_r_vs_gr/synthetic42.gr | 0 .../data/synthetic_r_vs_gr/synthetic43.gr | 0 .../data/synthetic_r_vs_gr/synthetic44.gr | 0 .../data/synthetic_r_vs_gr/synthetic45.gr | 0 .../data/synthetic_r_vs_gr/synthetic46.gr | 0 .../data/synthetic_r_vs_gr/synthetic47.gr | 0 .../data/synthetic_r_vs_gr/synthetic48.gr | 0 .../data/synthetic_r_vs_gr/synthetic49.gr | 0 .../data/synthetic_r_vs_gr/synthetic5.gr | 0 .../data/synthetic_r_vs_gr/synthetic6.gr | 0 .../data/synthetic_r_vs_gr/synthetic7.gr | 0 .../data/synthetic_r_vs_gr/synthetic8.gr | 0 .../data/synthetic_r_vs_gr/synthetic9.gr | 0 doc/make.bat | 36 +++ doc/source/_static/.placeholder | 0 .../diffpy.nmf_mapping.example_package.rst | 31 ++ doc/source/api/diffpy.nmf_mapping.rst | 30 ++ doc/source/conf.py | 289 ++++++++++++++++++ doc/source/index.rst | 44 +++ doc/source/license.rst | 39 +++ doc/source/release.rst | 5 + 115 files changed, 668 insertions(+) create mode 100644 doc/Makefile rename {docs => doc}/examples/NMFBatching.ipynb (100%) rename {docs => doc}/examples/data/edited.INP (100%) rename {docs => doc}/examples/data/example.INP (100%) rename {docs => doc}/examples/data/example_phases/LiO2.cif (100%) rename {docs => doc}/examples/data/example_phases/RuO2_tetragonal.cif (100%) rename {docs => doc}/examples/data/example_phases/Ru_mp-8639_conventional_standard.cif (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_0/synthetic0.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_0/synthetic1.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_0/synthetic2.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_0/synthetic3.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_0/synthetic4.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic10.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic11.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic12.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic5.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic6.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic7.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic8.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_1/synthetic9.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic13.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic14.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic15.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic16.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic17.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic18.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic19.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic20.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic21.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic22.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic23.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic24.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_2/synthetic25.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic26.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic27.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic28.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic29.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic30.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic31.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic32.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic33.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic34.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic35.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic36.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic37.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic38.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic39.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic40.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic41.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic42.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic43.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic44.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic45.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic46.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic47.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic48.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/batch_3/synthetic49.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic0.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic1.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic10.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic11.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic12.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic13.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic14.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic15.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic16.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic17.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic18.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic19.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic2.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic20.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic21.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic22.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic23.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic24.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic25.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic26.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic27.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic28.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic29.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic3.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic30.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic31.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic32.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic33.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic34.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic35.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic36.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic37.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic38.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic39.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic4.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic40.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic41.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic42.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic43.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic44.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic45.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic46.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic47.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic48.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic49.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic5.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic6.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic7.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic8.gr (100%) rename {docs => doc}/examples/data/synthetic_r_vs_gr/synthetic9.gr (100%) create mode 100644 doc/make.bat create mode 100644 doc/source/_static/.placeholder create mode 100644 doc/source/api/diffpy.nmf_mapping.example_package.rst create mode 100644 doc/source/api/diffpy.nmf_mapping.rst create mode 100644 doc/source/conf.py create mode 100644 doc/source/index.rst create mode 100644 doc/source/license.rst create mode 100644 doc/source/release.rst diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..b638db2 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,194 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build +BASENAME = $(subst .,,$(subst $() $(),,diffpy.nmf_mapping)) + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +# Manual publishing to the gh-pages branch + +GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) +GITREMOTE = origin +GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) +GITLASTCOMMIT = $(shell git rev-parse --short HEAD) + +publish: + @test -d build/html || \ + ( echo >&2 "Run 'make html' first!"; false ) + git show-ref --verify --quiet refs/heads/gh-pages || \ + git branch --track gh-pages $(GITREMOTE)/gh-pages + test -d build/gh-pages || \ + git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages + cd build/gh-pages && \ + git pull $(GITREMOTEURL) gh-pages + rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ + --exclude-from=build/gh-pages/.rsync-exclude \ + --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ + cd build/gh-pages && \ + git add --all . && \ + git diff --cached --quiet || \ + git commit -m "Sync with the source at $(GITLASTCOMMIT)." + cd build/gh-pages && \ + git push origin gh-pages diff --git a/docs/examples/NMFBatching.ipynb b/doc/examples/NMFBatching.ipynb similarity index 100% rename from docs/examples/NMFBatching.ipynb rename to doc/examples/NMFBatching.ipynb diff --git a/docs/examples/data/edited.INP b/doc/examples/data/edited.INP similarity index 100% rename from docs/examples/data/edited.INP rename to doc/examples/data/edited.INP diff --git a/docs/examples/data/example.INP b/doc/examples/data/example.INP similarity index 100% rename from docs/examples/data/example.INP rename to doc/examples/data/example.INP diff --git a/docs/examples/data/example_phases/LiO2.cif b/doc/examples/data/example_phases/LiO2.cif similarity index 100% rename from docs/examples/data/example_phases/LiO2.cif rename to doc/examples/data/example_phases/LiO2.cif diff --git a/docs/examples/data/example_phases/RuO2_tetragonal.cif b/doc/examples/data/example_phases/RuO2_tetragonal.cif similarity index 100% rename from docs/examples/data/example_phases/RuO2_tetragonal.cif rename to doc/examples/data/example_phases/RuO2_tetragonal.cif diff --git a/docs/examples/data/example_phases/Ru_mp-8639_conventional_standard.cif b/doc/examples/data/example_phases/Ru_mp-8639_conventional_standard.cif similarity index 100% rename from docs/examples/data/example_phases/Ru_mp-8639_conventional_standard.cif rename to doc/examples/data/example_phases/Ru_mp-8639_conventional_standard.cif diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic0.gr b/doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic0.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic0.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic0.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic1.gr b/doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic1.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic1.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic1.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic2.gr b/doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic2.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic2.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic2.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic3.gr b/doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic3.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic3.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic3.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic4.gr b/doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic4.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_0/synthetic4.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_0/synthetic4.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic10.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic10.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic10.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic10.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic11.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic11.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic11.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic11.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic12.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic12.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic12.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic12.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic5.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic5.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic5.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic5.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic6.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic6.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic6.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic6.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic7.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic7.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic7.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic7.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic8.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic8.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic8.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic8.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic9.gr b/doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic9.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_1/synthetic9.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_1/synthetic9.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic13.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic13.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic13.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic13.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic14.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic14.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic14.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic14.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic15.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic15.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic15.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic15.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic16.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic16.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic16.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic16.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic17.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic17.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic17.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic17.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic18.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic18.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic18.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic18.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic19.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic19.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic19.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic19.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic20.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic20.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic20.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic20.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic21.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic21.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic21.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic21.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic22.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic22.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic22.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic22.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic23.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic23.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic23.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic23.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic24.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic24.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic24.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic24.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic25.gr b/doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic25.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_2/synthetic25.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_2/synthetic25.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic26.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic26.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic26.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic26.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic27.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic27.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic27.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic27.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic28.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic28.