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| """Installed command-line interface for FlowPK workflows.""" | |
| from __future__ import annotations | |
| import argparse | |
| import sys | |
| from importlib import import_module | |
| from pathlib import Path | |
| from typing import Sequence | |
| from pff_pk.training.runtime import bootstrap | |
| _COMMANDS = { | |
| "run": "pff_pk.pipeline.experiment", | |
| "train": "pff_pk.pipeline.train", | |
| "posttrain": "pff_pk.pipeline.curriculum", | |
| "consolidate": "pff_pk.pipeline.consolidate", | |
| } | |
| _EVALUATION_COMMANDS = { | |
| "annotate-lenuzza-censoring": "pff_pk.commands.annotate_lenuzza_censoring", | |
| "sample-generation": "pff_pk.commands.generate_empirical_samples", | |
| "plot-trajectories": "pff_pk.commands.plot_empirical_trajectories_from_samples", | |
| "plot-vpc": "pff_pk.commands.plot_empirical_vpc_from_samples", | |
| "plot-tsne": "pff_pk.commands.plot_empirical_tsne", | |
| "evaluate-generation": "pff_pk.commands.compare_generation_models", | |
| "evaluate-validation": "pff_pk.commands.evaluate_validation_bank", | |
| "evaluate-vpc": "pff_pk.commands.evaluate_pharmpy_vpc", | |
| "upload-vpc": "pff_pk.commands.upload_vpc_artifacts", | |
| "upload-empirical": "pff_pk.commands.upload_empirical_artifacts", | |
| } | |
| def build_parser() -> argparse.ArgumentParser: | |
| parser = argparse.ArgumentParser( | |
| prog="pff-pk", | |
| description="Train, sample, evaluate, plot, and publish FlowPK runs.", | |
| ) | |
| parser.add_argument( | |
| "command", | |
| choices=(*_COMMANDS, *_EVALUATION_COMMANDS), | |
| help="workflow to run", | |
| ) | |
| parser.add_argument("arguments", nargs=argparse.REMAINDER) | |
| return parser | |
| def main(argv: Sequence[str] | None = None) -> None: | |
| args = build_parser().parse_args(argv) | |
| bootstrap(Path.cwd()) | |
| if args.command in _COMMANDS: | |
| module = import_module(_COMMANDS[args.command]) | |
| module.main(args.arguments) | |
| return | |
| module = import_module(_EVALUATION_COMMANDS[args.command]) | |
| previous = sys.argv | |
| try: | |
| sys.argv = [f"pff-pk {args.command}", *args.arguments] | |
| module.main() | |
| finally: | |
| sys.argv = previous | |
| if __name__ == "__main__": | |
| main() | |