Simple Cell Tuning with bmtool¶
This tutorial demonstrates how to perform parameter tuning on a simple cell model using bmtool's single cell analysis tools. We'll cover:
- Setup and Compilation: Importing libraries and compiling NEURON mechanisms
- Cell Model Definition: Creating a Python class-based cell model
- Parameter Modification: Changing cell parameters on-the-fly
- Simulation Re-running: Resetting and re-executing simulations efficiently
- Automated Tuning: Iteratively optimizing parameters to achieve target behavior
Part 1: Setup and Compilation¶
First, we import the necessary libraries and compile the NEURON MOD files. This section sets up the environment for single cell analysis.
In [1]:
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import os
import glob
import logging
import numpy as np
import matplotlib.pyplot as plt
from neuron import h
from bmtool.singlecell import (CurrentClamp,Profiler, run_and_plot)
%matplotlib inline
# Disable warnings for cleaner output
logging.disable(logging.WARNING)
import os
import glob
import logging
import numpy as np
import matplotlib.pyplot as plt
from neuron import h
from bmtool.singlecell import (CurrentClamp,Profiler, run_and_plot)
%matplotlib inline
# Disable warnings for cleaner output
logging.disable(logging.WARNING)
Warning: no DISPLAY environment variable. --No graphics will be displayed.
In [2]:
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# if already compiled then lets delete the folder and force a recompile
if os.path.isdir('modfiles/x86_64'):
os.system("rm -rf modfiles/x86_64")
if os.path.isdir('modfiles/arm64'):
os.system("rm -rf modfiles/arm64")
# compile the mod files
if not os.path.isdir("modfiles/x86_64"):
os.chdir('modfiles')
os.system("nrnivmodl")
os.chdir("..")
# if already compiled then lets delete the folder and force a recompile
if os.path.isdir('modfiles/x86_64'):
os.system("rm -rf modfiles/x86_64")
if os.path.isdir('modfiles/arm64'):
os.system("rm -rf modfiles/arm64")
# compile the mod files
if not os.path.isdir("modfiles/x86_64"):
os.chdir('modfiles')
os.system("nrnivmodl")
os.chdir("..")
/Users/gregglickert/miniconda3/envs/bmtk/bin/nrnivmodl:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import working_set
/usr/bin/xcrun /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles Mod files: "./AMPA_NMDA_STP.mod" "./CaDynamics.mod" "./Ca_HVA.mod" "./Ca_LVA.mod" "./GABA_A_STP.mod" "./Gfluct.mod" "./Ih.mod" "./Im.mod" "./Im_v2.mod" "./K_P.mod" "./K_T.mod" "./Kd.mod" "./Kv2like.mod" "./Kv3_1.mod" "./NaTa.mod" "./NaTs.mod" "./NaV.mod" "./Nap.mod" "./SK.mod" "./cadad.mod" "./cal2.mod" "./can_mig.mod" "./exp2syn_stp.mod" "./gap.mod" "./h_kole.mod" "./imCA3.mod" "./k.mod" "./kBK.mod" "./kap_BS.mod" "./kdmc_BS.mod" "./kdrCA3.mod" "./kdr_BS.mod" "./kdrinter.mod" "./leak.mod" "./na.mod" "./nainter.mod" "./napCA3.mod" "./natCA3.mod" "./nax_BS.mod" "./vecevent_coreneuron.mod" Creating 'arm64' directory for .o files. -> NMODL ../Ca_HVA.mod -> NMODL ../AMPA_NMDA_STP.mod -> Compiling mod_func.cpp -> NMODL ../CaDynamics.mod -> NMODL ../GABA_A_STP.mod -> NMODL ../Ca_LVA.mod -> NMODL ../Gfluct.mod -> NMODL ../Ih.mod -> NMODL ../Im.mod -> NMODL ../Im_v2.mod -> NMODL ../K_P.mod -> NMODL ../K_T.mod -> NMODL ../Kd.mod -> NMODL ../NaTa.mod -> NMODL ../Kv2like.mod -> NMODL ../Kv3_1.mod -> NMODL ../NaTs.mod -> NMODL ../NaV.mod -> NMODL ../Nap.mod -> NMODL ../SK.mod -> NMODL ../cadad.mod -> NMODL ../cal2.mod -> NMODL ../can_mig.mod -> NMODL ../exp2syn_stp.mod Warning: Default 2 of PARAMETER cao will be ignored and set by NEURON. Warning: Default 5e-05 of PARAMETER cai will be ignored and set by NEURON. Warning: Default 2 of PARAMETER cao will be ignored and set by NEURON. Warning: Default 5e-05 of PARAMETER cai will be ignored and set by NEURON. -> NMODL ../gap.mod -> NMODL ../h_kole.mod -> NMODL ../imCA3.mod -> NMODL ../k.mod Warning: Default 6.3 of PARAMETER celsius will be ignored and set by NEURON. -> NMODL ../kBK.mod -> NMODL ../kap_BS.mod -> NMODL ../kdmc_BS.mod -> NMODL ../kdrCA3.mod -> NMODL ../kdr_BS.mod -> NMODL ../kdrinter.mod -> NMODL ../leak.mod -> NMODL ../na.mod Warning: Default -80 of PARAMETER ek will be ignored and set by NEURON. Warning: Default 6.3 of PARAMETER celsius will be ignored and set by NEURON. -> NMODL ../nainter.mod -> NMODL ../napCA3.mod -> NMODL ../natCA3.mod -> NMODL ../nax_BS.mod Warning: Default 45 of PARAMETER ena will be ignored and set by NEURON. -> NMODL ../vecevent_coreneuron.mod -> Compiling AMPA_NMDA_STP.c -> Compiling CaDynamics.c -> Compiling Ca_HVA.c Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it only affects and is affected by discrete events. As such it is not located in a section and is not associated with an integrator -> Compiling Ca_LVA.c -> Compiling GABA_A_STP.c -> Compiling Gfluct.c -> Compiling Ih.c -> Compiling Im.c -> Compiling Im_v2.c -> Compiling K_P.c -> Compiling K_T.c -> Compiling Kd.c
