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Convert priors in benchmark problems to measurements
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Add a script to replace all objectivePriors in the PEtab benchmark problems
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dweindl committed Oct 24, 2024
1 parent aec9456 commit 2bf4949
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5 changes: 3 additions & 2 deletions .github/workflows/benchmark_models.yml
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Expand Up @@ -64,11 +64,12 @@ jobs:
BM_REPO_URL: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git
run: |
cd $PARPE_BASE/benchmark_collection \
&& git clone --depth 1 $BM_REPO_URL
&& git clone --depth 1 $BM_REPO_URL \
&& echo "export BENCHMARK_COLLECTION=$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" >> $GITHUB_ENV
- name: Benchmark models --- tests
run: |
cd $PARPE_BASE/benchmark_collection \
&& $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./priors_to_measurements.py
&& AMICI_PARALLEL_COMPILE="" \
BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
$PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh
83 changes: 83 additions & 0 deletions benchmark_collection/priors_to_measurements.py
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#!/usr/bin/env python3
"""For all benchmark collection problems, convert objectivePriors to
measurements."""
import os
import sys
from pathlib import Path
from petab.v1 import (Problem, write_observable_df, write_measurement_df,
write_parameter_df)
from petab.v1.priors import priors_to_measurements
from petab.v1.yaml import load_yaml
from petab.v1.C import (MEASUREMENT_FILES, OBSERVABLE_FILES, PARAMETER_FILE,
PROBLEMS)


def get_problems_dir() -> Path:
"""Get the directory containing the benchmark collection problems."""
if len(sys.argv) == 2:
problems_dir = sys.argv[1]
elif "BENCHMARK_COLLECTION" in os.environ:
problems_dir = os.environ["BENCHMARK_COLLECTION"]
else:
print("Usage: prior_to_measurements.py <benchmark_collection_dir>")
sys.exit(1)

problems_dir = Path(problems_dir)
if not problems_dir.is_dir():
print(f"Directory {problems_dir} does not exist.")
sys.exit(1)

return problems_dir


def save_problem(yaml_path: Path, petab_problem: Problem):
"""Save the updated PEtab problem."""
# only meausrements, observables, and parameters are changed
config = load_yaml(yaml_path)
assert len(config[PROBLEMS]) == 1
problem_config = config[PROBLEMS][0]
assert len(problem_config[MEASUREMENT_FILES]) == 1
assert len(problem_config[OBSERVABLE_FILES]) == 1
parameter_file = yaml_path.parent / config[PARAMETER_FILE]
measurement_file = yaml_path.parent / problem_config[MEASUREMENT_FILES][0]
observable_file = yaml_path.parent / problem_config[OBSERVABLE_FILES][0]
# back up the original files
parameter_file.rename(parameter_file.with_suffix(".tsv.bak"))
measurement_file.rename(measurement_file.with_suffix(".tsv.bak"))
observable_file.rename(observable_file.with_suffix(".tsv.bak"))
# write the updated files
write_parameter_df(petab_problem.parameter_df, parameter_file)
write_observable_df(petab_problem.observable_df, observable_file)
write_measurement_df(petab_problem.measurement_df, measurement_file)


def main():
problems_dir = get_problems_dir()

for problem_dir in sorted(problems_dir.iterdir()):
if not problem_dir.is_dir():
continue

problem_id = problem_dir.name
yaml_path = problem_dir / f"{problem_id}.yaml"

if not yaml_path.is_file():
continue
print(f"{problem_id}...")
petab_problem = Problem.from_yaml(yaml_path)
num_measurements_old = len(petab_problem.measurement_df)

try:
petab_problem = priors_to_measurements(petab_problem)
num_measurements_new = len(petab_problem.measurement_df)
if num_measurements_new != num_measurements_old:
print(f"\tConverting {problem_id}...")
save_problem(yaml_path, petab_problem)
else:
print(f"\tNothing to do for {problem_id}.")
except NotImplementedError as e:
print(f"\t{problem_id}: {e}")


if __name__ == "__main__":
main()

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