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JBbrowse 4 fixes #751

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garrettjstevens wants to merge 9 commits into from
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JBbrowse 4 fixes #751

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07e0b54
Pass feature instead of getting from model again
garrettjstevens Jan 20, 2026
c4b2eae
Improve typing of JBrowse feature
garrettjstevens Jan 20, 2026
51ddddb
Remove custom z-index that broke sub-menus
garrettjstevens Jan 20, 2026
b8797dd
Lots of dependency upgrades
garrettjstevens Jan 27, 2026
b5aeb55
More strict react versions
garrettjstevens Jan 27, 2026
d1960b1
Remove unused and disable broken tests
garrettjstevens Jan 27, 2026
e62c4b9
Get Jest tests working again
garrettjstevens Jan 27, 2026
613dc82
Fix lint
garrettjstevens Jan 28, 2026
9556045
Update node version on GitHub actions
garrettjstevens Jan 28, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/cypress_debug.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn

- name: Install
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2 changes: 1 addition & 1 deletion .github/workflows/deploy.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn
- name: Install
if: inputs.environment == 'staging'
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27 changes: 19 additions & 8 deletions .github/workflows/pull_request.yml
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Expand Up @@ -15,19 +15,27 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn
- name: Install
run: yarn --immutable
# Have to build shared before linting so type-based lint rules can
# run correctly
- name: Lint codebase
run: yarn eslint --max-warnings 0

# apollo-shared tests
- name: Build shared
run: yarn build
working-directory: packages/apollo-shared
- name: Lint codebase
run: yarn eslint --max-warnings 0
- name: Run Jest tests
run: yarn test
- name: Run apollo-shared tests
run: yarn run test:ci
working-directory: packages/apollo-shared

# jbrowse-plugin-apollo tests
- name: Run jbrowse-plugin-apollo tests
run: yarn run test:ci
working-directory: packages/jbrowse-plugin-apollo

# Cypress tests
- name: Get latest JBrowse
run: yarn run jbrowse create --nightly .jbrowse
working-directory: packages/jbrowse-plugin-apollo
Expand All @@ -43,13 +51,16 @@ jobs:
- name: Run Cypress tests
run: yarn run test:e2e
working-directory: packages/jbrowse-plugin-apollo

# CLI tests
- name: Start apollo
run: |
yarn --cwd packages/apollo-shared start &
yarn --cwd packages/apollo-collaboration-server test:cli:start &
- name: Run CLI tests
run: yarn test:cli
run: yarn run test:ci
working-directory: packages/apollo-cli

# - name: Run docker tests
# working-directory: packages/apollo-cli
# run: python3 ./src/test/test_docker.py
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9 changes: 2 additions & 7 deletions .github/workflows/push.yml
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Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn
- name: Install
run: yarn --immutable
Expand All @@ -36,15 +36,10 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn
- name: Install
run: yarn --immutable
# Have to build shared before linting so type-based lint rules can
# run correctly
- name: Build shared
run: yarn build
working-directory: packages/apollo-shared
- name: Lint codebase
run: yarn eslint --max-warnings 0
docker:
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2 changes: 1 addition & 1 deletion .github/workflows/website.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
- name: Use Node.js 20.x
uses: actions/setup-node@v4
with:
node-version: 20
node-version: 24
cache: yarn
- name: Install
run: yarn --immutable
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3 changes: 0 additions & 3 deletions .yarnrc.yml
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Expand Up @@ -5,9 +5,6 @@ enableGlobalCache: false
npmMinimalAgeGate: 2880

packageExtensions:
"@jbrowse/cli@*":
dependencies:
tmp: ^0.2.1
"@jbrowse/core@*":
peerDependencies:
"@emotion/react": "*"
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2 changes: 1 addition & 1 deletion eslint.config.mjs
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Expand Up @@ -40,7 +40,7 @@ export default [
globals: { ...globals.browser, ...globals.node },
parserOptions: {
projectService: {
allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'],
allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.{c,m,}js'],
},
defaultProject: 'tsconfig.json',
tsconfigRootDir: import.meta.dirname,
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2 changes: 1 addition & 1 deletion package.json
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Expand Up @@ -41,7 +41,7 @@
"npm-run-all": "^4.1.5",
"prettier": "^3.3.2",
"prettier-plugin-packagejson": "^2.5.2",
"react": "^18.2.0",
"react": "^18.3.1",
"semver": "^7.6.3",
"tslib": "^2.3.1",
"tsx": "^4.6.2",
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