Translating AMPA_NMDA_STP.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/AMPA_NMDA_STP.c
Translating Ca_HVA.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Ca_HVA.c
Translating CaDynamics.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/CaDynamics.c
Thread Safe
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Translating Ca_LVA.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Ca_LVA.c
Translating Gfluct.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Gfluct.c
Translating GABA_A_STP.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/GABA_A_STP.c
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Notice: This mechanism cannot be used with CVODE
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Translating Ih.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Ih.c
Translating Im.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Im.c
Translating Im_v2.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Im_v2.c
Thread Safe
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Translating K_P.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/K_P.c
Translating K_T.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/K_T.c
Translating Kd.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Kd.c
Thread Safe
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Translating Kv2like.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Kv2like.c
Translating Kv3_1.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Kv3_1.c
Translating NaTa.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/NaTa.c
Thread Safe
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Translating NaTs.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/NaTs.c
Translating NaV.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/NaV.c
Translating Nap.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/Nap.c
Thread Safe
Translating SK.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/SK.c
NEURON's CVode method ignores conservation
Notice: LINEAR is not thread safe.
Thread Safe
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Translating cal2.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/cal2.c
Translating can_mig.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/can_mig.c
Translating exp2syn_stp.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/exp2syn_stp.c
Translating cadad.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/cadad.c
Thread Safe
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Translating gap.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/gap.c
Translating h_kole.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/h_kole.c
Translating imCA3.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/imCA3.c
Thread Safe
Translating k.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/k.c
Thread Safe
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Thread Safe
Translating kBK.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kBK.c
Translating kdmc_BS.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kdmc_BS.c
Translating kap_BS.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kap_BS.c
Translating kdrCA3.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kdrCA3.c
Thread Safe
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Translating leak.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/leak.c
Translating kdrinter.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kdrinter.c
Translating na.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/na.c
Translating kdr_BS.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/kdr_BS.c
Thread Safe
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Translating nainter.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/nainter.c
Translating napCA3.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/napCA3.c
Thread Safe
Translating nax_BS.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/nax_BS.c
Thread Safe
Translating natCA3.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/natCA3.c
Thread Safe
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Translating vecevent_coreneuron.mod into /Users/gregglickert/Documents/GitHub/bmtool/docs/examples/notebooks/single_cell/modfiles/arm64/vecevent_coreneuron.c
Thread Safe
Ca_HVA.cAMPA_NMDA_STP.c::4342::18CaDynamics.c:42:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype] 42 | exter
18n: dwarning: oa function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]u
ble *getarg();
| ^
42 | extern double 43 | *g/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.he :ext15eta:r17g:( )note: ;expanded from macro 'getarg'
| ^
r n /Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.hd:o15u15b:l17 | #def: note: expanded from macro 'getarg'
e15ine ge t*getarg();
| a ^r
| g hoc_#g/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17d: note: expanded from macro 'getarg'
15 | #define getarg eefinheo targc
