readme pyproject.toml

Author: sbillinge

README.rst

@@ -1,108 +1,112 @@
+|Icon| `diffpy.pdfmorph <https://diffpy.github.io/diffpy.pdfmorph>`_
+=========================================================
 
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.pdfmorph
+        :height: 100px
 
-.. image:: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml/badge.svg 
-   :target: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml
+|PyPi| |Forge| |PythonVersion| |PR|
 
-.. image:: http://codecov.io/github/diffpy/diffpy.pdfmorph/coverage.svg?branch=master
-   :target: http://codecov.io/github/diffpy/diffpy.pdfmorph?branch=master
+|CI| |Codecov| |Black| |Tracking|
 
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
 
-PDFmorph
-========================================================================
+.. |CI| image:: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml
 
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.pdfmorph/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.pdfmorph
 
-PDFmorph is a Python software package designed to increase the insight 
-researchers can obtain from measured atomic pair distribution functions 
-(PDFs) in a model-independent way. The program was designed to help a 
-researcher answer the question: "Has my material undergone a phase 
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.pdfmorph
+        :target: https://anaconda.org/conda-forge/diffpy.pdfmorph
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdfmorph
+        :target: https://pypi.org/project/diffpy.pdfmorph/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdfmorph
+        :target: https://pypi.org/project/diffpy.pdfmorph/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.pdfmorph/issues
+
+Tools for manipulating and comparing PDF profiles
+
+PDFmorph is a Python software package designed to increase the insight
+researchers can obtain from measured atomic pair distribution functions
+(PDFs) in a model-independent way. The program was designed to help a
+researcher answer the question: "Has my material undergone a phase
 transition between these two measurements?"
 
-One approach is to compare the two PDFs in a plot and view the difference 
-curve underneath. However, significant signal can be seen in the 
-difference curve from benign effects such as thermal expansion (peak 
-shifts) and increased thermal motion (peak broadening) or a change in 
-scale due to differences in incident flux, for example. PDFmorph will 
-do its best to correct for these benign effects before computing and 
+One approach is to compare the two PDFs in a plot and view the difference
+curve underneath. However, significant signal can be seen in the
+difference curve from benign effects such as thermal expansion (peak
+shifts) and increased thermal motion (peak broadening) or a change in
+scale due to differences in incident flux, for example. PDFmorph will
+do its best to correct for these benign effects before computing and
 plotting the difference curve. One measured PDF (typically that collected
-at higher temperature) is identified as the target PDF and the second 
-PDF is then morphed by "stretching" (changing the r-axis to simulate a 
-uniform lattice expansion), "smearing" (broadening peaks through a 
-uniform convolution to simulate increased thermal motion), and "scaling" 
-(self-explanatory). PDFmorph will vary the amplitude of the morphing 
-transformations to obtain the best fit between the morphed and the target 
-PDFs, then plot them on top of each other with the difference plotted 
+at higher temperature) is identified as the target PDF and the second
+PDF is then morphed by "stretching" (changing the r-axis to simulate a
+uniform lattice expansion), "smearing" (broadening peaks through a
+uniform convolution to simulate increased thermal motion), and "scaling"
+(self-explanatory). PDFmorph will vary the amplitude of the morphing
+transformations to obtain the best fit between the morphed and the target
+PDFs, then plot them on top of each other with the difference plotted
 below.
 
 There are also a few other morphing transformations in the program.
 
-Finally, we note that PDFmorph should work on other spectra that are not 
+Finally, we note that PDFmorph should work on other spectra that are not
 PDFs, though it has not been extensively tested beyond the PDF.
 
 
-LICENSE
-------------------------------------------------------------------------
-
-This software is subject to license and copyright restrictions listed
-`here. <https://github.com/diffpy/diffpy.pdfmorph/blob/master/LICENSE.txt/>`_
+For more information about the diffpy.pdfmorph library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdfmorph>`_.
 
+Citation
+--------
 
-REQUIREMENTS
-------------------------------------------------------------------------
+If you use diffpy.pdfmorph in a scientific publication, we would like you to cite this package as
 
-PDFmorph is currently run from the command line, which requires opening
-and typing into a terminal window or Windows command prompt. It is 
-recommended that you consult online resources and become somewhat 
-familiar before using PDFmorph.
+        diffpy.pdfmorph Package, https://github.com/diffpy/diffpy.pdfmorph
 
-PDFmorph can be run with Python 3.10 or higher. It makes use of several third party
-libraries that you'll need to run the app and its components.
+Installation
+------------
 
-* `NumPy`              - library for scientific computing with Python
-* `matplotlib`         - Python 2D plotting library
-* `SciPy`              - library for highly technical Python computing
-* `diffpy.utils`       - `shared helper utilities <https://github.com/diffpy/diffpy.utils/>`_ for wx GUI
+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.
 
