Add tests

tests/conftest.py

@@ -24,6 +24,15 @@
 from tests.utils import DATA, cwd
 
 
+@pytest.fixture(scope="session")
+def nrnivmodl(tmp_path_factory):
+    """Compile the mechanisms only once per session."""
+    path = tmp_path_factory.mktemp("nrnivmodl_dir")
+    with cwd(path):
+        os.popen(f"nrnivmodl {DATA}/mechanisms").read()
+    return path
+
+
 @pytest.fixture
 def workspace(tmp_path):
     """Change the working directory to tmp_path.
@@ -35,7 +44,7 @@ def workspace(tmp_path):
 
 
 @pytest.fixture
-def emodel_dir(workspace):
+def emodel_dir(workspace, nrnivmodl):
     """Copy the required files to workspace/emodel."""
     dirs = ["config", "mechanisms", "morphology", "ephys_data"]
     files = ["final.json"]
@@ -44,6 +53,7 @@ def emodel_dir(workspace):
         shutil.copytree(DATA / name, dst / name)
     for name in files:
         shutil.copyfile(DATA / name, dst / name)
+    shutil.copytree(nrnivmodl / "x86_64", workspace / "x86_64")
     yield dst
 
 
@@ -72,7 +82,10 @@ def db_restart(emodel_dir):
 
 
 @pytest.fixture
-def evaluator(db, emodel_dir):
-    os.popen(f"nrnivmodl {emodel_dir}/mechanisms").read()
-    db.get_mechanisms_directory = lambda: None
-    return get_evaluator_from_access_point(access_point=db)
+def db_from_nexus(emodel_dir):
+    return get_access_point(
+        "local",
+        emodel="L5PC",
+        emodel_dir=emodel_dir,
+        recipes_path=emodel_dir / "config/recipes_nexus.json",
+    )

tests/functional_tests/test_protocols.py

@@ -20,13 +20,15 @@
 from numpy.testing import assert_allclose
 from pandas.testing import assert_frame_equal
 
+from bluepyemodel.evaluation.evaluation import get_evaluator_from_access_point
 
-def test_protocols(db, evaluator, tmp_path):
 
+def test_protocols(db, tmp_path):
     logging.basicConfig(level=logging.DEBUG)
     logging.getLogger().setLevel(logging.DEBUG)
 
     params = db.get_emodel().parameters
+    evaluator = get_evaluator_from_access_point(access_point=db)
 
     responses = evaluator.run_protocols(
         protocols=evaluator.fitness_protocols.values(), param_values=params

tests/functional_tests/test_protocols_from_nexus.py

@@ -0,0 +1,58 @@
+"""
+Copyright 2024, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+import logging
+
+import pandas as pd
+from numpy.testing import assert_allclose
+from pandas.testing import assert_frame_equal
+
+from bluepyemodel.evaluation.evaluation import get_evaluator_from_access_point
+
+
+def test_protocols(db_from_nexus, tmp_path):
+    logging.basicConfig(level=logging.DEBUG)
+    logging.getLogger().setLevel(logging.DEBUG)
+
+    params = db_from_nexus.get_emodel().parameters
+    evaluator = get_evaluator_from_access_point(access_point=db_from_nexus)
+
+    responses = evaluator.run_protocols(
+        protocols=evaluator.fitness_protocols.values(), param_values=params
+    )
+
+    # FIXME: remove print after clarifying the different result when executing the test alone
+    print(responses)
+    assert_allclose(responses["bpo_rmp"], -82.61402706564716, rtol=1e-06)
+    assert_allclose(responses["bpo_holding_current"], -0.05, rtol=1e-06)
+    assert_allclose(responses["bpo_rin"], 41.13626022273351, rtol=1e-06)
+    assert_allclose(responses["bpo_threshold_current"], 0.3757011543411314, rtol=1e-06)
+
+    for prot_name in [
+        "APWaveform_280.soma.v",
+        "IDrest_150.soma.v",
+        "IDrest_250.soma.v",
+        "IV_-100.soma.v",
+        "RinProtocol.soma.v",
+        "RMPProtocol.soma.v",
+        "SearchHoldingCurrent.soma.v",
+        "SearchThresholdCurrent.soma.v",
+    ]:
+        output_path = f"{tmp_path}/test_{prot_name}.csv"
+        responses[prot_name].response.to_csv(output_path, index=False)
+        expected_df = pd.read_csv(output_path)
+        response = responses[prot_name].response
+        assert_frame_equal(response, expected_df)

tests/functional_tests/test_validation.py

@@ -57,4 +57,4 @@ def test_validation(db):
     )
 
     assert len(emodels) == 1
-    assert emodels[0].passed_validation
+    assert emodels[0].passed_validation is True

tests/functional_tests/test_validation_from_nexus.py

@@ -0,0 +1,70 @@
+"""
+Copyright 2024, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+import logging
+
+from bluepyemodel.validation.validation import define_validation_function, validate
+
+
+def _always_true_validation(model, threshold=5.0, validation_protocols_only=False):
+    return True
+
+
+def test_define_validation_function(db_from_nexus):
+
+    model = {
+        "scores": {"a": 0.0, "b": 4.9, "c": 0.5, "d": 9.9},
+        "scores_validation": {"c": 0.5, "d": 9.9},
+    }
+
+    db_from_nexus.pipeline_settings.validation_function = _always_true_validation
+
+    validation_function = define_validation_function(db_from_nexus)
+
+    validated = bool(
+        validation_function(
+            model,
+            db_from_nexus.pipeline_settings.validation_threshold,
+            False,
+        )
+    )
+
+    assert validated
+
+
+def test_validation(db_from_nexus):
+
+    logging.basicConfig(level=logging.DEBUG)
+    logging.getLogger().setLevel(logging.DEBUG)
+
+    def _get_final_content(lock_file=True):
+        # enforce validated to None to ensure that the validation is run
+        result = get_final_content(lock_file=lock_file)
+        for key, value in result.items():
+            assert "validated" in value
+            value["validated"] = None
+        return result
+
+    get_final_content = db_from_nexus.get_final_content
+    db_from_nexus.get_final_content = _get_final_content
+    db_from_nexus.get_mechanisms_directory = lambda: None
+    emodels = validate(
+        access_point=db_from_nexus,
+        mapper=map,
+    )
+
+    assert len(emodels) == 1
+    assert emodels[0].passed_validation is True