Add tests to PR checks (#361)

* Setup pytest

* Add some tests for resource classes

* Add instructions for running tests to contributing docs

* Use a gnomAD bucket for test paths

Author: nawatts

.github/workflows/ci.yml

@@ -30,7 +30,9 @@ jobs:
       - name: Run Pylint
         run: ./lint --disable=W
       - name: Check formatting
-        run: black --check gnomad
+        run: black --check gnomad tests
+      - name: Run tests
+        run: python -m pytest
   docs:
     name: Build documentation
     runs-on: ubuntu-latest

CONTRIBUTING.md

@@ -36,6 +36,14 @@ Use [Black](https://black.readthedocs.io/) to format code.
 black gnomad
 ```
 
+## Running tests
+
+Run tests using [pytest](https://docs.pytest.org/en/stable/).
+
+```
+python -m pytest
+```
+
 ## Building documentation
 
 See instructions in [docs/README.md](./docs/README.md).

lint

@@ -2,4 +2,4 @@
 
 cd "$(dirname "$0")"
 
-PYTHONPATH=$PYTHONPATH:$(pwd) pylint "$@" gnomad
+PYTHONPATH=$PYTHONPATH:$(pwd) pylint "$@" gnomad tests

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+testpaths = tests

requirements-dev.txt

@@ -1,3 +1,4 @@
 black==19.10b0
 pre-commit==2.10.1
 pylint
+pytest==6.2.3

tests/resources/test_resource_utils.py

@@ -0,0 +1,58 @@
+from unittest.mock import patch
+
+from gnomad.resources import resource_utils
+
+
+class TestTableResource:
+    @patch("hail.read_table")
+    def test_read_table(self, read_table):
+        resource = resource_utils.TableResource("gs://gnomad-public/table.ht")
+
+        ds = resource.ht()
+        read_table.assert_called_with("gs://gnomad-public/table.ht")
+        assert ds == read_table.return_value
+
+
+class TestMatrixTableResource:
+    @patch("hail.read_matrix_table")
+    def test_read_matrix_table(self, read_matrix_table):
+        resource = resource_utils.MatrixTableResource(
+            "gs://gnomad-public/matrix_table.mt"
+        )
+
+        ds = resource.mt()
+        read_matrix_table.assert_called_with("gs://gnomad-public/matrix_table.mt")
+        assert ds == read_matrix_table.return_value
+
+
+class TestPedigreeResource:
+    @patch("hail.Pedigree.read")
+    def test_read_pedigree(self, read_pedigree):
+        resource = resource_utils.PedigreeResource("gs://gnomad-public/pedigree.ped")
+
+        ds = resource.pedigree()
+        read_pedigree.assert_called()
+        print(read_pedigree.call_args)
+        assert read_pedigree.call_args[0][0] == "gs://gnomad-public/pedigree.ped"
+        assert ds == read_pedigree.return_value
+
+    @patch("hail.import_fam")
+    def test_read_fam(self, import_fam):
+        resource = resource_utils.PedigreeResource("gs://gnomad-public/pedigree.fam")
+
+        ds = resource.ht()
+        import_fam.assert_called()
+        assert import_fam.call_args[0][0] == "gs://gnomad-public/pedigree.fam"
+        assert ds == import_fam.return_value
+
+
+class TestBlockMatrixResource:
+    @patch("hail.linalg.BlockMatrix.read")
+    def test_read_block_matrix(self, read_block_matrix):
+        resource = resource_utils.BlockMatrixResource(
+            "gs://gnomad-public/block_matrix.bm"
+        )
+
+        ds = resource.bm()
+        read_block_matrix.assert_called_with("gs://gnomad-public/block_matrix.bm")
+        assert ds == read_block_matrix.return_value