Clean up sphinx config

reichlab · Oct 11, 2024 · 26b8004 · 26b8004
1 parent df86eaf
commit 26b8004
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Showing 8 changed files with 25 additions and 26 deletions.
diff --git a/docs/_static/cladetime_logo dark_mode.png b/docs/_static/cladetime_logo dark_mode.png
diff --git a/docs/_static/cladetime_logo_light_mode.png b/docs/_static/cladetime_logo_light_mode.png
diff --git a/docs/_static/reichlab_favicon.png b/docs/_static/reichlab_favicon.png
diff --git a/docs/conf.py b/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 = [
@@ -40,12 +38,22 @@
 
 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 +63,12 @@
            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",
@@ -88,11 +84,14 @@
 # Open Graph metadata
 ogp_title = "cladetime documentation"
 ogp_type = "website"
-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."
+ogp_social_cards = {"image": "_static/cladetime_logo_light_mode.png", "line_color": "#F09837"}
+ogp_description = "Cladetime is a Python interface for accessing Nextstraing Sars-Cov-2 sequence and clade data."
 
-# Test code blocks only when explicitly specified
-doctest_test_doctest_blocks = ""
+# Warn about all references to unknown targets
+nitpicky = True
+nitpick_ignore = [
+    ("py:class", "datetime"),
+]
 
 
 # -- Options for EPUB output

diff --git a/docs/images/reichlab.png b/docs/images/reichlab.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -26,7 +26,7 @@ Cladetime can be installed with `pip <https://pip.pypa.io/>`_:
 Usage
 -----
 
-The CladeTime :class:`CladeTime` class provides a lightweight wrapper around historical and current
+The CladeTime :any:`CladeTime` class provides a lightweight wrapper around historical and current
 SARS-CoV-2 GenBank sequence and sequence metadata created by `nextstrain.org's <https://nextstrain.org/>`_
 daily workflow pipeline.
 

diff --git a/docs/reference/cladetime.rst b/docs/reference/cladetime.rst
@@ -1,4 +1,4 @@
 CladeTime
 ==========
 
-.. automodule:: cladetime.CladeTime
+.. autoclass:: cladetime.CladeTime
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,7 +45,7 @@ docs = [
     "furo",
     "matplotlib",
     "myst-parser",
-    "sphinx",
+    "sphinx>=5.0,<6.0",
     "sphinx-copybutton",
     "sphinxext-opengraph",
     ]