Merge pull request #646 from MetaCell/master

re-align development to release/0.9.0

Author: ddelpiano

requirements.txt

@@ -47,6 +47,7 @@ netpyne==1.0.3
 NEURON==8.0.2
 numpy==1.18.5
 oauthlib==3.0.1
+optuna==2.10.1
 ordered-set==4.0.2
 pamela==1.0.0
 pandas==0.23.4

setup.py

@@ -15,7 +15,7 @@
 
 setuptools.setup(
     name="netpyne_ui",
-    version="0.8.1",
+    version="0.9.0",
     url="https://github.com/MetaCell/NetPyNE-UI",
     author="MetaCell",
     author_email="info@metacell.us",

tests/frontend/e2e/package-lock.json

@@ -1950,7 +1950,7 @@ component-emitter@^1.2.1:
 concat-map@0.0.1:
   version "0.0.1"
   resolved "https://registry.yarnpkg.com/concat-map/-/concat-map-0.0.1.tgz#d8a96bd77fd68df7793a73036a3ba0d5405d477b"
-  integrity sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=
+  integrity sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==
 
 concat-stream@^1.6.2:
   version "1.6.2"
@@ -2071,9 +2071,9 @@ decamelize@^1.2.0:
   integrity sha1-9lNNFRSCabIDUue+4m9QH5oZEpA=
 
 decode-uri-component@^0.2.0:
-  version "0.2.0"
-  resolved "https://registry.yarnpkg.com/decode-uri-component/-/decode-uri-component-0.2.0.tgz#eb3913333458775cb84cd1a1fae062106bb87545"
-  integrity sha1-6zkTMzRYd1y4TNGh+uBiEGu4dUU=
+  version "0.2.2"
+  resolved "https://registry.yarnpkg.com/decode-uri-component/-/decode-uri-component-0.2.2.tgz#e69dbe25d37941171dd540e024c444cd5188e1e9"
+  integrity sha512-FqUYQ+8o158GyGTrMFJms9qh3CqTKvAqgqsTnkLI8sKu0028orqBhxNMFkFen0zGyg6epACD32pjVk58ngIErQ==
 
 deep-is@~0.1.3:
   version "0.1.4"
@@ -3905,9 +3905,9 @@ load-json-file@^4.0.0:
     strip-bom "^3.0.0"
 
 loader-utils@^1.4.0:
-  version "1.4.0"
-  resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.4.0.tgz#c579b5e34cb34b1a74edc6c1fb36bfa371d5a613"
-  integrity sha512-qH0WSMBtn/oHuwjy/NucEgbx5dbxxnxup9s4PVXJUDHZBQY+s0NWA9rJf53RBnQZxfch7euUui7hpoAPvALZdA==
+  version "1.4.2"
+  resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.4.2.tgz#29a957f3a63973883eb684f10ffd3d151fec01a3"
+  integrity sha512-I5d00Pd/jwMD2QCduo657+YM/6L3KZu++pmX9VFncxaxvHcru9jx1lBaFft+r4Mt2jK0Yhp41XlRAihzPxHNCg==
   dependencies:
     big.js "^5.2.2"
     emojis-list "^3.0.0"
@@ -4045,9 +4045,9 @@ mimic-fn@^2.1.0:
   integrity sha512-OqbOk5oEQeAZ8WXWydlu9HJjz9WVdEIvamMCcXmuqUYjTknH/sqsWvhQ3vgwKFRR1HpjvNBKQ37nbJgYzGqGcg==
 
 minimatch@^3.0.4:
-  version "3.1.1"
-  resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.1.1.tgz#879ad447200773912898b46cd516a7abbb5e50b0"
-  integrity sha512-reLxBcKUPNBnc/sVtAbxgRVFSegoGeLaSjmphNhcwcolhYLRgtJscn5mRl6YRZNQv40Y7P6JM2YhSIsbL9OB5A==
+  version "3.1.2"
+  resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.1.2.tgz#19cd194bfd3e428f049a70817c038d89ab4be35b"
+  integrity sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==
   dependencies:
     brace-expansion "^1.1.7"
 
@@ -4056,6 +4056,11 @@ minimist@^1.1.1, minimist@^1.2.0, minimist@^1.2.5:
   resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.6.tgz#8637a5b759ea0d6e98702cfb3a9283323c93af44"
   integrity sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q==
 
