Track filename in the errors

R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.

1 files changed, 6 insertions, 5 deletions

diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index 90beb8a..00b1ac6 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -4,17 +4,18 @@ from typing import Union
 from .utils import cell_error
 from .errors import InvalidValue
 
-def invalid_value(
-        line_number: int, column_number: int, val: str) -> Union[
-            InvalidValue, None]:
+def invalid_value(filename: str,
+                  line_number: int,
+                  column_number: int,
+                  val: str) -> Union[InvalidValue, None]:
     """
     Returns a `quality_control.errors.InvalidValue` object in the case where
     `val` is not a valid input for standard error files, otherwise, it returns
     `None`.
     """
     return cell_error(
-        r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, line=line_number,
-        column=column_number, value=val, message=(
+        r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, filename=filename,
+        line=line_number, column=column_number, value=val, message=(
             f"Invalid value '{val}'. "
             "Expected string representing a number with at least six "
             "decimal places."))