Fix tests, refactor pywake_api, and clean up test infrastructure

- Add test cleanup fixtures and output_dir management (conftest.py)
- Simplify foxes engine handling and fix test compatibility
- Split run_pywake into focused helper functions
- Add foxes turbine-based data test with density support
- Fix wayve test performance (510s to 6s)
- Pin numpy<2.0 for wayve compatibility (np.trapz removal)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: bjarketol

examples/cases/KUL_LES/wind_energy_system/analysis_US.yaml

@@ -64,7 +64,7 @@ HPC_config:
   mesh_node_number: 2
   mesh_ntasks_per_node: 48
   mesh_wall_time_hours: 1
-  run_partition: ""
+  mesh_partition: ""
   #
   wckey: ""
 

pyproject.toml

@@ -43,6 +43,7 @@ dependencies = [
     "windIO @ git+https://github.com/EUFlow/windIO.git",
     "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve@dev_foxes",
     "floris @ git+https://github.com/lejeunemax/floris.git@windIO",
+    "numpy<2.0",
     "xarray>=2022.0.0,<2025",
     "mpmath",
 ]

tests/conftest.py

@@ -1,4 +1,110 @@
+"""
+Pytest configuration and fixtures for WIFA tests.
+
+Provides:
+- Pre-test cleanup of leftover output directories
+- Output directory fixtures with conditional cleanup (preserved on failure)
+"""
+
+import shutil
+from pathlib import Path
+
 import numpy as np
+import pytest
+
+# Store test outcomes for conditional cleanup
+_test_outcomes = {}
+
+
+@pytest.hookimpl(hookwrapper=True)
+def pytest_runtest_makereport(item, call):
+    """Track test outcomes to conditionally preserve output on failure."""
+    outcome = yield
+    report = outcome.get_result()
+    if report.failed:
+        _test_outcomes[item.nodeid] = True
+
+
+def pytest_configure(config):
+    """Register custom markers."""
+    config.addinivalue_line(
+        "markers", "slow: marks tests as slow (deselect with '-m \"not slow\"')"
+    )
+
+
+@pytest.fixture(scope="session", autouse=True)
+def cleanup_old_outputs():
+    """Remove test output directories from previous test runs at session start."""
+    patterns = [
+        "output_pywake_*",
+        "output_test_*",
+    ]
+    for pattern in patterns:
+        for path in Path(".").glob(pattern):
+            if path.is_dir():
+                shutil.rmtree(path)
+            elif path.is_file():
+                path.unlink()
+    yield
+
+
+@pytest.fixture
+def output_dir(request, tmp_path):
+    """
+    Provide a unique temporary output directory for tests.
+
+    Cleans up automatically on test success, preserves on failure for debugging.
+    """
+    yield tmp_path
+
+    # Only clean up if test passed
+    test_failed = _test_outcomes.get(request.node.nodeid, False)
+    if not test_failed:
+        if tmp_path.exists():
+            shutil.rmtree(tmp_path)
+
+
+@pytest.fixture
+def named_output_dir(request):
+    """
+    Provide a named output directory based on test name.
+
+    Use this when tests need output in the current working directory
+    (e.g., for Code Saturne integration).
+
+    Cleans up automatically on test success, preserves on failure.
+    """
+    test_name = request.node.name.replace("[", "_").replace("]", "_").rstrip("_")
+    output_path = Path(f"output_test_{test_name}")
+    output_path.mkdir(parents=True, exist_ok=True)
+
+    yield output_path
+
+    # Only clean up if test passed
+    test_failed = _test_outcomes.get(request.node.nodeid, False)
+    if not test_failed:
+        if output_path.exists():
+            shutil.rmtree(output_path)
+
+
+@pytest.fixture
+def cleanup_output_dir(request):
+    """
+    Cleanup fixture for tests that write to the default 'output/' directory.
+
+    Use this when tests can't control their output location (e.g., when YAML
+    specifies output_folder). Only cleans up directories created during the test.
+    """
+    output_path = Path("output")
+    existed_before = output_path.exists()
+
+    yield output_path
+
+    # Only clean up if test passed and the directory was created by the test
+    test_failed = _test_outcomes.get(request.node.nodeid, False)
+    if not test_failed and not existed_before:
+        if output_path.exists():
+            shutil.rmtree(output_path)
 
