Clean up sphinx config

docs/conf.py

@@ -1,13 +1,12 @@
 import os
 import sys
-from datetime import date
 
 # Configuration file for the Sphinx documentation builder.
 
 # -- Project information
 
 project = "Cladetime"
-copyright = f"{date.today().year}, Reich Lab @ The University of Massachusetts Amherst"
+project_copyright = "%Y, Reich Lab @ The University of Massachusetts Amherst"
 author = "Reich Lab"
 
 # Add cladetime location to the path, so we can use autodoc to
@@ -19,7 +18,6 @@
 # FIXME: get the version dynamically
 version = "0.1.0"
 
-
 # -- General configuration
 
 extensions = [
@@ -32,6 +30,9 @@
     "sphinx.ext.napoleon",
 ]
 
+# Warn about all references to unknown targets
+nitpicky = True
+
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
     "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
@@ -40,12 +41,22 @@
 
 templates_path = ["_templates"]
 
+# The root toctree document.
+# root_doc = "index"
+
+# Test code blocks only when explicitly specified
+doctest_test_doctest_blocks = ""
+
+# Only look for source files in the docs directory
+include_patterns = ["**/docs"]
+
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_static_path = ["_static"]
 html_theme = "furo"
-html_favicon = "images/reichlab.png"
+html_favicon = "_static/reichlab_favicon.png"
 html_title = "Cladetime"
+html_last_updated_fmt = "%Y-%m-%d"
 
 # These folders are copied to the documentation's HTML output
 html_theme_options = {
@@ -55,24 +66,12 @@
            This is an announcement!
         </a>
     """,
-    "light_logo": "reichlab.png",
-    "dark_logo": "reichlab.png",
+    "sidebar_hide_name": True,
+    "light_logo": "cladetime_logo_light_mode.png",
+    "dark_logo": "cladetime_logo_dark_mode.png",
     "navigation_with_keys": True,
 }
 
-# Order sidebar content, placing ads in the left sidebar
-# html_sidebars = {
-#     "**": [
-#         "sidebar/brand.html",
-#         "sidebar/search.html",
-#         "sidebar/scroll-start.html",
-#         "sidebar/navigation.html",
-#         "sidebar/scroll-end.html",
-#         "sidebar/ethical-ads.html",
-#     ]
-# }
-
-
 # from https://myst-parser.readthedocs.io/en/latest/syntax/optional.html
 myst_enable_extensions = [
     "amsmath",
@@ -91,9 +90,5 @@
 ogp_social_cards = {"image": "images/reichlab.png", "line_color": "#F09837"}
 ogp_description = "cladetime is a user-friendly library for accessing Sars-Cov-2 clade data from Nextstrain."
 
-# Test code blocks only when explicitly specified
-doctest_test_doctest_blocks = ""
-
-
 # -- Options for EPUB output
 epub_show_urls = "footnote"