From e54067aa73f5c6390a3b7b9cad563bee1a1c6d51 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Mon, 24 Nov 2025 10:06:21 +0100
Subject: [PATCH] Fix regeneration of expected results hdf5

* Restore deleted data file
* Update to changed locations and names
---
 tests/cpp/generate_expected_results.py        |  52 ++++++++++--------
 .../example_jakstat_adjoint.py                |   7 +--
 ...ple_jakstat_adjoint_pnas_data_original.xls | Bin 0 -> 21504 bytes
 .../generateTestConfig/example_steadystate.py |   2 +-
 4 files changed, 33 insertions(+), 28 deletions(-)
 create mode 100644 tests/generateTestConfig/example_jakstat_adjoint_pnas_data_original.xls

diff --git a/tests/cpp/generate_expected_results.py b/tests/cpp/generate_expected_results.py
index a155a455c5..e5cef3a1a3 100755
--- a/tests/cpp/generate_expected_results.py
+++ b/tests/cpp/generate_expected_results.py
@@ -1,17 +1,23 @@
 #!/usr/bin/env python3
-"""Generate HDF5 file with expected results for the C++ tests."""
+"""
+Generate HDF5 file with expected results for the C++ tests.
+
+Delete `tests/cpp/expected_results_py.h5` and re-run this script to
+regenerate the expected results.
+Check the diff carefully before committing!
+"""
 
 import subprocess
 from pathlib import Path
 
 import amici
 import h5py
-from amici import (
-    readModelDataFromHDF5,
-    readSimulationExpData,
-    readSolverSettingsFromHDF5,
-    runAmiciSimulation,
-    writeReturnData,
+from amici.sim.sundials import (
+    read_exp_data_from_hdf5,
+    read_model_data_from_hdf5,
+    read_solver_settings_from_hdf5,
+    run_simulation,
+    write_return_data_to_hdf5,
 )
 from amici.testing.models import (
     import_model_calvetti,
@@ -28,7 +34,7 @@
 outfile = Path(__file__).parent / "expected_results_py.h5"
 
 
-def handle_model(id_: str, model: amici.Model):
+def handle_model(id_: str, model: amici.sim.sundials.Model):
     # write model settings to h5
     script = repo_root / "tests" / "generateTestConfig" / f"example_{id_}.py"
     subprocess.run([script, str(outfile)])
@@ -42,36 +48,36 @@ def handle_model(id_: str, model: amici.Model):
     for case in cases:
         # create a new model instance for each case, to ensure no interference
         model = model.module.get_model()
-        readModelDataFromHDF5(
-            str(outfile), model.get(), f"/model_{id_}/{case}/options"
-        )
-        solver = model.getSolver()
-        readSolverSettingsFromHDF5(
-            str(outfile), solver, f"/model_{id_}/{case}/options"
-        )
+        options_path = f"/model_{id_}/{case}/options"
+        data_path = f"/model_{id_}/{case}/data"
+        result_path = f"/model_{id_}/{case}/results"
+
+        read_model_data_from_hdf5(str(outfile), model.get(), options_path)
+        solver = model.create_solver()
+        read_solver_settings_from_hdf5(str(outfile), solver, options_path)
         # read ExpData if data/ exists
         try:
-            edata = readSimulationExpData(
-                str(outfile), f"/model_{id_}/{case}/data", model.get()
+            edata = read_exp_data_from_hdf5(
+                str(outfile), data_path, model.get()
             )
         except RuntimeError:
             edata = None
 
-        rdata = runAmiciSimulation(model, solver, edata)
-        writeReturnData(
-            rdata._swigptr.get(), str(outfile), f"/model_{id_}/{case}/results"
+        rdata = run_simulation(model, solver, edata)
+        write_return_data_to_hdf5(
+            rdata._swigptr.get(), str(outfile), result_path
         )
 
 
 def main():
     """Generate expected results for the C++ tests."""
+    handle_model("calvetti", import_model_calvetti())
     handle_model("dirac", import_model_dirac())
     handle_model("events", import_model_events())
-    handle_model("neuron", import_model_neuron())
-    handle_model("calvetti", import_model_calvetti())
-    handle_model("robertson", import_model_robertson())
     handle_model("jakstat_adjoint", import_model_jakstat())
     handle_model("nested_events", import_model_nested_events())
+    handle_model("neuron", import_model_neuron())
+    handle_model("robertson", import_model_robertson())
     handle_model("steadystate", import_model_steadystate())
 
 
diff --git a/tests/generateTestConfig/example_jakstat_adjoint.py b/tests/generateTestConfig/example_jakstat_adjoint.py
index 75ce991a14..01bdb4722f 100755
--- a/tests/generateTestConfig/example_jakstat_adjoint.py
+++ b/tests/generateTestConfig/example_jakstat_adjoint.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
-import os
 import sys
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -16,10 +16,9 @@ def __init__(self):
         self.numP = 17
         self.numK = 2
 
-        curPath = os.path.dirname(os.path.realpath(__file__))
         dataPath = (
-            curPath
-            + "/../../matlab/examples/example_jakstat_adjoint/pnas_data_original.xls"
+            Path(__file__).parent
+            / "example_jakstat_adjoint_pnas_data_original.xls"
         )
         xls = pd.ExcelFile(dataPath).parse()
         self.modelOptions["ts"] = xls.time
diff --git a/tests/generateTestConfig/example_jakstat_adjoint_pnas_data_original.xls b/tests/generateTestConfig/example_jakstat_adjoint_pnas_data_original.xls
new file mode 100644
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diff --git a/tests/generateTestConfig/example_steadystate.py b/tests/generateTestConfig/example_steadystate.py
index 70d1c9b476..0f5e01208e 100755
--- a/tests/generateTestConfig/example_steadystate.py
+++ b/tests/generateTestConfig/example_steadystate.py
@@ -2,7 +2,7 @@
 import sys
 
 import numpy as np
-from amici import (
+from amici.sim.sundials import (
     SensitivityOrder,
     SteadyStateComputationMode,
     SteadyStateSensitivityMode,