add bio helper utility#1055
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kumare3
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May 13, 2026
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@samhita-alla some small fixes #1062 and adding a defaults={...} parameter on shell.create() |
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) Stacked on top of #1055 — depends on the shell extra introduced there. ## Summary - New `defaults={...}` parameter on `shell.create()` — per-input fallback values applied when the caller omits an input, independent of `T | None` (which controls flag suppression). - Three rendering bugs found while building a `bedtools intersect` wrapper: - Positional indices ≥ 10 emitted as bare `$10`; bash parses that as `$1` + literal `"0"`. Tasks with 10+ scalar/bool inputs had values 10..N silently corrupted. Fixed by always-braced `${10}`. - Optional File / Dir flags emitted unconditionally — the renderer hardcoded `-flag /var/inputs/name` regardless of whether the caller supplied the file. Now guarded with `if [ -e <path> ]; then …; else <flag>=""; fi`. - Inputs whose names differ only in case (e.g. `c` vs `C`, common in bio CLIs) collided on the same `_VAL_*`/`_FLAG_*` bash variable and silently overwrote each other. `create()` now rejects this at declaration time. - New `examples/shell/12_bedtools_intersect_example.py` + `examples/shell/modules/bedtools_intersect.py` demonstrating a wider-flag-surface bedtools wrapper as a reference. This should probably just go in your plugins but leaving for your reference. ## Test plan - [x] 146 unit tests pass (28 new across the four areas above) - [x] Local Docker run of the bedtools example produces correct output for \`wa\`, \`v\`, \`count_overlaps\` against a small BED fixture - [ ] Remote run against demo cluster (needs the dev wheel to land on the cluster) --------- Signed-off-by: Kyle Hazen <kyle@union.ai> Signed-off-by: Samhita Alla <aallasamhita@gmail.com> Co-authored-by: Samhita Alla <aallasamhita@gmail.com>
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samhita-alla
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May 13, 2026
) Stacked on top of #1055 — depends on the shell extra introduced there. ## Summary - New `defaults={...}` parameter on `shell.create()` — per-input fallback values applied when the caller omits an input, independent of `T | None` (which controls flag suppression). - Three rendering bugs found while building a `bedtools intersect` wrapper: - Positional indices ≥ 10 emitted as bare `$10`; bash parses that as `$1` + literal `"0"`. Tasks with 10+ scalar/bool inputs had values 10..N silently corrupted. Fixed by always-braced `${10}`. - Optional File / Dir flags emitted unconditionally — the renderer hardcoded `-flag /var/inputs/name` regardless of whether the caller supplied the file. Now guarded with `if [ -e <path> ]; then …; else <flag>=""; fi`. - Inputs whose names differ only in case (e.g. `c` vs `C`, common in bio CLIs) collided on the same `_VAL_*`/`_FLAG_*` bash variable and silently overwrote each other. `create()` now rejects this at declaration time. - New `examples/shell/12_bedtools_intersect_example.py` + `examples/shell/modules/bedtools_intersect.py` demonstrating a wider-flag-surface bedtools wrapper as a reference. This should probably just go in your plugins but leaving for your reference. ## Test plan - [x] 146 unit tests pass (28 new across the four areas above) - [x] Local Docker run of the bedtools example produces correct output for \`wa\`, \`v\`, \`count_overlaps\` against a small BED fixture - [ ] Remote run against demo cluster (needs the dev wheel to land on the cluster) --------- Signed-off-by: Kyle Hazen <kyle@union.ai> Signed-off-by: Samhita Alla <aallasamhita@gmail.com> Co-authored-by: Samhita Alla <aallasamhita@gmail.com> Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
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) Stacked on top of #1055 — depends on the shell extra introduced there. ## Summary - New `defaults={...}` parameter on `shell.create()` — per-input fallback values applied when the caller omits an input, independent of `T | None` (which controls flag suppression). - Three rendering bugs found while building a `bedtools intersect` wrapper: - Positional indices ≥ 10 emitted as bare `$10`; bash parses that as `$1` + literal `"0"`. Tasks with 10+ scalar/bool inputs had values 10..N silently corrupted. Fixed by always-braced `${10}`. - Optional File / Dir flags emitted unconditionally — the renderer hardcoded `-flag /var/inputs/name` regardless of whether the caller supplied the file. Now guarded with `if [ -e <path> ]; then …; else <flag>=""; fi`. - Inputs whose names differ only in case (e.g. `c` vs `C`, common in bio CLIs) collided on the same `_VAL_*`/`_FLAG_*` bash variable and silently overwrote each other. `create()` now rejects this at declaration time. - New `examples/shell/12_bedtools_intersect_example.py` + `examples/shell/modules/bedtools_intersect.py` demonstrating a wider-flag-surface bedtools wrapper as a reference. This should probably just go in your plugins but leaving for your reference. ## Test plan - [x] 146 unit tests pass (28 new across the four areas above) - [x] Local Docker run of the bedtools example produces correct output for \`wa\`, \`v\`, \`count_overlaps\` against a small BED fixture - [ ] Remote run against demo cluster (needs the dev wheel to land on the cluster) --------- Signed-off-by: Kyle Hazen <kyle@union.ai> Signed-off-by: Samhita Alla <aallasamhita@gmail.com> Co-authored-by: Samhita Alla <aallasamhita@gmail.com> (cherry picked from commit f53a8bc)
Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
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