From 19b5479386960d2f4c86ab83fdf0967c06a4275f Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 13 Sep 2024 14:04:07 -0700
Subject: [PATCH 1/2] Fix rST docs conversion

Follow-up to "Convert markdown pages to reStructuredText" (7b8e45e2).
---
 docs/releases/v2.rst | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/docs/releases/v2.rst b/docs/releases/v2.rst
index abe58e855..f7b03fefc 100644
--- a/docs/releases/v2.rst
+++ b/docs/releases/v2.rst
@@ -83,7 +83,16 @@ v1 Auspice JSONs used 0-based starts for the gene positions and ``1``/``-1`` for
 Changes to how node data is stored
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Each tree node (internal & terminal) can now contain the following properties \* ``name`` (required) -- formerly this was ``strain`` \* ``node_attrs`` -- attributes associated with the node (sequence, date, location) as opposed to changes from one node to another. \* Node attributes can now be objects and contain confidence information if available. \* A ``hidden`` node attribute can control Auspice's display of the node \* Author information is now contained under the ``author`` key, and the ``author_info`` dictionary is no longer present in the JSON. \* ``branch_attrs`` -- attributes associated with the branch from the parent node to this node, such as branch lengths, mutations, support values \* ``branch_attrs.mutations`` -- both AA & nucleotide mutations are now defined in the same object. \* ``children`` (unchanged)
+Each tree node (internal & terminal) can now contain the following properties
+
+* ``name`` (required) -- formerly this was ``strain``
+* ``node_attrs`` -- attributes associated with the node (sequence, date, location) as opposed to changes from one node to another.
+* Node attributes can now be objects and contain confidence information if available.
+* A ``hidden`` node attribute can control Auspice's display of the node
+* Author information is now contained under the ``author`` key, and the ``author_info`` dictionary is no longer present in the JSON.
+* ``branch_attrs`` -- attributes associated with the branch from the parent node to this node, such as branch lengths, mutations, support values
+* ``branch_attrs.mutations`` -- both AA & nucleotide mutations are now defined in the same object.
+* ``children`` (unchanged)
 
 Colorings, geographic resolutions, and defaults
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

From 478de1a5b0f1f84b12e25873744728001b4b3984 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 13 Sep 2024 16:26:21 -0700
Subject: [PATCH 2/2] Fix inline code syntax

---
 docs/advanced-functionality/view-settings.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/advanced-functionality/view-settings.rst b/docs/advanced-functionality/view-settings.rst
index 00c152423..b453a1e77 100644
--- a/docs/advanced-functionality/view-settings.rst
+++ b/docs/advanced-functionality/view-settings.rst
@@ -17,7 +17,7 @@ Auspice has some hardcoded defaults, largely for historical reasons. Each of the
 -  Default geographic resolution is "country", if available.
 -  Default colouring is "country", if available.
 -  Default branch labelling is "clade", if available.
--  Default tip labelling is the sample / strain name (`node.name`)
+-  Default tip labelling is the sample / strain name (``node.name``)
 
 Dataset (JSON) configurable defaults
 ------------------------------------