g _| ge ^teatarg hoc_rg
ge
t a| r ^
g
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: /Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.hconflicting prototype is here:49:16 :49 | note: econflicting prototype is herex
t
ern do u49 | ext49 | belxerent*ern do gdeutargo(uibnbt)l;el
e *| ^ *g geett
aarrg/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h(gint()i;n
t:15: 17: note: expanded from macro 'getarg'
| ^) ;
15 | #define getarg ho
c_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg | ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h: 15:17h:o cnote: _getargexpanded from macro 'getarg'
15 | #d
e fine getarg hoc_getarg
| | ^ ^
AMPA_NMDA_STP.c:414:32: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
414 | if (_tsav > t){ extern char* hoc_object_name(); hoc_execerror(hoc_object_name(_pnt->ob), ":Event arrived out of order. Must call ParallelContext.set_maxstep AFTER assigning minimum NetCon.delay");}
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:46:14: note: conflicting prototype is here
46 | extern char* hoc_object_name(Object*);
| ^
Ca_LVA.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
2 warnings generated.
Gfluct.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
GABA_A_STP.c:42:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
42 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
GABA_A_STP.c:356:32: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
356 | if (_tsav > t){ extern char* hoc_object_name(); hoc_execerror(hoc_object_name(_pnt->ob), ":Event arrived out of order. Must call ParallelContext.set_maxstep AFTER assigning minimum NetCon.delay");}
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:46:14: note: conflicting prototype is here
46 | extern char* hoc_object_name(Object*);
| ^
Ih.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
Im.c:43:18: warning: 43a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype] | extern doubl
e *getarg();
43 | | ^
extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_ge/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.ht:a15r:g17
: | note: ^expanded from macro 'getarg'
15
| #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern dou/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16b:le* getar note: conflicting prototype is here
49 | extern double* getarg(int)g;
| (int);
| ^
^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17:/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h :note: 15expanded from macro 'getarg':
17: note: expanded from macro 'getarg'
15 | #15d | e#fdienfei ngee tgaertga r gh o ch_ogce_tgaertga
r g|
^
| ^
1 warning generated.
2 warnings generated.
1 warning generated.
1 warning generated.
Im_v2.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
K_P.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
K_T.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
Kd.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
Kv3_1.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getargKv2like.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
| ^
43 | extern double *geta/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.hr:g49(:)16;:
note: | conflicting prototype is here ^
49 | extern double* getarg(/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.hi:n15t:)17;:
note: | expanded from macro 'getarg' ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | 15# | d#edfeifnien eg egteatragr g h ohco_cg_egteatragr
g
| ^|
^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
NaTs.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
NaTa.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
Nap.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
NaV.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
NaV.c:404:17: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
404 | extern double *_getelm();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/nrniv_mf.h:26:16: note: conflicting prototype is here
26 | extern double* _getelm(int, int);
| ^
SK.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
cadad.c:42:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
42 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
cal2.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
can_mig.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
exp2syn_stp.c:42:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
42 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
exp2syn_stp.c:343:32: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
343 | if (_tsav > t){ extern char* hoc_object_name(); hoc_execerror(hoc_object_name(_pnt->ob), ":Event arrived out of order. Must call ParallelContext.set_maxstep AFTER assigning minimum NetCon.delay");}
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:46:14: note: conflicting prototype is here
46 | extern char* hoc_object_name(Object*);
| ^
2 warnings generated.
1 warning generated.
1 warning generated.
