Add codecov for code coverage of python and javascript (#1170)

* Add codecov to Push Test workflow

* Empty commit

* Clear reports and tag each with flags

* Tag code reports by test

* Fix codecov tags

* One more fix

.github/workflows/push_tests.yml

@@ -4,6 +4,7 @@ on: [push]
 
 env:
   JEST_ENV: prod
+  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 jobs:
   lint:
@@ -44,7 +45,10 @@ jobs:
     - name: Install dependencies
       run: make pydist install-dist dev-env-server
     - name: Unit tests
-      run: make unit-test
+      run: |
+        make unit-test
+        bash <(curl -s https://codecov.io/bash) -k server -cF backend,python,unitTest
+        cd client && ./node_modules/codecov/bin/codecov --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
 
   smoke-tests:
     runs-on: ubuntu-latest
@@ -71,7 +75,9 @@ jobs:
     - name: Install dependencies
       run: make pydist install-dist
     - name: Smoke tests (without annotations feature)
-      run: cd client && make smoke-test
+      run: |
+        cd client && make smoke-test
+        ./node_modules/codecov/bin/codecov --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
 
   smoke-tests-annotations:
     runs-on: ubuntu-latest
@@ -98,4 +104,6 @@ jobs:
     - name: Install dependencies
       run: make pydist install-dist
     - name: Smoke tests (with annotations feature)
-      run: cd client && make smoke-test-annotations
+      run: |
+        cd client && make smoke-test-annotations
+        ./node_modules/codecov/bin/codecov --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTestAnnotations

.gitignore

@@ -3,6 +3,8 @@ node_modules/
 
 # coverage
 coverage
+coverage.xml
+.coverage
 .nyc_output
 
 .pytest_cache/

README.md

@@ -5,6 +5,7 @@ _an interactive explorer for single-cell transcriptomics data_
 [![DOI](https://zenodo.org/badge/105615409.svg)](https://zenodo.org/badge/latestdoi/105615409) [![PyPI](https://img.shields.io/pypi/v/cellxgene)](https://pypi.org/project/cellxgene/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/cellxgene)](https://pypistats.org/packages/cellxgene) [![GitHub last commit](https://img.shields.io/github/last-commit/chanzuckerberg/cellxgene)](https://github.com/chanzuckerberg/cellxgene/pulse)
 ![Push Tests](https://github.com/chanzuckerberg/cellxgene/workflows/Push%20Tests/badge.svg)
 ![Compatability Tests](https://github.com/chanzuckerberg/cellxgene/workflows/Compatability%20Tests/badge.svg)
+![Code Coverage](https://codecov.io/gh/chanzuckerberg/cellxgene/branch/master/graph/badge.svg)
 
 cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
 

client/Makefile

@@ -88,7 +88,8 @@ smoke-test-annotations:
 
 .PHONY: unit-test
 unit-test:
-	node node_modules/jest/bin/jest.js --testPathIgnorePatterns e2e
+	node node_modules/jest/bin/jest.js \
+	    --testPathIgnorePatterns e2e
 
