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Set PEtab benchmark collection path via $BENCHMARK_COLLECTION (#2236)
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More convenient to use locally. Avoids having multiple copies of the PEtab benchmark collection lying around for different projects.
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dweindl authored Dec 13, 2023
1 parent 9e26037 commit eba9557
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions tests/benchmark-models/test_petab_benchmark.py
Original file line number Diff line number Diff line change
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"""Tests for simulate_petab on PEtab benchmark problems."""

import os
from pathlib import Path

import amici
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ATOL: float = 1e-3
RTOL: float = 1e-2

benchmark_path = (
Path(__file__).parent.parent.parent
/ "Benchmark-Models-PEtab"
/ "Benchmark-Models"
)
repo_root = Path(__file__).parent.parent.parent
benchmark_path = repo_root / "Benchmark-Models-PEtab" / "Benchmark-Models"
if not benchmark_path.exists():
benchmark_path = Path(os.environ["BENCHMARK_COLLECTION"])

# reuse compiled models from test_benchmark_collection.sh
benchmark_outdir = Path(__file__).parent.parent.parent / "test_bmc"
benchmark_outdir = repo_root / "test_bmc"
models = [
str(petab_path.stem)
for petab_path in benchmark_path.glob("*")
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