Add test coverage for multi-channel writing and fix bounding box bug

[Copilot]

Codecov reported 33% patch coverage with 6 uncovered lines in the multi-channel writing feature (n_channels parameter and channel axis handling).

Changes

• Added tests for n_channels parameter in CellMapDatasetWriter covering automatic channel axis addition and deduplication when axis already exists
• Added tests for channel axis detection in ImageWriter covering automatic detection from shape, explicit specification, and no-op when unnecessary
• Added tests for CellMapDataset.empty() verifying has_data and _sampling_box_shape initialization
• Fixed bug in ImageWriter.__init__: bounding_box now correctly includes channel dimension {"c": [0, n_channels]} when channel axis is detected or specified
• Fixed scale assignment: prepended channel axis now uses 1.0 (unitless) instead of copying first spatial scale

Example

# Channel axis automatically detected and bounding_box updated
writer = ImageWriter(
    path="output.zarr",
    target_class="predictions",
    scale=(4.0, 4.0, 4.0),
    write_voxel_shape=(3, 32, 32, 32),  # 4D: channels + spatial
    axis_order="zyx",                    # 3D spatial only
    bounding_box={"z": [0, 256], "y": [0, 256], "x": [0, 256]},
)
# Now: axes="czyx", bounding_box includes "c": [0, 3]

Coverage Impact

• dataset_writer.py: 33% → 57%
• image_writer.py: 47% → 75%
• dataset.py: 29% → 76%

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[Copilot]

Pull request overview

This PR adds test coverage for multi-channel writing features and fixes two critical bugs in ImageWriter: incorrect bounding_box handling for channel dimensions and incorrect scale assignment for channel axes. The changes improve code coverage from 33% to 57% for dataset_writer.py, 47% to 75% for image_writer.py, and 29% to 76% for dataset.py.

Changes:

• Added tests for automatic channel axis detection and deduplication in ImageWriter and CellMapDatasetWriter
• Added tests for CellMapDataset.empty() method initialization
• Fixed ImageWriter to correctly add channel dimension to bounding_box when channel axis is detected
• Fixed scale assignment to use 1.0 (unitless) for channel axis instead of copying first spatial scale

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 6 comments.

File	Description
tests/test_empty_image_writer.py	Added three tests for channel axis detection scenarios: automatic detection, explicit specification, and no-op when dimensions match
tests/test_dataset_writer.py	Added two tests for n_channels parameter: automatic channel axis addition and deduplication when axis already exists
tests/test_cellmap_dataset.py	Added two tests verifying CellMapDataset.empty() correctly initializes has_data and _sampling_box_shape
src/cellmap_data/image_writer.py	Fixed bounding_box to include channel dimension and scale to use 1.0 for channel axis; added tracking variable for channel axis addition

[codecov]

Codecov Report

❌ Patch coverage is 11.86441% with 52 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.77%. Comparing base (42f2cec) to head (25aa8a4).
⚠️ Report is 9 commits behind head on multi_channel_writing.

Files with missing lines	Patch %	Lines
src/cellmap_data/utils/view.py	0.00%	51 Missing ⚠️
src/cellmap_data/image_writer.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@                    Coverage Diff                    @@
##           multi_channel_writing      #57      +/-   ##
=========================================================
+ Coverage                  60.48%   68.77%   +8.29%     
=========================================================
  Files                         27       27              
  Lines                       2528     2527       -1     
=========================================================
+ Hits                        1529     1738     +209     
+ Misses                       999      789     -210     

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