Prepare napari-curvealign for merge and fix ROI mode-switch desync

[Phil-Dua]

Closes #29 , #38

Summary

• Align napari-curvealign with the current source-based workflow by removing legacy Docker paths, restoring the secure two-lane CI (test-basic + test-curvelab), and keeping CurveLab setup via .github/ci_setup_curvelab.sh.
• Restore plugin runtime dependencies and install paths for segmentation (cellpose + cellcast) so Cellpose/StarDist workflows work out of the box via the segmentation extra.
• Stabilize ROI editing behavior by fixing a shape-layer sync regression where previously drawn ROIs could disappear from the canvas when switching drawing tools even though they remained in the ROI list.
• Make headless testing safer (_tkinter import removal, conditional Agg backend under offscreen runs), and document curvelet and strict MATLAB parity test controls.

Plugin capabilities (current state)

• Interactive ROI creation/editing in napari (rectangle, ellipse, polygon, freehand) with ROI list management and annotation typing.
• Segmentation-assisted ROI generation from Cellpose/StarDist (via Cellcast) with analysis pipeline integration.
• Curvelet-based and CT-FIRE analysis hooks with export flows across multiple ROI formats.
• Per-image ROI scoping and overlay-assisted review in the napari dock workflow.

Review and test instructions

• Install base + segmentation runtime:
  • uv sync --extra segmentation
• Full local setup (CurveLab + FFTW + optional extras):
  • bash bin/install.sh
• Run default suite (headless):
  • QT_QPA_PLATFORM=offscreen make test
• Run curvelet-dependent tests:
  • TMEQ_RUN_CURVELETS=1 QT_QPA_PLATFORM=offscreen uv run pytest -q tests/test_get_ct.py tests/test_new_curv.py tests/test_process_image.py -rs
• Run strict MATLAB-reference parity assertions:
  • TMEQ_VALIDATE_MATLAB=1

Notes on MATLAB parity tests

• Strict MATLAB-reference assertions are opt-in via TMEQ_VALIDATE_MATLAB=1 so regular plugin validation and CI can remain reliable while preserving parity checks for dedicated calibration runs.
• No algorithmic behavior for strict checks was removed; the flag only controls when exact historical-reference assertions are enforced.

[elevans]

@Phil-Dua I pulled your branch and ran pytest in my tme-quant environment which was created via the new merged instructions. On Ubuntu 25.10 I get this error:

___________________________________ TestStarDistFormat.test_save_stardist_format ___________________________________

self = <test_roi_formats.TestStarDistFormat object at 0x7064db33dbd0>
roi_manager = <napari_curvealign.roi_manager.ROIManager object at 0x7064dacdf1d0>
sample_rois = [ROI(id=0, name='test_rect', shape=<ROIShape.RECTANGLE: 'Rectangle'>, coordinates=array([[10., 10.],
       [30., 30.]...age_label': 'test_image', 'stardist_compatible': True}, annotation_type='organelle', source_object_ids=[], metrics={})]
tmp_path = PosixPath('/tmp/pytest-of-edward/pytest-0/test_save_stardist_format0')

    def test_save_stardist_format(self, roi_manager, sample_rois, tmp_path):
        """Test saving ROIs in StarDist format."""
        output_path = tmp_path / "stardist_test.zip"
    
        # Save all ROIs (delegates to Fiji format)
        roi_manager.save_rois_stardist(str(output_path))
    
        # Check that file was created
>       assert output_path.exists()
E       AssertionError: assert False
E        +  where False = exists()
E        +    where exists = PosixPath('/tmp/pytest-of-edward/pytest-0/test_save_stardist_format0/stardist_test.zip').exists                                                                                                            

tests/test_roi_formats.py:199: AssertionError

Can you replicate this failure? Did you test on Windows too? I didn't dive into this but my guess is some OS specific path shenanigans at play.

[elevans]

Ahh woops I did not uv pip install -e . your latest version 🙃 . Tests look good. I'll continue with review!