From 949ea71eb721a3f5bdff3ba10f7dd7c70899d560 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 12:11:43 +0300
Subject: Fix linting and type errors.

---
 r_qtl/r_qtl2_qc.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index 261d300..853c34b 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -7,23 +7,23 @@ from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl.r_qtl2 import __FILE_TYPES__
 
-def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
+def bundle_files_list(cdata: dict) -> tuple[str, ...]:
     """Retrieve files listed in control file."""
     def __merge__(alist: tuple[str, ...], member: Union[str, Sequence[str]]) -> tuple[str, ...]:
         if isinstance(cdata[member], str):
             return alist + (cdata[member],)
         return alist + tuple(cdata[member])
 
-    fileslist = tuple()
-    fileslist = reduce(__merge__,
-                       (key for key in cdata.keys() if key in __FILE_TYPES__),
-                       tuple())
+    fileslist: tuple[str, ...] = reduce(
+        __merge__,
+        (key for key in cdata.keys() if key in __FILE_TYPES__),
+        tuple())
 
     if "file" in cdata.get("sex", {}):
         sexfile = cdata["sex"]["file"]
         fileslist = fileslist + (
             (sexfile,) if isinstance(sexfile, str) else tuple(sexfile))
-        
+
     if "file" in cdata.get("cross_info", {}):
         crossinfofile = cdata["cross_info"]["file"]
         fileslist = fileslist + (
@@ -32,7 +32,7 @@ def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
 
     return fileslist
 
-def missing_files(zfile: ZipFile) -> tuple[str]:
+def missing_files(zfile: ZipFile) -> tuple[str, ...]:
     """
     Retrieve a list of files listed in the control file that do not exist in the
     bundle.
@@ -45,7 +45,7 @@ def missing_files(zfile: ZipFile) -> tuple[str]:
             return True
 
     return tuple(filter(__missing_p__,
-                        bundle_files_list(zfile, rqtl2.control_data(zfile))))
+                        bundle_files_list(rqtl2.control_data(zfile))))
 
 def validate_bundle(zfile: ZipFile):
     """Ensure the R/qtl2 bundle is valid."""
-- 
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