 # DTU 10MW turbine data
 # (from examples/cases/windio_4turbines/plant_energy_turbine/DTU_10MW_turbine.yaml)

tests/test_cs.py

@@ -11,51 +11,46 @@
 
 
 def _run_cs(wes_dir, output_dir):
+    """Run Code Saturne on all system* files in the given directory."""
     i = 1
     for yaml_input in wes_dir.glob("system*"):
         print("\nRUNNING CODE_SATURNE ON", yaml_input, "\n")
         validate_yaml(yaml_input, Path("plant/wind_energy_system"))
+        # Pass subdirectory path - run_code_saturne will create it
+        sub_output_dir = output_dir / f"run_{i}"
         run_code_saturne(
             yaml_input,
             test_mode=False,
-            output_dir="output_test_" + output_dir + "_" + str(i),
+            output_dir=str(sub_output_dir),
         )
         i += 1
 
 
-def test_cs_KUL():
+def test_cs_KUL(output_dir):
     wes_dir = test_path / "../examples/cases/KUL_LES/wind_energy_system/"
-    _run_cs(wes_dir, "KUL")
+    _run_cs(wes_dir, output_dir)
 
 
-def test_cs_4wts():
+def test_cs_4wts(output_dir):
     wes_dir = test_path / "../examples/cases/windio_4turbines/wind_energy_system/"
-    _run_cs(wes_dir, "4wts")
+    _run_cs(wes_dir, output_dir)
 
 
-def test_cs_abl():
+def test_cs_abl(output_dir):
     wes_dir = test_path / "../examples/cases/windio_4turbines_ABL/wind_energy_system/"
-    _run_cs(wes_dir, "abl")
+    _run_cs(wes_dir, output_dir)
 
 
-def test_cs_abl_stable():
+def test_cs_abl_stable(output_dir):
     wes_dir = (
         test_path / "../examples/cases/windio_4turbines_ABL_stable/wind_energy_system/"
     )
-    _run_cs(wes_dir, "abl_stable")
+    _run_cs(wes_dir, output_dir)
 
 
-def test_cs_profiles():
+def test_cs_profiles(output_dir):
     wes_dir = (
         test_path
         / "../examples/cases/windio_4turbines_profiles_stable/wind_energy_system/"
     )
-    _run_cs(wes_dir, "profiles")
-
-
-if __name__ == "__main__":
-    test_cs_KUL()
-    test_cs_4wts()
-    test_cs_abl()
-    test_cs_abl_stable()
-    test_cs_profiles()
+    _run_cs(wes_dir, output_dir)

tests/test_foxes.py

@@ -12,112 +12,93 @@
 windIO_path = Path(wiop[0])
 
 
-def _run_foxes(wes_dir):
+def _run_foxes(wes_dir, output_dir):
+    """Run FOXES on all system.yaml files in the given directory."""
     assert wes_dir.is_dir(), f"{wes_dir} is not a directory"
 
     for yaml_input in wes_dir.glob("system.yaml"):
         print("\nRUNNING FOXES ON", yaml_input, "\n")
         validate_yaml(yaml_input, Path("plant/wind_energy_system"))
-        output_dir_name = Path("output_test_foxes")
-        output_dir_name.mkdir(parents=True, exist_ok=True)
-        run_foxes(yaml_input, output_dir=output_dir_name)
-        rmtree(output_dir_name)
+        run_foxes(yaml_input, output_dir=output_dir)
 
