ci: Run coverage with GitHub actions

.codecov.yml

@@ -1,2 +1,5 @@
 fixes:
-  - "datalad_service/::services/datalad/datalad_service/"
+  - "datalad_service/::services/datalad/datalad_service/"
+ignore:
+  - ".pnp.js"
+  - ".pnp.loader.mjs"

.github/workflows/python.yml

@@ -0,0 +1,45 @@
+name: Python tests and coverage
+
+on:
+  push: { branches: [master] }
+  pull_request: { branches: [master] }
+
+defaults:
+  run:
+    working-directory: ./services/datalad
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Use Node.js 18.x
+        uses: actions/setup-node@v3
+        with:
+          node-version: 18.x
+      - name: Setup Deno stable
+        uses: denoland/setup-deno@v1
+        with:
+          deno-version: v1.x
+      - name: Install git-annex 
+        run: curl -L http://archive.org/download/git-annex-builds/SHA256E-s53868494--3400215acc1f7f052351d60d17603b36c1338d743b9d8a700eead3dfcd52ad92.tar.gz | tar -C /usr/local/bin --strip-components 1 -xvz
+      - name: Install pipenv
+        run: pip install 'pipenv==2023.7.23'
+      - name: Install dependencies
+        run: pipenv install --dev
+      - name: Configure git defaults
+        run: |
+          git config --global user.name "Git Worker"
+          git config --global user.email "ci@openneuro.org"
+          git config --global receive.denyCurrentBranch updateInstead
+      - name: Run tests and collect coverage
+        run: pipenv run pytest -n 4 --cov=./datalad_service --cov-report=xml:coverage.xml ./tests
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/typescript.yml

@@ -0,0 +1,25 @@
+name: TypeScript tests and coverage
+
+on:
+  push: { branches: [master] }
+  pull_request: { branches: [master] }
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v3
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'yarn'
+    - run: yarn install
+    - run: yarn test --coverage
+    - name: Upload coverage reports to Codecov with GitHub Action
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitlab-ci.yml

@@ -32,7 +32,7 @@ test_nodejs:
     - ci_env=$(/bin/sh ./scripts/codecov-env)
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
     - docker pull $CI_REGISTRY_IMAGE/node:latest || true
-    - docker run $ci_env -e CI=true $CI_REGISTRY_IMAGE/node:$CI_COMMIT_SHA yarn ci-coverage
+    - docker run $ci_env -e CI=true $CI_REGISTRY_IMAGE/node:$CI_COMMIT_SHA yarn test
 
 build_server:
   tags: [ saas-linux-medium-amd64 ]

packages/openneuro-app/src/scripts/dataset/files/viewers/__tests__/file-viewer-json.spec.jsx

@@ -1,5 +1,5 @@
 import React from 'react'
-import { render } from '@testing-library/react'
+import { render, screen } from '@testing-library/react'
 import { FileViewerJsonRaw } from '../file-viewer-json.jsx'
 
 describe('File Viewer - JSON', () => {
@@ -9,7 +9,7 @@ describe('File Viewer - JSON', () => {
     expect(asFragment()).toMatchSnapshot()
   })
   it('renders with invalid JSON', () => {
-    const { asFragment } = render(<FileViewerJsonRaw jsonRaw="1234;" />)
-    expect(asFragment()).toMatchSnapshot()
+    render(<FileViewerJsonRaw jsonRaw="1234;" />)
+    expect(screen.getByText('JSON failed to parse')).toBeInTheDocument()
   })
 })