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bluepyemodel | ||
bluepyemodelnexus | ||
neuron |
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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 |
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import os | ||
from pathlib import Path | ||
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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 | ||
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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)) | ||
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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, | ||
) | ||
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def _get_nexus_access_point(etype, iteration_tag): | ||
return NexusAccessPoint( | ||
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"), | ||
) | ||
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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, | ||
} | ||
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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, | ||
) | ||
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@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()]} |