Fix linting issues

9 files changed, 48 insertions, 25 deletions

diff --git a/quality_control/average.py b/quality_control/average.py
index c552ba3..3261e1c 100644
--- a/quality_control/average.py
+++ b/quality_control/average.py
@@ -4,7 +4,8 @@ import re
 from .errors import InvalidCellValue
 
 def valid_value(val):
-    if re.search("^[0-9]+\.[0-9]{3}$", val):
+    """Checks whether `val` is a valid value for averages"""
+    if re.search(r"^[0-9]+\.[0-9]{3}$", val):
         return float(val)
     raise InvalidCellValue(
         f"Invalid value '{val}'.\n"
diff --git a/quality_control/errors.py b/quality_control/errors.py
index 993748c..0802159 100644
--- a/quality_control/errors.py
+++ b/quality_control/errors.py
@@ -19,5 +19,6 @@ class DuplicateHeader(Exception):
         super().__init__(self, *args)
 
 class ParseError(Exception):
-    def __init(self, *args):
-        super().__init__(*args)
+    """Raised if any of the above exceptions are raised"""
+    def __init__(self, *args):
+        super().__init__(self, *args)
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index 8b2715a..6e5bb8f 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -1,3 +1,5 @@
+"""Module handling the high-level parsing of the files"""
+
 import csv
 from enum import Enum
 from functools import reduce
@@ -9,11 +11,13 @@ from quality_control.errors import (
     ParseError, DuplicateHeader, InvalidCellValue, InvalidHeaderValue)
 
 class FileType(Enum):
+    """Enumerate the expected file types"""
     AVERAGE = 1
     STANDARD_ERROR = 2
 
 def parse_strains(filepath):
-    with open(filepath) as strains_file:
+    """Parse the strains file"""
+    with open(filepath, encoding="utf8") as strains_file:
         reader = csv.DictReader(
             strains_file,
             fieldnames=[
@@ -43,6 +47,7 @@ LINE_PARSERS = {
 }
 
 def strain_names(strains):
+    """Retrieve a complete list of the names of the strains"""
     def __extract_strain_names(acc, strain):
         return acc + tuple(
             item for item in (strain["Name"], strain["Name2"])
@@ -50,6 +55,7 @@ def strain_names(strains):
     return reduce(__extract_strain_names, strains, tuple())
 
 def parse_file(filepath: str, filetype: FileType, strains: list):
+    """Parse the given file"""
     seek_pos = 0
     try:
         with open(filepath, encoding="utf-8") as input_file:
@@ -66,5 +72,6 @@ def parse_file(filepath: str, filetype: FileType, strains: list):
             "filepath": filepath,
             "filetype": filetype,
             "position": seek_pos,
-            "line_number": line_number
-        })
+            "line_number": line_number,
+            "error": err
+        }) from err
diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index 7b49913..805c30e 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -4,7 +4,8 @@ import re
 from .errors import InvalidCellValue
 
 def valid_value(val):
-    if re.search("^[0-9]+\.[0-9]{6,}$", val):
+    """Checks whether `val` is a valid value for standard errors"""
+    if re.search(r"^[0-9]+\.[0-9]{6,}$", val):
         return float(val)
     raise InvalidCellValue(
         f"Invalid value '{val}'.\n"
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}"