Skip to content

change python version in README.rst #107

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
Sep 26, 2024
Merged

change python version in README.rst #107

Changes from 3 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
9477191
change python version in READNME.rst
stevenhua0320 Sep 4, 2024
0facd1a
README.rst rebuild followed cookiecutter standard
stevenhua0320 Sep 4, 2024
0d2793a
update long description for README.rst
stevenhua0320 Sep 4, 2024
6f5010d
change reference to paper
stevenhua0320 Sep 5, 2024
2f11c69
Merge branch 'diffpy:main' into readme
stevenhua0320 Sep 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
223 changes: 86 additions & 137 deletions README.rst
View file
Open in desktop
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/main.yml/badge.svg
:target: https://github.com/diffpy/diffpy.srmise/actions/workflows/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

implementation of the ParSCAPE algorithm for peak extraction from atomic pair distribution functions (PDFs)

SrMise is an implementation of the `ParSCAPE algorithm
<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
Expand Down Expand Up @@ -38,166 +70,83 @@ necessary to provide the most reliable results, but historically such PDFs
are rare. In the absence of accurate uncertainties an *ad hoc* uncertainty
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
-------
For more information about the diffpy.srmise library, please consult our `online documentation <https://diffpy.github.io/diffpy.srmise>`_.

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.

* `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 ::

sudo port install \
python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib
If you use diffpy.srmise in a scientific publication, we would like you to cite this package as

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::
diffpy.srmise Package, https://github.com/diffpy/diffpy.srmise

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This one has a published paper to cite, so please replace (here and in the docs) this line with:
L. Granlund, Billinge, S. J. L., and P. M. Duxbury. “Algorithm for systematic peak extraction from atomic
pair distribution functions”. In: Acta Crystallogr. A 71.4 (2015), pp. 392–409. DOI:
10.1107/S2053273315005276.

sudo port select --set python python27
Installation
------------

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>`_. ::
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.

sudo pip install diffpy.srmise
To add "conda-forge" to the conda channels, run the following in a terminal. ::

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 ::
conda config --add channels conda-forge

sudo python setup.py install
We want to install our packages in a suitable conda environment.
The following creates and activates a new environment named ``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.
conda create -n diffpy.srmise_env python=3
conda activate diffpy.srmise_env

Then, to fully install ``diffpy.srmise`` in our active environment, run ::

Linux
-----
conda install diffpy.srmise

On Ubuntu and Debian Linux, the required software can easily be installed using
the system package manager::
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, we will also have to install dependencies ::

sudo apt-get install \
python-setuptools python-numpy python-scipy python-matplotlib
pip install -r https://raw.githubusercontent.com/diffpy/diffpy.srmise/main/requirements/run.txt

Similarly, on Fedora::
and then install the package ::

sudo yum install python-setuptools numpy scipy python-matplotlib
pip install diffpy.srmise

For other Linux distributions consult the appropriate package manager.
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 ::

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>`_. ::
pip install .

sudo pip install diffpy.srmise
Support and Contribute
----------------------

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 ::
`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!

sudo python setup.py install
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>`_.

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.
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 ::

pip install -e .

DEVELOPMENT
===========
To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
hooks.

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.
1. Install pre-commit in your working environment by running ``conda install pre-commit``.

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

python setup.py develop --user
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.

Improvements and fixes are always appreciated.

ACKNOWLEDGEMENT
===============

The source code of *pdfdataset.py* was derived from diffpy.pdfgui.
Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srmise/blob/main/CODE_OF_CONDUCT.rst>`_.

Contact
-------

CONTACTS
========

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

http://www.diffpy.org/

or email Prof. Simon Billinge at [email protected].
For more information on diffpy.srmise please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
Loading