2 warnings generated.
h_kole.c:42:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
42 | exgap.ct:e41r:n18 :d owarning: ua function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]b
le *getarg() ;41
| extern do u| b ^l
e *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #de/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.hf:i15n:e17 :g enote: texpanded from macro 'getarg'a
rg 15h | o#cd_egfeitnaer gg
e t| a ^r
g hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | 49e | xetxetrenr nd oduobulbel*e *g egteatragr(gi(nitn)t;)
;
| ^|
^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h15::1517::17 :note: expanded from macro 'getarg'note:
expanded from macro 'getarg'
15 | 15# | d#edfeifnien eg egteatragr g h ohco_cg_egteatragr
g
| ^|
^
-> Compiling Kv2like.c -> Compiling Kv3_1.c -> Compiling NaTa.c -> Compiling NaTs.c -> Compiling Nap.c -> Compiling NaV.c -> Compiling SK.c -> Compiling cadad.c -> Compiling cal2.c -> Compiling can_mig.c -> Compiling exp2syn_stp.c -> Compiling gap.c -> Compiling h_kole.c -> Compiling imCA3.c -> Compiling k.c -> Compiling kBK.c -> Compiling kap_BS.c
imCA3.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
k.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
kBK.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
kap_BS.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
kdmc_BS.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
kdrCA3.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
kdr_BS.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
kdrinter.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
leak.c:41:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
41 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
na.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
nainter.cnapCA3.c::43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern d44ouble *getarg();
:18| : ^
warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #def ine getarg h44o | c_getarg
| ^
extern double *ge/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.ht:a49r:g();
| ^
16: note: conflicting prototype is here
49 | extern double/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h*: 15g:e17t: argnote: (expanded from macro 'getarg'int)
;
| ^
15 | #define get/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.ha:r15g: 17: note: expanded from macro 'getarg'
15 | #define geta horg hocc_geta_rgge
t a| r ^g
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
natCA3.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
nax_BS.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
-> Compiling kdmc_BS.c -> Compiling kdrCA3.c -> Compiling kdr_BS.c -> Compiling kdrinter.c -> Compiling leak.c -> Compiling na.c -> Compiling nainter.c -> Compiling napCA3.c -> Compiling natCA3.c -> Compiling nax_BS.c -> Compiling vecevent_coreneuron.c => LINKING shared library ./libnrnmech.dylib
vecevent_coreneuron.c:43:18: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
43 | extern double *getarg();
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:49:16: note: conflicting prototype is here
49 | extern double* getarg(int);
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/hocdec.h:15:17: note: expanded from macro 'getarg'
15 | #define getarg hoc_getarg
| ^
vecevent_coreneuron.c:242:32: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype]
242 | if (_tsav > t){ extern char* hoc_object_name(); hoc_execerror(hoc_object_name(_pnt->ob), ":Event arrived out of order. Must call ParallelContext.set_maxstep AFTER assigning minimum NetCon.delay");}
| ^
/Users/gregglickert/miniconda3/envs/bmtk/lib/python3.11/site-packages/neuron/.data/include/oc_ansi.h:46:14: note: conflicting prototype is here
46 | extern char* hoc_object_name(Object*);
| ^
2 warnings generated.
=> LINKING executable ./special LDFLAGS are:
Successfully created arm64/special
ld: warning: ignoring duplicate libraries: '-lnrnmech'
In [3]:
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profiler = Profiler(template_dir='.', mechanism_dir='modfiles', dt=0.05)
profiler = Profiler(template_dir='.', mechanism_dir='modfiles', dt=0.05)
Part 2: Creating the Profiler¶
The Profiler manages the NEURON environment and handles cell loading. We'll use it to work with our custom Python cell class.
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h.load_file("stdrun.hoc")
class SimpleSoma(object):
"""Single-section cell: A soma with leak, sodium, and potassium channels."""
def __init__(self):
self.create_sections()
self.build_topology()
self.build_subsets()
self.define_geometry()
self.define_biophysics()
#
def create_sections(self):
"""Create the sections of the cell."""
# NOTE: cell=self is required to tell NEURON of this object.
self.soma = h.Section(name='soma', cell=self)
#
def build_topology(self):
"""Connect the sections of the cell to build a tree."""
# Single section - no connections needed
pass
#
def define_geometry(self):
"""Set the 3D geometry of the cell."""
self.soma.L = 500 # soma length um
self.soma.diam = 500 # soma diameter um
h.define_shape() # Translate into 3D points.
#
def define_biophysics(self):
"""Assign the membrane properties across the cell."""
for sec in self.all: # 'all' defined in build_subsets
sec.cm = 1 # membrane capacitance uF/cm2
sec.Ra = 30 # ohm-cm
# Insert leak channel
self.soma.insert('leak') # Leak channel
self.soma.glbar_leak = 0.0003 # S/cm2
self.soma.el_leak = -60 # mV
# Insert sodium channel
self.soma.insert('na') # Sodium channel
self.soma.gnabar_na = 0.12 # S/cm2
self.soma.nao = 79.8 # extracellular Na concentration
# Insert potassium channel
self.soma.insert('k') # Potassium channel
self.soma.gkbar_k = 0.036 # S/cm2
self.soma.ki = 69.35 # intracellular K concentration
#
def build_subsets(self):
"""Build subset lists. For now we define 'all'."""
