pytest cov

Author: pranathivemuri

.github/workflows/ci.yml

@@ -37,6 +37,7 @@ jobs:
           pip install -r requirements_testing.txt
           make coverage
       - name: Send coverage to codecov.io
-        uses: codecov/codecov-action@v1
-        with:
-          fail_ci_if_error: true
+        shell: bash -l {0}
+        run: |
+          pip install codecov
+          bash <(curl -s https://codecov.io/bash)

Makefile

@@ -1,15 +1,34 @@
+PYTHON ?= python
+
 help:
 	@echo "lint - check code style with flake8"
+	@echo "code_format - check code style with black"
 	@echo "test - run tests only"
 	@echo "coverage - run tests and check code coverage"
 	@echo "conda_install (recommended) - Install requirements "
 
+clean:
+	$(PYTHON) setup.py clean --all
+
+install:
+	pip install -r requirements.txt
+	pip install .
+
+dist: FORCE
+	$(PYTHON) setup.py sdist
+
 test:
-	py.test
+	pip install -e '.[test]'
+	$(PYTHON) -m pytest
 
 coverage:
-	coverage run --source orpheum --omit="*/test*" --module py.test
-	coverage report --show-missing
+	$(PYTHON) setup.py clean --all
+	$(PYTHON) -m pytest --cov=. --cov-report term-missing
+
+FORCE:
+
+code_format:
+	black .
 
 lint:
 	# ignore:
@@ -22,11 +41,3 @@ conda_install:
 	pip install -r requirements.txt
 	pip install .
 
-install:
-	pip install -r requirements.txt
-	pip install .
-
-dist: FORCE
-	python setup.py sdist
-
-FORCE:

environment_minimal.yml

@@ -12,6 +12,8 @@ dependencies:
   - notebook
   - numpy
   - pandas
+  - pytest
+  - pytest-cov
   - pip
   - pyarrow
   - scikit-learn

requirements.txt

@@ -15,3 +15,4 @@ pyarrow
 s3fs
 fastparquet
 pytest
+pytest-cov

requirements_minimal.txt

@@ -7,4 +7,6 @@ khmer
 httmock
 seaborn
 scikit-learn
-networkx
+networkx
+pytest-cov
+pytest

requirements_testing.txt

@@ -1,3 +1,5 @@
 pytest
 coverage
-flake8
+flake8
+pytest-cov
+black