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic28.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic28.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic29.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic29.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic29.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic29.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic30.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic30.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic30.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic30.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic31.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic31.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic31.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic31.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic32.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic32.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic32.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic32.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic33.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic33.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic33.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic33.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic34.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic34.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic34.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic34.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic35.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic35.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic35.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic35.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic36.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic36.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic36.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic36.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic37.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic37.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic37.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic37.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic38.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic38.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic38.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic38.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic39.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic39.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic39.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic39.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic40.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic40.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic40.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic40.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic41.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic41.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic41.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic41.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic42.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic42.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic42.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic42.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic43.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic43.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic43.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic43.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic44.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic44.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic44.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic44.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic45.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic45.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic45.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic45.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic46.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic46.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic46.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic46.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic47.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic47.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic47.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic47.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic48.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic48.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic48.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic48.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic49.gr b/doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic49.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/batch_3/synthetic49.gr rename to doc/examples/data/synthetic_r_vs_gr/batch_3/synthetic49.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic0.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic0.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic0.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic0.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic1.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic1.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic1.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic1.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic10.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic10.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic10.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic10.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic11.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic11.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic11.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic11.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic12.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic12.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic12.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic12.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic13.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic13.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic13.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic13.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic14.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic14.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic14.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic14.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic15.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic15.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic15.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic15.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic16.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic16.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic16.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic16.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic17.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic17.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic17.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic17.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic18.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic18.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic18.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic18.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic19.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic19.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic19.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic19.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic2.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic2.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic2.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic2.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic20.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic20.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic20.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic20.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic21.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic21.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic21.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic21.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic22.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic22.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic22.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic22.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic23.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic23.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic23.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic23.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic24.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic24.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic24.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic24.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic25.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic25.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic25.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic25.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic26.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic26.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic26.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic26.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic27.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic27.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic27.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic27.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic28.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic28.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic28.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic28.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic29.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic29.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic29.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic29.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic3.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic3.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic3.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic3.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic30.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic30.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic30.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic30.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic31.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic31.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic31.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic31.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic32.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic32.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic32.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic32.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic33.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic33.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic33.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic33.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic34.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic34.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic34.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic34.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic35.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic35.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic35.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic35.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic36.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic36.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic36.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic36.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic37.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic37.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic37.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic37.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic38.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic38.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic38.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic38.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic39.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic39.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic39.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic39.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic4.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic4.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic4.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic4.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic40.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic40.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic40.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic40.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic41.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic41.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic41.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic41.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic42.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic42.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic42.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic42.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic43.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic43.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic43.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic43.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic44.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic44.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic44.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic44.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic45.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic45.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic45.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic45.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic46.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic46.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic46.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic46.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic47.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic47.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic47.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic47.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic48.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic48.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic48.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic48.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic49.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic49.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic49.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic49.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic5.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic5.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic5.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic5.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic6.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic6.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic6.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic6.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic7.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic7.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic7.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic7.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic8.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic8.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic8.