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add MANIFEST.in and README.rst #119

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f435e05
add MANIFEST.in and README.rst
stevenhua0320 Sep 25, 2024
b092cd5
add citation & acknowledgement
stevenhua0320 Sep 27, 2024
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19 changes: 10 additions & 9 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
recursive-include diffpy *.py
include AUTHORS.txt LICENSE*.txt README.rst
exclude MANIFEST.in
include diffpy/srmise/version.cfg
graft src
graft tests
graft requirements

recursive-include doc/examples *.py *.gr *.srmise *.pwa *.dat *.png
include doc/examples/README
include AUTHORS.rst LICENSE*.rst README.rst

recursive-include doc/manual/source *.rst *.txt
include doc/manual/source/conf.py
include doc/manual/Makefile
# 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.
220 changes: 84 additions & 136 deletions README.rst
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Original file line number Diff line number Diff line change
@@ -1,9 +1,41 @@
#########################
SrMise
#########################
|Icon| |title|_
===============

.. |title| replace:: diffpy.srmise
.. _title: https://diffpy.github.io/diffpy.srmise

.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
:target: https://diffpy.github.io/diffpy.srmise
: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.srmise/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
:target: https://github.com/diffpy/diffpy.srmise/actions/workflows/matrix-and-codecov-on-merge-to-main.yml

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

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

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

`DiffPy project <http://www.diffpy.org>`_ tool for unbiased peak extraction from
atomic pair distribution functions.
.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.srmise
:target: https://pypi.org/project/diffpy.srmise/

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

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

Peak extraction and peak fitting tool for atomic pair distribution functions.

SrMise is an implementation of the `ParSCAPE algorithm
<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
Expand Down Expand Up @@ -41,163 +73,79 @@ must be specified.
For more information about SrMise, see the users manual at
http://diffpy.github.io/diffpy.srmise.

Getting Started
=================

The diffpy.srmise package requires Python 2.6 or 2.7 and the following software:

* ``setuptools`` - software distribution tools for Python
* ``NumPy`` - numerical mathematics and fast array operations for Python
* ``SciPy`` - scientific libraries for Python
* ``matplotlib`` - python plotting library

See the `SrMise license <LICENSE.txt>`__ for terms and conditions of use.
Detailed installation instructions for the `Windows`_, `Mac OS X`_, and
`Linux`_ platforms follow.

Windows
-------

Several prebuilt Python distributions for Windows include all the
prerequisite software required to run SrMise, and installing one of these is the
simplest way to get started. These distributions are usually free for
individual and/or academic use, but some also have commercial version. Links to
executables, installation instructions, and licensing information
for some popular options are listed below.
For more information about the diffpy.srmise library, please consult our `online documentation <https://diffpy.github.io/diffpy.srmise>`_.

* `Anaconda <https://www.anaconda.com/download>`_
* `Enthought Canopy <https://www.enthought.com/products/canopy/>`_
* `Python(x,y) <https://code.google.com/p/pythonxy/>`_
* `WinPython <http://winpython.github.io>`_

Alternately, individual Windows executables for Python and the required
components can be downloaded and installed. The official Windows releases of
Numpy and SciPy do not currently support 64-bit Python installations, so be
sure to download the 32-bit versions of these packages.

* `Python 2.6/2.7 <https://www.python.org/downloads/windows/>`_
* `NumPy <http://sourceforge.net/projects/numpy/files/NumPy/>`_
* `SciPy <http://sourceforge.net/projects/scipy/files/scipy/>`_
* `matplotlib <http://matplotlib.org/downloads.html>`_

After installing Python and the required packages, the simplest way to obtain
SrMise is using ``pip`` to download and install the latest release from the
`Python Package Index <https://pypi.python.org>`_ (PyPI). Open a command window
by running ``cmd`` from the Start Menu's application search box (Windows 7/8/10)
or Run command (Windows Vista and earlier). Verify that the
``pip`` program is installed by running ::

pip --version

If this command is not found, download and run
`get-pip.py <https://bootstrap.pypa.io/get-pip.py>`_, which will install both it
and setuptools. For example, if the file were downloaded to the desktop, a
Windows user named ``MyName`` should run the following from the command
line: ::

cd C:\Users\MyName\Desktop
python get-pip.py

Finally, install the latest version of SrMise by running ::

pip install diffpy.srmise


Mac OS X
Citation
--------

For Mac OS X systems with the MacPorts package manager, the required
software can be installed with ::
If you use diffpy.srmise in a scientific publication, we would like you to cite this package as

sudo port install \
python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib
diffpy.srmise Package, https://github.com/diffpy/diffpy.srmise

sbillinge marked this conversation as resolved.
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When installing for MacPorts, make sure the MacPorts bin directory is the first
in the system PATH and that python27 is selected as the default Python version
in MacPorts::
Installation
------------

sudo port select --set python python27
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.