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
cell = SimpleSoma()
h.load_file("stdrun.hoc")
class SimpleSoma(object):
"""Single-section cell: A soma with leak, sodium, and potassium channels."""
def __init__(self):
self.create_sections()
self.build_topology()
self.build_subsets()
self.define_geometry()
self.define_biophysics()
#
def create_sections(self):
"""Create the sections of the cell."""
# NOTE: cell=self is required to tell NEURON of this object.
self.soma = h.Section(name='soma', cell=self)
#
def build_topology(self):
"""Connect the sections of the cell to build a tree."""
# Single section - no connections needed
pass
#
def define_geometry(self):
"""Set the 3D geometry of the cell."""
self.soma.L = 500 # soma length um
self.soma.diam = 500 # soma diameter um
h.define_shape() # Translate into 3D points.
#
def define_biophysics(self):
"""Assign the membrane properties across the cell."""
for sec in self.all: # 'all' defined in build_subsets
sec.cm = 1 # membrane capacitance uF/cm2
sec.Ra = 30 # ohm-cm
# Insert leak channel
self.soma.insert('leak') # Leak channel
self.soma.glbar_leak = 0.0003 # S/cm2
self.soma.el_leak = -60 # mV
# Insert sodium channel
self.soma.insert('na') # Sodium channel
self.soma.gnabar_na = 0.12 # S/cm2
self.soma.nao = 79.8 # extracellular Na concentration
# Insert potassium channel
self.soma.insert('k') # Potassium channel
self.soma.gkbar_k = 0.036 # S/cm2
self.soma.ki = 69.35 # intracellular K concentration
#
def build_subsets(self):
"""Build subset lists. For now we define 'all'."""
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
cell = SimpleSoma()
Part 3: Defining a Python Class Cell Model¶
Here we define a simple soma cell model as a Python class. This approach allows us to easily modify parameters and re-run simulations without rebuilding the entire cell structure.
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analysis_settings = {
'CurrentClamp': {
'celsius': 34.0,
'kwargs': {
'inj_amp': 100,
'inj_delay': 1500.0,
'inj_dur': 1000.0,
'tstop': 3000.0,
'threshold': -15.0
}
},
}
analysis_settings = {
'CurrentClamp': {
'celsius': 34.0,
'kwargs': {
'inj_amp': 100,
'inj_delay': 1500.0,
'inj_dur': 1000.0,
'tstop': 3000.0,
'threshold': -15.0
}
},
}
Part 4: Running the First Simulation¶
We run the current clamp simulation with the initial parameters and visualize the membrane potential response.
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proc_settings = analysis_settings['CurrentClamp']
h.celsius = proc_settings['celsius']
# Create ReusableCurrentClamp instance
sim_cc = CurrentClamp(cell, **proc_settings['kwargs'])
# First run
t1, v1 = sim_cc.run()
plt.figure(figsize=(10, 5))
plt.plot(t1, v1)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title('Current Clamp Response')
plt.tight_layout()
plt.show()
proc_settings = analysis_settings['CurrentClamp']
h.celsius = proc_settings['celsius']
# Create ReusableCurrentClamp instance
sim_cc = CurrentClamp(cell, **proc_settings['kwargs'])
# First run
t1, v1 = sim_cc.run()
plt.figure(figsize=(10, 5))
plt.plot(t1, v1)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title('Current Clamp Response')
plt.tight_layout()
plt.show()
Injection location: <__main__.SimpleSoma object at 0x318013b90>.soma(0.5) Recording: <__main__.SimpleSoma object at 0x318013b90>.soma(0.5)._ref_v Current clamp simulation running... Number of spikes: 0
Part 5: Modifying Cell Parameters¶
Since our cell is a Python class, we can directly modify its parameters. Here we increase the sodium conductance to see how it affects spiking behavior.
