Fix Windows virtual workspace path separator issue

[trissim]

Problem

Windows CI tests were failing with two separate issues:

Issue 1: Virtual workspace path separator mismatch

The virtual workspace mapping keys were being created with backslashes on Windows, causing "No wells found for processing" errors.

Root Cause: When building the workspace_mapping dictionary, the code used str(Path(...)) which converts to backslashes on Windows:

• Windows: 'Images\\r01c01f007p001-ch1sk1fk1fl1.tiff'
• Linux: 'Images/r01c01f007p001-ch1sk1fk1fl1.tiff'

The mapping lookup code normalizes incoming paths to forward slashes with .replace('\\', '/'), but the mapping keys themselves had backslashes on Windows, causing all lookups to fail.

Issue 2: Atomic file write failure on Windows

After fixing issue 1, tests failed with:

[WinError 183] Cannot create a file when that file already exists:
'.tmpopenhcs_metadata.json0g40hqyz.json' -> 'openhcs_metadata.json'

Root Cause: os.rename() fails on Windows when the destination file already exists. The code needs to use os.replace() which atomically replaces the destination on both Unix and Windows.

Solution

Fix 1: Use .as_posix() for virtual workspace mapping keys

Ensure forward slashes on all platforms:

OperaPhenix (openhcs/microscopes/opera_phenix.py):

# Before
virtual_relative = str(Path("Images") / new_name)
real_relative = str(Path("Images") / file_name)

# After
virtual_relative = (Path("Images") / new_name).as_posix()
real_relative = (Path("Images") / file_name).as_posix()

ImageXpress (openhcs/microscopes/imagexpress.py):

# Before
virtual_relative = str(directory.relative_to(plate_path) / new_filename)
real_relative = str(Path(img_file).relative_to(plate_path))

# After
virtual_relative = (directory.relative_to(plate_path) / new_filename).as_posix()
real_relative = Path(img_file).relative_to(plate_path).as_posix()

Fix 2: Use os.replace() for atomic file writes

atomic.py (openhcs/io/atomic.py):

# Before
os.rename(tmp_path, str(file_path))

# After
os.replace(tmp_path, str(file_path))  # Atomic on both Unix and Windows

Testing

This PR will trigger Windows CI to verify both fixes work on Windows. The mapping keys should now be stored with forward slashes in the JSON file, and atomic file writes should work correctly in multiprocessing mode.

Files Changed

• openhcs/microscopes/opera_phenix.py - Use .as_posix() for mapping keys
• openhcs/microscopes/imagexpress.py - Use .as_posix() for mapping keys
• openhcs/io/atomic.py - Use os.replace() instead of os.rename()