@jbrowse/cli 3.1.0 → 3.2.0

package/README.md

@@ -206,7 +206,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -257,7 +257,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -338,7 +338,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -368,7 +368,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -400,7 +400,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -457,7 +457,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -478,7 +478,7 @@ DESCRIPTION
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.26/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.27/src/commands/help.ts)_
 
 ## `jbrowse make-pif FILE`
 
@@ -508,7 +508,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -536,7 +536,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -578,7 +578,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-bed FILE`
 
@@ -609,7 +609,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/sort-bed.ts)_
+[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/sort-bed.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -640,7 +640,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -701,13 +701,13 @@ EXAMPLES
 
 
 
-  # create index for some files for use in @jbrowse/react-linear-genome-view or similar
+  # create index for some files for use in @jbrowse/react-linear-genome-view2 or similar
 
   $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -770,7 +770,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v3.1.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v3.2.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/text-index.js

@@ -201,8 +201,8 @@ class TextIndex extends base_1.default {
             .map(file => (0, common_1.guessAdapterFromFileName)(file))
             .filter(fileConfig => (0, common_1.supported)(fileConfig.adapter?.type));
         if (fileId?.length) {
-            for (let i = 0; i < fileId.length; i++) {
-                trackConfigs[i].trackId = fileId[i];
+            for (const [i, element] of fileId.entries()) {
+                trackConfigs[i].trackId = element;
             }
         }
         await this.indexDriver({
@@ -323,7 +323,7 @@ TextIndex.examples = [
     '# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)',
     '$ jbrowse text-index -a hg19 --force',
     '',
-    '# create index for some files for use in @jbrowse/react-linear-genome-view or similar',
+    '# create index for some files for use in @jbrowse/react-linear-genome-view2 or similar',
     '$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes',
 ];
 TextIndex.flags = {

package/lib/commands/upgrade.js

@@ -44,11 +44,11 @@ class Upgrade extends base_1.default {
         }
         if (clean) {
             fs_1.default.rmSync(path_1.default.join(argsPath, 'static'), { recursive: true, force: true });
-            fs_1.default.readdirSync(argsPath)
-                .filter(f => f.includes('worker.js'))
-                .forEach(f => {
+            for (const f of fs_1.default
+                .readdirSync(argsPath)
+                .filter(f => f.includes('worker.js'))) {
                 fs_1.default.unlinkSync(path_1.default.join(argsPath, f));
-            });
+            }
         }
         await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
         this.log(`Unpacked ${locationUrl} at ${argsPath}`);

package/oclif.manifest.json

@@ -952,7 +952,7 @@
         "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)",
         "$ jbrowse text-index -a hg19 --force",
         "",
-        "# create index for some files for use in @jbrowse/react-linear-genome-view or similar",
+        "# create index for some files for use in @jbrowse/react-linear-genome-view2 or similar",
         "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes"
       ],
       "flags": {
@@ -1165,5 +1165,5 @@
       ]
     }
   },
-  "version": "3.1.0"
+  "version": "3.2.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.1.0",
+  "version": "3.2.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }