initial commit of project files

Author: sbillinge

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# pycharm
+.idea/
+# Mac
+.DS_Store
+# Rever
+rever/

AUTHORS.rst

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+Authors
+====================
+
+Ran Gu, Adeolu Ajayi, Qiang Du,  Simon J.L. Billinge
+
+Contributors
+------------
+For a full list of contributors, visit
+https://github.com/diffpy/diffpy.snmf/graphs/contributors

CHANGELOG.rst

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+===========
+ Change Log
+===========
+
+.. current developments
+

diffpy/__init__.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy            by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2008 Trustees of the Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""snmf - implements the stretchednmf algorithm
+
+"""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+
+# End of file

diffpy/snmf/__init__.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# pdfmorph          by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2006 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Chris Farrow
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Tools for manipulating and comparing PDFs.
+"""
+
+# obtain version information
+__version__ = '0.0.1'
+
+# top-level import
+#from diffpy.snmf.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
+
+# End of file

diffpy/snmf/version.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# Structure         by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2008 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Definition of __version__ and __date__ for diffpy.pdfmorph.
+"""
+
+
+# obtain version information
+from pkg_resources import get_distribution
+
+__version__ = get_distribution('diffpy.snmf').version
+
+# we assume that tag_date was used and __version__ ends in YYYYMMDD
+__date__ = __version__[-8:-4] + '-' + __version__[-4:-2] + '-' + __version__[-2:]
+
+# End of file

environment.yml

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+name: diffpy.snmf
+channels:
+  - conda-forge
+dependencies:
+  - python=3
+  - pip

rever.xsh

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+$ACTIVITIES = [
+              'version_bump',  # Changes the version number in various source files (setup.py, __init__.py, etc)
+              'changelog',  # Uses files in the news folder to create a changelog for release
+              'tag',  # Creates a tag for the new version number
+              #'pypi',  # Sends the package to pypi
+              #'conda_forge',  # Creates a PR into your package's feedstock
+              'ghrelease'  # Creates a Github release entry for the new tag
+               ]
+$VERSION_BUMP_PATTERNS = [  # These note where/how to find the version numbers
+                         ('snmf/__init__.py', '__version__\s*=.*', "__version__ = '$VERSION'"),
+                         ('setup.py', 'version\s*=.*,', "version='$VERSION',")
+                         ]
+$CHANGELOG_FILENAME = 'CHANGELOG.rst'  # Filename for the changelog
+$CHANGELOG_TEMPLATE = 'TEMPLATE.rst'  # Filename for the news template
+$TAG_REMOTE = 'https://github.com/diffpy/snmf.git'  # Repo to push tags to
+
+$GITHUB_ORG = 'diffpy'  # Github org for Github releases and conda-forge
+$GITHUB_REPO = 'diffpy.snmf'  # Github repo for Github releases  and conda-forge

run_tests.py

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+#!/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))
+    # # compute coverage stats for xpdAcq
+    # 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)

setup.py

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+