Add tests for dataset

Author: jeromekelleher

.github/workflows/ci.yml

@@ -103,7 +103,7 @@ jobs:
         run: |
           # We are careful to pull in the minimum dependencies here
           # and only operate on files stored in the repo
-          python -m pytest -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
+          python -m pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
 
   packaging:
     name: Packaging tests

tests/data/v0.1_dataset_ex.vcz.zip

@@ -5,22 +5,39 @@
 
 
 @pytest.fixture
-def fx_v1_ex():
+def fx_ts_v1():
     return tszip.load("tests/data/v0.1_output_ex.ts.tsz")
 
 
-class TestBasics:
+@pytest.fixture
+def fx_ds_v1():
+    return sc2ts.Dataset("tests/data/v0.1_dataset_ex.vcz.zip")
+
+
+class TestStatFuncs:
 
-    def test_top_level_md(self, fx_v1_ex):
-        ts = fx_v1_ex
+    def test_top_level_md(self, fx_ts_v1):
+        ts = fx_ts_v1
         assert ts.metadata == {"time_zero_date": "2020-02-15"}
 
-    def test_node_data(self, fx_v1_ex):
-        ts = fx_v1_ex
+    def test_node_data(self, fx_ts_v1):
+        ts = fx_ts_v1
         df = sc2ts.node_data(ts)
         assert df.shape[0] == ts.num_nodes
 
-    def test_mutation_data(self, fx_v1_ex):
-        ts = fx_v1_ex
+    def test_mutation_data(self, fx_ts_v1):
+        ts = fx_ts_v1
         df = sc2ts.mutation_data(ts)
         assert df.shape[0] == ts.num_mutations
+
+
+class TestDataset:
+
+    def test_basics(self, fx_ds_v1):
+        ds = fx_ds_v1
+        G = ds["call_genotype"][:].squeeze()
+        pos = ds["variant_position"][:]
+        assert G.shape == (29903, 55)
+        assert pos.shape == (29903,)
+        assert pos[0] == 1
+        assert pos[-1] == 29903