@jbrowse/cli - npm Package Compare versions

Comparing version 2.11.2 to 2.12.0

lib/commands/create.js

@@ -49,3 +49,3 @@ "use strict";
         if (allFiles.length > 0) {
-            this.error(`${userPath} This directory has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
+            this.error(`This directory (${userPath}) has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
         }
@@ -52,0 +52,0 @@ }

lib/commands/set-default-session.js

@@ -28,3 +28,3 @@ "use strict";
         else if (!session) {
-            this.error(`Please either provide a default session file`, { exit: 120 });
+            this.error(`Please provide a --session file`, { exit: 120 });
         }
@@ -63,5 +63,9 @@ else if (session) {
 SetDefaultSession.examples = [
+    '# set default session for the config.json in your current directory',
     '$ jbrowse set-default-session --session /path/to/default/session.json',
-    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json',
-    '$ jbrowse set-default-session --view LinearGenomeView, --name newName',
+    '',
+    '# make session.json the defaultSession on the specified target config.json file',
+    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json',
+    '',
+    '# print current default session',
     '$ jbrowse set-default-session --currentSession # Prints out current default session',
@@ -72,3 +76,3 @@ ];
         char: 's',
-        description: 'set path to a file containing session in json format',
+        description: 'set path to a file containing session in json format (required, unless using delete/currentSession flags)',
     }),
@@ -75,0 +79,0 @@ name: core_1.Flags.string({

oclif.manifest.json

@@ -786,5 +786,9 @@ {
       "examples": [
+        "# set default session for the config.json in your current directory",
         "$ jbrowse set-default-session --session /path/to/default/session.json",
-        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json",
-        "$ jbrowse set-default-session --view LinearGenomeView, --name newName",
+        "",
+        "# make session.json the defaultSession on the specified target config.json file",
+        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json",
+        "",
+        "# print current default session",
         "$ jbrowse set-default-session --currentSession # Prints out current default session"
@@ -795,3 +799,3 @@ ],
           "char": "s",
-          "description": "set path to a file containing session in json format",
+          "description": "set path to a file containing session in json format (required, unless using delete/currentSession flags)",
           "name": "session",
@@ -1128,3 +1132,3 @@ "hasDynamicHelp": false,
   },
-  "version": "2.11.2"
+  "version": "2.12.0"
 }

package.json

 {
   "name": "@jbrowse/cli",
-  "version": "2.11.2",
+  "version": "2.12.0",
   "description": "A command line tool for working with JBrowse 2",
@@ -48,3 +48,3 @@ "keywords": [
   "dependencies": {
-    "@oclif/core": "^3.22.0",
+    "@oclif/core": "^4.0.6",
     "@oclif/plugin-help": "^6.0.15",
@@ -78,3 +78,3 @@ "boxen": "^4.2.0",
   },
-  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }

README.md

@@ -70,5 +70,5 @@ ---
 USAGE
-  $ jbrowse add-assembly SEQUENCE [-t indexedFasta|bgzipFasta|twoBit|chromSizes|custom] [-n <value>] [-a <value>]
-    [--displayName <value>] [--faiLocation <value>] [--gziLocation <value>] [--refNameAliasesType aliases|custom
-    --refNameAliases <value>] [--refNameColors <value>] [--target <value>] [--out <value>] [-h] [-l
+  $ jbrowse add-assembly SEQUENCE [-t indexedFasta|bgzipFasta|twoBit|chromSizes|custom] [-n <value>] [-a
+    <value>...] [--displayName <value>] [--faiLocation <value>] [--gziLocation <value>] [--refNameAliasesType
+    aliases|custom --refNameAliases <value>] [--refNameColors <value>] [--target <value>] [--out <value>] [-h] [-l
     copy|symlink|move|inPlace] [--skipCheck] [--overwrite] [-f]
@@ -209,3 +209,3 @@
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
@@ -261,3 +261,3 @@ ## `jbrowse add-connection CONNECTIONURLORPATH`
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
@@ -343,3 +343,3 @@ ## `jbrowse add-track TRACK`
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
@@ -374,3 +374,3 @@ ## `jbrowse add-track-json TRACK`
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
@@ -407,3 +407,3 @@ ## `jbrowse admin-server`
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
@@ -465,3 +465,3 @@ ## `jbrowse create LOCALPATH`
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/create.ts)_
 
@@ -487,3 +487,3 @@ ## `jbrowse help [COMMAND]`
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.22/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.3/src/commands/help.ts)_
 
@@ -518,3 +518,3 @@ ## `jbrowse make-pif FILE`
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
@@ -547,3 +547,3 @@ ## `jbrowse remove-track TRACK`
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
@@ -562,3 +562,4 @@ ## `jbrowse set-default-session`
   -n, --name=<value>     [default: New Default Session] Give a name for the default session
-  -s, --session=<value>  set path to a file containing session in json format
+  -s, --session=<value>  set path to a file containing session in json format (required, unless using
+                         delete/currentSession flags)
       --delete           Delete any existing default session.
@@ -572,8 +573,16 @@ --out=<value>      synonym for target
 EXAMPLES
+  # set default session for the config.json in your current directory
+
   $ jbrowse set-default-session --session /path/to/default/session.json
 
