one test

PMBio · Apr 12, 2024 · 05e4578 · 05e4578
1 parent ff78d30
commit 05e4578
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 17 deletions.
diff --git a/.github/workflows/test-runner.yml b/.github/workflows/test-runner.yml
@@ -40,5 +40,5 @@ jobs:
         shell: micromamba-shell {0}
 
       - name: Run pytest preprocessing
-        run: pytest -v ${{ github.workspace }}/tests/preprocessing --log-cli-level DEBUG 
+        run: pytest -v ${{ github.workspace }}/preprocessing/test_preprocess.py::test_process_and_combine_sparse_gt --log-cli-level DEBUG
         shell: micromamba-shell {0}
diff --git a/tests/preprocessing/test_preprocess.py b/tests/preprocessing/test_preprocess.py
@@ -229,18 +229,6 @@ def test_add_variant_ids(
 @pytest.mark.parametrize(
     "test_data_name_dir, extra_cli_params, input_h5, result_h5",
     [
-        (
-            "no_filters_minimal_split",
-            [
-                "--chromosomes",
-                "1,2",
-            ],
-            [
-                "genotypes_chr1.h5",
-                "genotypes_chr2.h5",
-            ],
-            "genotypes.h5",
-        ),
         (
             "filter_calls_variants_samples_minimal_split",
             [
@@ -317,7 +305,9 @@ def test_process_and_combine_sparse_gt(
     )
 
     expected_data = np.load(expected_array_archive.as_posix(), allow_pickle=True)
-
-    assert np.array_equal(written_variant_matrix, expected_data["variant_matrix"])
-    assert np.array_equal(written_genotype_matrix, expected_data["genotype_matrix"])
-    assert np.array_equal(written_samples, expected_data["samples"])
+    expected_data_variant_matrix = expected_data["variant_matrix"]
+    expected_data_genotype_matrix = expected_data["genotype_matrix"]
+    expected_data_samples = expected_data["samples"]
+    assert np.array_equal(written_variant_matrix, expected_data_variant_matrix)
+    assert np.array_equal(written_genotype_matrix, expected_data_genotype_matrix)
+    assert np.array_equal(written_samples, expected_data_samples)