From 5897b6ec7fbd1226cd68a292122cc494e46f6829 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 20 Apr 2022 13:26:20 +0300 Subject: Fix linting issues --- tests/qc/test_cells.py | 27 ++++++++++++++++++++------- tests/qc/test_header.py | 2 ++ tests/qc/test_parsing.py | 9 +++++++-- 3 files changed, 29 insertions(+), 9 deletions(-) (limited to 'tests/qc') diff --git a/tests/qc/test_cells.py b/tests/qc/test_cells.py index 5e25a9a..d4ef911 100644 --- a/tests/qc/test_cells.py +++ b/tests/qc/test_cells.py @@ -8,33 +8,46 @@ from quality_control.errors import InvalidCellValue from quality_control.average import valid_value as avg_valid_value from quality_control.standard_error import valid_value as se_valid_value -@given(num_str=st.from_regex("^(?!([0-9]+\.([0-9]{3}|[0-9]{6,}))).*", fullmatch=True)) +@given(num_str=st.from_regex( + r"^(?!([0-9]+\.([0-9]{3}|[0-9]{6,}))).*", fullmatch=True)) def test_cell_value_errors_with_invalid_inputs(num_str): + """Check that an error is raised for a cell with an invalid value.""" with pytest.raises(InvalidCellValue): avg_valid_value(num_str) with pytest.raises(InvalidCellValue): se_valid_value(num_str) -@given(num_str=st.from_regex("^[0-9]+\.([0-9]{1,2}|[0-9]{4,}$)", fullmatch=True)) +@given(num_str=st.from_regex( + r"^[0-9]+\.([0-9]{1,2}|[0-9]{4,}$)", fullmatch=True)) def test_cell_average_value_errors_if_not_three_decimal_places(num_str): + """Check that an error is raised if the average value does not have 3 decimal places""" with pytest.raises(InvalidCellValue): avg_valid_value(num_str) -@given(num_str=st.from_regex("^[0-9]+\.[0-9]{3}$", fullmatch=True)) +@given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{3}$", fullmatch=True)) def test_cell_average_value_pass_if_three_decimal_places(num_str): + """Check that there is no error if the average value has 3 decimal places.""" processed = avg_valid_value(num_str) assert ( isinstance(processed, float) and - processed == float(num_str)) + processed == float(num_str)) -@given(num_str=st.from_regex("^[0-9]+\.([0-9]{0,5}$)", fullmatch=True)) +@given(num_str=st.from_regex(r"^[0-9]+\.([0-9]{0,5}$)", fullmatch=True)) def test_cell_standard_error_value_errors_if_less_than_six_decimal_places(num_str): + """ + Check that an error is raised if the standard error value does not have 6 + decimal places + """ with pytest.raises(InvalidCellValue): se_valid_value(num_str) -@given(num_str=st.from_regex("^[0-9]+\.[0-9]{6,}$", fullmatch=True)) +@given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{6,}$", fullmatch=True)) def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str): + """ + Check that there is no error if the standard error value has 3 decimal + places. + """ processed = se_valid_value(num_str) assert ( isinstance(processed, float) and - processed == float(num_str)) + processed == float(num_str)) diff --git a/tests/qc/test_header.py b/tests/qc/test_header.py index a474834..6ca9376 100644 --- a/tests/qc/test_header.py +++ b/tests/qc/test_header.py @@ -1,3 +1,4 @@ +"""Test the parsing of headers""" import pytest from hypothesis import given from hypothesis import strategies as st @@ -27,5 +28,6 @@ def test_valid_header_strains_passes_with_valid_headers(strains, headers): ("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain", "AStrain"))]) def test_valid_header_fails_with_duplicate_headers(strains, headers): + """Check that parsing fails if any header is duplicated""" with pytest.raises(DuplicateHeader): valid_header(strains, headers) diff --git a/tests/qc/test_parsing.py b/tests/qc/test_parsing.py index be13d9b..6c784d5 100644 --- a/tests/qc/test_parsing.py +++ b/tests/qc/test_parsing.py @@ -1,3 +1,4 @@ +"""Test the parsing of the files""" import pytest from quality_control.errors import ParseError @@ -14,8 +15,9 @@ from quality_control.parsing import FileType, parse_file ("tests/test_data/duplicated_headers_no_data_errors.tsv", FileType.STANDARD_ERROR),)) def test_parse_file_fails_with_wrong_filetype_declaration(filepath, filetype, strains): + """Check that parsing fails if the wrong file type is declared""" with pytest.raises(ParseError): - for line in parse_file(filepath, filetype, strains): + for line in parse_file(filepath, filetype, strains): # pylint: disable=[unused-variable] pass @pytest.mark.parametrize( @@ -24,6 +26,7 @@ def test_parse_file_fails_with_wrong_filetype_declaration(filepath, filetype, st ("tests/test_data/average.tsv", FileType.AVERAGE), ("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR))) def test_parse_file_passes_with_valid_files(filepath, filetype, strains): + """Check that parsing succeeds with valid files""" for line in parse_file(filepath, filetype, strains): assert bool(line) @@ -33,6 +36,7 @@ def test_parse_file_passes_with_valid_files(filepath, filetype, strains): ("tests/test_data/average.tsv", FileType.AVERAGE), ("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR))) def test_parse_file_works_with_large_files(filepath, filetype, strains): + """Check that parsing succeeds even with large files.""" for line in parse_file(filepath, filetype, strains): assert bool(line) @@ -43,6 +47,7 @@ def test_parse_file_works_with_large_files(filepath, filetype, strains): ("tests/test_data/standarderror_1_error_at_end.tsv", FileType.STANDARD_ERROR), ("tests/test_data/duplicated_headers_no_data_errors.tsv", FileType.AVERAGE))) def test_parse_file_raises_exception_on_error_in_file(filepath, filetype, strains): + "Check that parsing fails if any error is found in a file" with pytest.raises(ParseError): - for line in parse_file(filepath, filetype, strains): + for line in parse_file(filepath, filetype, strains): # pylint: disable=[unused-variable] pass -- cgit v1.2.3