Fixes - #196
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The cellposev4 segmentation component exists but was not listed in any run script, so it never ran. Add it to segmentation_methods alongside cellpose (active in the seqeracloud scripts, commented in the local/test scripts, matching the existing convention). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Promote gene_efficiency_correction from an expression-correction method to its own stage (methods_gene_efficiency_correction) that runs after expression correction, offering two options: no_correction (pass-through) and gene_efficiency_correction. - New API src/api/comp_method_gene_efficiency_correction.yaml (input and output on file_spatial_corrected_counts). - New components under methods_gene_efficiency_correction/; the moved gene_efficiency_correction now reads --input and preserves an upstream normalized_uncorrected layer. - Remove gene_efficiency_correction from methods_expression_correction. - run_benchmark: insert the gene_eff stage between expression correction and aggregate_spatial_data; it overwrites the output_correction state key so aggregate_spatial_data and the similarity metric need no rewiring and controls keep working. Add --gene_efficiency_correction_methods and alias the colliding no_correction dependency (gene_eff_no_correction). - Update run scripts' method lists for the new stage. Verified: viash config view, viash ns build (components + workflow, deps and alias resolve), and viash test on both new components (output spec-conformant). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
…tangram, resolvi) Cloud-only tune-method sweeps under scripts/run_benchmark/param_sweep/. Each sweeps only already-exposed config args so it runs against the build/main container with no rebuild. Params read at launch from the committed yaml via raw-GitHub URL. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Same cloud-only param_sweep/ convention; sweeps only already-exposed args so they run against build/main with no rebuild. (singler intentionally omitted: its only exposed knob celltype_key is dead code in script.py, so a sweep would be a no-op until a wiring fix + rebuild.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The celltype_key arg (from comp_method_cell_type_annotation.yaml, default cell_type) was declared but never used — script.py hardcoded the reference label column, so any celltype_key override was a no-op. Now it selects the reference obs column, enabling a granularity sweep (cell_type -> cell_type_level2/3/4). Backward-compatible: default is still cell_type. Verified with `viash test` (2/2 scripts pass). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Proposed changes are described in the CHANGELOG.md
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