Merge pull request #758 from MetaCell/release/1.0.0

Release/1.0.0

.github/workflows/tests.yml

@@ -0,0 +1,258 @@
+name: Tests Workflow
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the specified branch
+  push:
+    branches:
+     - "master"
+     - "development"
+  pull_request:
+    branches:
+     - "master"
+     - "development"
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs: 
+  EEG_Dipole-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: EEG and Dipole Plot snapshot test using Tut#1
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run EEG and Dipole Plot test
+          npm run EEG_Dipole_test
+      env:
+          CI: true
+  Experiment_Manager-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Experiment Manager snapshot test using Tut#1
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Experiment Manager test
+          npm run Experiment_Manager_test
+      env:
+          CI: true
+  Control_Panel-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Control Panel test using Tut#2
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Control Panel test
+          npm run Control_Panel_test
+      env:
+          CI: true
+  Save_and_Open_File-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Test for Opening and Saving a file
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Control Panel test
+          npm run Save_Open_File_test
+      env:
+          CI: true
+  RxD-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Test for RxD plot
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run RxD Plot test
+          npm run RxD_test
+      env:
+          CI: true
+  Tutorial_1-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 1 Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 1 Plot Tests
+          npm run Tutorial_1_test
+      env:
+          CI: true
+  Tutorial_2-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 2 Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 2 Plot Tests
+          npm run Tutorial_2_test
+      env:
+          CI: true
+  Tutorial_3a-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 3a Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 3a Plot Tests
+          npm run Tutorial_3A_test
+      env:
+          CI: true
+  Tutorial_3b-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 3b Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 3b Plot Tests
+          npm run Tutorial_3B_test
+      env:
+          CI: true
+  Tutorial_3c-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 3c Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 3c Plot Tests
+          npm run Tutorial_3C_test
+      env:
+          CI: true
+  Tutorial_4-SmokeTest:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Tutorial 4 Plot Tests
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Tutorial 4 Plot Tests
+          npm run Tutorial_4_test
+      env:
+          CI: true

.gitignore

@@ -27,4 +27,8 @@ utilities/x86_64
 x86_64
 .jupyter-config
 venv
+webapp/build
+webapp/.yalc
 node_modules
+sa_nyhead.mat
+workspace

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:13.14 as jsbuild
+FROM node:14.21.3-bullseye as jsbuild
 
 WORKDIR /app
 
@@ -18,48 +18,50 @@ RUN rm -Rf node_modules/*
 FROM jupyter/base-notebook:hub-1.5.0
 ENV NB_UID=jovyan
 ENV FOLDER=netpyne
-ARG GEPPETTO_VERSION=development
 ARG BUILD_ARGS=""
+ARG WORKSPACE_VERSION=master
+# ARG GEPPETTO_VERSION=development
+# ARG NETPYNE_VERSION=master
 
 ENV FOLDER=/home/jovyan/work/NetPyNE-UI
 
 USER root
 
 RUN rm -rf /var/lib/apt/lists
 RUN apt-get update -qq &&\
-    apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
+    apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev  openjdk-11-jre-headless -y -y
 RUN conda install python=3.7 -y
 
-
 WORKDIR $FOLDER
 COPY --chown=1000:1000 requirements.txt requirements.txt
-RUN pip install -r requirements.txt --no-cache-dir --prefer-binary
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip && pip install -r requirements.txt --prefer-binary
 
-COPY --chown=$NB_UID:1000 . .
-COPY --from=jsbuild --chown=$NB_UID:1000 /app webapp
+COPY --chown=jovyan:1000 . .
+COPY --from=jsbuild --chown=jovyan:1000 /app webapp
 
 
 RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
 RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
 RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
 RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
 
-RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --npm-skip
+RUN python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION
 
 RUN jupyter labextension disable @jupyterlab/hub-extension
 
 RUN chown  $NB_UID .
 RUN chown -R $NB_UID workspace
 
 # Temp fixes for eeg plots
-RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
+ENV NEURON_HOME=/opt/conda
+# For lfpykit 0.4
+# RUN wget -P $(pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}') https://www.parralab.org/nyhead/sa_nyhead.mat
+# For lpfykit 0.5
+ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
+RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
 
 USER $NB_UID
 
-
 EXPOSE 8888
 
 
-
-
-

NetPyNE-UI

@@ -1,4 +1,4 @@
 #!/bin/sh
 CONFIG=$(pwd)/.jupyter-config
 export JUPYTER_CONFIG_DIR=$CONFIG
-exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True
+exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --NotebookApp.notebook_dir=workspace --library=netpyne_ui --NotebookApp.disable_check_xsrf=True

netpyne_ui/__init__.py

@@ -11,21 +11,23 @@
     "https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6"
 )
 
+HEAD_MODEL_FILE = os.getenv("NP_LFPYKIT_HEAD_FILE", "sa_nyhead.mat")
+
 def init_eeg():
     import sys
     from netpyne_ui.constants import HERE
     # FIXES library asking for input to download
     sys.stdin = open(os.path.join(HERE, "resources/stdin.txt"),'r') 
     from lfpykit.eegmegcalc import NYHeadModel
     try:
-        NYHeadModel() # Downloads the model if does not exist
+        NYHeadModel(HEAD_MODEL_FILE) # Downloads the model if does not exist
     except:
         logging.error("Error initializing the EEG head model", exc_info=True)
 
-from multiprocessing import Process
-thread = Process(target = init_eeg)
-thread.start()
-
+if not os.path.exists(HEAD_MODEL_FILE):
+    from multiprocessing import Process
+    thread = Process(target = init_eeg)
+    thread.start()
 
 RouteManager.add_controller(api.NetPyNEController)