__skimindex_stamping.sh

Exposes the Python stamp API as shell functions (prefixed ski_). They map boolean returns to POSIX exit codes (True → 0, False → 1), so they work directly in if statements.

Pass --help to any function to see the full argument reference:

ski_needs_run --help

Functions

Function	Description
ski_stamp <path>	Mark path as successfully completed
ski_is_stamped <path>	Return 0 if path has a stamp
ski_unstamp <path>	Remove the stamp (force re-run)
ski_remove_if_not_stamped <path>	Delete path if it has no stamp
ski_needs_run <path> [sources…] [--dry-run] [--label L] [--action A]	Three-way branch: already done / dry-run / must run
ski_newer_than_stamp <path> <stamped>	Return 0 if path is newer than the stamp of stamped
ski_unstamp_if_newer <path> [sources…]	Invalidate stamp when a dependency changes
ski_stamp_gz <path>	Verify gzip integrity then stamp

Example

OUTPUT_DIR="/processed_data/Human/split"

if ski_needs_run "$OUTPUT_DIR" "$INPUT_FILE" \
        --label "human:split" --action "split sequences"; then
    ski_remove_if_not_stamped "$OUTPUT_DIR"
    mkdir -p "$OUTPUT_DIR"

    # … do the work …

    ski_stamp "$OUTPUT_DIR"
fi