fix: remove unnecessary deprecation attribute

ivan-aksamentov · claude · ivan-aksamentov · commit 3e15cd471e26 · 2026-01-13T14:48:28.000+01:00
Co-Authored-By: Claude &lt;noreply@anthropic.com&gt;
diff --git a/packages/nextclade-schemas/input-pathogen-json.schema.json b/packages/nextclade-schemas/input-pathogen-json.schema.json
@@ -933,7 +933,6 @@
           ]
         },
         "mutationsThreshold": {
-          "deprecated": true,
           "type": [
             "integer",
             "null"
diff --git a/packages/nextclade-schemas/input-pathogen-json.schema.yaml b/packages/nextclade-schemas/input-pathogen-json.schema.yaml
@@ -597,7 +597,6 @@ definitions:
         - $ref: '#/definitions/QcRecombConfigMultiAncestor'
         - type: 'null'
       mutationsThreshold:
-        deprecated: true
         type:
         - integer
         - 'null'
diff --git a/packages/nextclade-schemas/nextclade-auspice-extensions.schema.json b/packages/nextclade-schemas/nextclade-auspice-extensions.schema.json
@@ -1192,7 +1192,6 @@
           ]
         },
         "mutationsThreshold": {
-          "deprecated": true,
           "type": [
             "integer",
             "null"
diff --git a/packages/nextclade-schemas/nextclade-auspice-extensions.schema.yaml b/packages/nextclade-schemas/nextclade-auspice-extensions.schema.yaml
@@ -756,7 +756,6 @@ definitions:
         - $ref: '#/definitions/QcRecombConfigMultiAncestor'
         - type: 'null'
       mutationsThreshold:
-        deprecated: true
         type:
         - integer
         - 'null'
diff --git a/packages/nextclade/src/qc/qc_config.rs b/packages/nextclade/src/qc/qc_config.rs
@@ -378,13 +378,11 @@ pub struct QcRulesConfigRecombinants {
   #[serde(default, skip_serializing_if = "Option::is_none")]
   pub multi_ancestor: Option<QcRecombConfigMultiAncestor>,
 
-  #[deprecated(note = "Use weighted_threshold.threshold instead")]
   #[serde(default, skip_serializing_if = "Option::is_none")]
   pub mutations_threshold: Option<usize>,
 }
 
 impl QcRulesConfigRecombinants {
-  #[allow(deprecated)]
   pub const fn example() -> Self {
     Self {
       enabled: true,
@@ -398,7 +396,6 @@ impl QcRulesConfigRecombinants {
     }
   }
 
-  #[allow(deprecated)]
   pub fn get_weighted_threshold_config(&self) -> QcRecombConfigWeightedThreshold {
     if let Some(config) = &self.weighted_threshold {
       config.clone()

Original file line number	Diff line number	Diff line change
`@@ -933,7 +933,6 @@`
`933`	`933`	`]`
`934`	`934`	`},`
`935`	`935`	`"mutationsThreshold": {`
`936`		`- "deprecated": true,`
`937`	`936`	`"type": [`
`938`	`937`	`"integer",`
`939`	`938`	`"null"`
Original file line number	Diff line number	Diff line change
`@@ -1192,7 +1192,6 @@`
`1192`	`1192`	`]`
`1193`	`1193`	`},`
`1194`	`1194`	`"mutationsThreshold": {`
`1195`		`- "deprecated": true,`
`1196`	`1195`	`"type": [`
`1197`	`1196`	`"integer",`
`1198`	`1197`	`"null"`
Original file line number	Diff line number	Diff line change
`@@ -378,13 +378,11 @@ pub struct QcRulesConfigRecombinants {`
`378`	`378`	`#[serde(default, skip_serializing_if = "Option::is_none")]`
`379`	`379`	`pub multi_ancestor: Option<QcRecombConfigMultiAncestor>,`
`380`	`380`
`381`		`- #[deprecated(note = "Use weighted_threshold.threshold instead")]`
`382`	`381`	`#[serde(default, skip_serializing_if = "Option::is_none")]`
`383`	`382`	`pub mutations_threshold: Option<usize>,`
`384`	`383`	`}`
`385`	`384`
`386`	`385`	`impl QcRulesConfigRecombinants {`
`387`		`- #[allow(deprecated)]`
`388`	`386`	`pub const fn example() -> Self {`
`389`	`387`	`Self {`
`390`	`388`	`enabled: true,`
`@@ -398,7 +396,6 @@ impl QcRulesConfigRecombinants {`
`398`	`396`	`}`
`399`	`397`	`}`
`400`	`398`
`401`		`- #[allow(deprecated)]`
`402`	`399`	`pub fn get_weighted_threshold_config(&self) -> QcRecombConfigWeightedThreshold {`
`403`	`400`	`if let Some(config) = &self.weighted_threshold {`
`404`	`401`	`config.clone()`