Tag release v0.3.11

Author: garrettjstevens

packages/apollo-cli/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.10 linux-x64 node-v24.6.0
+@apollo-annotation/cli/0.3.11 linux-x64 node-v24.6.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -117,7 +117,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -153,7 +153,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -195,7 +195,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -223,7 +223,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -245,7 +245,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -280,7 +280,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -304,7 +304,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -356,7 +356,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -384,7 +384,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add [FEATURE-JSON]`
 
@@ -440,7 +440,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/add.ts)_
+[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add.ts)_
 
 ## `apollo feature add-child`
 
@@ -471,7 +471,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -504,7 +504,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -535,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -559,7 +559,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -601,7 +601,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -641,7 +641,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -675,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -699,7 +699,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -733,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -761,7 +761,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature get-indexed-id ID`
 
@@ -793,7 +793,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
+[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -824,7 +824,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -875,7 +875,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -902,7 +902,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -930,7 +930,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -957,7 +957,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -994,7 +994,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -1060,7 +1060,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
 
 ## `apollo jbrowse get-config`
 
@@ -1086,7 +1086,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -1115,7 +1115,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1154,7 +1154,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1184,7 +1184,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1215,7 +1215,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1247,7 +1247,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1269,7 +1269,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1305,6 +1305,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

packages/apollo-cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",

packages/apollo-common/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/common",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",

packages/apollo-mst/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"

packages/apollo-schemas/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/schemas",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"

packages/apollo-shared/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",

packages/jbrowse-plugin-apollo/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",