Add httomo version comment to pipeline file copied to output dir

Author: yousefmoazzam

httomo/cli.py

@@ -1,7 +1,6 @@
 from contextlib import AbstractContextManager, nullcontext
 from datetime import datetime
 from pathlib import Path, PurePath
-from shutil import copy
 import sys
 import tempfile
 from typing import List, Optional, TextIO, Union, Any
@@ -340,7 +339,11 @@ def initialise_output_directory(pipeline: Union[Path, str]) -> None:
 
     # If pipeline is a file path, copy it to output directory
     if isinstance(pipeline, Path):
-        copy(pipeline, httomo.globals.run_out_dir)
+        with open(pipeline, "r") as input:
+            pipeline_contents = input.read()
+        with open(Path(httomo.globals.run_out_dir) / pipeline.name, "a") as output:
+            output.write(f"# Created with HTTomo version {__version__}\n")
+            output.write(pipeline_contents)
     # If pipeline is a JSON string, write it to a file in the output directory
     else:
         with open(httomo.globals.run_out_dir / "pipeline.json", "w") as f:

tests/test_cli.py

@@ -192,27 +192,25 @@ def test_initialise_output_directory_handles_json_string(tmp_path):
     assert written_content == json_string
 
 
-def test_initialise_output_directory_handles_path_input(mocker, tmp_path):
+def test_initialise_output_directory_handles_path_input(
+    mocker, tmp_path, standard_loader: str
+):
     """Test that initialise_output_directory correctly handles Path input (existing behavior)."""
     from httomo.cli import initialise_output_directory
 
     # Set up the global output directory
     output_dir = tmp_path / "output"
     httomo.globals.run_out_dir = output_dir
-
-    # Mock copy to avoid actual file operations
-    mock_copy = mocker.patch("httomo.cli.copy")
-
-    pipeline_path = Path("some/pipeline.yaml")
+    pipeline_path = Path(__file__).parent.parent / standard_loader
 
     # Call the function with a Path
     initialise_output_directory(pipeline_path)
 
     # Verify directory was created
     assert output_dir.exists()
 
-    # Verify that copy was called for the file
-    mock_copy.assert_called_once_with(pipeline_path, output_dir)
+    # Verify that pipeline file was copied to output dir
+    assert (output_dir / pipeline_path.name).exists()
 
 
 @pytest.mark.cupy