Merge branch 'development' into test_gha_osb3

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:16 as jsbuild
+FROM node:20 as jsbuild
 
 ENV FOLDER=nwb-explorer
 
@@ -21,26 +21,27 @@ RUN jupyter labextension disable @jupyterlab/hub-extension
 RUN apt-get update -qq &&\
     apt-get install python3-tk vim nano unzip git g++ -qq
 
+USER $NB_UID
 COPY --chown=1000:1000 requirements.txt .   
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
     pip install -r requirements.txt
-USER $NB_UID
+
 
 COPY --chown=$NB_UID:$NB_UID . $FOLDER 
-COPY --from=jsbuild --chown=1000:1000 $FOLDER $FOLDER
+COPY --from=jsbuild --chown=$NB_UID:$NB_UID $FOLDER $FOLDER
 
 WORKDIR $FOLDER
 RUN mkdir workspace
 
 
 
 # Temporary fix for deprecated api usage on some requirement
-# RUN pip install setuptools==45
+RUN pip install setuptools==45
+
 
-USER root
 
-RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
-    python utilities/install.py --npm-skip
+# RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+#     python utilities/install.py --npm-skip
 
 
 RUN rm -rf /var/lib/apt/lists

README.md

@@ -38,7 +38,7 @@ source nwb-explorer/bin/activate
 Or, with conda
 
 ```bash
-conda create -n nwb-explorer python=3.9
+conda create -n nwb-explorer python=3.12
 conda activate nwb-explorer
 ```
 

requirements-test.txt

@@ -1,3 +1,3 @@
-pytest==4.6.2
-pytest-cov==2.7.1
-tox==3.12.1
+pytest>8
+pytest-cov
+tox>4

requirements.txt

@@ -1,66 +1,39 @@
-airspeed==0.5.20
-attrs==19.3.0
-cachetools==0.8.0
-cffi==1.14.0
-cryptography==2.9.2
-cycler==0.10.0
-decorator==4.4.2
-defusedxml==0.6.0
-Deprecated==1.2.10
-entrypoints==0.3
-h5py==3.7.0
-idna==2.9
-ipython-genutils==0.2.0
-imageio==2.5.0
-ipysheet>=0.5.0
-jedi==0.17.0
-Jinja2==2.11.2
-jsonschema==3.2.0
-jupyter_geppetto==1.1.5
+
 jupyter-client==7.0.6
-jupyter-core==4.9.1
-jupyter-server==1.11.2
-jupyterhub==1.5.0
-jupyterlab==3.2.4
+jupyter-core<6.0.0
+# jupyterhub==4.0.2
 jupyterthemes==0.20.0
-kiwisolver==1.2.0
-markupsafe==2.0.1
-mistune==0.8.4
-multimethod==1.3
-nbconvert==5.6.1
-nbformat==5.0.6
-ordered-set==4.0.2
-pandocfilters==1.4.2
-parso==0.7.0
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow>=7.2.0
-prompt-toolkit==3.0.5
-ptyprocess==0.6.0
-pycparser==2.20
-pyecore==0.11.7
-pygeppetto==0.8.1
-Pygments==2.6.1
-pyparsing==2.4.7
-pyrsistent==0.16.0
-python-dateutil==2.8.1
-python-json-logger==0.1.11
-pytz==2020.1
-PyYAML==5.3.1
-pyzmq==19.0.1
-qtconsole==4.7.5
-QtPy==1.9.0
-quantities==0.12.3
-RestrictedPython==5.0
-Send2Trash==1.5.0
-terminado==0.8.3
-tornado==6.1.0
-traitlets==4.3.3
-urllib3==1.25.9
-webencodings==0.5.1
-wrapt==1.12.1
-zipp==3.1.0
+nbclient==0.10.0
 jupyter_geppetto==1.1.5
+pynwb==2.8.3
 nwbwidgets==0.11.3
-pygeppetto==0.8.1
-pynwb==2.5.0
+nwbinspector==0.6.0
+quantities
+pyecore==0.15.2
+pygeppetto==0.9.0
+# from nwbwidgets
+botocore==1.35.35
+etelemetry==0.3.0
+dandischema==0.10.3
+numpy
+matplotlib
+scikit-image
+ipympl
+ipydatagrid
+ipyvolume==0.6.2
+# ipywidgets>=8.0.0
+plotly==5.13.1
+tqdm>=4.36.0
+zarr
+tifffile
+ndx-spectrum
+ndx-icephys-meta
+ndx-grayscalevolume
+trimesh
+dandi>=0.55.0
+importlib-metadata <5.0
+fsspec
+requests
+aiohttp
+# ipydatawidgets==4.3.2
+ipyfilechooser==0.6.0

