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Merge pull request #758 from MetaCell/release/1.0.0
Release/1.0.0
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‎.github/workflows/tests.yml

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

‎.gitignore

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

‎Dockerfile

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@@ -1,4 +1,4 @@
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FROM node:13.14 as jsbuild
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FROM node:14.21.3-bullseye as jsbuild
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WORKDIR /app
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@@ -18,48 +18,50 @@ RUN rm -Rf node_modules/*
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FROM jupyter/base-notebook:hub-1.5.0
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ENV NB_UID=jovyan
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ENV FOLDER=netpyne
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ARG GEPPETTO_VERSION=development
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ARG BUILD_ARGS=""
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ARG WORKSPACE_VERSION=master
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# ARG GEPPETTO_VERSION=development
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# ARG NETPYNE_VERSION=master
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ENV FOLDER=/home/jovyan/work/NetPyNE-UI
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USER root
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RUN rm -rf /var/lib/apt/lists
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RUN apt-get update -qq &&\
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apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
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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
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RUN conda install python=3.7 -y
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WORKDIR $FOLDER
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COPY --chown=1000:1000 requirements.txt requirements.txt
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RUN pip install -r requirements.txt --no-cache-dir --prefer-binary
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RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip && pip install -r requirements.txt --prefer-binary
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38-
COPY --chown=$NB_UID:1000 . .
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COPY --from=jsbuild --chown=$NB_UID:1000 /app webapp
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COPY --chown=jovyan:1000 . .
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COPY --from=jsbuild --chown=jovyan:1000 /app webapp
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4142

4243
RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
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RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
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47-
RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --npm-skip
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RUN python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION
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4950
RUN jupyter labextension disable @jupyterlab/hub-extension
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5152
RUN chown $NB_UID .
5253
RUN chown -R $NB_UID workspace
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# Temp fixes for eeg plots
55-
RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
56+
ENV NEURON_HOME=/opt/conda
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# For lfpykit 0.4
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# RUN wget -P $(pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}') https://www.parralab.org/nyhead/sa_nyhead.mat
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# For lpfykit 0.5
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ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
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RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
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5763
USER $NB_UID
5864

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6065
EXPOSE 8888
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63-
64-
65-

‎NetPyNE-UI

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#!/bin/sh
22
CONFIG=$(pwd)/.jupyter-config
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export JUPYTER_CONFIG_DIR=$CONFIG
4-
exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True
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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

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@@ -11,21 +11,23 @@
1111
"https://[email protected]/6"
1212
)
1313

14+
HEAD_MODEL_FILE = os.getenv("NP_LFPYKIT_HEAD_FILE", "sa_nyhead.mat")
15+
1416
def init_eeg():
1517
import sys
1618
from netpyne_ui.constants import HERE
1719
# FIXES library asking for input to download
1820
sys.stdin = open(os.path.join(HERE, "resources/stdin.txt"),'r')
1921
from lfpykit.eegmegcalc import NYHeadModel
2022
try:
21-
NYHeadModel() # Downloads the model if does not exist
23+
NYHeadModel(HEAD_MODEL_FILE) # Downloads the model if does not exist
2224
except:
2325
logging.error("Error initializing the EEG head model", exc_info=True)
2426

25-
from multiprocessing import Process
26-
thread = Process(target = init_eeg)
27-
thread.start()
28-
27+
if not os.path.exists(HEAD_MODEL_FILE):
28+
from multiprocessing import Process
29+
thread = Process(target = init_eeg)
30+
thread.start()
2931

3032
RouteManager.add_controller(api.NetPyNEController)
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