finishing the recut

.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

@@ -1,32 +1,13 @@
-# Configuration of the coverage.py tool for reporting test coverage.
-
+[run]
+source =
+    diffpy.utils
 [report]
-# RE patterns for lines to be excluded from consideration.
-exclude_lines =
-    ## Have to re-enable the standard pragma
-    pragma: no cover
-    ## Don't complain if tests don't hit defensive assertion code:
-    raise AssertionError
-    raise NotImplementedError
-    ^[ ]*assert False
-
-    ## Don't complain if non-runnable code isn't run:
-    ^[ ]*@unittest.skip\b
-    ^[ ]{4}unittest.main()
-    if __name__ == .__main__.:
 omit =
     */python?.?/*
     */site-packages/nose/*
     # ignore _version.py and versioneer.py
     .*version.*
     *_version.py
-    # ignore wx directory
-    */wx/*
 
-
-[run]
-source =
-    src/diffpy/utils/
-omit =
-    ## exclude debug.py from codecov report
-    */tests/debug.py
+exclude_lines =
+    if __name__ == '__main__':

.flake8

@@ -4,9 +4,8 @@ exclude =
     __pycache__,
     build,
     dist,
-    versioneer.py,
-    doc/manual/source/conf.py
+    doc/source/conf.py
 max-line-length = 115
-# Ignore some style 'errors' produced while formatting by 'black' (see link below)
+# Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
 extend-ignore = E203

.gitignore

@@ -1,49 +1,99 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
 
-# Packages
-*.egg
-*.egg-info
-dist
-build
-eggs
-parts
-bin
-var
-sdist
-temp
-develop-eggs
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+venv/
+*.egg-info/
 .installed.cfg
-lib
-lib64
-tags
+*.egg
+bin/
+temp/
+tags/
 errors.err
 
+# 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
 MANIFEST
 
 # Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-.tox
+.coverage.*
+.cache
 nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
 
 # Translations
 *.mo
+*.pot
 
 # Mr Developer
 .mr.developer.cfg
 .project
 .pydevproject
 
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Editor files
+# mac
+.DS_Store
+*~
+
+# vim
+*.swp
+*.swo
+
+# pycharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Ipython Notebook
+.ipynb_checkpoints
+
 # version information
 setup.cfg
 /src/diffpy/*/version.cfg
 
 # Rever
 rever/
-
-# PyCharm
-.idea/

MANIFEST.in

@@ -1,15 +1,12 @@
-recursive-include src *
-include AUTHORS.txt LICENSE*.txt README.rst
-recursive-exclude src *.py[co]
-global-exclude .gitattributes .gitignore .gitarchive.cfg
-global-exclude .DS_Store
+graft src
+graft tests
+graft requirements
 
-# Avoid user content in setup.cfg to make distribution reproducible.
-exclude setup.cfg
+include AUTHORS.rst LICENSE*.rst README.rst
 
-# Exclude git-tracked files spuriously added by setuptools_scm
-exclude .coveragerc
-exclude .travis*
-prune conda-recipe
-prune devutils
-prune doc
+# 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

@@ -1,9 +1,39 @@
-.. image:: https://github.com/diffpy/diffpy.utils/actions/workflows/main.yml/badge.svg
-   :target: https://github.com/diffpy/diffpy.utils/actions/workflows/main.yml
+|Icon| |title|_
+===============
 
-.. image:: https://codecov.io/gh/diffpy/diffpy.utils/branch/main/graph/badge.svg
-  :target: https://codecov.io/gh/diffpy/diffpy.utils
+.. |title| replace:: diffpy.utils
+.. _title: https://diffpy.github.io/diffpy.utils
 
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.utils
+        :height: 100px
+
+|PyPi| |Forge| |PythonVersion| |PR|
+
+|CI| |Codecov| |Black| |Tracking|
+
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
+
+.. |CI| image:: https://github.com/diffpy/diffpy.utils/actions/workflows/codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.utils/actions/workflows/codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.utils/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.utils
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.utils
+        :target: https://anaconda.org/conda-forge/diffpy.utils
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.utils/issues
 
 diffpy.utils
 ========================================================================
@@ -16,78 +46,81 @@ program.  The package also includes an interpolation function based on the
 Whittaker-Shannon formula that can be used to resample a PDF or other profile
 function over a new grid.
 
