Remove export v1

CHANGES.md

@@ -6,6 +6,7 @@
 
 * Updated default latitudes and longitudes for geography traits that includes location name changes. See the pull request for more details. [#1744][] (@joverlee521)
 * curate apply-geolocation-rules: Augur's standard geolocation rules are used by default and rules provided via `--geolocation-rules` are considered custom rules that have precedence over the default rules. The `--no-default-rules` flag can be used to ignore the default rules. See the pull request for more details. [#1745][] (@joverlee521)
+* export v1 has been removed (deprecated in v22.2.0, July 2023). `augur export v2` was introduced in Augur version 6.0.0. Migrate by following the [official guide](https://docs.nextstrain.org/projects/augur/page/releases/migrating-v5-v6.html).
 
 ### Features
 

DEPRECATED.md

@@ -26,8 +26,7 @@ We recognize the existing usage of this function, so it has been moved to
 
 ## `augur export v1`
 
-*Deprecated in version 22.2.0 (July 2023). Planned for [removal](https://github.com/nextstrain/augur/issues/1266)
-January 2024 or after.*
+*Deprecated in version 22.2.0 (July 2023). Removed in version TKTK (TKTK 2025)*
 
 `augur export v2` was introduced in Augur version 6.0.0. Migrate by following
 the [official guide](https://docs.nextstrain.org/projects/augur/page/releases/migrating-v5-v6.html).

augur/data/schema-auspice-config-v2.json

@@ -3,7 +3,7 @@
     "$id": "https://nextstrain.org/schemas/auspice/config/v2",
     "type": "object",
     "title": "Auspice config file to be supplied to `augur export v2`",
-    "$comment": "This schema includes deprecated-but-handled-by-augur-export-v1 properties, but their schema definitions are somewhat incomplete",
+    "$comment": "This schema includes properties which were used in `augur export v1` as these are still handled by `augur export v2`. The should all be considered deprecated.",
     "additionalProperties": false,
     "required": [],
     "properties" : {

augur/data/schema-export-root-sequence.json

@@ -2,32 +2,20 @@
   "$schema": "http://json-schema.org/draft-06/schema#",
   "$id": "https://nextstrain.org/schemas/dataset/root-sequence",
   "title": "Nextstrain root-sequence sidecar for datasets",
-  "description": "Typically produced by Augur and consumed by Auspice.  Applicable to the `--root-sequence` output of `augur export v2` as well as the `--output-sequence` option of `augur export v1`.",
-  "oneOf": [
-    {
-      "$comment": "This is sort of weird, but `augur export v1` can explicitly produce an empty object.",
-      "description": "An empty object",
-      "type": "object",
-      "properties": {},
-      "additionalProperties": false
-    },
-    {
-      "description": "An object containing at least a \"nuc\" key and optionally additional keys for genome annotations (e.g. genes)",
-      "type": "object",
-      "required": ["nuc"],
-      "properties": {
-        "nuc": {
-          "description": "Nucleotide sequence of whole genome (from the output of `augur ancestral`)",
-          "type": "string"
-        }
-      },
-      "patternProperties": {
-        "^[a-zA-Z0-9*_-]+$": {
-          "$comment": "This pattern is the same pattern used in the corresponding parts of schema-export-v2.json.",
-          "description": "Amino acid sequence of genome annotation (e.g. gene) identified by this key (from the output of `augur translate`)",
-          "type": "string"
-        }
-      }
+  "description": "Typically produced by Augur and consumed by Auspice. Applicable to the `--root-sequence` output of `augur export v2`. An object containing at least a \"nuc\" key and optionally additional keys for genome annotations (CDSs / genes)",
+  "type": "object",
+  "required": ["nuc"],
+  "properties": {
+    "nuc": {
+      "description": "Nucleotide sequence of whole genome (from the output of `augur ancestral`)",
+      "type": "string"
     }
-  ]
+  },
+  "patternProperties": {
+    "^[a-zA-Z0-9*_-]+$": {
+      "$comment": "This pattern is the same pattern used in the corresponding parts of schema-export-v2.json.",
+      "description": "Amino acid sequence of genome annotation (e.g. gene) identified by this key (from the output of `augur translate`)",
+      "type": "string"
+    }
+  }
 }