From 42b743a5ef07d3c75524df3e58acd65e9f85456f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 24 Oct 2024 16:05:08 -0500
Subject: Fix linting and typing errors.

---
 r_qtl/r_qtl2.py                |  2 +-
 scripts/rqtl2/phenotypes_qc.py | 11 +++++------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 5b926d1..c6307f5 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -566,7 +566,7 @@ def read_text_file(filepath: Union[str, Path]) -> Iterator[str]:
 
 def read_csv_file(filepath: Union[str, Path],
                   separator: str = ",",
-                  comment_char: str = "#") -> Iterator[str]:
+                  comment_char: str = "#") -> Iterator[tuple[str, ...]]:
     """Read a file as a csv file."""
     for line in read_text_file(filepath):
         if line.startswith(comment_char):
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index 4191df9..3448790 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -169,7 +169,7 @@ def merge_dicts(*dicts):
     return reduce(lambda merged, dct: {**merged, **dct}, dicts, {})
 
 
-def decimal_points_error(
+def decimal_points_error(# pylint: disable=[too-many-arguments]
         filename: str,
         rowtitle: str,
         coltitle: str,
@@ -178,7 +178,7 @@ def decimal_points_error(
         decimal_places: int = 1
 ) -> Optional[InvalidValue]:
     """Returns an error if the value does not meet the checks."""
-    if not bool(decimal_places_pattern(1).match(cellvalue)):
+    if not bool(decimal_places_pattern(decimal_places).match(cellvalue)):
         return InvalidValue(filename, rowtitle, coltitle, cellvalue, message)
     return None
 
@@ -188,8 +188,7 @@ def integer_error(
         rowtitle: str,
         coltitle: str,
         cellvalue: str,
-        message: str,
-        decimal_places: int = 1
+        message: str
 ) -> Optional[InvalidValue]:
     """Returns an error if the value does not meet the checks."""
     try:
@@ -201,7 +200,7 @@ def integer_error(
         return InvalidValue(filename, rowtitle, coltitle, cellvalue, message)
 
 
-def qc_pheno_file(
+def qc_pheno_file(# pylint: disable=[too-many-arguments]
         filepath: Path,
         samples: tuple[str, ...],
         phenonames: tuple[str, ...],
@@ -281,7 +280,7 @@ def run_qc(# pylint: disable=[too-many-arguments]
         logger.error("We found the following errors:\n%s",
                      "\n".join(f" - {error}" for error in errors))
         return 1
-    # TODO: Run QC on actual values
+    # Run QC on actual values
     #       Steps:
     #       - Extract file to specific directory
     extractiondir, *_bundlefiles = extract_bundle(phenobundle, workingdir)
-- 
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