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# Modify cell parameter
cell.soma.gnabar_na = 0.22 # S/cm2
# Modify cell parameter
cell.soma.gnabar_na = 0.22 # S/cm2
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# Reset NEURON state and re-run with modified parameter (no cell rebuild!)
sim_cc.reset_state()
t2, v2 = sim_cc.run()
plt.figure(figsize=(10, 5))
plt.plot(t2, v2)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title('Current Clamp Response')
plt.tight_layout()
plt.show()
# Reset NEURON state and re-run with modified parameter (no cell rebuild!)
sim_cc.reset_state()
t2, v2 = sim_cc.run()
plt.figure(figsize=(10, 5))
plt.plot(t2, v2)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title('Current Clamp Response')
plt.tight_layout()
plt.show()
Current clamp simulation running... Number of spikes: 179
Part 6: Automated Parameter Tuning¶
Finally, we demonstrate automated tuning: iteratively adjusting the sodium conductance until the cell produces the desired number of spikes. This shows how Python class-based models enable efficient parameter optimization. This simple example could be expanded and you could tune other parameters such as passive properties and FI curves.
In [9]:
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# Automatically adjust gnabar_na to achieve target number of spikes
target_spikes = 5 # Set desired number of spikes
gnabar_na_start = 0.12 # Starting value
gnabar_na_step = 0.01 # Increment step
max_iterations = 100 # Safety limit
gnabar_na = gnabar_na_start
iteration = 0
# Clear any previous spike detections
sim_cc.nspks = 0
while sim_cc.nspks < target_spikes and iteration < max_iterations:
cell.soma.gnabar_na = gnabar_na
sim_cc.reset_state()
t, v = sim_cc.run()
current_spikes = sim_cc.nspks
print(f"Iteration {iteration}: gnabar_na = {gnabar_na:.3f}, spikes = {current_spikes}")
if current_spikes >= target_spikes:
break
gnabar_na += gnabar_na_step
iteration += 1
if iteration >= max_iterations:
print("Warning: Maximum iterations reached without achieving target spikes")
else:
print(f"Target achieved with gnabar_na = {gnabar_na:.3f}")
# Plot the final result
plt.figure(figsize=(10, 5))
plt.plot(t, v)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title(f'Current Clamp Response (gnabar_na = {gnabar_na:.3f}, spikes = {sim_cc.nspks})')
plt.tight_layout()
plt.show()
# Automatically adjust gnabar_na to achieve target number of spikes
target_spikes = 5 # Set desired number of spikes
gnabar_na_start = 0.12 # Starting value
gnabar_na_step = 0.01 # Increment step
max_iterations = 100 # Safety limit
gnabar_na = gnabar_na_start
iteration = 0
# Clear any previous spike detections
sim_cc.nspks = 0
while sim_cc.nspks < target_spikes and iteration < max_iterations:
cell.soma.gnabar_na = gnabar_na
sim_cc.reset_state()
t, v = sim_cc.run()
current_spikes = sim_cc.nspks
print(f"Iteration {iteration}: gnabar_na = {gnabar_na:.3f}, spikes = {current_spikes}")
if current_spikes >= target_spikes:
break
gnabar_na += gnabar_na_step
iteration += 1
if iteration >= max_iterations:
print("Warning: Maximum iterations reached without achieving target spikes")
else:
print(f"Target achieved with gnabar_na = {gnabar_na:.3f}")
# Plot the final result
plt.figure(figsize=(10, 5))
plt.plot(t, v)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane Potential (mV)')
plt.title(f'Current Clamp Response (gnabar_na = {gnabar_na:.3f}, spikes = {sim_cc.nspks})')
plt.tight_layout()
plt.show()
Current clamp simulation running... Number of spikes: 0 Iteration 0: gnabar_na = 0.120, spikes = 0 Current clamp simulation running... Number of spikes: 0 Iteration 1: gnabar_na = 0.130, spikes = 0 Current clamp simulation running... Number of spikes: 0 Iteration 2: gnabar_na = 0.140, spikes = 0 Current clamp simulation running... Number of spikes: 0 Iteration 3: gnabar_na = 0.150, spikes = 0 Current clamp simulation running... Number of spikes: 0 Iteration 4: gnabar_na = 0.160, spikes = 0 Current clamp simulation running... Number of spikes: 0 Iteration 5: gnabar_na = 0.170, spikes = 0 Current clamp simulation running... Number of spikes: 172 Iteration 6: gnabar_na = 0.180, spikes = 172 Target achieved with gnabar_na = 0.180
