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start work on docs
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‎.flake8

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[flake8]
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ignore = E731, W503, W504, E203
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ignore = E731, W503, W504, E203, W605
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max-line-length=80
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exclude = .git,__pycache__,*__init__.py,alnur

‎doc/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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@if [ "$@" = "html" ]; then \
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touch $(BUILDDIR)/html/.nojekyll; \
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fi

‎doc/make.bat

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎doc/source/.conf.py.swp

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‎doc/source/.index.rst.swp

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‎doc/source/_static/css/.custom.css.swp

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‎doc/source/_static/css/custom.css

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@import url('https://fonts.googleapis.com/css2?family=Raleway:ital,wght@0,300;0,400;0,600;1,300;1,400;1,600&display=swap');
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:root {
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--sidebarcolor: #102133;
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--sidebarfontcolor: #ffffff;
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--sidebarhover: #295e97;
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--bodyfontcolor: #333;
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--webfont: 'Raleway';
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--contentwidth: 1000px;
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}
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/* Fonts and text */
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h1, h2, h3, h4, h5, h6 {
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font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
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font-weight: 400;
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}
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h1 {
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font-size: 225%;
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}
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body {
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font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
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color: var(--bodyfontcolor);
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}
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p {
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font-size: 1em;
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line-height: 150%;
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}
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/* Sidebar */
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.wy-side-nav-search {
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background-color: var(--sidebarcolor);
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}
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.wy-nav-side {
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background: var(--sidebarcolor);
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}
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.wy-menu-vertical header, .wy-menu-vertical p.caption {
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color: var(--sidebarfontcolor);
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}
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.wy-menu-vertical a {
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color: var(--sidebarfontcolor);
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}
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.wy-menu-vertical a:hover {
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background-color: var(--sidebarhover);
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}
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/* Main content */
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.wy-nav-content {
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max-width: var(--contentwidth);
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}

‎doc/source/api/index.rst

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.. _api:
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API
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===
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MDE
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~~~
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.. autoclass:: pymde.MDE
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:members:
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:exclude-members: forward
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.. automethod:: __init__
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.. autofunction:: pymde.preserve_neighbors
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.. autofunction:: pymde.preserve_distances
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Distortion functions
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~~~~~~~~~~~~~~~~~~~~
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Penalties
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^^^^^^^^^
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.. automodule:: pymde.penalties
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.. autoclass:: pymde.penalties.Linear
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Quadratic
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Cubic
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Power
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Huber
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Logistic
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Log1p
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:exclude-members: forward
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.. autoclass:: pymde.penalties.Log
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:exclude-members: forward
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.. autoclass:: pymde.penalties.InvPower
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:exclude-members: forward
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.. autoclass:: pymde.penalties.LogRatio
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:exclude-members: forward
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.. autoclass:: pymde.penalties.PushAndPull
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:exclude-members: forward
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Losses
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^^^^^^^^^
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.. automodule:: pymde.losses
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.. autoclass:: pymde.losses.Absolute
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:exclude-members: forward
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.. autoclass:: pymde.losses.Quadratic
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:exclude-members: forward
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.. autoclass:: pymde.losses.Cubic
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:exclude-members: forward
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.. autoclass:: pymde.losses.Power
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:exclude-members: forward
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.. autoclass:: pymde.losses.WeightedQuadratic
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:exclude-members: forward
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.. autoclass:: pymde.losses.Fractional
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:exclude-members: forward
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.. autoclass:: pymde.losses.SoftFractional
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:exclude-members: forward
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Constraints
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~~~~~~~~~~~
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.. autoclass:: pymde.constraints.Constraint
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:members:
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.. autofunction:: pymde.Centered
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.. autofunction:: pymde.Standardized
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.. autoclass:: pymde.Anchored
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.. automethod:: __init__
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Preprocessing
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~~~~~~~~~~~~~
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.. autoclass:: pymde.Graph
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:members:
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.. autofunction:: pymde.preprocess.graph.k_nearest_neighbors
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.. autofunction:: pymde.preprocess.graph.shortest_paths
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.. autofunction:: pymde.preprocess.data_matrix.k_nearest_neighbors
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Utilities
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~~~~~~~~~
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.. autofunction:: pymde.all_edges
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.. autofunction:: pymde.align
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.. autofunction:: pymde.center
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.. autofunction:: pymde.rotate
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.. autofunction:: pymde.plot

‎doc/source/citing/.index.rst.swp

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‎doc/source/citing/index.rst

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.. _citing:
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Citing
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======
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If you use PyMDE in academic work, please consider citing the paper it
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accompanies (*Minimum-Distortion Embedding*.) You can use the following
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BibTex entry:
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.. code:: bibtex
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@article{agrawal2020minimum,
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author = {Agrawal, Akshay and Ali, Alnur and Boyd, Stephen},
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title = {Minimum-Distortion Embedding},
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url = {https://web.stanford.edu/~boyd/papers/min_dist_emb.html},
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year = {2020},
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}
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If you want to keep tabs on the development of PyMDE (or just want to send
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a virtual kudos), consider leaving a star on the
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`Github repository <https://github.com/cvxgrp/pymde>`_.

‎doc/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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# -- Project information -----------------------------------------------------
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project = 'pymde'
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copyright = '2021, Akshay Agrawal'
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author = 'Akshay Agrawal'
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# The full version, including alpha/beta/rc tags
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release = '0.1.0'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx_rtd_theme',
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'sphinx.ext.autodoc',
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'sphinx.ext.napoleon',
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]
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'autumn'
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_css_files = [
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'css/custom.css',
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]

‎doc/source/datasets/index.rst

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.. _datasets:
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Datasets
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========
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