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Merge pull request #39 from broadinstitute/ziq
Ziq
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‎docs/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)

‎docs/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

‎docs/requirements.txt‎

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sphinx==4.0.2
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nbsphinx==0.8.6
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nbsphinx-link==1.3.0
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sphinx-rtd-theme
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torch
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pandas==1.1.0
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numpy==1.19.1
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scipy==1.5.2
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seaborn==0.11.1
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scanpy>=1.6.0
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scikit-learn
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tqdm
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sphinx-gallery==0.9.0

‎docs/source/_contributors.rst‎

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.. sidebar:: Contributors
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* `Tommaso Biancalani`_: author of method, PyPI maintainer :mod:`Contact: [email protected]`
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* Gabriele Scalia: author of method :mod:`Contact: [email protected]`
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* Ziqing Lu: PyPI maintainer :mod:`Contact: [email protected]`
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* Shreya Gaddam: PyPI maintainer :mod:`Contact: [email protected]`
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* Anna Hupalowska: Artwork :mod:`Contact: [email protected]`
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.. _Tommaso Biancalani: https://twitter.com/tbyanc?lang=en

‎docs/source/_static/css/custom.css‎

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.small {
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font-size: 55%;
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}
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/*size of the page*/
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.wy-nav-content {
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max-width: 1500px !important;
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}
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div.version {
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color: #4d79ff!important;
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}
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/*side-bar background color*/
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.wy-nav-side {
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background: #4d79ff!important;
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}
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/*logo area*/
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.wy-side-nav-search {
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background-color: #ffffff!important;
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}
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.wy-side-nav-search {
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border: 4px solid #4d79ff;
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}
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.wy-side-nav-search input[type="text"] {
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border-radius: 6px!important;
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}
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.wy-nav-content{
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max-width: 950px;
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}
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/* color for hovering over the topics */
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.wy-menu-vertical a:hover {
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background-color: #00e6e6
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}
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/*color for text when hovering*/
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.wy-menu-vertical a:hover {
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color: #0000ff
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}
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/* color for hovering over the selected topic */
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.wy-menu-vertical li.current a:hover {
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background: #00e6e6;
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}
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.wy-menu > .caption > span.caption-text {
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color: #ffffff;
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}
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‎docs/source/_static/images/tangram.png‎

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‎docs/source/_static/images/tangram_loss.gif‎

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‎docs/source/_static/images/tangram_overview.png‎

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‎docs/source/_templates/autosummary/base.rst‎

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{{ fullname | escape | underline}}
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.. currentmodule:: {{ module }}
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.. auto{{ objtype }}:: {{ objname }}

‎docs/source/_templates/autosummary/class.rst‎

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{{ fullname | escape | underline}}
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.. currentmodule:: {{ module }}
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.. autoclass:: {{ objname }}
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{% block methods %}
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{% block attributes %}
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{% if attributes %}
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.. autosummary::
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:toctree:
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{% for item in all_attributes %}
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{%- if not item.startswith('_') %}
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{{ name }}.{{ item }}
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{%- endif -%}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% if methods %}
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.. autosummary::
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:toctree:
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{% for item in all_methods %}
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{%- if not item.startswith('_') or item in ['__call__'] %}
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{{ name }}.{{ item }}
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{%- endif -%}
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{%- endfor %}
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{% endif %}
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{% endblock %}

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