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>

.codecov.yml

@@ -20,7 +20,7 @@ coverage:
         target: auto
         if_no_uploads: error
         if_not_found: success
-        if_ci_failed: failure
+        if_ci_failed: error
         paths: '!*/tests/.*'
 
       tests:

.coveragerc

@@ -6,7 +6,7 @@ omit =
     */python?.?/*
     */site-packages/nose/*
     # ignore _version.py and versioneer.py
-    *version.*
+    .*version.*
     *_version.py
 
 exclude_lines =

.github/workflows/check-news-item.yml

@@ -6,7 +6,7 @@ on:
     - main
 
 jobs:
-  check-news-item:
+  build:
     uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.snmf

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

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  CI:
+  coverage:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.snmf

.github/workflows/publish-docs-on-release.yml

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

.github/workflows/tests-on-pr.yml

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

.gitignore

@@ -20,9 +20,14 @@ lib64/
 parts/
 sdist/
 var/
+venv/
 *.egg-info/
 .installed.cfg
 *.egg
+bin/
+temp/
+tags/
+errors.err
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -33,6 +38,7 @@ var/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+MANIFEST
 
 # Unit test / coverage reports
 htmlcov/
@@ -49,48 +55,45 @@ coverage.xml
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
 
 # PyBuilder
 target/
 
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
+# Editor files
+# mac
+.DS_Store
+*~
 
-# celery beat schedule file
-celerybeat-schedule
+# vim
+*.swp
+*.swo
 
-# dotenv
-.env
+# pycharm
+.idea/
 
-# virtualenv
-venv/
-ENV/
+# VSCode
+.vscode/
 
-# Spyder project settings
-.spyderproject
+# Ipython Notebook
+.ipynb_checkpoints
 
-# Rope project settings
-.ropeproject
+# version information
+setup.cfg
+/src/diffpy/*/version.cfg
 
-# pycharm
-.idea/
-# Mac
-.DS_Store
 # Rever
 rever/

.pre-commit-config.yaml

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

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contibutors.
+Billinge Group and community contributors.
 
 Contributors
 ------------

MANIFEST.in

@@ -1,14 +1,12 @@
-include AUTHORS.rst
-include LICENSE
-include README.rst
-include requirements.txt
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat
-
-include diffpy.snmf/version.py
-
-# If including data files in the package, add them like:
-# include path/to/data_file
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.

README.rst

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.snmf/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.snmf
@@ -83,11 +83,7 @@ Then, to fully install ``diffpy.snmf`` in our active environment, run ::
 
 Another option is to use ``pip`` to download and install the latest release from
 `Python Package Index <https://pypi.python.org>`_.
-To install using ``pip`` into your ``diffpy.snmf_env`` environment, we will also have to install dependencies ::
-
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.snmf/main/requirements/run.txt
-
-and then install the package ::
+To install using ``pip`` into your ``diffpy.snmf_env`` environment, type ::
 
         pip install diffpy.snmf
 
@@ -102,7 +98,7 @@ Support and Contribute
 
 `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!
 
-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>`_. 
+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>`_.
 
 Feel free to fork the project and contribute. To install diffpy.snmf
 in a development mode, with its sources being directly used by Python

doc/make.bat

@@ -1,36 +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
+@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

doc/source/index.rst

@@ -2,7 +2,7 @@ Welcome to SNMF's Documentation!
 ====================================
 
 ``SNMF``: This library implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF
-(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023), 
+(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023),
 which is referenced under the Citation section below.
 
 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.
 This software implementation was developed by members of the Billinge Group at Columbia University and Brookhaven
 National Laboratory including Ran Gu, Adeolu Ajayi, Qiang Du, and Simon J. L. Billinge.
 
-For a detailed list of contributors, check `here 
+For a detailed list of contributors, check `here
 <https://github.com/diffpy/diffpy.snmf/graphs/contributors>`_.
 
 To get started, please go to :ref:`quick_start`

doc/source/license.rst

@@ -9,9 +9,9 @@ OPEN SOURCE LICENSE AGREEMENT
 =============================
 BSD 3-Clause License
 
-Copyright (c) 2023-2024, The Trustees of Columbia University in 
+Copyright (c) 2023-2024, The Trustees of Columbia University in
 the City of New York.
-All Rights Reserved. 
+All Rights Reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

doc/source/release.rst

@@ -1,3 +1,5 @@
+:tocdepth: -1
+
 .. index:: release notes
 
-.. include:: /../../CHANGELOG.rst
+.. include:: ../../CHANGELOG.rst

news/recut.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* re-cookiecuter repo to groupd's package standard
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "diffpy.snmf"
-dynamic=['version']
+dynamic=['version', 'dependencies']
 authors = [
   { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
@@ -45,9 +45,12 @@ dirty_template = "{tag}"
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
-exclude = ["diffpy.snmf.tests*"]  # exclude packages matching these glob patterns (empty by default)
+exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements/run.txt"]}
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

requirements/build.txt

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