 
-def test_foxes_KUL():
+def test_foxes_KUL(output_dir):
     wes_dir = test_path / "../examples/cases/KUL_LES/wind_energy_system/"
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_4wts():
+def test_foxes_4wts(output_dir):
     wes_dir = test_path / "../examples/cases/windio_4turbines/wind_energy_system/"
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_abl():
+def test_foxes_abl(output_dir):
     wes_dir = test_path / "../examples/cases/windio_4turbines_ABL/wind_energy_system/"
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_abl_stable():
+def test_foxes_abl_stable(output_dir):
     wes_dir = (
         test_path / "../examples/cases/windio_4turbines_ABL_stable/wind_energy_system/"
     )
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_profiles():
+def test_foxes_profiles(output_dir):
     wes_dir = (
         test_path
         / "../examples/cases/windio_4turbines_profiles_stable/wind_energy_system/"
     )
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_heterogeneous_wind_rose_at_turbines():
+def test_foxes_heterogeneous_wind_rose_at_turbines(output_dir):
     wes_dir = (
         test_path
         / "../examples/cases/heterogeneous_wind_rose_at_turbines/wind_energy_system/"
     )
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_heterogeneous_wind_rose_map():
+def test_foxes_heterogeneous_wind_rose_map(output_dir):
     wes_dir = (
         test_path / "../examples/cases/heterogeneous_wind_rose_map/wind_energy_system/"
     )
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_simple_wind_rose():
+def test_foxes_simple_wind_rose(output_dir):
     wes_dir = test_path / "../examples/cases/simple_wind_rose/wind_energy_system/"
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_foxes_timeseries_with_operating_flag():
+def test_foxes_timeseries_with_operating_flag(output_dir):
     wes_dir = (
         test_path
         / "../examples/cases/timeseries_with_operating_flag/wind_energy_system/"
     )
-    _run_foxes(wes_dir)
+    _run_foxes(wes_dir, output_dir)
 
 
-def test_timeseries_per_turbine_with_density(tmp_path=Path(".")):
+def test_timeseries_per_turbine_with_density(output_dir):
     import foxes.variables as FV
     from conftest import make_timeseries_per_turbine_system_dict
 
     # Run with density
     system_dict = make_timeseries_per_turbine_system_dict("foxes")
-    output_dir = tmp_path / "output_foxes_ts"
-    farm_results = run_foxes(system_dict, verbosity=0, output_dir=str(output_dir))[0]
+    out_with = output_dir / "output_foxes_ts"
+    farm_results = run_foxes(system_dict, verbosity=0, output_dir=str(out_with))[0]
     farmP_with = farm_results[FV.P].sum()
-    # print("Farm power with density:", farmP_with)
     assert np.isfinite(farmP_with) and farmP_with > 0
 
     # Run without density — same config but density removed
     system_dict_no = make_timeseries_per_turbine_system_dict("foxes")
     del system_dict_no["site"]["energy_resource"]["wind_resource"]["density"]
-    output_dir_no = tmp_path / "output_foxes_ts_no_density"
+    out_without = output_dir / "output_foxes_ts_no_density"
     farm_results_no = run_foxes(
-        system_dict_no, verbosity=0, output_dir=str(output_dir_no)
+        system_dict_no, verbosity=0, output_dir=str(out_without)
     )[0]
     farmP_without = farm_results_no[FV.P].sum()
-    # print("Farm power without density:", farmP_without)
-
-    rmtree(output_dir)
-    rmtree(output_dir_no)
 
     # Density correction should change AEP (test data varies around 1.225)
     assert farmP_with != farmP_without
-
-
-if __name__ == "__main__":
-    test_foxes_KUL()
-    test_foxes_4wts()
-    test_foxes_abl()
-    test_foxes_abl_stable()
-    test_foxes_profiles()
-    test_foxes_heterogeneous_wind_rose_at_turbines()
-    test_foxes_heterogeneous_wind_rose_map()
-    test_foxes_simple_wind_rose()
-    test_timeseries_per_turbine_with_density()