-For more information about the diffpy.utils library, see the users manual at
-http://diffpy.github.io/diffpy.utils.
+Citation
+--------
+
+If you use diffpy.utils in a scientific publication, we would like you to cite this package as
+
+        diffpy.utils Package, https://github.com/diffpy/diffpy.utils
 
-INSTALLATION
-------------------------------------------------------------------------
+Installation
+------------
 
 The preferred method is to use `Miniconda Python
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
 and install from the "conda-forge" channel of Conda packages.
 
 To add "conda-forge" to the conda channels, run the following in a terminal. ::
 
-   conda config --add channels conda-forge
+        conda config --add channels conda-forge
 
 We want to install our packages in a suitable conda environment.
-The following creates and activates a new environment named ``diffpy-utils`` ::
+The following creates and activates a new environment named ``diffpy.utils_env`` ::
 
-    conda create -n diffpy-utils python=3
-    conda activate diffpy-utils
+        conda create -n diffpy.utils_env python=3
+        conda activate diffpy.utils_env
 
 Then, to fully install ``diffpy.utils`` in our active environment, run ::
 
-    conda install diffpy.utils
+        conda install diffpy.utils
 
 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-utils`` environment, we will also have to install dependencies ::
+To install using ``pip`` into your ``diffpy.utils_env`` environment, we will also have to install dependencies ::
 
-   pip install numpy
-   pip install diffpy.utils
+        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.utils/main/requirements/run.txt
 
-For those planning to use functions in the ``diffpy.utils.wx`` module, you will also need to install ``wxPython``.
-Both of the following lines will install this package. ::
+and then install the package ::
 
-    conda install wxPython
-    pip install wxPython
+        pip install diffpy.utils
 
 If you prefer to install from sources, after installing the dependencies, obtain the source archive from
 `GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` directory
 and run the following ::
 
-   pip install .
+        pip install .
 
-To check the installation integrity, if the following passes all checks, you are good! ::
+Support and Contribute
+----------------------
 
-   pip install pytest
-   python -m diffpy.utils.tests.run
+`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.utils. Please join the diffpy.utils users community by joining the Google group. The diffpy.utils 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.utils/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.utils/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
 
-DEVELOPMENT
-------------------------------------------------------------------------
-
-diffpy.utils is an open-source software developed as a part of the
-DiffPy-CMI complex modeling initiative at the Brookhaven National
-Laboratory.  The diffpy.utils sources are hosted at
-https://github.com/diffpy/diffpy.utils.
-
-Feel free to fork the project and contribute.  To install diffpy.utils
+Feel free to fork the project and contribute. To install diffpy.utils
 in a development mode, with its sources being directly used by Python
 rather than copied to a package directory, use the following in the root
 directory ::
 
-   pip install -e .
+        pip install -e .
+
+To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
+hooks.
+
+1. Install pre-commit in your working environment by running ``conda install pre-commit``.
 
-Note that this is only supported for `setuptools` version 62.0 and above.
+2. Initialize pre-commit (one time only) ``pre-commit install``.
 
+Thereafter your code will be linted by black and isort and checked against flake8 before you can commit.
+If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should
+pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before
+trying to commit again.
 
-CONTACTS
-------------------------------------------------------------------------
+Improvements and fixes are always appreciated.
 
-For more information on diffpy.utils please visit the project web-page
+Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.utils/blob/main/CODE_OF_CONDUCT.rst>`_.
 
-http://www.diffpy.org/
+Contact
+-------
 
-or email Prof. Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.utils please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

doc/Makefile

@@ -6,6 +6,7 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
+BASENAME      = $(subst .,,$(subst $() $(),,diffpy.utils))
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -85,17 +86,17 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/diffpyutils.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/diffpyutils.qhc"
+	@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 $$HOME/.local/share/devhelp/diffpyutils"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/diffpyutils"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)"
 	@echo "# devhelp"
 
 epub: