more config messing around

docs/conf.py

@@ -22,6 +22,7 @@
 # -- General configuration
 
 extensions = [
+    "myst_parser",
     "sphinx.ext.autodoc",
     "sphinx_copybutton",
     "sphinx.ext.doctest",
@@ -37,8 +38,13 @@
 }
 intersphinx_disabled_domains = ["std"]
 
-copybutton_prompt_text = r">>> |\$ "
-copybutton_only_copy_prompt_lines = True
+# Copied these settings from the copybutton's config
+# https://github.com/executablebooks/sphinx-copybutton/blob/master/docs/conf.py
+copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: "
+copybutton_prompt_is_regexp = True
+copybutton_line_continuation_character = "\\"
+copybutton_here_doc_delimiter = "EOT"
+copybutton_selector = "div:not(.no-copybutton) > div.highlight > pre"
 
 templates_path = ["_templates"]
 
@@ -48,9 +54,6 @@
 # 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"]
@@ -74,6 +77,15 @@
     "light_logo": "cladetime_logo_light_mode.png",
     "dark_logo": "cladetime_logo_dark_mode.png",
     "navigation_with_keys": True,
+    "source_repository": "https://github.com/reichlab/cladetime/",
+}
+
+html_context = {
+    # Enable the "Edit in GitHub link within the header of each page.
+    "display_github": True,
+    "github_user": "reichlab",
+    "github_repo": "cladetime",
+    "github_version": "main/source/",
 }
 
 # from https://myst-parser.readthedocs.io/en/latest/syntax/optional.html

docs/index.rst

@@ -37,14 +37,14 @@ daily workflow pipeline.
 
    >>> ct = CladeTime()
    >>> filtered_sequence_metadata = (
-      ct.sequence_metadata.select(["country", "division", "date", "host", "clade_nextstrain"])
-      .filter(
-         pl.col("country") == "USA",
-         pl.col("date").is_not_null(),
-         pl.col("host") == "Homo sapiens",
-      )
-      .cast({"date": pl.Date}, strict=False)
-   )
+   ...    ct.sequence_metadata.select(["country", "division", "date", "host", "clade_nextstrain"])
+   ...    .filter(
+   ...        pl.col("country") == "USA",
+   ...        pl.col("date").is_not_null(),
+   ...        pl.col("host") == "Homo sapiens",
+   ...    )
+   ...    .cast({"date": pl.Date}, strict=False)
+   ...)
 
    >>> filtered_sequence_metadata.head(5).collect()
 

docs/user-guide.rst

@@ -77,8 +77,8 @@ a Python datetime object. Both will be treated as UTC dates/times.
     # ct operations now reference the version of the sequence metadata
     # that was available at midnight UTC on August 2, 2024.
     >>> ct.sequence_metadata \
-        .cast({"date": pl.Date}, strict=False) \
-        .select(pl.max("date")).collect()
+    ...     .cast({"date": pl.Date}, strict=False) \
+    ...     .select(pl.max("date")).collect()
 
     shape: (1, 1)
     ┌────────────┐