setup.py

@@ -49,6 +49,7 @@
         'msgpack-python==0.5.6',
         'nose>=1.3.7',
         'Pillow>=7.0.0',
+        'quantities>=0.12.3',
         'redis>=2.10.6',
         'seaborn>=0.8.1',
         'uuid>=1.30',

utilities/install.py

@@ -9,8 +9,7 @@
 
 
 # repos
-JUPYTER = 'https://github.com/openworm/org.geppetto.frontend.jupyter.git'
-PYGEPPETTO = 'https://github.com/openworm/pygeppetto.git'
+GEPPETTO_META = '[email protected]:MetaCell/geppetto-meta.git'
 
 
 ROOT_DIR = os.path.join(HERE, os.pardir)
@@ -83,27 +82,24 @@ def main(branch=branch, skipNpm=False, skipTest=False, development=False):
         os.chdir(DEPS_DIR)
         # install pygeppetto
         cprint("Installing pygeppetto")
-        clone(repository=PYGEPPETTO,
-              folder='pygeppetto',
-              default_branch_or_tag='development'
+        clone(repository=GEPPETTO_META,
+              folder='geppetto-meta',
+              default_branch_or_tag='develop'
               )
-        execute(cmd=['pip', 'install', '-e', '.'], cwd='pygeppetto')
+        execute(cmd=['pip', 'install', '-e', '.'], cwd='geppetto-meta/pygeppetto')
 
         # install jupyter geppetto
         cprint("Installing org.geppetto.frontend.jupyter")
-        clone(repository=JUPYTER,
-              folder=JUPYTER_DIR,
-              default_branch_or_tag='development'
-              )
+
         os.chdir(ROOT_DIR)
-        execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, JUPYTER_DIR))
+        execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, "geppetto-meta/jupyter-geppetto"))
     else:
         # install requirements
         cprint("Installing requirements")
         execute(cmd=['pip', 'install', '-r', 'requirements.txt'], cwd=ROOT_DIR)
 
         cprint("Installing UI python package...")
-        execute(cmd=['pip', 'install', '.', '--no-deps'], cwd=ROOT_DIR)
+        execute(cmd=['pip', 'install', '-e', '.', '--no-deps'], cwd=ROOT_DIR)
 
     if not skipNpm and os.path.exists(os.path.join(DEPS_DIR, JUPYTER_DIR)):
         cprint("Building Jupyter Geppetto extension...")

webapp/Main.js

@@ -3,6 +3,8 @@ global.GEPPETTO_CONFIGURATION = require('./GeppettoConfiguration.json');
 const { initGeppetto } = require('@metacell/geppetto-meta-client/GEPPETTO');
 import { LoadingSpinner } from '@metacell/geppetto-meta-client/components';
 import ErrorDialog from './components/reduxconnect/ErrorDialogContainer';
+
+
 require('babel-polyfill');
 const { Provider } = require('react-redux');
 const configureStore = require('./redux/store').default;
@@ -27,7 +29,7 @@ window.updateFile = nwbFileService.setNWBFileUrl;
 
 
 const store = configureStore();
-
+import './styles/main.less';
 
 (function init () {
 

webapp/components/App.js

@@ -1,9 +1,7 @@
 import React from 'react';
 import WelcomePage from './pages/WelcomePage';
-import nwbFileService from '../services/NWBFileService';
 import FileExplorerPage from './pages/FileExplorerPage';
 
-// import { Route, Switch, Redirect, BrowserRouter as Router } from 'react-router-dom';
 
 export default class App extends React.Component {
   constructor () {

webapp/components/pages/WelcomePage.js

@@ -6,7 +6,7 @@ import FileSampleSelector from '../reduxconnect/FileSampleSelectorContainer';
 
 import logo_osb from '../../resources/logos/osb.png';
 import logo_openworm from '../../resources/logos/openworm.png';
-import logo_metacell from '../../resources/logos/metacell_new.png';
+import logo_metacell from '../../resources/logos/metacell-blue.png';
 import logo_wellcome from '../../resources/logos/wellcome.png';
 import logo_nwb_explorer from '../../resources/logos/nwb-explorer.png';
 

webapp/geppetto.ejs

@@ -68,6 +68,9 @@
       href="<%= cssPaths%><%=htmlWebpackPlugin.options.GEPPETTO_CONFIGURATION.properties.icon%>"
     />
     <% } %>
+
+
+
   </head>
   <body style="margin: 0px;">
     <!-- For index purposes -->