Merge pull request #8 from YosefLab/docs

use simpler rtd theme

README.md

@@ -10,3 +10,6 @@ Skeleton repository for creating novel models with
 [scvi-tools](https://www.scvi-tools.org/en/stable/). For questions about
 using this skeleton, please use the scvi-tools
 [forum](https://discourse.scvi-tools.org/).
+
+
+Getting started development using this skeleton is similar to [getting started](https://docs.scvi-tools.org/en/stable/contributing/index.html) with scvi-tools.

docs/_static/css/custom.css

@@ -0,0 +1,78 @@
+/* influenced by and borrowed from: https://github.com/cvxgrp/pymde/blob/main/docs_src/source/_static/css/custom.css */
+
+@import url('https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,300;0,400;0,600;1,300;1,400;1,600&display=swap');
+
+:root {
+    --sidebarcolor: #003262;
+    --sidebarfontcolor: #ffffff;
+	--sidebarhover: #295e97;
+
+    --bodyfontcolor: #333;
+	--webfont: 'Roboto';
+
+	--contentwidth: 1000px;
+}
+
+/* Fonts and text */
+h1, h2, h3, h4, h5, h6 {
+	font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
+	font-weight: 400;
+}
+
+h2, h3, h4, h5, h6 {
+  padding-top: 0.25em;
+  margin-bottom: 0.5em;
+}
+
+h1 {
+	font-size: 225%;
+}
+
+body {
+	font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
+	color: var(--bodyfontcolor);
+}
+
+p {
+	font-size: 1em;
+	line-height: 150%;
+}
+
+
+/* Sidebar */
+.wy-side-nav-search {
+    background-color: var(--sidebarcolor);
+}
+
+.wy-nav-side {
+    background: var(--sidebarcolor);
+}
+
+.wy-menu-vertical header, .wy-menu-vertical p.caption {
+    color: var(--sidebarfontcolor);
+}
+
+.wy-menu-vertical a {
+    color: var(--sidebarfontcolor);
+}
+
+.wy-side-nav-search > div.version {
+    color: var(--sidebarfontcolor);
+}
+
+.wy-menu-vertical a:hover {
+    background-color: var(--sidebarhover);
+}
+
+/* Main content */
+.wy-nav-content {
+    max-width: var(--contentwidth);
+}
+
+
+html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) dl:not(.field-list) > dt{
+    margin-bottom: 6px;
+    border-left: none;
+    background: none;
+    color: #555;
+}

docs/conf.py

@@ -1,23 +1,11 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
+# Configuration file for the Sphinx documentation builder.
 #
-# scvi documentation build configuration file, created by
-# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
 
-# If extensions (or modules to document with autodoc) are in another
-# directory, add these directories to sys.path here. If the directory is
-# relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-#
 import sys
 from pathlib import Path
 
@@ -122,70 +110,31 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "default"
+pygments_style = "tango"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
-# -- Options for HTML output -------------------------------------------
+# -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_show_sourcelink = True
-html_sidebars = {
-    "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
-}
-html_theme = "sphinx_material"
-
-# Theme options are theme-specific and customize the look and feel of a
-# theme further.  For a list of options available for each theme, see the
-# documentation.
-#
+html_theme = "sphinx_rtd_theme"
+
+html_show_sourcelink = False
+
+html_show_copyright = False
+
+display_version = True
 
-# Set link name generated in the top bar.
-html_title = "scvi-tools project skeleton"
-
-# Material theme options (see theme.conf for more information)
-html_theme_options = {
-    "base_url": "https://project.github.io/project",
-    # Set the color and the accent color
-    "color_primary": "white",
-    "color_accent": "light-blue",
-    "repo_type": "github",
-    # Set the repo location to get a badge with stats
-    "repo_url": "https://github.com/YosefLab/scvi-tools-skeleton",
-    "repo_name": "scvi-tools-skeleton",
-    "nav_links": [],
-    "html_minify": True,
-    "css_minify": True,
-    "nav_title": "scvi-tools-skeleton",
-    "globaltoc_depth": 3,
-    "globaltoc_collapse": True,
-    "globaltoc_includehidden": True,
-    "master_doc": False,
-    "logo_icon": "&#xe869",
-}
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-html_show_sphinx = False
-
-
-# -- Options for HTMLHelp output ---------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = "skeletondoc"
+html_css_files = [
+    "css/custom.css",
+]
 
-mathjax_config = {
-    "extensions": ["tex2jax.js"],
-    "jax": ["input/TeX", "output/HTML-CSS"],
-    "tex2jax": {
-        "inlineMath": [["$", "$"], ["\\(", "\\)"]],
-        "displayMath": [["$$", "$$"], ["\\[", "\\]"]],
-        "processEscapes": True,
-    },
-}
+html_favicon = "favicon.ico"

pyproject.toml

@@ -54,7 +54,7 @@ scikit-misc = {version = ">=0.1.3", optional = true}
 scvi-tools = ">=0.10.0"
 sphinx = {version = "^3.0", optional = true}
 sphinx-autodoc-typehints = {version = "*", optional = true}
-sphinx-material = {version = "*", optional = true}
+sphinx-rtd-theme = {version = "*", optional = true}
 typing_extensions = {version = "*", python = "<3.8"}
 
 [tool.poetry.extras]
@@ -68,7 +68,7 @@ docs = [
   "pydata-sphinx-theme",
   "typing_extensions",
   "sphinx-autodoc-typehints",
-  "sphinx-material",
+  "sphinx-rtd-theme",
 ]
 tutorials = ["scanpy", "leidenalg", "python-igraph", "loompy", "scikit-misc"]