refactor: extract inline Python from 5 modules to module binaries (P1/P2 sweep) - #151

Merged

heylf merged 14 commits into

nf-core:devfrom

an-altosian:feature/inline-python-sweep

May 4, 2026

Commits on Apr 30, 2026

docs(base.config): explain errorStrategy exit codes
an-altosian
committed
style(modules.config): replace findAll().join(' ') with join(' ').trim() for STARDIST ext.args
an-altosian
committed
chore: remove orphan modules/local/utility/Dockerfile
an-altosian
committed
feat(schema): add format validators (directory-path, file-path) to schema_input.json
an-altosian
committed
fix(xenium_patch/stitch): thread baysor_tiling_min_transcripts_per_cell via ext.args
an-altosian
committed
refactor(segger): extract create_dataset orchestration to module binary
an-altosian
committed
refactor(segger): extract predict orchestration to module binary
an-altosian
committed
refactor(utility/convert_mask_uint32): extract dtype conversion to module binary
an-altosian
committed
refactor(utility/extract_dapi): extract DAPI channel slicing to module binary
an-altosian
committed
refactor(utility/downscale_morphology): extract image downscaling to module binary
an-altosian
committed
refactor(utility/upscale_mask): extract mask upscaling to module binary
an-altosian
committed
refactor(xenium_patch/stitch): extract postprocess cleanup to module binary
an-altosian
committed
revert(schema): drop format validators on bundle/image — incompatible with tar.gz test data
an-altosian
committed
chore(segger): drop versions.yml heredocs from create_dataset and predict
an-altosian
committed