Fix a typo and formatting (#376)

* Fix a typo and formatting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update

* udpdate

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

DEVELOPMENT.md

@@ -40,7 +40,6 @@ node server.js --data-file tfci.jsonl.gz
 
 This will launch the backend server on port 8000, from a small tree file. (Though sometimes this checked in tree file gets out of date in terms of format, you can also use the latest full public tree: `https://cov2tree.nyc3.cdn.digitaloceanspaces.com/latest_public.jsonl.gz` but this will need more RAM).
 
-
 ### Linking taxonium_data_handling
 
 A small amount of backend code comes from the `taxonium_data_handling` repo. If you need to work on this code then you can "link" the `taxonium_data_handling` to the backend repo.

docs/taxoniumtools.md

@@ -47,7 +47,7 @@ Some people ask what the "L" in JSONL is for. JSONL means "JSON Lines". Each lin
    :func: get_parser
    :prog: usher_to_taxonium
 
-   This tool with convert an UShER protobuf file into a Taxonium file. At its simplest it just takes the `-i` and `-o` parameters, describing the input and output files. But for the most complete results you can add metadata, a reference genome, or even create a time tree.
+   This tool will convert an UShER protobuf file into a Taxonium file. At its simplest it just takes the `-i` and `-o` parameters, describing the input and output files. But for the most complete results you can add metadata, a reference genome, or even create a time tree.
 
    j
       This file controls many aspects of the UI for Taxonium, such as what searches are available. You can see an example file at https://github.com/theosanderson/taxonium/blob/master/taxonium_backend/config_public.json.

taxonium_web_client/src/hooks/useLayers.js

@@ -313,8 +313,9 @@ const useLayers = ({
 
   // If leaves are fewer than max_text_number, add a text layer
   if (
-    data.data.nodes && proportionalToNodesOnScreen <
-    0.8 * 10 ** settings.thresholdForDisplayingText
+    data.data.nodes &&
+    proportionalToNodesOnScreen <
+      0.8 * 10 ** settings.thresholdForDisplayingText
   ) {
     const node_label_layer = new TextLayer({
       id: "main-text-node",

taxoniumtools/src/taxoniumtools/usher_to_taxonium.py

@@ -249,7 +249,7 @@ def get_parser():
         "--overlay_html",
         type=str,
         help=
-        "A file containing HTML to put in the About box when this tree is loaded. This could contain information about who you are who built the tree and what data you used.",
+        "A file containing HTML to put in the About box when this tree is loaded. This could contain information about who built the tree and what data you used.",
         default=None)
     parser.add_argument(
         '--remove_after_pipe',
@@ -261,7 +261,7 @@ def get_parser():
         "--clade_types",
         type=str,
         help=
-        "Optionally specify clade types provided in the UShER file, comma separated - e.g. 'nextstrain,pango'. Order must match that used in the UShER pb file.",
+        "Optionally specify clade types provided in the UShER file, comma separated - e.g. 'nextstrain,pango'. Order must match that used in the UShER pb file. If you haven't specifically annotated clades in your protobuf, don't use this",
         default=None)
     parser.add_argument('--name_internal_nodes',
                         action='store_true',
@@ -282,7 +282,7 @@ def get_parser():
         '--only_variable_sites',
         action='store_true',
         help=
-        "Only store information about the root sequence if there is variation somewhere in the tree. This may be removed in future versions."
+        "Only store information about the root sequence at a particular position if there is variation at that position somewhere in the tree. This helps to speed up the loading of larger genomes such as MPXV."
     )
 
     parser.add_argument(