Enable running benchmark/sbml tests from repo root (#2807)

* Allow running benchmark tests from repo root

* rename benchmark models

* Update run-SBMLTestsuite.sh

* more path cleanup

* Update evaluate_benchmark.py

Author: FFroehlich

.github/workflows/test_benchmark_collection_models.yml

@@ -66,7 +66,7 @@ jobs:
       env:
         AMICI_PARALLEL_COMPILE: ""
       run: |
-        cd tests/benchmark-models && pytest test_petab_benchmark.py \
+        pytest tests/benchmark_models/test_petab_benchmark.py \
           --durations=10 \
           --cov=amici \
           --cov-report=xml:"coverage_py.xml" \
@@ -85,14 +85,14 @@ jobs:
     # collect & upload results
     - name: Aggregate results
       run: |
-          cd tests/benchmark-models && python3 evaluate_benchmark.py
+          python3 tests/benchmark_models/evaluate_benchmark.py
 
     - uses: actions/upload-artifact@v4
       with:
         name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
         path: |
-          tests/benchmark-models/computation_times.csv
-          tests/benchmark-models/computation_times.png
+          tests/benchmark_models/computation_times.csv
+          tests/benchmark_models/computation_times.png
 
   jax:
     name: Benchmark Collection JAX
@@ -142,7 +142,7 @@ jobs:
       env:
         AMICI_PARALLEL_COMPILE: ""
       run: |
-        cd tests/benchmark-models && pytest test_petab_benchmark_jax.py \
+        pytest tests/benchmark_models/test_petab_benchmark_jax.py \
           --durations=10 \
           --cov=amici \
           --cov-report=xml:"coverage_py.xml" \

.gitignore

@@ -137,7 +137,7 @@ tests/sbml/sbml-test-suite/*
 tests/sbml/sbml-test-suite/
 */sbml-semantic-test-cases/*
 tests/sbml/SBMLTestModels/
-tests/benchmark-models/test_bmc
+tests/benchmark_models/test_bmc
 tests/petab_test_suite
 petab_test_suite
 */tests/BIOMD0000000529/*
@@ -193,6 +193,6 @@ Benchmark-Models-PEtab/
 CS_Signalling_ERBB_RAS_AKT/
 cache_fiddy/*
 debug/*
-tests/benchmark-models/cache_fiddy/*
+tests/benchmark_models/cache_fiddy/*
 venv/*
 .coverage

doc/AGENTS.md

@@ -48,16 +48,15 @@ source ./venv/bin/activate
 
 This project uses `pre-commit` for linting and `pytest` for tests. Run them on changed files whenever you make modifications.
 
-When running the tests locally, change into the test directory first:
+When running the tests locally, invoke `pytest` from the repository root:
 
 ```bash
-cd tests/benchmark-models
-pytest test_petab_benchmark.py
-pytest test_petab_benchmark_jax.py
+pytest tests/benchmark_models/test_petab_benchmark.py
+pytest tests/benchmark_models/test_petab_benchmark_jax.py
 ```
 
 To quickly verify the benchmark tests, you can limit execution to a small model:
 
 ```bash
-pytest -k Boehm_JProteomeRes2014 test_petab_benchmark.py
+pytest tests/benchmark_models/test_petab_benchmark.py -k Boehm_JProteomeRes2014
 ```

scripts/run-SBMLTestsuite.sh

@@ -10,7 +10,6 @@ if [[ ! -d "tests/sbml/sbml-test-suite" ]]; then
 fi
 
 source venv/bin/activate
-export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}."
 pip show pytest-xdist > /dev/null 2>&1 || pip install pytest-xdist
 pip install coverage pytest-cov
 

tests/README.md

@@ -7,4 +7,4 @@ This directory contains:
   interface (`sbml/`)
 - Scripts for running the PEtab test suite, exercising the Python interface (`petab_test_suite/`)
 - Scripts for testing AMICI performance for importing a somewhat larger model (`performance/`)
-- Scripts for running the PEtab benchmark suite, exercising the Python interface (`benchmark-models/`)
+- Scripts for running the PEtab benchmark suite, exercising the Python interface (`benchmark_models/`)

tests/benchmark-models/benchmark_models.yaml renamed to tests/benchmark_models/benchmark_models.yaml

@@ -1,5 +1,6 @@
 import copy
 from pathlib import Path
+import sys
 
 import pytest
 import petab.v1 as petab
@@ -8,9 +9,12 @@
 import benchmark_models_petab
 from amici.petab.petab_import import import_petab_problem
 
+script_dir = Path(__file__).parent.resolve()
+if str(script_dir) not in sys.path:
+    sys.path.insert(0, str(script_dir))
+
 from test_petab_benchmark import problems
 
-script_dir = Path(__file__).parent
 repo_root = script_dir.parent.parent
 benchmark_outdir = repo_root / "test_bmc"
 

tests/benchmark-models/conftest.py renamed to tests/benchmark_models/conftest.py

@@ -9,16 +9,19 @@
 import matplotlib.pyplot as plt
 import pandas as pd
 import seaborn as sns
+from pathlib import Path
 
 # read benchmark results for different models
 
+benchmark_dir = Path(__file__).parent.resolve()
+
 outfile = "computation_times.csv"
 df = pd.concat(
     [
-        pd.read_csv(f, header=[0], index_col=[0])
+        pd.read_csv(benchmark_dir / f, header=[0], index_col=[0])
         .rename(columns={"0": "_".join(f.split("_")[:2])})
         .T
-        for f in os.listdir()
+        for f in os.listdir(benchmark_dir)
         if f.endswith(".csv")
         if f != outfile
     ]

tests/benchmark-models/evaluate_benchmark.py renamed to tests/benchmark_models/evaluate_benchmark.py

@@ -12,11 +12,11 @@
 from amici.jax.petab import run_simulations, JAXProblem
 from amici.petab.petab_import import import_petab_problem
 from amici.petab.simulations import simulate_petab, LLH, SLLH
-import test_petab_benchmark as common
-
-settings = common.settings
-problems_for_gradient_check = common.problems_for_gradient_check
-benchmark_outdir = common.benchmark_outdir
+from test_petab_benchmark import (
+    benchmark_outdir,
+    problems_for_gradient_check,
+    settings,
+)
 
 jax.config.update("jax_enable_x64", True)