fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-15 12:47:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

chore: replace deprecated codecov with GitHub Action (#2747)

Browse Source 
Migrate from the deprecated codecov npm package and bash uploader to the
official codecov/codecov-action@v5. This fixes gcov errors on macOS runners
and provides better reliability for coverage uploads.

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Timmy Huang
2026-01-16 09:28:12 -08:00
committed by GitHub
parent 5ac256fc8b
commit 7c7203bdfe
4 changed files with 17 additions and 201 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
.github/workflows/push_tests.yml vendored
View File

@@ -69,10 +69,21 @@ jobs:
- name: Install dependencies
run: make pydist install-dist dev-env-server
- name: Unit tests
run: |
make unit-test-server unit-test-client
bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
run: make unit-test-server unit-test-client
- name: Generate server coverage XML
run: coverage xml -o server/coverage.xml
- name: Upload server coverage
uses: codecov/codecov-action@v5
with:
flags: server,python,unitTest
files: ./server/coverage.xml
fail_ci_if_error: false
- name: Upload client coverage
uses: codecov/codecov-action@v5
with:
flags: frontend,javascript,unitTest
files: ./client/coverage/lcov.info
fail_ci_if_error: false
smoke-tests:
runs-on: macos-latest
@@ -102,9 +113,7 @@ jobs:
pip install setuptools
make pydist install-dist
- name: Smoke tests (without annotations feature)
run: |
cd client && make smoke-test
./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
run: cd client && make smoke-test
# TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
# smoke-tests-annotations:

192
client/package-lock.json generated
View File

@@ -71,7 +71,6 @@
"cheerio": "^1.0.0-rc.6",
"clean-css": "^5.1.2",
"clean-webpack-plugin": "^4.0.0-alpha.0",
"codecov": "^3.7.1",
"css-loader": "^5.2.4",
"css-minimizer-webpack-plugin": "^4.0.0",
"eslint": "^7.24.0",
@@ -5371,16 +5370,6 @@
"sprintf-js": "~1.0.2"
}
},
"node_modules/argv": {
"version": "0.0.2",
"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
"deprecated": "Package no longer supported. Contact Support at https://www.npmjs.com/support for more info.",
"dev": true,
"engines": {
"node": ">=0.6.10"
}
},
"node_modules/aria-query": {
"version": "4.2.2",
"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
@@ -6448,26 +6437,6 @@
"node": ">=0.10.0"
}
},
"node_modules/codecov": {
"version": "3.8.3",
"resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
"integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
"deprecated": "https://about.codecov.io/blog/codecov-uploader-deprecation-plan/",
"dev": true,
"dependencies": {
"argv": "0.0.2",
"ignore-walk": "3.0.4",
"js-yaml": "3.14.1",
"teeny-request": "7.1.1",
"urlgrey": "1.0.0"
},
"bin": {
"codecov": "bin/codecov"
},
"engines": {
"node": ">=4.0"
}
},
"node_modules/collect-v8-coverage": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
@@ -9173,21 +9142,6 @@
"resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
"integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
},
"node_modules/fast-url-parser": {
"version": "1.1.3",
"resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
"integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
"dev": true,
"dependencies": {
"punycode": "^1.3.2"
}
},
"node_modules/fast-url-parser/node_modules/punycode": {
"version": "1.4.1",
"resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
"integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
"dev": true
},
"node_modules/fastest-levenshtein": {
"version": "1.0.12",
"resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
@@ -10251,15 +10205,6 @@
"node": ">= 4"
}
},
"node_modules/ignore-walk": {
"version": "3.0.4",
"resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
"integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
"dev": true,
"dependencies": {
"minimatch": "^3.0.4"
}
},
"node_modules/import-fresh": {
"version": "3.3.0",
"resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
@@ -16921,15 +16866,6 @@
"node": ">= 0.8"
}
},
"node_modules/stream-events": {
"version": "1.0.5",
"resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
"integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
"dev": true,
"dependencies": {
"stubs": "^3.0.0"
}
},
"node_modules/string_decoder": {
"version": "1.1.1",
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
@@ -17089,12 +17025,6 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
"node_modules/stubs": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
"dev": true
},
"node_modules/stylehacks": {
"version": "5.1.0",
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
@@ -17353,22 +17283,6 @@
"node": ">= 6"
}
},
"node_modules/teeny-request": {
"version": "7.1.1",
"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
"dev": true,
"dependencies": {
"http-proxy-agent": "^4.0.0",
"https-proxy-agent": "^5.0.0",
"node-fetch": "^2.6.1",
"stream-events": "^1.0.5",
"uuid": "^8.0.0"
},
"engines": {
"node": ">=10"
}
},
"node_modules/terminal-link": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
@@ -17957,15 +17871,6 @@
"requires-port": "^1.0.0"
}
},
"node_modules/urlgrey": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
"integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
"dev": true,
"dependencies": {
"fast-url-parser": "^1.1.3"
}
},
"node_modules/use": {
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
@@ -17996,15 +17901,6 @@
"node": ">= 0.4.0"
}
},
"node_modules/uuid": {
"version": "8.3.2",
"resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
"integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
"dev": true,
"bin": {
"uuid": "dist/bin/uuid"
}
},
"node_modules/v8-compile-cache": {
"version": "2.3.0",
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
@@ -22694,12 +22590,6 @@
"sprintf-js": "~1.0.2"
}
},
"argv": {
"version": "0.0.2",
"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
"dev": true
},
"aria-query": {
"version": "4.2.2",
"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
@@ -23489,19 +23379,6 @@
"integrity": "sha512-RpAVKQA5T63xEj6/giIbUEtZwJ4UFIc3ZtvEkiaUERylqe8xb5IvqcgOurZLahv93CLKfxcw5YI+DZcUBRyLXA==",
"dev": true
},
"codecov": {
"version": "3.8.3",
"resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
"integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
"dev": true,
"requires": {
"argv": "0.0.2",
"ignore-walk": "3.0.4",
"js-yaml": "3.14.1",
"teeny-request": "7.1.1",
"urlgrey": "1.0.0"
}
},
"collect-v8-coverage": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
@@ -25575,23 +25452,6 @@
"resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
"integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
},
"fast-url-parser": {
"version": "1.1.3",
"resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
"integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
"dev": true,
"requires": {
"punycode": "^1.3.2"
},
"dependencies": {
"punycode": {
"version": "1.4.1",
"resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
"integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
"dev": true
}
}
},
"fastest-levenshtein": {
"version": "1.0.12",
"resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
@@ -26382,15 +26242,6 @@
"resolved": "https://registry.npmjs.org/ignore/-/ignore-4.0.6.tgz",
"integrity": "sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg=="
},
"ignore-walk": {
"version": "3.0.4",
"resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
"integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
"dev": true,
"requires": {
"minimatch": "^3.0.4"
}
},
"import-fresh": {
"version": "3.3.0",
"resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
@@ -31562,15 +31413,6 @@
"integrity": "sha512-RwNA9Z/7PrK06rYLIzFMlaF+l73iwpzsqRIFgbMLbTcLD6cOao82TaWefPXQvB2fOC4AjuYSEndS7N/mTCbkdQ==",
"dev": true
},
"stream-events": {
"version": "1.0.5",
"resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
"integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
"dev": true,
"requires": {
"stubs": "^3.0.0"
}
},
"string_decoder": {
"version": "1.1.1",
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
@@ -31693,12 +31535,6 @@
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
"integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig=="
},
"stubs": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
"dev": true
},
"stylehacks": {
"version": "5.1.0",
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
@@ -31896,19 +31732,6 @@
}
}
},
"teeny-request": {
"version": "7.1.1",
"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
"dev": true,
"requires": {
"http-proxy-agent": "^4.0.0",
"https-proxy-agent": "^5.0.0",
"node-fetch": "^2.6.1",
"stream-events": "^1.0.5",
"uuid": "^8.0.0"
}
},
"terminal-link": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
@@ -32347,15 +32170,6 @@
"requires-port": "^1.0.0"
}
},
"urlgrey": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
"integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
"dev": true,
"requires": {
"fast-url-parser": "^1.1.3"
}
},
"use": {
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
@@ -32380,12 +32194,6 @@
"integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==",
"dev": true
},
"uuid": {
"version": "8.3.2",
"resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
"integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
"dev": true
},
"v8-compile-cache": {
"version": "2.3.0",
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",

1
client/package.json
View File

@@ -101,7 +101,6 @@
"cheerio": "^1.0.0-rc.6",
"clean-css": "^5.1.2",
"clean-webpack-plugin": "^4.0.0-alpha.0",
"codecov": "^3.7.1",
"css-loader": "^5.2.4",
"css-minimizer-webpack-plugin": "^4.0.0",
"eslint": "^7.24.0",

2
server/requirements-dev.txt
View File

@@ -1,6 +1,6 @@
black
bumpversion>=0.5
codecov>=2.0.15
coverage>=5.0
parameterized>=0.7.0
pytest>=3.6.3
python-jose>=3.2.0