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Revert "change python version in README.rst" #123

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Revert "change python version in README.rst (#107)"
stevenhua0320 Sep 27, 2024
6ca891e
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Sep 27, 2024
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225 changes: 137 additions & 88 deletions README.rst
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|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
#########################
SrMise
#########################

.. |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)
`DiffPy project <http://www.diffpy.org>`_ tool for unbiased peak extraction from
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 @@ -70,85 +38,166 @@ 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 the diffpy.srmise library, please consult our `online documentation <https://diffpy.github.io/diffpy.srmise>`_.
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
-------

Citation
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
--------

If you use diffpy.srmise in a scientific publication, we would like you to cite this package as
For Mac OS X systems with the MacPorts package manager, the required
software can be installed 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 install \
python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib

Installation
------------
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::

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 port select --set python python27

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

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

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

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

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 ::
Linux
-----

pip install -r https://raw.githubusercontent.com/diffpy/diffpy.srmise/main/requirements/run.txt
On Ubuntu and Debian Linux, the required software can easily be installed using
the system package manager::

and then install the package ::
sudo apt-get install \
python-setuptools python-numpy python-scipy python-matplotlib

pip install diffpy.srmise
Similarly, on Fedora::

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 ::
sudo yum install python-setuptools numpy scipy python-matplotlib

pip install .
For other Linux distributions consult the appropriate package manager.

Support and Contribute
----------------------
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>`_. ::

`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 pip install diffpy.srmise

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>`_.
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 ::

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 ::
sudo python setup.py install

pip install -e .
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.

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``.
DEVELOPMENT
===========

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

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.
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 ::

Improvements and fixes are always appreciated.
python setup.py develop --user

Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srmise/blob/main/CODE_OF_CONDUCT.rst>`_.

Contact
-------
ACKNOWLEDGEMENT
===============

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/

For more information on diffpy.srmise please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
or email Prof. Simon Billinge at [email protected].
24 changes: 12 additions & 12 deletions doc/source/extending.rst
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Expand Up @@ -27,14 +27,14 @@ subpackges, as shown below.
* .. py:class:: BaseFunction

+ .. py:class:: BaselineFunction

- .. py:class:: FromSequence
- .. py:class:: NanoSpherical
- .. py:class:: Polynomial
- *etc.*

+ .. py:class:: PeakFunction

- .. py:class:: Gaussian
- .. py:class:: GaussianOverR
- *etc.*
Expand All @@ -57,7 +57,7 @@ for examples.
.. py:method:: estimate_parameters(r, y)

Return a Numpy array of parameters estimated from the data.

:param r: Grid on which the data are defined.
:param y: The data.
:type r: `Sequence`
Expand All @@ -69,9 +69,9 @@ for examples.


.. py:method:: _jacobian_raw(pars, r, free)

Return Jacobian for parameters evaluated over `r`.

:param pars: The parameters of the baseline.
:param r: Scalar or grid on which to calculate the Jacobian.
:param free: Boolean values indicating if corresponding parameter is free (True) or fixed (False).
Expand All @@ -84,7 +84,7 @@ for examples.
.. py:method:: _transform_derivativesraw(pars, in_format, out_format)

Return the gradient matrix of `pars` represented in format 'out_format'.

:param pars: The parameters of the baseline.
:param in_format: The format of `pars`.
:param out_format: The desired format of `pars`.
Expand All @@ -97,7 +97,7 @@ for examples.
.. py:method:: _transform_parametersraw(pars, in_format, out_format)

Return parameters transformed into format 'out_format'.

:param pars: The parameters of the baseline.
:param in_format: The format of `pars`.
:param out_format: The desired format of `pars`.
Expand All @@ -106,11 +106,11 @@ for examples.
:type out_format: `str`
:returns: The transformed parameters.
:rtype: `numpy.ndarray`

.. py:method:: _valueraw(pars, r)

Return value of baseline with given parameters at r.

:param pars: The parameters of the baseline.
:param r: Scalar or grid on which to calculate the baseline.
:type pars: `Sequence(float)`
Expand All @@ -130,12 +130,12 @@ following differences:
1) The ``estimate_parameters`` method is required.
2) The "position" key must be defined in the ``parameterdict`` class member.
3) Peak functions must implement the additional method ``scale_at``.

.. py:method:: scale_at(pars, r, scale)

Return peak parameters such that the value at ``r`` is scaled by ``scale``
while the position of the peak's maxima remains unchanged.

:param pars: The parameters of the peak.
:param r: Position where the peak will be rescaled.
:param scale: A scale factor > 0.
Expand Down
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