Restore original names and instead ignore specific linter errors.

1 files changed, 13 insertions, 10 deletions

diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index 98b855f..9f11f57 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -41,15 +41,18 @@ logging.basicConfig(
             "(%(pathname)s: %(lineno)d) %(message)s"))
 logger = logging.getLogger(__MODULE__)
 
-def validate(phenobundle: Path, alogger: Logger) -> dict:
+def validate(
+        phenobundle: Path,
+        logger: Logger# pylint: disable=[redefined-outer-name]
+) -> dict:
     """Check that the bundle is generally valid"""
     try:
         rqc.validate_bundle(phenobundle)
     except rqe.RQTLError as rqtlerr:
-        # alogger.error("Bundle file validation failed!", exc_info=True)
+        # logger.error("Bundle file validation failed!", exc_info=True)
         return {
             "skip": True,
-            "logger": alogger,
+            "logger": logger,
             "phenobundle": phenobundle,
             "errors": (" ".join(rqtlerr.args),)
         }
@@ -57,20 +60,20 @@ def validate(phenobundle: Path, alogger: Logger) -> dict:
         "errors": tuple(),
         "skip": False,
         "phenobundle": phenobundle,
-        "logger": alogger
+        "logger": logger
     }
 
 
 def check_for_mandatory_pheno_keys(
         phenobundle: Path,
-        alogger: Logger,
+        logger: Logger,# pylint: disable=[redefined-outer-name]
         **kwargs
 ) -> dict:
     """Check that the mandatory keys exist for phenotypes."""
     if kwargs.get("skip", False):
         return {
             **kwargs,
-            "logger": alogger,
+            "logger": logger,
             "phenobundle": phenobundle
         }
 
@@ -81,7 +84,7 @@ def check_for_mandatory_pheno_keys(
         for key in _mandatory_keys if key not in _cdata.keys())
     return {
         **kwargs,
-        "logger": alogger,
+        "logger": logger,
         "phenobundle": phenobundle,
         "errors": _errors,
         "skip": len(_errors) > 0
@@ -90,14 +93,14 @@ def check_for_mandatory_pheno_keys(
 
 def check_for_averages_files(
         phenobundle: Path,
-        alogger: Logger,
+        logger: Logger,# pylint: disable=[redefined-outer-name]
         **kwargs
 ) -> dict:
     """Check that averages files appear together"""
     if kwargs.get("skip", False):
         return {
             **kwargs,
-            "logger": alogger,
+            "logger": logger,
             "phenobundle": phenobundle
         }
 
@@ -110,7 +113,7 @@ def check_for_averages_files(
         if ((first in _cdata.keys()) and (second not in _cdata.keys())))
     return {
         **kwargs,
-        "logger": alogger,
+        "logger": logger,
         "phenobundle": phenobundle,
         "errors": _errors,
         "skip": len(_errors) > 0