-  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json
 
-  $ jbrowse set-default-session --view LinearGenomeView, --name newName
 
+  # make session.json the defaultSession on the specified target config.json file
+
+  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json
+
+
+
+  # print current default session
+
   $ jbrowse set-default-session --currentSession # Prints out current default session
@@ -583,3 +592,3 @@ ```
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
@@ -615,3 +624,3 @@ ## `jbrowse sort-gff FILE`
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
@@ -625,4 +634,4 @@ ## `jbrowse text-index`
   $ jbrowse text-index [-h] [--tracks <value>] [--target <value>] [--out <value>] [--attributes <value>] [-a
-    <value>] [--force] [-q] [--perTrack] [--exclude <value>] [--prefixSize <value>] [--file <value>] [--fileId <value>]
-    [--dryrun]
+    <value>] [--force] [-q] [--perTrack] [--exclude <value>] [--prefixSize <value>] [--file <value>...] [--fileId
+    <value>...] [--dryrun]
 
@@ -684,3 +693,3 @@ FLAGS
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
@@ -748,3 +757,3 @@ ## `jbrowse upgrade [LOCALPATH]`
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
@@ -751,0 +760,0 @@ <!-- commandsstop -->

New alerts

Network access

Supply chain risk

This module accesses the network.

Found 1 instance in 1 package

Shell access

Supply chain risk

This module accesses the system shell. Accessing the system shell increases the risk of executing arbitrary code.

Found 1 instance in 1 package

Environment variable access

Supply chain risk

Package accesses environment variables, which may be a sign of credential stuffing or data theft.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

AI-detected potential code anomaly

Supply chain risk

AI has identified unusual behaviors that may pose a security risk.

Found 1 instance in 1 package

Long strings

Supply chain risk

Contains long string literals, which may be a sign of obfuscated or packed code.

Found 1 instance in 1 package

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Fixed alerts

Network access

Supply chain risk

This module accesses the network.

Found 1 instance in 1 package

Shell access

Supply chain risk

This module accesses the system shell. Accessing the system shell increases the risk of executing arbitrary code.

Found 1 instance in 1 package

Environment variable access

Supply chain risk

Package accesses environment variables, which may be a sign of credential stuffing or data theft.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

AI-detected potential code anomaly

Supply chain risk

AI has identified unusual behaviors that may pose a security risk.

Found 1 instance in 1 package

Long strings

Supply chain risk

Contains long string literals, which may be a sign of obfuscated or packed code.

Found 1 instance in 1 package

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

195735

0.34%

Lines of code

3956

0.2%

Number of lines in readme file

752

1.21%

Dependency changes

• - Removed

  @nodelib/fs.scandir@2.1.5
  (transitive)

• - Removed

  @nodelib/fs.stat@2.0.5
  (transitive)

• - Removed

  @nodelib/fs.walk@1.2.8
  (transitive)

• - Removed

  @oclif/core@3.27.0
  (transitive)

• - Removed

  @types/cli-progress@3.11.6
  (transitive)

• - Removed

  @types/node@25.6.0
  (transitive)

• - Removed

  ansicolors@0.3.2
  (transitive)

• - Removed

  argparse@1.0.10
  (transitive)

• - Removed

  array-union@2.1.0
  (transitive)

• - Removed

  astral-regex@2.0.0
  (transitive)

• - Removed

  braces@3.0.3
  (transitive)

• - Removed

  cardinal@2.1.1
  (transitive)

• - Removed

  color@4.2.3
  (transitive)

• - Removed

  color-string@1.9.1
  (transitive)

• - Removed

  dir-glob@3.0.1
  (transitive)

• - Removed

  esprima@4.0.1
  (transitive)

• - Removed

  fast-glob@3.3.3
  (transitive)

• - Removed

  fastq@1.20.1
  (transitive)

• - Removed

  fill-range@7.1.1
  (transitive)

• - Removed

  glob-parent@5.1.2
  (transitive)

• - Removed

  globby@11.1.0
  (transitive)

• - Removed

  hyperlinker@1.0.0
  (transitive)

• - Removed

  ignore@5.3.2
  (transitive)

• - Removed

  is-arrayish@0.3.4
  (transitive)

• - Removed

  is-extglob@2.1.1
  (transitive)

• - Removed

  is-glob@4.0.3
  (transitive)

• - Removed

  is-number@7.0.0
  (transitive)

• - Removed

  js-yaml@3.14.2
  (transitive)

• - Removed

  merge2@1.4.1
  (transitive)

• - Removed

  micromatch@4.0.8
  (transitive)

• - Removed

  natural-orderby@2.0.3
  (transitive)

• - Removed

  object-treeify@1.1.33
  (transitive)

• - Removed

  password-prompt@1.1.3
  (transitive)

• - Removed

  path-type@4.0.0
  (transitive)

• - Removed

  picomatch@2.3.2
  (transitive)

• - Removed

  queue-microtask@1.2.3
  (transitive)

• - Removed

  redeyed@2.1.1
  (transitive)

• - Removed

  reusify@1.1.0
  (transitive)

• - Removed

  run-parallel@1.2.0
  (transitive)

• - Removed

  simple-swizzle@0.2.4
  (transitive)

• - Removed

  slash@3.0.0
  (transitive)

• - Removed

  slice-ansi@4.0.0
  (transitive)

• - Removed

  sprintf-js@1.0.3
  (transitive)

• - Removed

  supports-hyperlinks@2.3.0
  (transitive)

• - Removed

  to-regex-range@5.0.1
  (transitive)

• - Removed

  undici-types@7.19.2
  (transitive)

• Updated

  @oclif/core@^4.0.6