Merge origin/main

package.json

@@ -118,6 +118,7 @@
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "3.14.1",
     "nock": "^12.0.3",
+    "npm-run-all": "^4.1.5",
     "open-cli": "^6.0.1",
     "postcss-flexbugs-fixes": "^4.1.0",
     "postcss-loader": "^3.0.0",

plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete.tsx

@@ -84,10 +84,11 @@ function RefNameAutocomplete({
   const [searchOptions, setSearchOptions] = useState<Option[]>([])
   const { assemblyManager } = session
   const { coarseVisibleLocStrings } = model
-  const assembly = assemblyName && assemblyManager.get(assemblyName)
-  const regions: Region[] = useMemo(() => {
-    return (assembly && assembly.regions) || []
-  }, [assembly])
+  const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined
+
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  const regions: Region[] = assembly?.regions || []
+
   const options: Option[] = useMemo(() => {
     const defaultOptions = regions.map(option => {
       return {

products/jbrowse-cli/package.json

@@ -32,10 +32,16 @@
   },
   "scripts": {
     "build": "oclif-dev pack",
-    "postpack": "rm -f oclif.manifest.json",
-    "prepack": "rm -rf lib && tsc -b && oclif-dev manifest && oclif-dev readme",
-    "version": "oclif-dev readme && git add README.md",
-    "docs": "oclif-dev readme && prettier --write README.md"
+    "build:typescript": "tsc --build",
+    "postpack": "rimraf oclif.manifest.json",
+    "clean": "rimraf lib",
+    "prepack": "npm-run-all clean build:typescript manifest docs",
+    "manifest": "oclif-dev manifest",
+    "version": "npm-run-all docs:**",
+    "docs": "npm-run-all docs:*",
+    "docs:create": "oclif-dev readme",
+    "docs:format": "prettier --write README.md",
+    "docs:version:add": "git add README.md"
   },
   "dependencies": {
     "@oclif/command": "^1",

yarn.lock

@@ -14794,6 +14794,11 @@ memory-fs@^0.5.0:
     errno "^0.1.3"
     readable-stream "^2.0.1"
 
+memorystream@^0.3.1:
+  version "0.3.1"
+  resolved "https://registry.yarnpkg.com/memorystream/-/memorystream-0.3.1.tgz#86d7090b30ce455d63fbae12dda51a47ddcaf9b2"
+  integrity sha1-htcJCzDORV1j+64S3aUaR93K+bI=
+
 meow@^3.3.0:
   version "3.7.0"
   resolved "https://registry.yarnpkg.com/meow/-/meow-3.7.0.tgz#72cb668b425228290abbfa856892587308a801fb"
@@ -15638,6 +15643,21 @@ npm-pick-manifest@^3.0.0:
     npm-package-arg "^6.0.0"
     semver "^5.4.1"
 
+npm-run-all@^4.1.5:
+  version "4.1.5"
+  resolved "https://registry.yarnpkg.com/npm-run-all/-/npm-run-all-4.1.5.tgz#04476202a15ee0e2e214080861bff12a51d98fba"
+  integrity sha512-Oo82gJDAVcaMdi3nuoKFavkIHBRVqQ1qvMb+9LHk/cF4P6B2m8aP04hGf7oL6wZ9BuGwX1onlLhpuoofSyoQDQ==
+  dependencies:
+    ansi-styles "^3.2.1"
+    chalk "^2.4.1"
+    cross-spawn "^6.0.5"
+    memorystream "^0.3.1"
+    minimatch "^3.0.4"
+    pidtree "^0.3.0"
+    read-pkg "^3.0.0"
+    shell-quote "^1.6.1"
+    string.prototype.padend "^3.0.0"
+
 npm-run-path@^2.0.0:
   version "2.0.2"
   resolved "https://registry.yarnpkg.com/npm-run-path/-/npm-run-path-2.0.2.tgz#35a9232dfa35d7067b4cb2ddf2357b1871536c5f"
@@ -16457,6 +16477,11 @@ picomatch@^2.0.4, picomatch@^2.0.5, picomatch@^2.2.1, picomatch@^2.2.2:
   resolved "https://registry.yarnpkg.com/picomatch/-/picomatch-2.2.2.tgz#21f333e9b6b8eaff02468f5146ea406d345f4dad"
   integrity sha512-q0M/9eZHzmr0AulXyPwNfZjtwZ/RBZlbN3K3CErVrk50T2ASYI7Bye0EvekFY3IP1Nt2DHu0re+V2ZHIpMkuWg==
 
+pidtree@^0.3.0:
+  version "0.3.1"
+  resolved "https://registry.yarnpkg.com/pidtree/-/pidtree-0.3.1.tgz#ef09ac2cc0533df1f3250ccf2c4d366b0d12114a"
+  integrity sha512-qQbW94hLHEqCg7nhby4yRC7G2+jYHY4Rguc2bjw7Uug4GIJuu1tvf2uHaZv5Q8zdt+WKJ6qK1FOI6amaWUo5FA==
+
 pify@^2.0.0, pify@^2.3.0:
   version "2.3.0"
   resolved "https://registry.yarnpkg.com/pify/-/pify-2.3.0.tgz#ed141a6ac043a849ea588498e7dca8b15330e90c"
@@ -19360,7 +19385,7 @@ [email protected]:
     array-reduce "~0.0.0"
     jsonify "~0.0.0"
 
-[email protected]:
+[email protected], shell-quote@^1.6.1:
   version "1.7.2"
   resolved "https://registry.yarnpkg.com/shell-quote/-/shell-quote-1.7.2.tgz#67a7d02c76c9da24f99d20808fcaded0e0e04be2"
   integrity sha512-mRz/m/JVscCrkMyPqHc/bczi3OQHkLTqXHEFu0zDhK/qfv3UcOA4SVmRCLmos4bhjr9ekVQubj/R7waKapmiQg==