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic8.gr diff --git a/docs/examples/data/synthetic_r_vs_gr/synthetic9.gr b/doc/examples/data/synthetic_r_vs_gr/synthetic9.gr similarity index 100% rename from docs/examples/data/synthetic_r_vs_gr/synthetic9.gr rename to doc/examples/data/synthetic_r_vs_gr/synthetic9.gr diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 0000000..ac53d5b --- /dev/null +++ b/doc/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/doc/source/_static/.placeholder b/doc/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/doc/source/api/diffpy.nmf_mapping.example_package.rst b/doc/source/api/diffpy.nmf_mapping.example_package.rst new file mode 100644 index 0000000..da17a67 --- /dev/null +++ b/doc/source/api/diffpy.nmf_mapping.example_package.rst @@ -0,0 +1,31 @@ +.. _example_package documentation: + +|title| +======= + +.. |title| replace:: diffpy.nmf_mapping.example_package package + +.. automodule:: diffpy.nmf_mapping.example_package + :members: + :undoc-members: + :show-inheritance: + +|foo| +----- + +.. |foo| replace:: diffpy.nmf_mapping.example_package.foo module + +.. automodule:: diffpy.nmf_mapping.example_package.foo + :members: + :undoc-members: + :show-inheritance: + +|bar| +----- + +.. |bar| replace:: diffpy.nmf_mapping.example_package.bar module + +.. automodule:: diffpy.nmf_mapping.example_package.foo + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/api/diffpy.nmf_mapping.rst b/doc/source/api/diffpy.nmf_mapping.rst new file mode 100644 index 0000000..0f03d4b --- /dev/null +++ b/doc/source/api/diffpy.nmf_mapping.rst @@ -0,0 +1,30 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: diffpy.nmf_mapping package + +.. automodule:: diffpy.nmf_mapping + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + diffpy.nmf_mapping.example_package + +Submodules +---------- + +|module| +-------- + +.. |module| replace:: diffpy.nmf_mapping.example_submodule module + +.. automodule:: diffpy.nmf_mapping.example_submodule + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/conf.py b/doc/source/conf.py new file mode 100644 index 0000000..fea3aa1 --- /dev/null +++ b/doc/source/conf.py @@ -0,0 +1,289 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# diffpy.nmf_mapping documentation build configuration file, created by +# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# +# 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. + +import sys +import time +from importlib.metadata import version +from pathlib import Path + +# 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 Path().resolve() to make it absolute, like shown here. +# sys.path.insert(0, str(Path(".").resolve())) +sys.path.insert(0, str(Path("../..").resolve())) +sys.path.insert(0, str(Path("../../src").resolve())) + +# abbreviations +ab_authors = "Billinge Group members and community contributors" + +# -- 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.napoleon", + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "m2r", +] + +# 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"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "diffpy.nmf_mapping" +copyright = "%Y, The Trustees of Columbia University in the City of New York" + +# 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. + +fullversion = version(project) +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# substitute YEAR in the copyright string +copyright = copyright.replace("%Y", year) + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["build"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ["diffpy.nmf_mapping"] + +# Display all warnings for missing links. +nitpicky = True + +# -- 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" + +# 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 = { + "navigation_with_keys": "true", +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "diffpy.nmf_mapping".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "doc" + + +# -- 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': '', +} + +# 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 = [ + ("index", "\.tex", "diffpy.nmf_mapping Documentation", ab_authors, "manual"), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [("index", "\", "diffpy.nmf_mapping Documentation", ab_authors, 1)] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- 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 = [ + ( + "index", + "\", + "diffpy.nmf_mapping Documentation", + ab_authors, + "diffpy.nmf_mapping", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/doc/source/index.rst b/doc/source/index.rst new file mode 100644 index 0000000..8ac8e89 --- /dev/null +++ b/doc/source/index.rst @@ -0,0 +1,44 @@ +####### +|title| +####### + +.. |title| replace:: diffpy.nmf_mapping documentation + +diffpy.nmf_mapping - Run NMF analysis on PDF and XRD data. + +| Software version |release|. +| Last updated |today|. + +======= +Authors +======= + +diffpy.nmf_mapping is developed by Billinge Group +and its community contributors. + +For a detailed list of contributors see +https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors. + +============ +Installation +============ + +See the `README `_ +file included with the distribution. + +================= +Table of contents +================= +.. toctree:: + :titlesonly: + + license + release + Package API + +======= +Indices +======= + +* :ref:`genindex` +* :ref:`search` diff --git a/doc/source/license.rst b/doc/source/license.rst new file mode 100644 index 0000000..cfab61c --- /dev/null +++ b/doc/source/license.rst @@ -0,0 +1,39 @@ +:tocdepth: -1 + +.. index:: license + +License +####### + +OPEN SOURCE LICENSE AGREEMENT +============================= +BSD 3-Clause License + +Copyright (c) 2024, The Trustees of Columbia University in +the City of New York. +All Rights Reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/doc/source/release.rst b/doc/source/release.rst new file mode 100644 index 0000000..27cd0cc --- /dev/null +++ b/doc/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst From e6da62ece4d64cd8fba1e77ba0e26c480f542b44 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:21:30 -0400 Subject: [PATCH 03/14] Remove older docs folder --- docs/Makefile | 194 -------------------------------------------------- docs/make.bat | 190 ------------------------------------------------ 2 files changed, 384 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/make.bat diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index f2f0753..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,194 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build -RELEASE = v0.1 - - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -DOCREPONAME = .github.io -DOCREPOURL = - - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - -rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/fief.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/fief.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/fief" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/fief" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -push-latest: - cd $(BUILDDIR) && \ - test -d $(DOCREPONAME) || git clone $(DOCREPOURL) $(DOCREPONAME) && \ - cd $(DOCREPONAME) && \ - git pull origin gh-pages && \ - test -d latest || mkdir latest && touch latest/_ && \ - rm -r latest/* && \ - cp -r ../html/* latest/ && \ - git add latest/ && \ - git commit -am "Pushed latest docs at $(date)" && \ - git push - -push-release: - cd $(BUILDDIR) && \ - test -d $(DOCREPONAME) || git clone $(DOCREPOURL) $(DOCREPONAME) && \ - cd $(DOCREPONAME) && \ - git pull origin gh-pages && \ - test -d $(RELEASE) || mkdir $(RELEASE) && touch $(RELEASE)/_ && \ - rm -r $(RELEASE)/* && \ - cp -r ../html/* $(RELEASE)/ && \ - git add $(RELEASE)/ && \ - git commit -am "Pushed $(RELEASE) docs at $(date)" && \ - git push - -push-root: - cd $(BUILDDIR) && \ - test -d $(DOCREPONAME) || git clone $(DOCREPOURL) $(DOCREPONAME) && \ - cd $(DOCREPONAME) && \ - git pull origin gh-pages && \ - rm -rf libref previous _sources _static *.html *.js *.inv && \ - cp -r ../html/* . && \ - git add . && \ - git commit -am "Pushed root-level docs at $(date)" && \ - git push diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index ec0e4c3..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,190 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run "qcollectiongenerator" with the ^ -.qhcp project file in %BUILDDIR%/qthelp, like this: - echo.^> qcollectiongenerator %BUILDDIR%\qthelp\fief.qhcp - echo.To view the help file: - echo.^> assistant -collectionFile %BUILDDIR%\qthelp\fief.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end From 46e201022a0f94d4a82c54435d4fe252ef1b528f Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:23:14 -0400 Subject: [PATCH 04/14] Add 2022 to copyright year --- doc/source/conf.py | 2 +- doc/source/license.