Add emodel_00

custom_analyses/src/emodel_00/requirements.in

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+bluepyemodel
+bluepyemodelnexus
+neuron

custom_analyses/src/emodel_00/requirements.txt

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+aiohttp==3.9.3
+aiosignal==1.3.1
+appnope==0.1.4
+asttokens==2.4.1
+async-timeout==4.0.3
+attrs==23.2.0
+bluepyefe==2.3.14
+bluepyemodel==0.0.83
+bluepyemodelnexus==0.0.7
+bluepyopt==1.14.10
+cachetools==5.3.2
+certifi==2024.2.2
+charset-normalizer==3.3.2
+click==8.1.7
+comm==0.2.1
+configparser==6.0.0
+contourpy==1.2.0
+currentscape==0.1.0
+cycler==0.12.1
+deap==1.4.1
+debugpy==1.8.1
+decorator==5.1.1
+deprecation==2.1.0
+devtools==0.12.2
+ecdsa==0.18.0
+efel==5.5.7
+elasticsearch==7.17.9
+elasticsearch-dsl==7.4.0
+entity-management==1.2.41
+entrypoints==0.4
+exceptiongroup==1.2.0
+executing==2.0.1
+fasteners==0.19
+find-libpython==0.3.1
+fonttools==4.48.1
+frozendict==2.4.0
+frozenlist==1.4.1
+gitdb==4.0.11
+GitPython==3.1.41
+h5py==3.10.0
+hjson==3.1.0
+ICSelector==0.0.3
+idna==3.6
+igor2==0.5.3
+ipykernel==6.29.2
+ipyparallel==8.6.1
+ipython==8.21.0
+isodate==0.6.1
+jedi==0.19.1
+Jinja2==3.1.3
+jupyter_client==8.6.0
+jupyter_core==5.7.1
+kiwisolver==1.4.5
+lxml==5.1.0
+MarkupSafe==2.1.5
+matplotlib==3.8.3
+matplotlib-inline==0.1.6
+more-itertools==10.2.0
+morph-tool==2.10.2
+MorphIO==3.3.7
+multidict==6.0.5
+neo==0.13.0
+nest-asyncio==1.6.0
+neurom==3.2.8
+NEURON==8.2.4
+nexus-sdk==0.3.2
+nexusforge==0.8.1
+numpy==1.26.4
+owlrl==5.2.3
+packaging==23.2
+palettable==3.3.3
+pandas==2.2.0
+parso==0.8.3
+Pebble==5.0.6
+pexpect==4.9.0
+pickleshare==0.7.5
+pillow==10.2.0
+platformdirs==4.2.0
+prettytable==2.5.0
+prompt-toolkit==3.0.43
+psutil==5.9.8
+ptyprocess==0.7.0
+pure-eval==0.2.2
+puremagic==1.20
+pyasn1==0.5.1
+Pygments==2.17.2
+PyJWT==2.8.0
+PyLD==2.0.3
+pyparsing==3.1.1
+pyshacl==0.17.2
+python-dateutil==2.8.2
+python-jose==3.3.0
+python-keycloak==3.8.4
+pytz==2024.1
+PyYAML==6.0.1
+pyzmq==25.1.2
+quantities==0.15.0
+rdflib==6.2.0
+requests==2.31.0
+requests-toolbelt==1.0.0
+rsa==4.9
+scipy==1.12.0
+six==1.16.0
+smmap==5.0.1
+SPARQLWrapper==2.0.0
+sseclient==0.0.27
+stack-data==0.6.3
+tornado==6.4
+tqdm==4.66.2
+traitlets==5.14.1
+typing_extensions==4.9.0
+tzdata==2024.1
+urllib3==1.26.18
+wcwidth==0.2.13
+xmltodict==0.13.0
+yarl==1.9.4

custom_analyses/src/emodel_00/run.py

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+import os
+from pathlib import Path
+
+from bluepyemodel.emodel_pipeline import plotting
+from bluepyemodel.evaluation import evaluation
+from bluepyemodelnexus.forge_access_point import NexusForgeAccessPoint
+from bluepyemodelnexus.nexus import NexusAccessPoint
+from common.utils import L, run_analysis
+
+
+def _debug_nexus_env():
+    keys = ["NEXUS_PROJ", "NEXUS_ORG", "NEXUS_BASE", "NEXUS_FORGE_PATH"]
+    L.info("Nexus env:\n%s", "\n".join(f"{k}={os.getenv(k, '')}" for k in keys))
+
+
+def _get_nexus_forge_access_point():
+    return NexusForgeAccessPoint(
+        project=os.getenv("NEXUS_PROJ"),
+        organisation=os.getenv("NEXUS_ORG"),
+        endpoint=os.getenv("NEXUS_BASE"),
+        access_token=os.getenv("NEXUS_TOKEN"),
+        forge_path=os.getenv("NEXUS_FORGE_PATH"),
+        cross_bucket=True,
+    )
+
+
+def _get_nexus_access_point(emodel, etype, iteration_tag):
+    return NexusAccessPoint(
+        emodel=emodel,
+        etype=etype,
+        iteration_tag=iteration_tag,
+        project=os.getenv("NEXUS_PROJ"),
+        organisation=os.getenv("NEXUS_ORG"),
+        endpoint=os.getenv("NEXUS_BASE"),
+        access_token=os.getenv("NEXUS_TOKEN"),
+        forge_path=os.getenv("NEXUS_FORGE_PATH"),
+    )
+
+
+def _get_metadata_from_id(emodel_id):
+    access_point = _get_nexus_forge_access_point()
+    resource = access_point.retrieve(emodel_id)
+    return {
+        "emodel": resource.emodel,
+        "etype": resource.etype,
+        "iteration": resource.iteration,
+    }
+
+
+def _get_recording_names(access_point, cell_evaluator):
+    return plotting.get_recording_names(
+        protocol_config=access_point.get_fitness_calculator_configuration().protocols,
+        stimuli=cell_evaluator.fitness_protocols["main_protocol"].protocols,
+    )
+
+
+@run_analysis
+def main(analysis_config: dict) -> dict:
+    _debug_nexus_env()
+    L.info("analysis_config:\n%s", analysis_config)
+    metadata = _get_metadata_from_id(analysis_config["emodel_id"])
+    access_point = _get_nexus_access_point(
+        emodel=metadata["emodel"],
+        etype=metadata["etype"],
+        iteration_tag=metadata["iteration"],
+    )
+    emodel = access_point.get_emodel()
+    cell_evaluator = evaluation.get_evaluator_from_access_point(
+        access_point,
+        stochasticity=False,
+        include_validation_protocols=False,
+    )
+    L.info("cell_evaluator:\n%s", cell_evaluator)
+    recording_names = _get_recording_names(access_point, cell_evaluator)
+    responses = cell_evaluator.run_protocols(
+        protocols=cell_evaluator.fitness_protocols.values(),
+        param_values=emodel.parameters,
+    )
+    figures_dir = Path(analysis_config["output"]) / "figures"
+    plotting.traces(
+        model=emodel,
+        responses=responses,
+        recording_names=recording_names,
+        figures_dir=figures_dir,
+    )
+    return {"outputs": [{"path": str(f)} for f in figures_dir.iterdir() if f.is_file()]}