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| author | Frederick Muriuki Muriithi | 2024-01-02 09:30:57 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-02 09:30:57 +0300 |
| commit | ee0cf7de526849f228c73b744bf66d22c30b34de (patch) | |
| tree | 97b2758adccae5bb3bc8e688d7d3b845d1a0ddb8 | |
| parent | b3b9ba3b5b4e516d6220668155f9b5c57a51eb7d (diff) | |
| download | gn-uploader-ee0cf7de526849f228c73b744bf66d22c30b34de.tar.gz | |
Mark tests as unit tests.
| -rw-r--r-- | tests/qc/test_cells.py | 4 | ||||
| -rw-r--r-- | tests/qc/test_error_collection.py | 3 | ||||
| -rw-r--r-- | tests/qc/test_header.py | 6 |
3 files changed, 12 insertions, 1 deletions
diff --git a/tests/qc/test_cells.py b/tests/qc/test_cells.py index f5411fe..51e8bcf 100644 --- a/tests/qc/test_cells.py +++ b/tests/qc/test_cells.py @@ -10,6 +10,7 @@ from quality_control.errors import InvalidValue from quality_control.average import invalid_value as avg_invalid_value from quality_control.standard_error import invalid_value as se_invalid_value +@pytest.mark.unit_test @given(num_str=st.from_regex( r"^(?!([0-9]+\.[0-9]{1,}|0+)).*", fullmatch=True)) def test_cell_value_errors_with_invalid_inputs2(num_str): @@ -48,6 +49,7 @@ def test_cell_average_value_errors_if_not_three_decimal_places2(num_str): f"Invalid value '{num_str}'. Expected string representing a number " "with exactly three decimal places.")) +@pytest.mark.unit_test @given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{1,}$", fullmatch=True)) def test_cell_average_value_pass_if_three_decimal_places(num_str): """ @@ -77,7 +79,7 @@ def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_s f"Invalid value '{num_str}'. Expected string representing a number " "with at least six decimal places.")) - +@pytest.mark.unit_test @given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{1,}$", fullmatch=True)) def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str): """ diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py index ee1e6c2..25f5d01 100644 --- a/tests/qc/test_error_collection.py +++ b/tests/qc/test_error_collection.py @@ -6,6 +6,7 @@ from quality_control.parsing import take, FileType, collect_errors from quality_control.errors import ( InvalidValue, DuplicateHeading, InconsistentColumns) +@pytest.mark.unit_test @pytest.mark.parametrize( "sample,num,expected", ((range(0,25), 5, [0, 1, 2, 3, 4]), @@ -18,6 +19,7 @@ def test_take(sample, num, expected): assert taken == expected @pytest.mark.slow +@pytest.mark.unit_test @pytest.mark.parametrize( "filepath,filetype,count", (("tests/test_data/average_crlf.tsv", FileType.AVERAGE, 10), @@ -36,6 +38,7 @@ def test_collect_errors(filepath, filetype, strains, count): return isinstance(item, (InvalidValue, DuplicateHeading)) assert all(__valid_instance(error) for error in results) +@pytest.mark.unit_test @pytest.mark.parametrize( "filepath,filetype,expected", (("tests/test_data/average_inconsistent_columns.tsv", FileType.AVERAGE, diff --git a/tests/qc/test_header.py b/tests/qc/test_header.py index 2557e85..5e54122 100644 --- a/tests/qc/test_header.py +++ b/tests/qc/test_header.py @@ -7,6 +7,7 @@ from quality_control.errors import InvalidValue, DuplicateHeading from quality_control.headers import ( invalid_header, invalid_headings, duplicate_headings) +@pytest.mark.unit_test @given(headers=st.lists(st.text(max_size=10), max_size=1)) def test_invalid_header_with_list_of_one_value(headers): """Test `invalid_header` with invalid header row""" @@ -14,6 +15,7 @@ def test_invalid_header_with_list_of_one_value(headers): 0, 0, "<TAB>".join(headers), "The header MUST contain at least 2 columns") +@pytest.mark.unit_test @given(headings=st.lists(st.text(min_size=2, max_size=10), min_size=2)) def test_invalid_headings_with_invalid_inputs(headings): "Verify that the check for header validity works" @@ -21,6 +23,7 @@ def test_invalid_headings_with_invalid_inputs(headings): InvalidValue(0, col, heading, f"'{heading}' not a valid strain.") for col, heading in enumerate(headings, start=2)) +@pytest.mark.unit_test @pytest.mark.parametrize( "headers", [ (("ProbeSet", "BXD3", "BXD1")), @@ -29,6 +32,7 @@ def test_invalid_header_with_valid_headers(headers): "Verify that the check for header validity works" assert invalid_header(0, headers) is None +@pytest.mark.unit_test @pytest.mark.parametrize( "strains,headings", [ (("BXD1", "BXD2", "BXD3"), ("BXD3", "BXD1")), @@ -38,6 +42,7 @@ def test_invalid_headings_with_valid_headings(strains, headings): "Verify that the check for header validity works" assert invalid_headings(0, strains, headings) == tuple() +@pytest.mark.unit_test @pytest.mark.parametrize( "headers,repeated", [ (("ProbeSet", "BXD3", "BXD1", "BXD1"), {"BXD1": (3, 4)}), @@ -51,6 +56,7 @@ def test_duplicate_headers_with_repeated_column_headings(headers, repeated): f"{','.join(str(i) for i in cols)}")) for head, cols in repeated.items()) +@pytest.mark.unit_test @pytest.mark.parametrize( "headers", [ (("ProbeSet", "BXD3", "BXD1")), |