+minimist@^1.2.0:
+  version "1.2.7"
+  resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.7.tgz#daa1c4d91f507390437c6a8bc01078e7000c4d18"
+  integrity sha512-bzfL1YUZsP41gmu/qjrEk0Q6i2ix/cVeAhbCbqH9u3zYutS1cLg00qhrD0M2MVdCcx4Sc0UpP2eBWo9rotpq6g==
+
 mixin-deep@^1.2.0:
   version "1.3.2"
   resolved "https://registry.yarnpkg.com/mixin-deep/-/mixin-deep-1.3.2.tgz#1120b43dc359a785dce65b55b82e257ccf479566"

tests/frontend/e2e/yarn.lock

@@ -116,12 +116,12 @@ def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False,
         execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR))
         # installing core dependencies
         execute(cmd=['pip', 'install', '-e', '.'], cwd=ROOT_DIR)
-    else:
-        # install requirements
         if netpyne_branch and netpyne_branch != 'master':
           cprint("Installing netpyne")
           clone(repository=NETPYNE, branch_or_tag=netpyne_branch)
           execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, NETPYNE_DIR))
+    else:
+        # install requirements
         cprint("Installing UI python package...")
         execute(cmd=['pip', 'install', '-e', '.', '--no-deps'], cwd=ROOT_DIR)
 

utilities/install.py

@@ -26,10 +26,10 @@ const AboutContent = withStyles(styles)(({ classes }) => (
     <img width="250" src={logoNetpyne} />
     <Box m={1}>
       <Link variant="h5" style={{ display: 'block' }} href="https://github.com/MetaCell/NetPyNE-UI" target="_blank">
-        NetPyNE-UI v0.8.1
+        NetPyNE-UI v0.9.0
       </Link>
       <Link variant="h5" style={{ display: 'block' }} href="https://github.com/Neurosim-lab/netpyne" target="_blank">
-        NetPyNE v1.0.2.1
+        NetPyNE v1.0.3
       </Link>
       <Link variant="h5" style={{ display: 'block' }} href="https://www.neuron.yale.edu/neuron/" target="_blank">
         NEURON v8.0.2

webapp/components/general/Dialog.js

@@ -1,6 +1,6 @@
 {
   "name": "geppetto-netpyne",
-  "version": "0.8.1",
+  "version": "0.9.0",
   "description": "Geppetto NetPyNE-UI frontend.",
   "repository": "https://github.com/MetaCell/NetPyNE-UI",
   "license": "MIT",

webapp/dev_package.json

@@ -1,6 +1,6 @@
 {
   "name": "geppetto-netpyne",
-  "version": "0.8.1",
+  "version": "0.9.0",
   "description": "Geppetto NetPyNE-UI frontend.",
   "repository": "https://github.com/MetaCell/NetPyNE-UI",
   "license": "MIT",
@@ -19,9 +19,9 @@
     "@material-ui/core": "4.12.1",
     "@material-ui/icons": "^4.11.2",
     "@material-ui/lab": "^4.0.0-alpha.60",
-    "@metacell/geppetto-meta-client": "1.0.0-final",
-    "@metacell/geppetto-meta-core": "1.0.0-final",
-    "@metacell/geppetto-meta-ui": "1.0.0-final",
+    "@metacell/geppetto-meta-client": "1.1.0",
+    "@metacell/geppetto-meta-core": "1.1.0",
+    "@metacell/geppetto-meta-ui": "1.1.0",
     "@nosferatu500/react-sortable-tree": "3.0.5",
     "@sentry/integrations": "^6.16.1",
     "@sentry/react": "^6.16.1",
@@ -37,7 +37,7 @@
     "react-json-view": "^1.21.3",
     "react-redux": "^7.2.0",
     "react-sortable-tree": "^2.8.0",
-    "redux": "^4.1.0",
+    "redux": "4.1.2",
     "sass": "^1.49.0",
     "sass-loader": "^7.2.0",
     "three": "0.111.0"

webapp/package.json

@@ -34,6 +34,11 @@ if (isWin) {
 }
 
 const availableExtensions = [
+  {
+    from: path.resolve(__dirname, geppettoClientPath, 'style/fonts/*'),
+    to: 'static/fonts',
+    flatten: true,
+  },
   {
     from: path.resolve(__dirname, geppettoClientPath, 'style/css/font-awesome.min.css'),
     to: 'static/css',