shell: defaults param, fix 3 rendering bugs, add bedtools example#1062
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shell.create now accepts `defaults={name: value}` — per-input fallback
values applied when the caller omits an input. Works independently of
`T | None`: required + no default raises, optional + no default suppresses
the flag, either + default uses the default.
Three rendering bugs surfaced while building a bedtools intersect wrapper:
1. Positional-arg indices >= 10 were emitted as bare `$10`, which bash
parses as `$1` followed by literal "0". Any task with 10+ scalar/bool
inputs had its 10..N values silently corrupted. Fixed by always braced
`${10}`.
2. Optional File / Dir flags emitted unconditionally — the renderer
hardcoded `-flag /var/inputs/name` regardless of whether the caller
supplied the file, so omitting an optional file flag pointed the tool
at a missing path. Now guarded with
`if [ -e <path> ]; then ...; else <flag>=""; fi`.
3. Inputs whose names differed only in case (e.g. `c` vs `C`, common in
bio CLIs like bedtools / samtools) collided on the same `_VAL_*` /
`_FLAG_*` bash variable and silently overwrote each other. create()
now rejects this at declaration time with an error naming both
offending inputs.
Adds 28 unit tests across the four-cell defaults matrix, optional
File/Dir flag emission, case-collision detection, and the positional-arg
brace regression.
New examples:
- examples/shell/12_bedtools_intersect_example.py — three intersect
queries in parallel against a small BED fixture.
- examples/shell/modules/bedtools_intersect.py — typed wrapper around
bedtools intersect; reference for bio-CLI shell-extra modules.
Signed-off-by: Kyle Hazen <kyle@union.ai>
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> Signed-off-by: Samhita Alla <aallasamhita@gmail.com>
samhita-alla
added a commit
that referenced
this pull request
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> (cherry picked from commit f53a8bc)
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Stacked on top of #1055 — depends on the shell extra introduced there.
Summary
defaults={...}parameter onshell.create()— per-input fallback values applied when the caller omits an input, independent ofT | None(which controls flag suppression).bedtools intersectwrapper:$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}.-flag /var/inputs/nameregardless of whether the caller supplied the file. Now guarded withif [ -e <path> ]; then …; else <flag>=""; fi.cvsC, common in bio CLIs) collided on the same_VAL_*/_FLAG_*bash variable and silently overwrote each other.create()now rejects this at declaration time.examples/shell/12_bedtools_intersect_example.py+examples/shell/modules/bedtools_intersect.pydemonstrating a wider-flag-surface bedtools wrapper as a reference. This should probably just go in your plugins but leaving for your reference.Test plan