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bobleesjpre-commit-ci[bot]
bobleesj
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authored
Re-cookiecut (#89)
* Move tests folder to top * Revert commit * Add codecov, remove gitattributes * Add test tests * Add .gitignore and precommit * Add MANIFEST * Add pyproject.toml * Add authors * Add requirements * Add readme * Add doc * Add 2023 to copyright in doc * Add 2023 to license.rst * [pre-commit.ci] auto fixes from pre-commit hooks * Add newds * Remove null in matrix codecov * Remove null in matrix --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
1 parent c7d4910 commit 1e3d023

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Diff for: ‎.codecov.yml

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target: auto
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if_no_uploads: error
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if_not_found: success
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if_ci_failed: failure
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if_ci_failed: error
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paths: '!*/tests/.*'
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tests:

Diff for: ‎.coveragerc

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*/python?.?/*
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*/site-packages/nose/*
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# ignore _version.py and versioneer.py
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*version.*
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.*version.*
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*_version.py
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exclude_lines =

Diff for: ‎.gitattributes

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This file was deleted.

Diff for: ‎.github/workflows/check-news-item.yml

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- main
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jobs:
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check-news-item:
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build:
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uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
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with:
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project: diffpy.snmf

Diff for: ‎.github/workflows/matrix-and-codecov-on-merge-to-main.yml

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workflow_dispatch:
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jobs:
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CI:
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coverage:
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uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
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with:
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project: diffpy.snmf

Diff for: ‎.github/workflows/publish-docs-on-release.yml

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@@ -7,7 +7,7 @@ on:
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workflow_dispatch:
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jobs:
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publish-docs-on-release:
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docs:
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uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
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with:
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project: diffpy.snmf

Diff for: ‎.github/workflows/tests-on-pr.yml

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@@ -8,7 +8,7 @@ on:
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workflow_dispatch:
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jobs:
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tests-on-pr:
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validate:
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uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
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with:
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project: diffpy.snmf

Diff for: ‎.gitignore

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@@ -20,9 +20,14 @@ lib64/
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parts/
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sdist/
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var/
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venv/
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*.egg-info/
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.installed.cfg
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*.egg
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bin/
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temp/
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tags/
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errors.err
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# PyInstaller
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# Usually these files are written by a python script from a template
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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MANIFEST
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# Unit test / coverage reports
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htmlcov/
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*.mo
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*.pot
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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docs/build/
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docs/source/generated/
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# pytest
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.pytest_cache/
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# PyBuilder
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target/
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# IPython Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# Editor files
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# mac
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.DS_Store
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*~
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# celery beat schedule file
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celerybeat-schedule
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# vim
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*.swp
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*.swo
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# dotenv
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.env
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# pycharm
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.idea/
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# virtualenv
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venv/
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ENV/
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# VSCode
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.vscode/
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# Spyder project settings
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.spyderproject
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# Ipython Notebook
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.ipynb_checkpoints
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# Rope project settings
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.ropeproject
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# version information
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setup.cfg
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/src/diffpy/*/version.cfg
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# pycharm
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.idea/
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# Mac
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.DS_Store
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# Rever
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rever/

Diff for: ‎.pre-commit-config.yaml

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@@ -16,7 +16,10 @@ repos:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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exclude: '\.(rst|txt)$'
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-toml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 24.4.2
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hooks:

Diff for: ‎AUTHORS.rst

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Authors
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=======
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Billinge Group and community contibutors.
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Billinge Group and community contributors.
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Contributors
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------------

Diff for: ‎MANIFEST.in

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include AUTHORS.rst
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include LICENSE
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include README.rst
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include requirements.txt
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recursive-exclude * __pycache__
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recursive-exclude * *.py[co]
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recursive-include docs *.rst conf.py Makefile make.bat
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include diffpy.snmf/version.py
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# If including data files in the package, add them like:
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# include path/to/data_file
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graft src
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graft tests
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graft requirements
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include AUTHORS.rst LICENSE*.rst README.rst
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# Exclude all bytecode files and __pycache__ directories
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global-exclude *.py[cod] # Exclude all .pyc, .pyo, and .pyd files.
9+
global-exclude .DS_Store # Exclude Mac filesystem artifacts.
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global-exclude __pycache__ # Exclude Python cache directories.
11+
global-exclude .git* # Exclude git files and directories.
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global-exclude .idea # Exclude PyCharm project settings.

