{ "info": { "author": "Ralf Banisch, Erik Henning Thiede, Zofia Trstanova", "author_email": "ralf.banisch@fu-berlin.de, ehthiede@gmail.com, zofia.trstanova@ed.ac.uk", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering" ], "description": "========\nOverview\n========\n\n\n\nThis 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. \n\n* Free software: MIT License.\n\nInstallation\n============\n\nPydiffmap is installable using pip. You can install it using the command\n\n::\n\n pip install pyDiffMap\n\nYou 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.\n\n::\n\n pip install [source_directory]\n\nDocumentation\n=============\n\nhttps://pyDiffMap.readthedocs.io/\n\nDevelopment\n===========\n\nTo run the all tests run::\n\n tox\n\nNote, to combine the coverage data from all the tox environments run:\n\n.. list-table::\n :widths: 10 90\n :stub-columns: 1\n\n - - Windows\n - ::\n\n set PYTEST_ADDOPTS=--cov-append\n tox\n\n - - Other\n - ::\n\n PYTEST_ADDOPTS=--cov-append tox\n\nIf you don't have tox installed, you can also run the python tests directly with \n\n::\n\n pytest\n\n\n\nChangelog\n=========\n\n0.2.0.1 (2019-02-04)\nNew Features\n~~~~~~~~~~~~\n* Added a more generous epsilon procedure for convenience.\n\n0.2.0 (2019-02-01)\n------------------\n\nNew Features\n~~~~~~~~~~~~\n* Added support for user-provided kernel functions. \n* Added a utility for building a sparse matrix from a function on the data.\n* (Re)added separate TMDmap class wrapping base diffusion map class to \n allow for easier construction of TMDmaps. \n* Added ability to explicitly provide the sampled density for q^alpha normalization.\n* Added Variable Bandwidth Diffusion Maps.\n* Added a new out-of-sample extension method that should work for variable bandwidth methods.\n\nTweaks and Modifications\n~~~~~~~~~~~~~~~~~~~~~~~~\n* Changed from exp^(-d^2) to exp^(-d^2/4) convention.\n* Moved weight functionality into a function provided on initialization, \n rather than input values, and added a helper function that allows values to\n be read from a lookup table.\n* Improved the Diffusion Map test suite.\n* Moved out-of-sample routines into separate functions.\n* Moved matrix symmetrization into newly made utility file.\n* Adjusted constructor for the diffusion map to take the kernel object directly.\n\nBugfixes\n~~~~~~~~\n* Fixed bug where weight matrices were not included for out of sample extension.\n\nOther\n~~~~~\n* Moved to MIT license.\n\n0.1.0 (2017-12-06)\n------------------\n\n* Fixed setup.py issues.\n\n0.1.0 (2017-12-06)\n------------------\n\n* Added base functionality to the code.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/DiffusionMapsAcademics/pyDiffMap", "keywords": "diffusion maps,manifold learning,molecular dynamics,dimensionality reduction", "license": "MIT license", "maintainer": "", "maintainer_email": "", "name": "pydiffmap", "package_url": "https://pypi.org/project/pydiffmap/", "platform": "", "project_url": "https://pypi.org/project/pydiffmap/", "project_urls": { "Homepage": "https://github.com/DiffusionMapsAcademics/pyDiffMap" }, "release_url": "https://pypi.org/project/pydiffmap/0.2.0.1/", 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