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index fea3aa1..d931754 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -62,7 +62,7 @@ # General information about the project. project = "diffpy.nmf_mapping" -copyright = "%Y, The Trustees of Columbia University in the City of New York" +copyright = "2022-%Y, The Trustees of Columbia University in the City of New York" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/doc/source/license.rst b/doc/source/license.rst index cfab61c..cc67702 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -9,7 +9,7 @@ OPEN SOURCE LICENSE AGREEMENT ============================= BSD 3-Clause License -Copyright (c) 2024, The Trustees of Columbia University in +Copyright (c) 2022-2024, The Trustees of Columbia University in the City of New York. All Rights Reserved. From 832f38d1cb08b809afefb3ccc790018597c40489 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:36:39 -0400 Subject: [PATCH 05/14] Keep conf.py like from diffpy.snmf --- doc/source/conf.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index d931754..4280239 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -62,7 +62,7 @@ # General information about the project. project = "diffpy.nmf_mapping" -copyright = "2022-%Y, The Trustees of Columbia University in the City of New York" +copyright = "2023-%Y, The Trustees of Columbia University in the City of New York" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -221,7 +221,7 @@ # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - ("index", "\.tex", "diffpy.nmf_mapping Documentation", ab_authors, "manual"), + ("index", "diffpy.nmf_mapping.tex", "diffpy.nmf_mapping Documentation", ab_authors, "manual"), ] # The name of an image file (relative to this directory) to place at the top of @@ -249,7 +249,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [("index", "\", "diffpy.nmf_mapping Documentation", ab_authors, 1)] +man_pages = [("index", "diffpy.nmf_mapping", "diffpy.nmf_mapping Documentation", ab_authors, 1)] # If true, show URL addresses after external links. # man_show_urls = False @@ -263,7 +263,7 @@ texinfo_documents = [ ( "index", - "\", + "diffpy.nmf_mapping", "diffpy.nmf_mapping Documentation", ab_authors, "diffpy.nmf_mapping", From 135964bb78dbe85f1a8a2fd692dfd4a53443bce1 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:52:53 -0400 Subject: [PATCH 06/14] Move file paths --- ...H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr | 0 ...0934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr | 0 .../diffpy}/nmf_mapping/tests/data/example_phases/LiO2.cif | 0 .../nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif | 0 .../data/example_phases/Ru_mp-8639_conventional_standard.cif | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr | 0 .../nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr | 0 .../tests/output/output_1/component_index_vs_RE_value.json | 0 .../tests/output/output_1/component_index_vs_pratio_col.json | 0 .../tests/output/output_1/x_index_vs_y_col_components.json | 0 .../tests/output/output_2/component_index_vs_RE_value.json | 0 .../tests/output/output_2/component_index_vs_pratio_col.json | 0 .../tests/output/output_2/x_index_vs_y_col_components.json | 0 .../tests/output/output_3/component_index_vs_RE_value.json | 0 .../tests/output/output_3/component_index_vs_pratio_col.json | 0 .../tests/output/output_3/x_index_vs_y_col_components.json | 0 .../diffpy}/nmf_mapping/tests/test_NMF_analysis_code.py | 0 {diffpy => src/diffpy}/nmf_mapping/tests/test_load_data.py | 0 66 files changed, 0 insertions(+), 0 deletions(-) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/different_r_grid/MgTi2O4_cryobraket_ly_20190524-200934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/example_phases/LiO2.cif (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/example_phases/Ru_mp-8639_conventional_standard.cif (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_1/x_index_vs_y_col_components.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_2/x_index_vs_y_col_components.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_3/component_index_vs_RE_value.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_3/component_index_vs_pratio_col.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/output/output_3/x_index_vs_y_col_components.json (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/test_NMF_analysis_code.py (100%) rename {diffpy => src/diffpy}/nmf_mapping/tests/test_load_data.py (100%) diff --git a/diffpy/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr b/src/diffpy/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr rename to src/diffpy/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr diff --git a/diffpy/nmf_mapping/tests/data/different_r_grid/MgTi2O4_cryobraket_ly_20190524-200934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr b/src/diffpy/nmf_mapping/tests/data/different_r_grid/MgTi2O4_cryobraket_ly_20190524-200934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/different_r_grid/MgTi2O4_cryobraket_ly_20190524-200934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr rename to src/diffpy/nmf_mapping/tests/data/different_r_grid/MgTi2O4_cryobraket_ly_20190524-200934_temperature_400,63_degK_33b844_0063_dark_corrected_img.gr diff --git a/diffpy/nmf_mapping/tests/data/example_phases/LiO2.cif b/src/diffpy/nmf_mapping/tests/data/example_phases/LiO2.cif similarity index 100% rename from diffpy/nmf_mapping/tests/data/example_phases/LiO2.cif rename to src/diffpy/nmf_mapping/tests/data/example_phases/LiO2.cif diff --git a/diffpy/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif b/src/diffpy/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif similarity index 100% rename from diffpy/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif rename to src/diffpy/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif diff --git a/diffpy/nmf_mapping/tests/data/example_phases/Ru_mp-8639_conventional_standard.cif b/src/diffpy/nmf_mapping/tests/data/example_phases/Ru_mp-8639_conventional_standard.cif similarity index 100% rename from diffpy/nmf_mapping/tests/data/example_phases/Ru_mp-8639_conventional_standard.cif rename to src/diffpy/nmf_mapping/tests/data/example_phases/Ru_mp-8639_conventional_standard.cif diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic0.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic1.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic10.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic11.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic12.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic13.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic14.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic15.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic16.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic17.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic18.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic19.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic2.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic20.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic21.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic22.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic23.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic24.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic25.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic26.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic27.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic28.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic29.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic3.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic30.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic31.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic32.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic33.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic34.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic35.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic36.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic37.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic38.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic39.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic4.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic40.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic41.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic42.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic43.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic44.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic45.