 # pass remaining commands through to npm run
 %:

client/package-lock.json

@@ -6138,6 +6138,12 @@
         "type-detect": "4.0.8"
       }
     },
+    "@tootallnate/once": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/@tootallnate/once/-/once-1.0.0.tgz",
+      "integrity": "sha512-KYyTT/T6ALPkIRd2Ge080X/BsXvy9O0hcWTtMWkPvwAwF99+vn6Dv4GzrFT/Nn1LePr+FFDbRXXlqmsy9lw2zA==",
+      "dev": true
+    },
     "@types/babel__core": {
       "version": "7.1.2",
       "resolved": "https://registry.npmjs.org/@types/babel__core/-/babel__core-7.1.2.tgz",
@@ -6663,6 +6669,12 @@
         "sprintf-js": "~1.0.2"
       }
     },
+    "argv": {
+      "version": "0.0.2",
+      "resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
+      "integrity": "sha1-7L0W+JSbFXGDcRsb2jNPN4QBhas=",
+      "dev": true
+    },
     "aria-query": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/aria-query/-/aria-query-3.0.0.tgz",
@@ -7967,6 +7979,19 @@
       "integrity": "sha1-bqa989hTrlTMuOR7+gvz+QMfsYQ=",
       "dev": true
     },
+    "codecov": {
+      "version": "3.6.5",
+      "resolved": "https://registry.npmjs.org/codecov/-/codecov-3.6.5.tgz",
+      "integrity": "sha512-v48WuDMUug6JXwmmfsMzhCHRnhUf8O3duqXvltaYJKrO1OekZWpB/eH6iIoaxMl8Qli0+u3OxptdsBOYiD7VAQ==",
+      "dev": true,
+      "requires": {
+        "argv": "0.0.2",
+        "ignore-walk": "3.0.3",
+        "js-yaml": "3.13.1",
+        "teeny-request": "6.0.1",
+        "urlgrey": "0.4.4"
+      }
+    },
     "collect-v8-coverage": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.0.tgz",
@@ -12685,6 +12710,37 @@
         "toidentifier": "1.0.0"
       }
     },
+    "http-proxy-agent": {
+      "version": "4.0.1",
+      "resolved": "https://registry.npmjs.org/http-proxy-agent/-/http-proxy-agent-4.0.1.tgz",
+      "integrity": "sha512-k0zdNgqWTGA6aeIRVpvfVob4fL52dTfaehylg0Y4UvSySvOq/Y+BOyPrgpUrA7HylqvU8vIZGsRuXmspskV0Tg==",
+      "dev": true,
+      "requires": {
+        "@tootallnate/once": "1",
+        "agent-base": "6",
+        "debug": "4"
+      },
+      "dependencies": {
+        "agent-base": {
+          "version": "6.0.0",
+          "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.0.tgz",
+          "integrity": "sha512-j1Q7cSCqN+AwrmDd+pzgqc0/NpC655x2bUf5ZjRIO77DcNBFmh+OgRNzF6OKdCC9RSCb19fGd99+bhXFdkRNqw==",
+          "dev": true,
+          "requires": {
+            "debug": "4"
+          }
+        },
+        "debug": {
+          "version": "4.1.1",
+          "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz",
+          "integrity": "sha512-pYAIzeRo8J6KPEaJ0VWOh5Pzkbw/RetuzehGM7QRRX5he4fPHx2rdKMB256ehJCkX+XRQm16eZLqLNS8RSZXZw==",
+          "dev": true,
+          "requires": {
+            "ms": "^2.1.1"
+          }
+        }
+      }
+    },
     "http-signature": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/http-signature/-/http-signature-1.2.0.tgz",
@@ -12764,6 +12820,15 @@
       "integrity": "sha512-Pgs951kaMm5GXP7MOvxERINe3gsaVjUWFm+UZPSq9xYriQAksyhg0csnS0KXSNRD5NmNdapXEpjxG49+AKh/ug==",
       "dev": true
     },
+    "ignore-walk": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.3.tgz",
+      "integrity": "sha512-m7o6xuOaT1aqheYHKf8W6J5pYH85ZI9w077erOzLje3JsB1gkafkAhHHY19dqjulgIZHFm32Cp5uNZgcQqdJKw==",
+      "dev": true,
+      "requires": {
+        "minimatch": "^3.0.4"
+      }
+    },
     "import-fresh": {
       "version": "3.2.1",
       "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.2.1.tgz",
@@ -19694,6 +19759,12 @@
         "lower-case": "^1.1.1"
       }
     },
+    "node-fetch": {
+      "version": "2.6.0",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.0.tgz",
+      "integrity": "sha512-8dG4H5ujfvFiqDmVu9fQ5bOHUC15JMjMY/Zumv26oOvvVJjM67KF8koCWIabKQ1GJIa9r2mMZscBq/TbdOcmNA==",
+      "dev": true
+    },
     "node-int64": {
       "version": "0.4.0",
       "resolved": "https://registry.npmjs.org/node-int64/-/node-int64-0.4.0.tgz",
@@ -22527,6 +22598,15 @@
         "stream-shift": "^1.0.0"
       }
     },
+    "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"
+      }
+    },
     "stream-http": {
       "version": "2.8.3",
       "resolved": "https://registry.npmjs.org/stream-http/-/stream-http-2.8.3.tgz",
@@ -22751,6 +22831,12 @@
       "integrity": "sha1-PFMZQukIwml8DsNEhYwobHygpgo=",
       "dev": true
     },
+    "stubs": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
+      "integrity": "sha1-6NK6H6nJBXAwPAMLaQD31fiavls=",
+      "dev": true
+    },
     "style-loader": {
       "version": "1.1.3",
       "resolved": "https://registry.npmjs.org/style-loader/-/style-loader-1.1.3.tgz",
@@ -22979,6 +23065,19 @@
       "integrity": "sha512-IlqtmLVaZA2qab8epUXbVWRn3aB1imbDMJtjB3nu4X0NqPkcY/JH9ZtCBWKHWPxs8Svi9tyo8w2dBoi07qZbBA==",
       "dev": true
     },
+    "teeny-request": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-6.0.1.tgz",
+      "integrity": "sha512-TAK0c9a00ELOqLrZ49cFxvPVogMUFaWY8dUsQc/0CuQPGF+BOxOQzXfE413BAk2kLomwNplvdtMpeaeGWmoc2g==",
+      "dev": true,
+      "requires": {
+        "http-proxy-agent": "^4.0.0",
+        "https-proxy-agent": "^4.0.0",
+        "node-fetch": "^2.2.0",
+        "stream-events": "^1.0.5",
+        "uuid": "^3.3.2"
+      }
+    },
     "term-size": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/term-size/-/term-size-1.2.0.tgz",
@@ -23664,6 +23763,12 @@
         "prepend-http": "^1.0.1"
       }
     },
+    "urlgrey": {
+      "version": "0.4.4",
+      "resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-0.4.4.tgz",
+      "integrity": "sha1-iS/pWWCAXoVRnxzUOJ8stMu3ZS8=",
+      "dev": true
+    },
     "use": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",

client/package.json

@@ -69,6 +69,7 @@
     "babel-loader": "^8.0.6",
     "babel-preset-modern-browsers": "^14.1.1",
     "chalk": "^3.0.0",
+    "codecov": "^3.6.5",
     "connect-history-api-fallback": "^1.6.0",
     "copy-webpack-plugin": "^5.1.1",
     "css-loader": "^3.4.2",
@@ -107,7 +108,9 @@
     "testURL": "http://localhost/",
     "setupFiles": [
       "./__tests__/setupMissingGlobals.js"
-    ]
+    ],
+    "coverageDirectory": "./coverage/",
+    "collectCoverage": true
   },
   "babel": {
     "env": {

server/Makefile

@@ -7,4 +7,11 @@ clean:
 
 .PHONY: unit-test
 unit-test:
-	pytest -s test
+	PYTHONWARNINGS=ignore:ResourceWarning coverage run \
+		--source=app,cli,common,compute,converters,data_anndata,data_common,data_cxg \
+		--omit=.coverage,data_common/fbs/NetEncoding,venv \
+		-m unittest discover \
+		--start-directory test/ \
+		--top-level-directory ../ \
+		--verbose
+

server/requirements-dev.txt

@@ -3,4 +3,5 @@ bumpversion>=0.5
 parameterized>=0.7.0
 pytest>=3.6.3
 twine>=1.12.1
+codecov>=2.0.15
 -r requirements.txt