added support for code coverage

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+branch = True
+source = cellxgene_gateway
+
+[report]
+exclude_lines =
+    if self.debug:
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True
+omit =
+    tests/*

.github/workflows/pr-checks.yaml

@@ -45,5 +45,16 @@ jobs:
         run: |
           eval "$(conda shell.bash hook)"
           conda activate cellxgene-gateway
-          python -m unittest discover tests
-          bash <(curl -s https://codecov.io/bash)
+          coverage run -m unittest discover tests
+
+      - name: Check coverage
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          coverage report --fail-under 41
+          coverage xml -i
+
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v1
+        with:
+          fail_ci_if_error: true

.gitignore

@@ -55,6 +55,7 @@ htmlcov/
 .nox/
 .coverage
 .coverage.*
+htmlcov
 .cache
 nosetests.xml
 coverage.xml

README.md

@@ -140,6 +140,12 @@ pre-commit install
     python -m unittest discover tests
 ```
 
+## Code Coverage
+```bash
+    coverage run -m unittest discover tests
+    coverage html
+```
+
 ## Running Linters
 
 pip install isort flake8 black

environment.yml

@@ -7,6 +7,7 @@ dependencies:
 - flask
 - psutil
 - black
+- coverage
 - pip
 - pip:
   - flask-api