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic46.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic47.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic48.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic49.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic5.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic6.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic7.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic8.gr diff --git a/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr b/src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr similarity index 100% rename from diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr rename to src/diffpy/nmf_mapping/tests/data/synthetic_r_vs_gr/synthetic9.gr diff --git a/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json b/src/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json rename to src/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json diff --git a/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json b/src/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json rename to src/diffpy/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json diff --git a/diffpy/nmf_mapping/tests/output/output_1/x_index_vs_y_col_components.json b/src/diffpy/nmf_mapping/tests/output/output_1/x_index_vs_y_col_components.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_1/x_index_vs_y_col_components.json rename to src/diffpy/nmf_mapping/tests/output/output_1/x_index_vs_y_col_components.json diff --git a/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json b/src/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json rename to src/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json diff --git a/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json b/src/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json rename to src/diffpy/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json diff --git a/diffpy/nmf_mapping/tests/output/output_2/x_index_vs_y_col_components.json b/src/diffpy/nmf_mapping/tests/output/output_2/x_index_vs_y_col_components.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_2/x_index_vs_y_col_components.json rename to src/diffpy/nmf_mapping/tests/output/output_2/x_index_vs_y_col_components.json diff --git a/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_RE_value.json b/src/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_RE_value.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_3/component_index_vs_RE_value.json rename to src/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_RE_value.json diff --git a/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_pratio_col.json b/src/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_pratio_col.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_3/component_index_vs_pratio_col.json rename to src/diffpy/nmf_mapping/tests/output/output_3/component_index_vs_pratio_col.json diff --git a/diffpy/nmf_mapping/tests/output/output_3/x_index_vs_y_col_components.json b/src/diffpy/nmf_mapping/tests/output/output_3/x_index_vs_y_col_components.json similarity index 100% rename from diffpy/nmf_mapping/tests/output/output_3/x_index_vs_y_col_components.json rename to src/diffpy/nmf_mapping/tests/output/output_3/x_index_vs_y_col_components.json diff --git a/diffpy/nmf_mapping/tests/test_NMF_analysis_code.py b/src/diffpy/nmf_mapping/tests/test_NMF_analysis_code.py similarity index 100% rename from diffpy/nmf_mapping/tests/test_NMF_analysis_code.py rename to src/diffpy/nmf_mapping/tests/test_NMF_analysis_code.py diff --git a/diffpy/nmf_mapping/tests/test_load_data.py b/src/diffpy/nmf_mapping/tests/test_load_data.py similarity index 100% rename from diffpy/nmf_mapping/tests/test_load_data.py rename to src/diffpy/nmf_mapping/tests/test_load_data.py From 93ab0f1f6c893e8e2de83baa25a25fea256d3c0b Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 17:54:01 -0400 Subject: [PATCH 07/14] Move source code --- {diffpy/nmf_mapping => src/diffpy}/nmf_mapping/main.py | 0 .../nmf_mapping => src/diffpy}/nmf_mapping/nmf_mapping_code.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename {diffpy/nmf_mapping => src/diffpy}/nmf_mapping/main.py (100%) rename {diffpy/nmf_mapping => src/diffpy}/nmf_mapping/nmf_mapping_code.py (100%) diff --git a/diffpy/nmf_mapping/nmf_mapping/main.py b/src/diffpy/nmf_mapping/main.py similarity index 100% rename from diffpy/nmf_mapping/nmf_mapping/main.py rename to src/diffpy/nmf_mapping/main.py diff --git a/diffpy/nmf_mapping/nmf_mapping/nmf_mapping_code.py b/src/diffpy/nmf_mapping/nmf_mapping_code.py similarity index 100% rename from diffpy/nmf_mapping/nmf_mapping/nmf_mapping_code.py rename to src/diffpy/nmf_mapping/nmf_mapping_code.py From 1cf04086692053aca3e72efa464e8813d7614bc0 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 18:00:55 -0400 Subject: [PATCH 08/14] Add test files --- src/diffpy/nmf_mapping/tests/__init__.py | 0 src/diffpy/nmf_mapping/tests/conftest.py | 19 +++++++++++++ src/diffpy/nmf_mapping/tests/debug.py | 35 ++++++++++++++++++++++++ src/diffpy/nmf_mapping/tests/run.py | 34 +++++++++++++++++++++++ 4 files changed, 88 insertions(+) create mode 100644 src/diffpy/nmf_mapping/tests/__init__.py create mode 100644 src/diffpy/nmf_mapping/tests/conftest.py create mode 100644 src/diffpy/nmf_mapping/tests/debug.py create mode 100644 src/diffpy/nmf_mapping/tests/run.py diff --git a/src/diffpy/nmf_mapping/tests/__init__.py b/src/diffpy/nmf_mapping/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/diffpy/nmf_mapping/tests/conftest.py b/src/diffpy/nmf_mapping/tests/conftest.py new file mode 100644 index 0000000..e3b6313 --- /dev/null +++ b/src/diffpy/nmf_mapping/tests/conftest.py @@ -0,0 +1,19 @@ +import json +from pathlib import Path + +import pytest + + +@pytest.fixture +def user_filesystem(tmp_path): + base_dir = Path(tmp_path) + home_dir = base_dir / "home_dir" + home_dir.mkdir(parents=True, exist_ok=True) + cwd_dir = base_dir / "cwd_dir" + cwd_dir.mkdir(parents=True, exist_ok=True) + + home_config_data = {"username": "home_username", "email": "home@email.com"} + with open(home_dir / "diffpyconfig.json", "w") as f: + json.dump(home_config_data, f) + + yield tmp_path diff --git a/src/diffpy/nmf_mapping/tests/debug.py b/src/diffpy/nmf_mapping/tests/debug.py new file mode 100644 index 0000000..46dad2c --- /dev/null +++ b/src/diffpy/nmf_mapping/tests/debug.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2024 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Billinge Group members and community contributors. +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# +# See LICENSE.rst for license information. +# +############################################################################## + +""" +Convenience module for debugging the unit tests using + +python -m diffpy.nmf_mapping.tests.debug + +Exceptions raised by failed tests or other errors are not caught. +""" + + +if __name__ == "__main__": + import sys + + from diffpy.nmf_mapping.tests import testsuite + + pattern = sys.argv[1] if len(sys.argv) > 1 else "" + suite = testsuite(pattern) + suite.debug() + + +# End of file diff --git a/src/diffpy/nmf_mapping/tests/run.py b/src/diffpy/nmf_mapping/tests/run.py new file mode 100644 index 0000000..389c772 --- /dev/null +++ b/src/diffpy/nmf_mapping/tests/run.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2024 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Billinge Group members and community contributors. +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# +# See LICENSE.rst for license information. +# +############################################################################## +"""Convenience module for executing all unit tests with +python -m \.tests.run +""" + +import sys + +import pytest + +if __name__ == "__main__": + # show output results from every test function + args = ["-v"] + # show the message output for skipped and expected failure tests + if len(sys.argv) > 1: + args.extend(sys.argv[1:]) + print("pytest arguments: {}".format(args)) + # call pytest and exit with the return code from pytest + exit_res = pytest.main(args) + sys.exit(exit_res) + +# End of file From 42a7090662ba631265bb4972f0d61a95f7cc975f Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Sun, 11 Aug 2024 18:01:16 -0400 Subject: [PATCH 09/14] Add source files --- src/diffpy/__init__.py | 24 ++++++++++++++++++++ src/diffpy/nmf_mapping/__init__.py | 25 +++++++++++++++++++++ src/diffpy/nmf_mapping/nmf_mapping_code.py | 3 ++- src/diffpy/nmf_mapping/version.py | 26 ++++++++++++++++++++++ 4 files changed, 77 insertions(+), 1 deletion(-) create mode 100644 src/diffpy/__init__.py create mode 100644 src/diffpy/nmf_mapping/__init__.py create mode 100644 src/diffpy/nmf_mapping/version.py diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py new file mode 100644 index 0000000..c8359ab --- /dev/null +++ b/src/diffpy/__init__.