Copy calibration_metadata.yml file to output directory instead of symlinking

src/xfel_calibrate/finalize.py

@@ -447,16 +447,16 @@ def finalize(joblist, finaljob, run_path, out_path, version, title, author, repo
     # Notebooks should have a karabo_id parameter, which we'll use to make a
     # unique name like calibration_metadata_MID_DET_AGIPD1M-1.yml in the output
     # folder. In case they don't, fall back to a name like the report.
-    # To replace any existing symlink, we create it in a temp folder & rename.
+    # To avoid interleaved writes, we'll copy it to a temp folder, then rename.
     det = metadata['calibration-configurations'].get('karabo-id', report_to.name)
     with TemporaryDirectory(dir=out_path) as td:
-        tlp = Path(td, f"calibration_metadata_{det}.yml")
-        tlp.symlink_to(md_path)
-        tlp.replace(out_path / f"calibration_metadata_{det}.yml")
+        tmp_path = Path(td, f"calibration_metadata_{det}.yml")
+        copy(md_path, tmp_path)
+        tmp_path.replace(out_path / f"calibration_metadata_{det}.yml")
 
         # For continuity, we'll also expose it as $out/calibration_metadata.yml.
         # This is only useful if there's 1 calibration run per output folder,
-        # otherwise the last one to create the link wins.
-        tlp = Path(td, f"calibration_metadata.yml")
-        tlp.symlink_to(md_path)
-        tlp.replace(out_path / "calibration_metadata.yml")
+        # otherwise the last one to create the file wins.
+        tmp_path = Path(td, f"calibration_metadata.yml")
+        copy(md_path, tmp_path)
+        tmp_path.replace(out_path / "calibration_metadata.yml")