feat: updated Nextflow workflows with profiles, auto-assess, rehoming#102
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FIrgolitsch wants to merge 4 commits intomainfrom
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feat: updated Nextflow workflows with profiles, auto-assess, rehoming#102FIrgolitsch wants to merge 4 commits intomainfrom
FIrgolitsch wants to merge 4 commits intomainfrom
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- Replace setup.py + requirements.txt with pyproject.toml (uv) - Add .pre-commit-config.yaml (ruff-format, ruff lint, ty advisory) - Update CI workflow to use uv + ruff + ty - Update Dockerfile for uv - Add uv.lock, linumpy/py.typed - Delete setup.py, requirements.txt, requirements-pytest.txt - Run ruff format on all Python files - Run ruff check --fix (341 auto-fixes applied)
…visualization New library modules: - linumpy/preproc/normalization.py, resampling.py - linumpy/utils/image_quality.py, orientation.py, visualization.py New scripts: - linum_fix_galvo_shift_zarr.py, linum_clean_raw_data.py - linum_compare_stitching.py, linum_extract_pyramid_levels.py - linum_normalize_z_intensity.py, linum_aip_png.py - linum_screenshot_omezarr_annotated.py, linum_generate_mosaic_aips.py Updated: preprocessing, stitching, registration, I/O, metrics modules Added tests for normalization, resampling, xyzcorr, orientation, visualization
New library modules: - linumpy/stitching/motor.py — motor-only stacking - linumpy/stitching/stacking.py — stacking improvements (confidence gating, z-consistency, drift limits) New scripts: - linum_stack_motor_only.py, linum_stack_slices_motor.py - linum_stitch_motor_only.py, linum_stitch_3d_refined.py - linum_auto_exclude_slices.py Updated scripts: - linum_stack_slices_3d.py, linum_stack_slices.py, linum_stitch_3d.py - linum_align_mosaics_3d_from_shifts.py Tests: test_stitching_motor.py, test_stitching_stacking.py
Updated workflows: - workflows/reconst_3d/soct_3d_reconst.nf — major expansion with auto-exclude, motor stacking, rehoming detection, MSE quality assessment, refined stitching - workflows/reconst_3d/nextflow.config — new profiles, parameter additions - workflows/preproc/preproc_rawtiles.nf — preprocessing improvements - workflows/preproc/nextflow.config — updated preprocessing config
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PR I — Nextflow Workflow Updates
Changes
workflows/reconst_3d/soct_3d_reconst.nf— Major expansion: auto-exclude slices, motor stacking, rehoming detection, MSE quality assessment, refined stitching, slice interpolation supportworkflows/reconst_3d/nextflow.config— New execution profiles, expanded parameters for all new featuresworkflows/preproc/preproc_rawtiles.nf— Preprocessing workflow improvementsworkflows/preproc/nextflow.config— Updated preprocessing configurationDependencies