CLI reference

Every command prints human-readable output by default, accepts --json for machine output, and exits 0 when there are no errors and 1 otherwise.

markinp validate

Validate one or more .inp files.

markinp validate FILE.inp [FILE.inp ...] [options]

Option	Meaning
--groups N	Assert the expected number of groups
--occasions N	Assert the expected history length
--covariates N	Assert the expected covariate count
--data-type TYPE	Hint the data type (live_recapture, closed_captures, occupancy, known_fate, dead_recovery, multistrata)
--strict	Treat warnings as errors
--json	Emit machine-readable JSON

With several files, --json emits an array of per-file objects. The command exits non-zero if any file has an error, so it works in CI and pre-commit.

markinp validate data/*.inp --strict

markinp inspect

Summarise the inferred structure of a file (read-only).

markinp inspect FILE.inp [--json]

Reports occasions, groups, covariates, number of records, number of individuals (sum of the absolute frequencies), and a data-type guess.

markinp build

Build a valid, deterministic .inp from a tidy CSV.

markinp build INPUT.csv -o OUTPUT.inp [options]

Option	Meaning
--format long\|wide	Layout (default: auto-detect)
--id-col NAME	Individual id column (long format)
--occasion-col NAME	Occasion column (long format)
--detect-col NAME	0/1 detection column (long format)
--history-col NAME	Prebuilt history column (wide alternative)
--group-col NAME	Column defining groups
--covariate-cols A,B,...	Comma-separated covariate columns
--comment-col NAME	Column written as /* value */ per record
--data-type TYPE	live_recapture (default) or occupancy
--collapse / --no-collapse	Aggregate identical histories (default: on)
--json	Emit a build report

build validates its own output and refuses to write a file that would not pass validate.

Long format

One row per (individual × occasion):

id,occasion,detected,sex,weight
A1,1,1,M,10.2
A1,2,0,M,10.2
A1,3,1,M,10.2

markinp build captures.csv -o out.inp \
    --id-col id --occasion-col occasion --detect-col detected \
    --group-col sex --covariate-cols weight

Wide format

One row per individual, with occasion columns (or a prebuilt history column):

id,o1,o2,o3,sex,weight
A1,1,0,1,M,10.2

markinp build captures.csv -o out.inp --format wide \
    --group-col sex --covariate-cols weight

Occupancy format

For occupancy / detection-history data, pass --data-type occupancy. A blank or NA detection cell is written as . (not surveyed) instead of 0, so a missing survey is never mistaken for a non-detection:

site,survey,detected,elev
A,1,1,120
A,2,0,120
A,3,,120      # not surveyed -> '.'

markinp build sites.csv -o out.inp --data-type occupancy \
    --id-col site --occasion-col survey --detect-col detected \
    --covariate-cols elev
# site A -> history "10."

Use as a library

The CLI is a thin wrapper; everything is importable:

from markinp import parse_text, validate

result = parse_text("1001 1;\n0101 2;\n")
for diag in validate(result.dataset):
    print(diag.code, diag.message)