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2024 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Billinge Group members and community contributors. +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# +# See LICENSE.rst for license information. +# +############################################################################## + +"""Blank namespace package for module diffpy.""" + + +from pkgutil import extend_path + +__path__ = extend_path(__path__, __name__) + +# End of file + diff --git a/src/diffpy/nmf_mapping/__init__.py b/src/diffpy/nmf_mapping/__init__.py new file mode 100644 index 0000000..4ebd82f --- /dev/null +++ b/src/diffpy/nmf_mapping/__init__.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2024 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Billinge Group members and community contributors. +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# +# See LICENSE.rst for license information. +# +############################################################################## + +"""Run NMF analysis on PDF and XRD data""" + +# package version +from diffpy.nmf_mapping.version import __version__ + +# silence the pyflakes syntax checker +assert __version__ or True + +# End of file + diff --git a/src/diffpy/nmf_mapping/nmf_mapping_code.py b/src/diffpy/nmf_mapping/nmf_mapping_code.py index 4ad293a..1d9b496 100644 --- a/src/diffpy/nmf_mapping/nmf_mapping_code.py +++ b/src/diffpy/nmf_mapping/nmf_mapping_code.py @@ -11,11 +11,12 @@ import numpy as np import pandas as pd from bg_mpl_stylesheets.styles import all_styles -from diffpy.utils.parsers.loaddata import loadData from scipy import interpolate from sklearn.decomposition import NMF, PCA from sklearn.exceptions import ConvergenceWarning +from diffpy.utils.parsers.loaddata import loadData + plt.style.use(all_styles["bg_style"]) warnings.filterwarnings("ignore", category=FutureWarning) warnings.filterwarnings("ignore", category=ConvergenceWarning) diff --git a/src/diffpy/nmf_mapping/version.py b/src/diffpy/nmf_mapping/version.py new file mode 100644 index 0000000..0991a0b --- /dev/null +++ b/src/diffpy/nmf_mapping/version.py @@ -0,0 +1,26 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2024 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Billinge Group members and community contributors. +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# +# See LICENSE.rst for license information. +# +############################################################################## + +"""Definition of __version__.""" + +# We do not use the other three variables, but can be added back if needed. +# __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"] + +# obtain version information +from importlib.metadata import version + +__version__ = version("diffpy.nmf_mapping") + +# End of file From 4534d174b97c72d94e5ec6a909a44f7dd2cdcf52 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 11 Aug 2024 22:02:25 +0000 Subject: [PATCH 10/14] [pre-commit.ci] auto fixes from pre-commit hooks --- src/diffpy/__init__.py | 1 - src/diffpy/nmf_mapping/__init__.py | 1 - 2 files changed, 2 deletions(-) diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index c8359ab..58c58be 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -21,4 +21,3 @@ __path__ = extend_path(__path__, __name__) # End of file - diff --git a/src/diffpy/nmf_mapping/__init__.py b/src/diffpy/nmf_mapping/__init__.py index 4ebd82f..e39ac48 100644 --- a/src/diffpy/nmf_mapping/__init__.py +++ b/src/diffpy/nmf_mapping/__init__.py @@ -22,4 +22,3 @@ assert __version__ or True # End of file - From a8816a62821366aa22ec2ccda969163b7ed2f00b Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:46:51 -0400 Subject: [PATCH 11/14] Fix typo in run.py to run flake8 --- src/diffpy/nmf_mapping/tests/run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/diffpy/nmf_mapping/tests/run.py b/src/diffpy/nmf_mapping/tests/run.py index 389c772..02b30c9 100644 --- a/src/diffpy/nmf_mapping/tests/run.py +++ b/src/diffpy/nmf_mapping/tests/run.py @@ -7,13 +7,13 @@ # File coded by: Billinge Group members and community contributors. # # See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors +# https://github.com/diffpy/diffpy.snmf/graphs/contributors # # See LICENSE.rst for license information. # ############################################################################## """Convenience module for executing all unit tests with -python -m \.tests.run +python -m diffpy.snmf.tests.run """ import sys From 451fd78966b1586753d2247a684fb54e6e262b76 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:49:12 -0400 Subject: [PATCH 12/14] Fix from snmf to nmf_mapping --- src/diffpy/nmf_mapping/tests/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/diffpy/nmf_mapping/tests/run.py b/src/diffpy/nmf_mapping/tests/run.py index 02b30c9..d38677f 100644 --- a/src/diffpy/nmf_mapping/tests/run.py +++ b/src/diffpy/nmf_mapping/tests/run.py @@ -13,7 +13,7 @@ # ############################################################################## """Convenience module for executing all unit tests with -python -m diffpy.snmf.tests.run +python -m diffpy.nmf_mapping.tests.run """ import sys From a9913c8253b499037c2187dd2e33cb58b6479a05 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:50:50 -0400 Subject: [PATCH 13/14] Fix snmf to nmf_mapping in comment --- src/diffpy/nmf_mapping/tests/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/diffpy/nmf_mapping/tests/run.py b/src/diffpy/nmf_mapping/tests/run.py index d38677f..db406fa 100644 --- a/src/diffpy/nmf_mapping/tests/run.py +++ b/src/diffpy/nmf_mapping/tests/run.py @@ -7,7 +7,7 @@ # File coded by: Billinge Group members and community contributors. # # See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.snmf/graphs/contributors +# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors # # See LICENSE.rst for license information. # From dd2d5c29d502563e6d2cd2947233c3a20f92fa5d Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 20:01:31 -0400 Subject: [PATCH 14/14] Remove files for testing --- run_tests.py | 16 -------------- src/diffpy/nmf_mapping/tests/run.py | 34 ----------------------------- 2 files changed, 50 deletions(-) delete mode 100644 run_tests.py delete mode 100644 src/diffpy/nmf_mapping/tests/run.py diff --git a/run_tests.py b/run_tests.py deleted file mode 100644 index 3fec742..0000000 --- a/run_tests.py +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env python -import sys - -import pytest - -if __name__ == "__main__": - # show output results from every test function - args = ["-v"] - # show the message output for skipped and expected failure tests - if len(sys.argv) > 1: - args.extend(sys.argv[1:]) - print("pytest arguments: {}".format(args)) - # call pytest and exit with the return code from pytest so that - # travis will fail correctly if tests fail - exit_res = pytest.main(args) - sys.exit(exit_res) diff --git a/src/diffpy/nmf_mapping/tests/run.py b/src/diffpy/nmf_mapping/tests/run.py deleted file mode 100644 index db406fa..0000000 --- a/src/diffpy/nmf_mapping/tests/run.py +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# (c) 2024 The Trustees of Columbia University in the City of New York. -# All rights reserved. -# -# File coded by: Billinge Group members and community contributors. -# -# See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors -# -# See LICENSE.rst for license information. -# -############################################################################## -"""Convenience module for executing all unit tests with -python -m diffpy.nmf_mapping.tests.run -""" - -import sys - -import pytest - -if __name__ == "__main__": - # show output results from every test function - args = ["-v"] - # show the message output for skipped and expected failure tests - if len(sys.argv) > 1: - args.extend(sys.argv[1:]) - print("pytest arguments: {}".format(args)) - # call pytest and exit with the return code from pytest - exit_res = pytest.main(args) - sys.exit(exit_res) - -# End of file