Formatting and theme updates

docs/conf.py

@@ -1,9 +1,11 @@
+from datetime import date
+
 # Configuration file for the Sphinx documentation builder.
 
 # -- Project information
 
 project = "Cladetime"
-copyright = "2024, Reich Lab @ The University of Massachusetts Amherst"
+copyright = f"{date.today().year}, Reich Lab @ The University of Massachusetts Amherst"
 author = "Reich Lab"
 
 release = "0.1"
@@ -28,18 +30,24 @@
 
 templates_path = ["_templates"]
 
-# These folders are copied to the documentation's HTML output
+# 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_title = "Cladetime"
+
+# These folders are copied to the documentation's HTML output
 html_theme_options = {
     "announcement": """
         <a style=\"text-decoration: none; color: white;\"
            href=\"https://reichlab.io">
            <img src=\"/en/latest/_static/reichlab.png\"/> This is an announcement!
         </a>
     """,
-    "sidebar_hide_name": True,
-    "light_logo": "banner.svg",
-    "dark_logo": "dark-logo.svg",
+    "light_logo": "images/reichlab.png",
+    "dark_logo": "images/reichlab.png",
+    "navigation_with_keys": True,
 }
 
 # from https://myst-parser.readthedocs.io/en/latest/syntax/optional.html
@@ -63,18 +71,6 @@
 # Test code blocks only when explicitly specified
 doctest_test_doctest_blocks = ""
 
-# -- Options for HTML output
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = "furo"
-html_favicon = "images/reichlab.png"
-html_title = "Cladetime"
-html_theme_options = {}
-
-# html_js_files = [
-#     "js/custom.js",
-# ]
 
 # -- Options for EPUB output
 epub_show_urls = "footnote"

docs/index.rst

@@ -2,12 +2,14 @@
  Cladetime
 ===============
 
-Cladetime is a lightweight Python library for manipulating SARS-CoV-2 sequence and clade data provided by [nextstrain.org](https://nextstrain.org/).
+Cladetime is a lightweight Python library for manipulating SARS-CoV-2 sequence and clade data provided by
+`nextstrain.org <https://nextstrain.org/>`_.
 
 Contents
 --------
 
 .. toctree::
+   :titlesonly:
 
    Home <self>
    user-guide

docs/user-guide.rst

@@ -5,15 +5,19 @@ Cladetime
 Installing
 ------------
 
-cladetime can be installed with [pip])(https://pip.pypa.io/): ::
+cladetime can be installed with `pip <https://pip.pypa.io/>`_:
+
+.. code-block:: bash
 
     pip install git+https://github.com/reichlab/cladetime.git
 
 
 Finding Nextstrain SARS-CoV-2 sequences and sequence metadata
 --------------------------------------------------------------
 
-Cladetime provides a CladeTime class that provides a lightweight interface to nextstrain.org files. ::
+Cladetime provides a CladeTime class that provides a lightweight interface to nextstrain.org files.
+
+.. code-block:: python
 
     from cladetime import CladeTime
 
@@ -42,10 +46,14 @@ Cladetime provides a CladeTime class that provides a lightweight interface to ne
 Working with SARS-CoV-2 sequence metadata
 ------------------------------------------
 
-The CladeTime class also provides a Polars LazyFrame object that points to the Nextstrain's sequence metadata file. This file is in .tsv format and contains information about the sequences, such as their collection date, host, and location.
+The CladeTime class also provides a Polars LazyFrame object that points to the Nextstrain's sequence metadata file.
+This file is in .tsv format and contains information about the sequences, such as their collection date,
+host, and location.
 
-The metadata also includes a clade assignment for each sequence. Nextstrain assigns clades based on a reference tree, and the reference tree varies over time. ::
+The metadata also includes a clade assignment for each sequence. Nextstrain assigns clades based on a reference tree,
+and the reference tree varies over time.
 
+.. code-block:: python
 
     import polars as pl
     from cladetime import CladeTime