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Fix: Load mod files after compile #20

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merged 2 commits into from
Dec 7, 2023
Merged

Fix: Load mod files after compile #20

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ddee324
Fix: Load mod files after compile
arnaudon Dec 7, 2023
da3f48d
lint
arnaudon Dec 7, 2023
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13 changes: 0 additions & 13 deletions emodel_generalisation/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,23 +22,10 @@
# pylint: disable=line-too-long
import logging
import os
from pathlib import Path

os.environ["NEURON_MODULE_OPTIONS"] = "-nogui"
logger = logging.getLogger(__name__)

_TMPDIR = os.environ.get("TMPDIR", None)
if _TMPDIR is not None:
try:
import neuron

if (Path(_TMPDIR) / "x86_64").exists():
if not neuron.load_mechanisms(_TMPDIR):
raise Exception("Could not load mod files")
except Exception as exc: # pylint: disable=broad-exception-caught
logger.debug("Could not load mod files from %s because of %s", _TMPDIR, exc)
os.environ["DASK_TEMPORARY_DIRECTORY"] = _TMPDIR


PARAM_LABELS = {
# passive
Expand Down
16 changes: 16 additions & 0 deletions emodel_generalisation/model/nexus_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from copy import copy
from pathlib import Path

import neuron
from tqdm import tqdm

L = logging.getLogger(__name__)
Expand Down Expand Up @@ -197,6 +198,19 @@ def convert_all_config(config_path, out_config_folder="config", mech_path="mecha
json.dump(final, final_file, indent=4)


def load_mechanisms():
"""Load mechanisms if present in TMPDIR."""
_TMPDIR = os.environ.get("TMPDIR", None)
if _TMPDIR is not None:
try:
if (Path(_TMPDIR) / "x86_64").exists():
if not neuron.load_mechanisms(_TMPDIR):
raise Exception("Could not load mod files")
except Exception as exc: # pylint: disable=broad-exception-caught
L.debug("Could not load mod files from %s because of %s", _TMPDIR, exc)
os.environ["DASK_TEMPORARY_DIRECTORY"] = _TMPDIR


def compile_mechanisms(mech_path="mechanisms", compiled_mech_path=None):
"""Compile mechanisms in custom location."""
if compiled_mech_path is None:
Expand All @@ -208,3 +222,5 @@ def compile_mechanisms(mech_path="mechanisms", compiled_mech_path=None):
os.chdir(compiled_mech_path)
subprocess.run(f"nrnivmodl {mech_path}", shell=True, check=True)
os.chdir(cwd)
# load mechs after compile
load_mechanisms()