From c261e60a8bd44a9c8c061b848e1a5b0eabd585d7 Mon Sep 17 00:00:00 2001
From: Becky Sweger <rsweger@umass.edu>
Date: Fri, 11 Oct 2024 14:42:26 -0400
Subject: [PATCH] Try github links extension

---
 docs/conf.py   | 8 ++++++--
 pyproject.toml | 9 ++++++++-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 471a6e0..6479e65 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -26,7 +26,7 @@
     "sphinx_copybutton",
     "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",
-    "myst_parser",  # markdown (NOTE: this is NOT mystmd)
+    "spinx_github_style",
     "sphinxext.opengraph",
     "sphinx.ext.napoleon",
 ]
@@ -37,7 +37,8 @@
 }
 intersphinx_disabled_domains = ["std"]
 
-copybutton_prompt_text = ">>> ,$"
+copybutton_prompt_text = r">>> |\$ "
+copybutton_only_copy_prompt_lines = True
 
 templates_path = ["_templates"]
 
@@ -58,6 +59,9 @@
 html_title = "Cladetime"
 html_last_updated_fmt = "%Y-%m-%d"
 
+# Settings for the GitHub link extension
+linkcode_url = "https://github.com/reichlab/cladetime"
+
 # These folders are copied to the documentation's HTML output
 html_theme_options = {
     "announcement": """
diff --git a/pyproject.toml b/pyproject.toml
index 352807c..74c8192 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,11 @@ authors = [
 
 requires-python = ">=3.11"
 readme = "README.md"
-license = {text = "MIT"}
+
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "License :: OSI Approved :: MIT License",
+]
 
 dependencies = [
     "awscli>=1.32.92",
@@ -47,11 +51,14 @@ docs = [
     "myst-parser",
     "sphinx>=5.0,<6.0",
     "sphinx-copybutton",
+    "sphinx-github-style",
     "sphinxext-opengraph",
     ]
 
 [project.urls]
 Repository = "https://github.com/reichlab/cladetime.git"
+Documentation = "https://cladetime.readthedocs.io/"
+Issues = "https://github.com/reichlab/cladetime/issues"
 
 [project.entry-points."console_scripts"]
 assign_clades = "cladetime.assign_clades:main"