From b182d228af7565043c7a58d6bbfa54c501a5fba6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 23 Mar 2026 21:30:09 +0000
Subject: [PATCH 1/3] Initial plan


From 8a3242607726f321fd0c94102249cbc3aaedb8c6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 23 Mar 2026 21:35:47 +0000
Subject: [PATCH 2/3] Fix PDF index: repair broken printindex in
 source/indices.rst, add latex section to scripting/scrpt-indices.rst,
 suppress auto printindex in conf.py

Co-authored-by: briantoby <9433704+briantoby@users.noreply.github.com>
Agent-Logs-Url: https://github.com/AdvancedPhotonSource/GSAS-II/sessions/1c45d811-b476-4c2b-9e8c-deba32cb152d
---
 docs/scripting/conf.py           | 3 +++
 docs/scripting/scrpt-indices.rst | 9 +++++++++
 docs/source/conf.py              | 3 +++
 docs/source/indices.rst          | 6 +-----
 4 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/docs/scripting/conf.py b/docs/scripting/conf.py
index 6572bab00..fde7dd954 100644
--- a/docs/scripting/conf.py
+++ b/docs/scripting/conf.py
@@ -249,6 +249,9 @@
 
 #this allows \AA to be used in equations 
 'preamble': '\\global\\renewcommand{\\AA}{\\text{\\r{A}}}',
+
+# Suppress auto-generated printindex at end; index is printed via scrpt-indices.rst
+'printindex': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
diff --git a/docs/scripting/scrpt-indices.rst b/docs/scripting/scrpt-indices.rst
index 9436dcbf5..3f9d2aedf 100644
--- a/docs/scripting/scrpt-indices.rst
+++ b/docs/scripting/scrpt-indices.rst
@@ -5,3 +5,12 @@
 
 	  `General Index <./genindex.html>`_
 	  --------------------------------------------
+
+.. only:: latex
+
+    Index
+    =====
+
+    .. raw:: latex
+
+        \printindex
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 145eded36..59eaa337c 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -253,6 +253,9 @@
 
 #this allows \AA to be used in equations 
 'preamble': '\\global\\renewcommand{\\AA}{\\text{\\r{A}}}',
+
+# Suppress auto-generated printindex at end; index is printed via indices.rst
+'printindex': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
diff --git a/docs/source/indices.rst b/docs/source/indices.rst
index cb046c523..7e5155c6f 100644
--- a/docs/source/indices.rst
+++ b/docs/source/indices.rst
@@ -16,8 +16,4 @@
 
     .. raw:: latex
 
-        \renewcommand{\printindex}{%
-          \begin{theindex}
-          \printindex
-          \end{theindex}
-        }
+        \printindex

From 3d1ebc489245537600d98abf25fac4ada4fd7f98 Mon Sep 17 00:00:00 2001
From: Brian Toby <briantoby@users.noreply.github.com>
Date: Mon, 23 Mar 2026 16:37:34 -0500
Subject: [PATCH 3/3] Update Python version from 3.11 to 3.13 in full doc file

---
 docs/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/environment.yml b/docs/environment.yml
index e919543f7..d6d106954 100644
--- a/docs/environment.yml
+++ b/docs/environment.yml
@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.11
+  - python=3.13
   - scipy
   - pyopengl
   - imageio