theislab · davidsebfischer · Jun 8, 2021 · May 31, 2021 · May 31, 2021 · May 31, 2021
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,15 @@
+# Cache
 cache/ontologies/cl/*
+
+# Docs
+docs/api/
+
+# Unit test temporary data:
 sfaira/unit_tests/test_data_loaders/*
 sfaira/unit_tests/test_data/*
 sfaira/unit_tests/template_data/*
-sfaira/unit_tests/data_contribution/test_data_template.py
+
+# General patterns:
 git abuild
 cache
 sfaira.egg-info
@@ -14,7 +21,6 @@ venv/*
 *.ipynb_checkpoints/
 */*.ipynb_checkpoints/
 **/.DS_Store
-docs/_templates/
 dist/
 !**/.gitignore
 

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -10,6 +10,6 @@ sphinx:
 formats: all
 
 python:
-  version: 3.9
+  version: 3.8
   install:
     - requirements: docs/requirements.txt
diff --git a/docs/_static/custom_sfaira.css b/docs/_static/custom_sfaira.css
@@ -1,140 +1,3 @@
-@import "basic.css";
-
-/*Color main components with a dark theme*/
-div, span, code {
-    background-color: #181a1b !important;
-}
-
-.wy-side-nav-search {
-    background-color: #005fff !important;
-}
-
-.wy-side-nav-search div {
-    background-color: #005fff !important;
-}
-
-/*Font color is mainly white*/
-.rst-content p, li, h1, h2, h3, h4, h5, h6, .highlight-console, .n, .section {
-    color: #FFFFFF;
-}
-
-/*The side menu is slightly more grey and lighter than the overall theme*/
-.wy-menu, .wy-menu-vertical {
-    background-color: #2D2E2F !important;
-}
-
-.wy-side-scroll {
-    background-color: #2D2E2F !important;
-}
-
-.wy-menu .caption-text {
-    background-color: #2D2E2F !important;
-}
-
-.caption-text {
-    background-color: #181a1b !important;
-}
-
-.figure p {
-    background-color: #181a1b !important;
-}
-
-/*Toctree wrapper on index page has a dark background unlike the other menu items*/
-.toctree-wrapper .compound ul .toctree-l1, .toctree-wrapper .compound ul .toctree-l2 {
-    background-color: #181a1b !important;
-    color: #005fff !important;
-}
-
-/*The current menu section has a blue background*/
-.wy-menu-vertical li.toctree-l1.current li.toctree-l2 > a:hover {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-}
-
-/*Subitems under the current section are displayed in grey again*/
-.wy-menu-vertical li.toctree-l1.current li.toctree-l2 > a {
-    color: #FFFFFF !important;
-    background: #2D2E2F !important;
-}
-
-/*Current hovered item has a blue background*/
-.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a:hover {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l2.current > a:hover {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a {
-    color: #FFFFFF !important;
-    background: #2D2E2F !important;
-}
-
-.wy-menu-vertical li.toctree-l1.current {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-    border-color: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l1.current > a {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-    border-color: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l1.current > a:hover {
-    color: #FFFFFF !important;
-    background: #005fff !important;
-    border-color: #005fff !important;
-}
-
-/*The expand toctree items have the same background as its corresponding section*/
-.wy-menu-vertical li.toctree-l1 a span.toctree-expand {
-    background-color: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l2 a span.toctree-expand {
-    background-color: #2D2E2F !important;
-}
-
-.wy-menu-vertical li.toctree-l2 a:hover span.toctree-expand {
-    background-color: #005fff !important;
-}
-
-.wy-menu-vertical li.toctree-l3 a span.toctree-expand {
-    background-color: #2D2E2F !important;
-}
-
-.wy-menu-vertical li.toctree-l3 a:hover span.toctree-expand {
-    background-color: #005fff !important;
-}
-
-.code .docutils .literal .notranslate .pre {
-    background-color: #181a1b !important;
-}
-
-/*Color footer separately corresponding to overall dark theme*/
-footer {
-    color: #FFFFFF;
-}
-
-/*Color footer buttons in blue*/
-.rst-footer-buttons a, .rst-footer-buttons a:hover, .rst-footer-buttons span {
-    background-color: #005fff !important;
-}
-
-.wy-side-nav-search a {
-    background-color: #005fff !important;
-}
-
-.version {
-    background-color: #005fff !important;
-    color: #FFFFFF !important;
-}
-
 /*Set max width to none so the theme uses all available width*/
 .wy-nav-content {
     max-width: none;

diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
@@ -0,0 +1,40 @@
+..
+    This code was adapted from https://github.com/theislab/cellrank/tree/master/docs/_templates/autosummary/base.rst
+    This file is therefore licensed under the license of the cellrank project,
+    available from https://github.com/theislab/cellrank and copied here at the time of accession.
+
+    BSD 3-Clause License
+
+    Copyright (c) 2019, Theis Lab
+    All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+
+    1. Redistributions of source code must retain the above copyright notice, this
+       list of conditions and the following disclaimer.
+
+    2. Redistributions in binary form must reproduce the above copyright notice,
+       this list of conditions and the following disclaimer in the documentation
+       and/or other materials provided with the distribution.
+
+    3. Neither the name of the copyright holder nor the names of its
+       contributors may be used to endorse or promote products derived from
+       this software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+    OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+:github_url: {{ fullname }}
+
+{% extends "!autosummary/base.rst" %}
+
+.. http://www.sphinx-doc.org/en/stable/ext/autosummary.html#customizing-templates
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,74 @@
+..
+    This code was adapted from https://github.com/theislab/cellrank/tree/master/docs/_templates/autosummary/class.rst
+    This file is therefore licensed under the license of the cellrank project,
+    available from https://github.com/theislab/cellrank and copied here at the time of accession.
+
+    BSD 3-Clause License
+
+    Copyright (c) 2019, Theis Lab
+    All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+
+    1. Redistributions of source code must retain the above copyright notice, this
+       list of conditions and the following disclaimer.
+
+    2. Redistributions in binary form must reproduce the above copyright notice,
+       this list of conditions and the following disclaimer in the documentation
+       and/or other materials provided with the distribution.
+
+    3. Neither the name of the copyright holder nor the names of its
+       contributors may be used to endorse or promote products derived from
+       this software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+    OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+:github_url: {{ fullname }}
+
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: .
+   {% for item in attributes %}
+      ~{{ fullname }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: .
+   {% for item in methods %}
+      {%- if item != '__init__' %}
+      ~{{ fullname }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   .. _sphx_glr_backref_{{fullname}}:
+
+   .. minigallery:: {{fullname}}
+       :add-heading: Examples
+       :heading-level: -
diff --git a/docs/_templates/autosummary/function.rst b/docs/_templates/autosummary/function.rst
@@ -0,0 +1,46 @@
+..
+    This code was adapted from https://github.com/theislab/cellrank/tree/master/docs/_templates/autosummary/function.rst
+    This file is therefore licensed under the license of the cellrank project,
+    available from https://github.com/theislab/cellrank and copied here at the time of accession.
+
+    BSD 3-Clause License
+
+    Copyright (c) 2019, Theis Lab
+    All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+
+    1. Redistributions of source code must retain the above copyright notice, this
+       list of conditions and the following disclaimer.
+
+    2. Redistributions in binary form must reproduce the above copyright notice,
+       this list of conditions and the following disclaimer in the documentation
+       and/or other materials provided with the distribution.
+
+    3. Neither the name of the copyright holder nor the names of its
+       contributors may be used to endorse or promote products derived from
+       this software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+    OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+:github_url: {{ fullname }}
+
+{{ fullname | escape | underline}}
+
+.. autofunction:: {{ fullname }}
+
+.. _sphx_glr_backref_{{fullname}}:
+
+.. minigallery:: {{fullname}}
+   :add-heading: Examples
+   :heading-level: -