Command-line interface¶

Installing PyMixEF creates the pymixef command. Use pymixef --help or pymixef COMMAND --help for the installed-version synopsis.

Global options¶

pymixef --version
pymixef --help

Inspect capabilities¶

pymixef capabilities
pymixef capabilities --json

The text view is intended for people. The JSON view is the automation contract for capability name, maturity, implemented state, evidence, limitations, and open gates.

Export traceability¶

pymixef traceability > traceability.json

This prints the requirement-to-implementation/specification/test/evidence matrix as JSON.

Explain a model¶

pymixef explain \
  "change ~ baseline + treatment * visit + (1 | subject)" \
  --data analysis.csv \
  --family gaussian \
  --engine lmm \
  --method reml

--data is optional for syntax/capability inspection but required for data-dependent design details. Options:

Argument	Meaning
`formula`	quoted PyMixEF formula
`--data PATH`	CSV input
`--family NAME`	response family
`--engine NAME`	backend selection
`--method NAME`	ML, REML, or Laplace as compatible

CLI family names include Gaussian/normal, Bernoulli, binomial, Poisson, NB1, NB2, gamma, and beta. Family recognition does not override backend compatibility; an unavailable combination is refused.

Fit a CSV model¶

pymixef fit \
  "change ~ baseline + treatment * visit + (1 | subject)" \
  --data analysis.csv \
  --family gaussian \
  --engine lmm \
  --method reml \
  --maxiter 1000 \
  --tolerance 1e-10 \
  --output result.json

Required arguments are formula, --data, and --output. Numerical controls are forwarded only to a compatible engine. The output is the same portable FitResult JSON contract used by FitResult.save.

By default a numerically suspect completed fit exits with code 4. --allow-warning changes that case to code 0; it does not erase warnings from the result.

Create and verify a validation bundle¶

pymixef bundle result.json --output validation-bundle
pymixef verify-bundle validation-bundle

bundle loads an existing result and creates deterministic evidence files. verify-bundle checks the manifest and internal hashes.

Parse an NM-TRAN control stream¶

pymixef parse-nonmem model.ctl --output parsed-records.json

The command preserves the documented record subset and writes a compatibility report. Structural $PK, $DES, and $ERROR code is not executed.

Exit codes¶

Code	Meaning
`0`	command completed under its success contract
`2`	fit failed
`3`	NM-TRAN parse found unsupported constructs
`4`	fit returned but is numerically suspect; use result warnings/convergence for detail

Argument parsing errors also follow the command parser’s standard nonzero behavior.

Shell automation¶

Prefer JSON output for capabilities, traceability, fitted results, and parsed interchange reports. Do not parse human summaries when a structured contract is available. Preserve the command, environment, input hash, exit code, and output artifact together.

The implementation reference is pymixef.cli.