fix: quick-export Excel race without overwrite

CHANGELOG.md

@@ -17,6 +17,7 @@ All notable changes are recorded here. The project follows semantic versioning a
 - Validated run-wide diffraction and discovery settings before copying local inputs, contacting providers, or starting GUI workers.
 - Snapshotted GUI run options on the Tk thread so background workers do not access mutable Tk state.
 - Required explicit overwrite authorization for existing quick-export workbooks and replaced authorized workbooks atomically.
+- Preserved workbooks created by another process during quick export when overwrite was not authorized.
 - Rechecked bundle and benchmark targets immediately before commit so files created during a long-running calculation are not silently replaced.
 - Rejected malformed or non-finite provider elasticity matrices instead of truncating oversized arrays to 6×6.
 - Applied Materials Project stability thresholds before server-side result limits, with strict local verification so qualifying candidates are not lost to post-filtering.

src/diffractscout/quick_export.py

@@ -7,6 +7,7 @@
 from __future__ import annotations
 
 import argparse
+import os
 import shutil
 import sys
 import tempfile
@@ -53,7 +54,18 @@ def _copy_excel_atomic(source: Path, target: Path, *, overwrite: bool) -> None:
             temporary_name = handle.name
         temporary = Path(temporary_name)
         shutil.copy2(source, temporary)
-        temporary.replace(target)
+        if overwrite:
+            temporary.replace(target)
+        else:
+            try:
+                # Publish the completed file atomically without replacing a
+                # target created after the preflight check.
+                os.link(temporary, target)
+            except FileExistsError as exc:
+                raise FileExistsError(
+                    f"Excel output was created while exporting: {target}. "
+                    "The new file was preserved; rerun with overwrite=True only if intended."
+                ) from exc
     finally:
         if temporary_name:
             Path(temporary_name).unlink(missing_ok=True)

tests/test_quick_export.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+import shutil
 
 import pytest
 from openpyxl import load_workbook
@@ -7,7 +8,7 @@
 from diffractscout.models import AnalysisSettings
 from diffractscout.pipeline import analyze_cifs
 from diffractscout.quick_export import main as quick_export_main
-from diffractscout.quick_export import quick_export
+from diffractscout.quick_export import _copy_excel_atomic, quick_export
 from diffractscout.validation import verify_bundle
 
 
@@ -37,6 +38,29 @@ def test_quick_export_does_not_replace_existing_excel_without_authorization(
     assert not (tmp_path / "existing_bundle").exists()
 
 
+def test_atomic_excel_copy_preserves_target_created_during_export(
+    tmp_path: Path, monkeypatch
+) -> None:
+    source = tmp_path / "source.xlsx"
+    target = tmp_path / "result.xlsx"
+    source.write_bytes(b"completed-workbook")
+
+    real_copy2 = shutil.copy2
+
+    def racing_copy(source_path: Path, temporary_path: Path) -> Path:
+        copied = real_copy2(source_path, temporary_path)
+        target.write_bytes(b"external-file")
+        return copied
+
+    monkeypatch.setattr("diffractscout.quick_export.shutil.copy2", racing_copy)
+
+    with pytest.raises(FileExistsError, match="created while exporting"):
+        _copy_excel_atomic(source, target, overwrite=False)
+
+    assert target.read_bytes() == b"external-file"
+    assert not list(tmp_path.glob(".result.xlsx.*.tmp"))
+
+
 def test_quick_export_can_atomically_replace_existing_excel_when_authorized(
     demo_inputs: Path, tmp_path: Path
 ) -> None: