Fix linting issues

5 files changed, 31 insertions, 18 deletions

diff --git a/tests/conftest.py b/tests/conftest.py
index 0cdba3e..f79166d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,4 @@
-from functools import reduce
+"""Set up fixtures for tests"""
 
 import pytest
 
@@ -6,4 +6,5 @@ from quality_control.parsing import strain_names, parse_strains
 
 @pytest.fixture(scope="session")
 def strains():
+    """Parse the strains once every test session"""
     return strain_names(parse_strains("strains.csv"))
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
diff --git a/tests/strategies.py b/tests/strategies.py
deleted file mode 100644
index ccda362..0000000
--- a/tests/strategies.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""Module holding custom data generation strategies"""
-
-from hypothesis.strategies import characters, composite
-
-@composite
-def average_numbers_string(draw):
-    num = draw(floats(allow_nan=False, allow_infinity=False,))
-    return f"{num:.3f}"