-These dependencies will be installed automatically if you use the conda
-installation procedure described below.
+To add "conda-forge" to the conda channels, run the following in a terminal. ::
 
+        conda config --add channels conda-forge
 
-INSTALLATION
-------------------------------------------------------------------------
+We want to install our packages in a suitable conda environment.
+The following creates and activates a new environment named ``diffpy.pdfmorph_env`` ::
 
-We recommend installing the software using conda. If you have anaconda
-or mini-conda installed on your computer, you can proceed directly to
-the instructions below. If not, we recommend that you install mini-
-conda and test that it is working by opening a terminal and typing
-``conda``.
- 
-To create and activate a conda environment to use this software, run 
-the following command from the command line ::
-	
-	conda create -n pdfmorph_env python=3 --yes
-	conda activate pdfmorph_env
+        conda create -n diffpy.pdfmorph_env python=3
+        conda activate diffpy.pdfmorph_env
 
-When you are finished with the session, exit the environment by running :: 
+Then, to fully install ``diffpy.pdfmorph`` in our active environment, run ::
 
-	conda deactivate pdfmorph_env
+        conda install diffpy.pdfmorph
 
-For your future sessions with the application: Make sure to run the 
-``conda activate pdfmorph_env`` command from your command line beforehand
-to ensure access to the software.
+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.pdfmorph_env`` environment, we will also have to install dependencies ::
 
-Once in your desired conda environment, you can install from either the
-"conda-forge" channel of Anaconda packages by running ::
+        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/run.txt
 
-	conda config --add channels conda-forge
-	conda install diffpy.pdfmorph
- 
-If you do not use conda or prefer to install from sources, please 
-consult online documentation.
+and then install the package ::
 
-With conda, PDFmorph can be later upgraded to the latest released
-version using ::
+        pip install diffpy.pdfmorph
 
-     conda update diffpy.pdfmorph
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.pdfmorph/>`_. Once installed, ``cd`` into your ``diffpy.pdfmorph`` directory
+and run the following ::
 
+        pip install .
 
 USING PDFmorph
 ------------------------------------------------------------------------
@@ -117,36 +121,34 @@ up a terminal and check installation has worked properly by running ::
 	pdfmorph -h			  #get some helpful information
 	pdfmorph --version
 
-If installed correctly, this last command should return the version 
-of PDFmorph that you have installed on your system. To begin using 
+If installed correctly, this last command should return the version
+of PDFmorph that you have installed on your system. To begin using
 PDFmorph, run a command like ::
 
 	pdfmorph <target PDF file> <morphed PDF file>
 
 where both PDFs file are text files which contain PDF data, such as ``.gr``
-or ``.cgr`` files that are produced by ``PDFgetX2``, ``PDFgetX3``, 
-or ``PDFgui``. Though some file extensions other than ``.gr`` or ``.cgr``, 
-but with the same content structure, have been shown to work with 
+or ``.cgr`` files that are produced by ``PDFgetX2``, ``PDFgetX3``,
+or ``PDFgui``. Though some file extensions other than ``.gr`` or ``.cgr``,
+but with the same content structure, have been shown to work with
 PDFmorph, it is recommended to stick with ``.gr`` files.
 
 Enjoy!
 
 
-DEVELOPMENT
-------------------------------------------------------------------------
+Support and Contribute
+----------------------
 
-PDFmorph is an open-source software project on Github:
-https://github.com/diffpy/diffpy.pdfmorph.
+`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdfmorph. Please join the diffpy.pdfmorph users community by joining the Google group. The diffpy.pdfmorph project welcomes your expertise and enthusiasm!
 
-Feel free to fork the project and contribute! To install PDFmorph
-in a development mode where the source files are used directly
-rather than copied to a system directory, use ::
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfmorph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfmorph/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_. 
 
-     python -m pip install -e .
+Feel free to fork the project and contribute. To install diffpy.pdfmorph
+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 ::
 
-CONTRIBUTING
-------------------------------------------------------------------------
-We welcome contributors from the community.  Please consider posting issues, and taking issues and posting PRs.
+        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.
@@ -157,12 +159,14 @@ hooks.
 
 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
+pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before
 trying to commit again.
 
+Improvements and fixes are always appreciated.
 
-CONTACTS
-------------------------------------------------------------------------
+Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfmorph/blob/main/CODE_OF_CONDUCT.rst>`_.
+
+Contact
+-------
 
-For more information on PDFmorph, visit the `PDFmorph project web-page, <https://github.com/diffpy/diffpy.github.io/blob/source/products/pdfmorph.rst/>`_
-or email Professor Simon Billinge at sb2896@columbia.edu
+For more information on diffpy.pdfmorph please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

pyproject.toml

@@ -11,13 +11,14 @@ authors = [
 maintainers = [
   { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
 ]
-description = "Tools for manipulating and comparing PDF profiles."
-keywords = ["diffpy PDF"]
+description = "Tools for manipulating and comparing PDF profiles"
+keywords = ['diffpy', 'pdf', 'data interpretation']
 readme = "README.rst"
 requires-python = ">=3.10"
 classifiers = [
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
+        'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
         'Operating System :: MacOS :: MacOS X',
@@ -27,8 +28,8 @@ classifiers = [
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
-	'Topic :: Scientific/Engineering :: Chemistry',
         'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
 [project.scripts]
@@ -49,7 +50,7 @@ dirty_template = "{tag}"
 
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
-include = ["diffpy*"]  # package names should match these glob patterns (["*"] by default)
+include = ["*"]  # package names should match these glob patterns (["*"] by default)
 exclude = ["diffpy.pdfmorph.tests*"]  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
@@ -75,7 +76,3 @@ exclude = '''
   | tests/data
 )/
 '''
-
-[tool.flake8]
-max-line-length = 115
-per-file-ignores="__init__.py:F401"