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Cookiecutting - update readme
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7 changes: 3 additions & 4 deletions LICENSE.rst
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Expand Up @@ -5,10 +5,9 @@ If you use this program to do productive scientific research that leads
to publication, we ask that you acknowledge use of the program by citing
the following paper in your publication:

C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin,
J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and
PDFgui: computer programs for studying nanostructure in
crystals, J. Phys.: Condens. Matter 19, 335219 (2007)
C\. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen
and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure
in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)

Copyright 2006-2007, Board of Trustees of Michigan State University,
Copyright 2008-2024, Board of Trustees of Columbia University in the
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139 changes: 97 additions & 42 deletions README.rst
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@@ -1,10 +1,39 @@
|Icon| |title|_
===============

.. image:: https://codecov.io/gh/diffpy/diffpy.pdffit2/branch/master/graph/badge.svg
:target: https://codecov.io/gh/diffpy/diffpy.pdffit2
.. |title| replace:: diffpy.pdffit2
.. _title: https://diffpy.github.io/diffpy.pdffit2

.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
:target: https://diffpy.github.io/diffpy.pdffit2
:height: 100px

PDFfit2
========================================================================
|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.pdffit2/actions/workflows/main.yml/badge.svg
:target: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/main.yml

.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.pdffit2/branch/main/graph/badge.svg
:target: https://codecov.io/gh/diffpy/diffpy.pdffit2

.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.pdffit2
:target: https://anaconda.org/conda-forge/diffpy.pdffit2

.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff

.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdffit2
:target: https://pypi.org/project/diffpy.pdffit2/

.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdffit2
:target: https://pypi.org/project/diffpy.pdffit2/

.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
:target: https://github.com/diffpy/diffpy.pdffit2/issues

Real space structure refinement to atomic pair distribution function.

Expand All @@ -29,11 +58,19 @@ To learn more about diffpy.pdffit2 library, see the examples directory
included in this distribution or the API documentation at
http://www.diffpy.org/doc/pdffit2.

Citation
--------

If you use diffpy.pdffit2 in a scientific publication, we would like you to cite the following paper:

REQUIREMENTS
------------------------------------------------------------------------
C\. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen
and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure
in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)

diffpy.pdffit2 requires Python 3.7 or later or 2.7 and
Installation
------------

diffpy.pdffit2 requires Python 3.10 or later and
the following external software:

* ``setuptools`` - software distribution tools for Python
Expand All @@ -43,50 +80,44 @@ the following external software:
* ``diffpy.structure`` - simple storage and manipulation of atomic
structures, https://github.com/diffpy/diffpy.structure

We recommend to use `Anaconda Python <https://www.anaconda.com/distribution>`_
as it allows to install all software dependencies together with
PDFfit2. For other Python distributions it is necessary to
install the required software separately. As an example, on Ubuntu
Linux some of the required software can be installed using ::

sudo apt-get install \
python-setuptools python-dev libgsl0-dev build-essential
----

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.

INSTALLATION
------------------------------------------------------------------------
To add "conda-forge" to the conda channels, run the following in a terminal. ::

The preferred method is to use Anaconda Python and install from the
"conda-forge" channel of Anaconda packages ::
conda config --add channels conda-forge

conda install -c conda-forge diffpy.pdffit2
We want to install our packages in a suitable conda environment.
The following creates and activates a new environment named ``diffpy.pdffit2_env`` ::

If you don't use Anaconda or prefer to install from sources, make
sure the required software is in place and run ::
conda create -n diffpy.pdffit2_env python=3
conda activate diffpy.pdffit2_env

python setup.py install
Then, to fully install ``diffpy.pdffit2`` in our active environment, run ::

By default the files get installed to standard system directories,
which may require the use of ``sudo`` for write permissions. If
administrator (root) access is not available, consult the output from
``python setup.py install --help`` for options to install as a regular
user to other locations. The installation integrity can be
verified by changing to the HOME directory and running ::
conda install diffpy.pdffit2

python -m diffpy.pdffit2.tests.rundeps
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.pdffit2_env`` environment, we will also have to install dependencies ::

Anaconda Python allows to later update PDFfit2 using ::
pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdffit2/main/requirements/run.txt

conda update diffpy.pdffit2
and then install the package ::

With other Python distributions use the easy_install program to
upgraded to the latest version ::
pip install diffpy.pdffit2

easy_install --upgrade diffpy.pdffit2
If you prefer to install from sources, after installing the dependencies, obtain the source archive from
`GitHub <https://github.com/diffpy/diffpy.pdffit2/>`_. Once installed, ``cd`` into your ``diffpy.pdffit2`` directory
and run the following ::

pip install .

DEVELOPMENT
------------------------------------------------------------------------
Support and Contribute
----------------------

PDFfit2 is not developed anymore and is only maintained due to its
status of a sole computational engine for PDFgui. We don't expect any
Expand All @@ -97,12 +128,36 @@ at https://github.com/diffpy/diffpy.pdffit2.
For an actively developed codes for PDF simulations see the
DiffPy-CMI framework at http://www.diffpy.org.

----

`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdffit2. Please join the diffpy.pdffit2 users community by joining the Google group. The diffpy.pdffit2 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.pdffit2/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdffit2/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.pdffit2
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 .

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``.

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.pdffit2 please visit the project web-page:
Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdffit2/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.pdffit2 please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

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