semvec/pypi-packages huggingface dataset:
pydiffmap 0.2.0.1
Library for constructing variable bandwidth diffusion maps
License: MIT license
Keywords: diffusion maps,manifold learning,molecular dynamics,dimensionality reduction

========
Overview
========



This is the home of the documentation for pyDiffMap, an open-source project to develop a robust and accessible diffusion map code for public use. Our documentation is currently under construction, please bear with us. 

* Free software: MIT License.

Installation
============

Pydiffmap is installable using pip.  You can install it using the command

::

    pip install pyDiffMap

You can also install the package directly from the source directly by downloading the package from github and running the command below, optionally with the "-e" flag for an editable install.

::

    pip install [source_directory]

Documentation
=============

https://pyDiffMap.readthedocs.io/

Development
===========

To run the all tests run::

    tox

Note, to combine the coverage data from all the tox environments run:

.. list-table::
    :widths: 10 90
    :stub-columns: 1

    - - Windows
      - ::

            set PYTEST_ADDOPTS=--cov-append
            tox

    - - Other
      - ::

            PYTEST_ADDOPTS=--cov-append tox

If you don't have tox installed, you can also run the python tests directly with 

::

    pytest



Changelog
=========

0.2.0.1 (2019-02-04)
New Features
~~~~~~~~~~~~
* Added a more generous epsilon procedure for convenience.

0.2.0 (2019-02-01)
------------------

New Features
~~~~~~~~~~~~
* Added support for user-provided kernel functions. 
* Added a utility for building a sparse matrix from a function on the data.
* (Re)added separate TMDmap class wrapping base diffusion map class to 
  allow for easier construction of TMDmaps. 
* Added ability to explicitly provide the sampled density for q^alpha normalization.
* Added Variable Bandwidth Diffusion Maps.
* Added a new out-of-sample extension method that should work for variable bandwidth methods.

Tweaks and Modifications
~~~~~~~~~~~~~~~~~~~~~~~~
* Changed from exp^(-d^2) to exp^(-d^2/4) convention.
* Moved weight functionality into a function provided on initialization, 
  rather than input values, and added a helper function that allows values to
  be read from a lookup table.
* Improved the Diffusion Map test suite.
* Moved out-of-sample routines into separate functions.
* Moved matrix symmetrization into newly made utility file.
* Adjusted constructor for the diffusion map to take the kernel object directly.

Bugfixes
~~~~~~~~
* Fixed bug where weight matrices were not included for out of sample extension.

Other
~~~~~
* Moved to MIT license.

0.1.0 (2017-12-06)
------------------

* Fixed setup.py issues.

0.1.0 (2017-12-06)
------------------

* Added base functionality to the code.