Merge branch 'development' of https://github.com/metacell/netpyne-ui into feature/netpyne-24

Author: ddelpiano

README.md

@@ -30,26 +30,59 @@ your system and you have had troubles installing it you can opt for the Virtual
 
 ### Python Dependencies
 
-We recommend the use of a new python 3 virtual environment:
+We recommend the use of a new python 3.7 virtual environment.
+Currently, NetPyNE-UI only supports Python 3.7, but that can change in the future.
+
+For NetPyNE-UI, the preferred way of creating a virtual env is to pass by conda/miniconda or mamba/micromamba.
+The pyenv tool can be also used, but it requires to be compiled with some special options to have NEURON running properly the simulation using `nrniv`.
+The reason behind this is that NEURON is distributed as a Python wheel with a specific option which force NEURON to look for the CPython dynamic lib.
+However, pyenv by default installs the static version of the CPython lib, resulting in `nrniv -python` not being able to run.
+
+The way of creating the virtualenv using (mini)conda is the following
+
+```bash
+conda create -n netpyne python=3.7
+conda activate netpyne
+```
+
+Here is how to create the virtualenv using (micro)mamba
+
+```bash
+mamba create -n netpyne python=3.7 -c conda-forge
+mamba activate netpyne
+```
+
+You can also directly create a virtualenv using your `python3` executable, obviously if it's the 3.7 version.
 
 ```bash
 python3 -m venv npenv
 source npenv/bin/activate
 ```
 
-Or, with conda
+If you want to use anyway pyenv, here is how to properly create the virtualenv and activate it.
 
 ```bash
-conda create -n netpyne python=3.7
-conda activate netpyne
+env PYTHON_CONFIGURE_OPTS="--enable-shared"  pyenv install --verbose 3.7.17
+pyenv virtualenv 3.7.17 netpyne
+pyenv shell netpyne
 ```
 
 ### Run install script
 
+When you are in your virtualenv, here is how you can install the "basic" version of NetPyNE-UI:
+
 ```bash
 python utilities/install.py
 ```
 
+If you want to have a different version of NetPyNE or geppetto meta, you can pass the version you want to the installer:
+
+```bash
+python utilities/install.py --dev --netpyne development --geppetto development --no-test
+```
+
+This command will install the `development` version of netpyne and geppetto and disable the tests during the installation.
+
 ### Start application
 
 ```bash
@@ -62,6 +95,15 @@ For debugging you can use `run.py` instead
 python run.py
 ```
 
+To run the UI in dev mode, you need to run `python run.py` in one terminal, and use `yarn` from the `webapp` folder, using node v14 (use `nvm` if you need to have a different version of node than the one installed on your system):
+
+```bash
+cd webapp
+yarn start
+```
+
+You can then navigate to `http://127.0.0.1:8081/` to access the dev version of the UI.
+
 ## Run NetPyNE User Interface in Docker
 
 Ensure that you have Docker installed on your system.
@@ -75,7 +117,7 @@ docker build -t netpyne-ui .
 Run the image
 
 ```bash
-docker run -p 8888:8888 netpyne-ui 
+docker run -p 8888:8888 netpyne-ui
 ```
 
 ## End-to-end tests

netpyne_ui/netpyne_geppetto.py

@@ -913,11 +913,15 @@ def getAvailableCellModels(self):
                     cell_models.add(cm)
         return list(cell_models)
 
-    def getAvailableCellTypes(self):
-        cell_types = set([])
-        for p in self.netParams.cellParams:
-            cell_types.add(p)
-        return list(cell_types)
+    def getAvailableCellModels(self):
+        return ["", "VecStim", "NetStim", "IntFire1"]
+
+    def getAvailableStimulationDistribution(self):
+        return ["normal", "uniform"]
+
+    def getAvailableStimulationPattern(self):
+        # self.netParams.popParams[name]['spikePattern'] = {}
+        return ["", "rhythmic", "evoked", "poisson", "gauss"]
 
     def getAvailableSections(self):
         sections = {}

tests/frontend/e2e/jest-puppeteer.config.js

@@ -1,6 +1,6 @@
 module.exports = {
   launch: {
-    headless: true,
+    headless: 'new',
     defaultViewport: {
       width: 1300,
       height: 1024

tests/frontend/e2e/tests/SaveOpenFile.test.js

@@ -39,7 +39,7 @@ const PASSWORD = 'testpassword'
 
 jest.setTimeout(300000);
 
-describe('Save / Open File testing', () => {
+describe.skip('Save / Open File testing', () => {
 
     beforeAll(async () => {
         await page.goto(baseURL);