From ebe34400325901a43e42c35fb9ad74f6c6ec0a6f Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Thu, 16 Jan 2025 14:48:27 -0800
Subject: [PATCH] Remove all options from cat utility

---
 micall/drivers/sample.py |  3 +--
 micall/utils/cat.py      | 38 ++++++++++----------------------------
 2 files changed, 11 insertions(+), 30 deletions(-)

diff --git a/micall/drivers/sample.py b/micall/drivers/sample.py
index 8f8fd33db..ffa8f4051 100644
--- a/micall/drivers/sample.py
+++ b/micall/drivers/sample.py
@@ -437,8 +437,7 @@ def run_denovo(self, excluded_seeds):
 
         concatenate_files(inputs=[self.unstitched_contigs_fasta,
                                   self.merged_contigs_fasta],
-                          output=self.combined_contigs_fasta,
-                          text=True, ignore_not_found=True)
+                          output=self.combined_contigs_fasta)
 
         with open(self.combined_contigs_fasta, 'r') as combined_contigs_fasta, \
              open(self.stitched_contigs_fasta, 'w') as stitched_contigs_fasta:
diff --git a/micall/utils/cat.py b/micall/utils/cat.py
index 3edd6e7d5..cd092f218 100644
--- a/micall/utils/cat.py
+++ b/micall/utils/cat.py
@@ -19,12 +19,7 @@
 from typing import Iterable, Sequence
 
 
-def cat(inputs: Iterable[Path],
-        output: Path,
-        text: bool,
-        ignore_not_found: bool,
-        ) -> int:
-
+def cat(inputs: Iterable[Path], output: Path) -> int:
     """
     Concatenates the contents of input inputs and writes the result to
     an output file.
@@ -42,40 +37,27 @@ def cat(inputs: Iterable[Path],
             for file in inputs:
                 try:
                     with open(file) as f:
-                        if text:
-                            for line in f:
-                                out.write(line)
-                        else:
-                            shutil.copyfileobj(f, out)
+                        shutil.copyfileobj(f, out)
                 except FileNotFoundError:
-                    if ignore_not_found:
-                        continue
-                    else:
-                        print(f"The file {str(file)!r} was not found."
-                              " Please check the file path and try again.",
-                              file=sys.stderr)
-                        raise
-                        return 1
+                    print(f"The file {str(file)!r} was not found."
+                          " Please check the file path and try again.",
+                          file=sys.stderr)
+                    return 1
                 except IOError as e:
                     print(f"IO Error while processing the file {str(file)!r}: {e}",
                           file=sys.stderr)
-                    raise
                     return 1
+
+            return 0
         except BaseException as e:
             print(f"An unexpected error occurred: {e}", file=sys.stderr)
-            raise
-        return 1
+            return 1
 
 
 def main(argv: Sequence[str]) -> int:
     parser = argparse.ArgumentParser(
         description="Concatenate inputs and write to an output file.")
 
-    parser.add_argument('--text', action='store_true',
-                        help='Operate on text inputs.')
-    parser.add_argument('--ignore-not-found', action='store_true',
-                        help='Treat non-existant inputs as empty.')
-
     parser.add_argument(
         'inputs',
         metavar='FILE',
@@ -92,7 +74,7 @@ def main(argv: Sequence[str]) -> int:
     )
 
     args = parser.parse_args(argv)
-    return cat(args.inputs, args.output, args.text, args.ignore_not_found)
+    return cat(args.inputs, args.output)
 
 
 def entry() -> None: