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Fix rST docs conversion #1858

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merged 2 commits into from
Sep 13, 2024
Merged

Fix rST docs conversion #1858

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19b5479
Fix rST docs conversion
victorlin Sep 13, 2024
478de1a
Fix inline code syntax
victorlin Sep 13, 2024
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2 changes: 1 addition & 1 deletion docs/advanced-functionality/view-settings.rst
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Expand Up @@ -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
------------------------------------
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11 changes: 10 additions & 1 deletion docs/releases/v2.rst
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Expand Up @@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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