The simplest way to obtain diffpy.srmise on Mac OS X systems
is using ``pip`` to download and install the latest release from
`PyPI <https://pypi.python.org>`_. ::
To add "conda-forge" to the conda channels, run the following in a terminal. ::

sudo pip install diffpy.srmise
conda config --add channels conda-forge

Those who prefer to install from sources may download them from the
`GitHub <https://github.com/diffpy/diffpy.srmise/releases>`__ or
`PyPI <https://pypi.python.org/pypi/diffpy.srmise>`__ pages for SrMise.
Uncompress them to a directory, and from that directory run ::
We want to install our packages in a suitable conda environment.
The following creates and activates a new environment named ``diffpy.srmise_env`` ::

sudo python setup.py install
conda create -n diffpy.srmise_env python=3
conda activate diffpy.srmise_env

This installs diffpy.srmise for all users in the default system location. If
administrator (root) access is not available, see the usage info from
``python setup.py install --help`` for options to install to user-writable
directories.
Then, to fully install ``diffpy.srmise`` in our active environment, run ::

conda install diffpy.srmise

Linux
-----
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.srmise_env`` environment, type ::

On Ubuntu and Debian Linux, the required software can easily be installed using
the system package manager::
pip install diffpy.srmise

sudo apt-get install \
python-setuptools python-numpy python-scipy python-matplotlib
If you prefer to install from sources, after installing the dependencies, obtain the source archive from
`GitHub <https://github.com/diffpy/diffpy.srmise/>`_. Once installed, ``cd`` into your ``diffpy.srmise`` directory
and run the following ::

Similarly, on Fedora::
pip install .

sudo yum install python-setuptools numpy scipy python-matplotlib
Support and Contribute
----------------------

For other Linux distributions consult the appropriate package manager.
`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.srmise. Please join the diffpy.srmise users community by joining the Google group. The diffpy.srmise project welcomes your expertise and enthusiasm!

The simplest way to obtain diffpy.srmise on Linux systems
is using ``pip`` to download and install the latest release from the
`PyPI <https://pypi.python.org>`_. ::
If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srmise/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srmise/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.

sudo pip install diffpy.srmise
Feel free to fork the project and contribute. To install diffpy.srmise
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 ::

Those who prefer to install from sources may download them from the
`GitHub <https://github.com/diffpy/diffpy.srmise/releases>`__ or
`PyPI <https://pypi.python.org/pypi/diffpy.srmise>`__ pages for SrMise.
Uncompress them to a directory, and from that directory run ::
pip install -e .

sudo python setup.py install
To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
hooks.

This installs diffpy.srmise for all users in the default system location. If
administrator (root) access is not available, see the usage info from
``python setup.py install --help`` for options to install to user-writable
directories.
1. Install pre-commit in your working environment by running ``conda install pre-commit``.

2. Initialize pre-commit (one time only) ``pre-commit install``.

DEVELOPMENT
===========
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.

diffpy.srmise is open-source software developed with support of the Center of
Research Excellence in Complex Materials at Michigan State University, in
cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven
National Laboratory. The diffpy.srmise sources are hosted at
https://github.com/diffpy/diffpy.srmise.
Improvements and fixes are always appreciated.

Feel free to fork the project and contribute. To install diffpy.srmise in a
development mode, with its sources being directly used by Python rather than
copied to a package directory, use ::
Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srmise/blob/main/CODE_OF_CONDUCT.rst>`_.

python setup.py develop --user


ACKNOWLEDGEMENT
===============
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Let's put this acknowledgement back in.


The source code of *pdfdataset.py* was derived from diffpy.pdfgui.


CONTACTS
========

For more information on SrMise please visit the DiffPy project web-page

http://www.diffpy.org/
Contact
-------

or email Prof. Simon Billinge at sb2896@columbia.edu.
For more information on diffpy.srmise please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.
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