Diff for: ‎README.rst

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.. |Black| image:: https://img.shields.io/badge/code_style-black-black
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:target: https://github.com/psf/black
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.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml/badge.svg
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:target: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml
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.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
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:target: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
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.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.snmf/branch/main/graph/badge.svg
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:target: https://codecov.io/gh/diffpy/diffpy.snmf
@@ -83,11 +83,7 @@ Then, to fully install ``diffpy.snmf`` in our active environment, run ::
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Another option is to use ``pip`` to download and install the latest release from
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`Python Package Index <https://pypi.python.org>`_.
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To install using ``pip`` into your ``diffpy.snmf_env`` environment, we will also have to install dependencies ::
87-
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pip install -r https://raw.githubusercontent.com/diffpy/diffpy.snmf/main/requirements/run.txt
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and then install the package ::
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To install using ``pip`` into your ``diffpy.snmf_env`` environment, type ::
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pip install diffpy.snmf
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@@ -102,7 +98,7 @@ Support and Contribute
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`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.snmf. Please join the diffpy.snmf users community by joining the Google group. The diffpy.snmf project welcomes your expertise and enthusiasm!
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If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.snmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
101+
If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.snmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
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Feel free to fork the project and contribute. To install diffpy.snmf
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in a development mode, with its sources being directly used by Python

Diff for: ‎doc/make.bat

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1-
@ECHO OFF
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3-
pushd %~dp0
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REM Command file for Sphinx documentation
6-
7-
if "%SPHINXBUILD%" == "" (
8-
set SPHINXBUILD=sphinx-build
9-
)
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set SOURCEDIR=source
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set BUILDDIR=build
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set SPHINXPROJ=PackagingScientificPython
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14-
if "%1" == "" goto help
15-
16-
%SPHINXBUILD% >NUL 2>NUL
17-
if errorlevel 9009 (
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echo.
19-
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
20-
echo.installed, then set the SPHINXBUILD environment variable to point
21-
echo.to the full path of the 'sphinx-build' executable. Alternatively you
22-
echo.may add the Sphinx directory to PATH.
23-
echo.
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echo.If you don't have Sphinx installed, grab it from
25-
echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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:end
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popd
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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
6+
7+
if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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set SPHINXPROJ=PackagingScientificPython
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14+
if "%1" == "" goto help
15+
16+
%SPHINXBUILD% >NUL 2>NUL
17+
if errorlevel 9009 (
18+
echo.
19+
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
20+
echo.installed, then set the SPHINXBUILD environment variable to point
21+
echo.to the full path of the 'sphinx-build' executable. Alternatively you
22+
echo.may add the Sphinx directory to PATH.
23+
echo.
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echo.If you don't have Sphinx installed, grab it from
25+
echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
30+
goto end
31+
32+
:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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:end
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popd

Diff for: ‎doc/source/index.rst

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====================================
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``SNMF``: This library implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF
5-
(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023),
5+
(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023),
66
which is referenced under the Citation section below.
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88
This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal
@@ -63,7 +63,7 @@ Jame R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge.
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This software implementation was developed by members of the Billinge Group at Columbia University and Brookhaven
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National Laboratory including Ran Gu, Adeolu Ajayi, Qiang Du, and Simon J. L. Billinge.
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66-
For a detailed list of contributors, check `here
66+
For a detailed list of contributors, check `here
6767
<https://github.com/diffpy/diffpy.snmf/graphs/contributors>`_.
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To get started, please go to :ref:`quick_start`

Diff for: ‎doc/source/license.rst

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=============================
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BSD 3-Clause License
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Copyright (c) 2023-2024, The Trustees of Columbia University in
12+
Copyright (c) 2023-2024, The Trustees of Columbia University in
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the City of New York.
14-
All Rights Reserved.
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All Rights Reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:

Diff for: ‎doc/source/release.rst

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:tocdepth: -1
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.. index:: release notes
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.. include:: /../../CHANGELOG.rst
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.. include:: ../../CHANGELOG.rst

Diff for: ‎news/recut.rst

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**Added:**
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* <news item>
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* re-cookiecuter repo to groupd's package standard
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**Security:**
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* <news item>

Diff for: ‎pyproject.toml

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[build-system]
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requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
2+
requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
33
build-backend = "setuptools.build_meta"
44

55
[project]
66
name = "diffpy.snmf"
7-
dynamic=['version']
7+
dynamic=['version', 'dependencies']
88
authors = [
99
{ name="Simon J.L. Billinge group", email="[email protected]" },
1010
]
@@ -45,9 +45,12 @@ dirty_template = "{tag}"
4545
[tool.setuptools.packages.find]
4646
where = ["src"] # list of folders that contain the packages (["."] by default)
4747
include = ["*"] # package names should match these glob patterns (["*"] by default)
48-
exclude = ["diffpy.snmf.tests*"] # exclude packages matching these glob patterns (empty by default)
48+
exclude = [] # exclude packages matching these glob patterns (empty by default)
4949
namespaces = false # to disable scanning PEP 420 namespaces (true by default)
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51+
[tool.setuptools.dynamic]
52+
dependencies = {file = ["requirements/run.txt"]}
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[tool.black]
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line-length = 115
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include = '\.pyi?$'

Diff for: ‎requirements/build.txt

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@@ -1,2 +0,0 @@
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python
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setuptools

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