From aedc81bcbb6eb929db208c6c9b5ac1befe71fd71 Mon Sep 17 00:00:00 2001
From: Austin Richardson <accounts@agdr.org>
Date: Thu, 21 Aug 2025 15:02:20 -0700
Subject: [PATCH 1/2] Expand JSON format documentation

---
 src/formats/json.rs | 52 +++++++++++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 9 deletions(-)

diff --git a/src/formats/json.rs b/src/formats/json.rs
index ccdccb7..983eb5f 100644
--- a/src/formats/json.rs
+++ b/src/formats/json.rs
@@ -12,17 +12,51 @@ use crate::Taxonomy;
 use serde::{de, Deserialize, Deserializer, Serialize, Serializer};
 use serde_json::{json, to_value, to_writer, Value};
 
+
 /// We can handle 2 kinds of JSON formats:
-/// 1. the node link format
-/// 2. the tree format
+/// 1. The Node Link format
+/// 2. The Tree format
+///
+/// The Node Link Format:
+/// 
+/// The taxonomy is represented as a directed acyclic graph (DAG) in JSON using a node-link
+/// structure:
+/// ```json
+/// {
+///   "nodes": [
+///     { "id": 0, "name": "root", "rank": "no rank" },
+///     { "id": 1, "name": "superkingdom A", "rank": "superkingdom" },
+///     { "id": 2, "name": "kingdom A", "rank": "kingdom" },
+///     { "id": 3, "name": "phylum A", "rank": "phylum" },
+///     { "id": 4, "name": "genus A", "rank": "genus" },
+///     { "id": 5, "name": "species A1", "rank": "species" }
+///   ],
+///   "links": [
+///     { "source": 5, "target": 4 },
+///     { "source": 4, "target": 3 },
+///     { "source": 3, "target": 2 },
+///     { "source": 2, "target": 1 },
+///     { "source": 1, "target": 0 }
+///   ]
+/// }
+/// ```
+/// 
+/// nodes:
+/// A list of taxonomic units. Each node has:
+///   id – unique integer identifier
+///   name – the scientific name or placeholder label
+///   rank – the taxonomic rank (e.g., "species", "genus", "family")
+/// 
+/// links:
+/// A list of directed edges between nodes. Each link has:
+///   source – the child node’s index in the nodes array
+///   target – the parent node’s index in the nodes array
 ///
-/// The node link format comes from an old version of [NetworkX](https://networkx.org)
-///  and looks like the following:
-/// ```{'nodes': [{'id': 'A'}, {'id': 'B'}], 'links': [{'source': 0, 'target': 1}]}```
-/// This format is only used as legacy and is not recommended for new projects
-/// as it's easy to mess up and not even supported anymore by NetworkX.
+/// The Tree Format
 ///
-/// The tree format is a more natural looking format (only `id` is required):
+/// In the tree format, child nodes are nested within their parent node. This format is more
+/// natural as the taxonomic structure is immediately apparent from reading it.
+/// 
 /// ```json
 /// {
 ///     "id": "1",
@@ -42,7 +76,7 @@ use serde_json::{json, to_value, to_writer, Value};
 ///             ]
 ///         }
 ///     ]
-// }
+/// }
 /// ```
 //
 /// For both formats, you can add more data on each node object and these will be available after loading.

From 5b10512aff2841051c3a76484776b91bdfc194c2 Mon Sep 17 00:00:00 2001
From: Austin Richardson <accounts@agdr.org>
Date: Thu, 21 Aug 2025 15:03:24 -0700
Subject: [PATCH 2/2] fmt

---
 src/formats/json.rs | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/formats/json.rs b/src/formats/json.rs
index 983eb5f..9d1d81a 100644
--- a/src/formats/json.rs
+++ b/src/formats/json.rs
@@ -12,13 +12,12 @@ use crate::Taxonomy;
 use serde::{de, Deserialize, Deserializer, Serialize, Serializer};
 use serde_json::{json, to_value, to_writer, Value};
 
-
 /// We can handle 2 kinds of JSON formats:
 /// 1. The Node Link format
 /// 2. The Tree format
 ///
 /// The Node Link Format:
-/// 
+///
 /// The taxonomy is represented as a directed acyclic graph (DAG) in JSON using a node-link
 /// structure:
 /// ```json
@@ -40,13 +39,13 @@ use serde_json::{json, to_value, to_writer, Value};
 ///   ]
 /// }
 /// ```
-/// 
+///
 /// nodes:
 /// A list of taxonomic units. Each node has:
 ///   id – unique integer identifier
 ///   name – the scientific name or placeholder label
 ///   rank – the taxonomic rank (e.g., "species", "genus", "family")
-/// 
+///
 /// links:
 /// A list of directed edges between nodes. Each link has:
 ///   source – the child node’s index in the nodes array
@@ -56,7 +55,7 @@ use serde_json::{json, to_value, to_writer, Value};
 ///
 /// In the tree format, child nodes are nested within their parent node. This format is more
 /// natural as the taxonomic structure is immediately apparent from reading it.
-/// 
+///
 /// ```json
 /// {
 ///     "id": "1",