From 4c75c50b73db837f97b98b6b1cded5bf9888330d Mon Sep 17 00:00:00 2001
From: Werner Van Geit <werner.vangeit@epfl.ch>
Date: Tue, 20 Nov 2018 09:14:39 +0100
Subject: [PATCH] First version of sim test suite

---
 .../soma_cm2/bmtk_build/build_network.py      |  24 +++++++
 .../one_cell/soma_cm2/bmtk_test/.gitignore    |   1 +
 .../one_cell/soma_cm2/bmtk_test/run.sh        |  10 +++
 .../soma_cm2/bmtk_test/test_output.py         |  58 +++++++++++++++
 .../expected_output/membrane_potential.h5     | Bin 0 -> 33712 bytes
 .../soma_cm2/expected_output/spikes.h5        | Bin 0 -> 7112 bytes
 .../soma_cm2/input/circuit_config.json        |  20 ++++++
 .../one_cell/soma_cm2/input/config.json       |   1 +
 .../input/network/biophysical_node_types.csv  |   2 +
 .../input/network/biophysical_nodes.h5        | Bin 0 -> 8536 bytes
 .../one_cell/soma_cm2/input/node_sets.json    |   5 ++
 .../soma_cm2/input/simulation_config.json     |  55 +++++++++++++++
 .../biophysical/one_cell/soma_cm2/pytest.ini  |   3 +
 .../one_cell/soma_cm2/shared_components       |   1 +
 .../soma_cm2_hh/bmtk_build/build_network.py   |  24 +++++++
 .../one_cell/soma_cm2_hh/bmtk_test/.gitignore |   1 +
 .../one_cell/soma_cm2_hh/bmtk_test/run.sh     |   8 +++
 .../soma_cm2_hh/bmtk_test/test_output.py      |  66 ++++++++++++++++++
 .../expected_output/membrane_potential.h5     | Bin 0 -> 33712 bytes
 .../soma_cm2_hh/expected_output/spikes.h5     | Bin 0 -> 7112 bytes
 .../soma_cm2_hh/input/circuit_config.json     |  20 ++++++
 .../one_cell/soma_cm2_hh/input/config.json    |   1 +
 .../input/network/biophysical_node_types.csv  |   2 +
 .../input/network/biophysical_nodes.h5        | Bin 0 -> 8536 bytes
 .../one_cell/soma_cm2_hh/input/node_sets.json |   5 ++
 .../soma_cm2_hh/input/simulation_config.json  |  55 +++++++++++++++
 .../one_cell/soma_cm2_hh/pytest.ini           |   3 +
 .../one_cell/soma_cm2_hh/shared_components    |   1 +
 .../shared_components/configs/config.json     |   4 ++
 .../shared_components/morphologies/soma1.swc  |   5 ++
 .../shared_components/scripts/run_bionet.py   |  19 +++++
 .../templates/nml/soma_cm2.nml                |   9 +++
 .../templates/nml/soma_cm2_hh.nml             |  13 ++++
 33 files changed, 416 insertions(+)
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_build/build_network.py
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/.gitignore
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/run.sh
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/test_output.py
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/membrane_potential.h5
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/spikes.h5
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2/input/circuit_config.json
 create mode 120000 examples/sim_tests/biophysical/one_cell/soma_cm2/input/config.json
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_node_types.csv
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_nodes.h5
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/input/node_sets.json
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2/input/simulation_config.json
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2/pytest.ini
 create mode 120000 examples/sim_tests/biophysical/one_cell/soma_cm2/shared_components
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_build/build_network.py
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/.gitignore
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/run.sh
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/test_output.py
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/membrane_potential.h5
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/spikes.h5
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/circuit_config.json
 create mode 120000 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/config.json
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_node_types.csv
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_nodes.h5
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/node_sets.json
 create mode 100755 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/simulation_config.json
 create mode 100644 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/pytest.ini
 create mode 120000 examples/sim_tests/biophysical/one_cell/soma_cm2_hh/shared_components
 create mode 100755 examples/sim_tests/shared_components/configs/config.json
 create mode 100644 examples/sim_tests/shared_components/morphologies/soma1.swc
 create mode 100755 examples/sim_tests/shared_components/scripts/run_bionet.py
 create mode 100755 examples/sim_tests/shared_components/templates/nml/soma_cm2.nml
 create mode 100755 examples/sim_tests/shared_components/templates/nml/soma_cm2_hh.nml

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_build/build_network.py b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_build/build_network.py
new file mode 100755
index 0000000..7174787
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_build/build_network.py
@@ -0,0 +1,24 @@
+#!/bin/env python
+
+# Sonata Simulator Test Suite
+# 1-cell circuit, single soma, only cm, 1 step current
+
+# Authors: Werner Van Geit @ BBP
+
+import bmtk.builder
+
+cell_models = [
+    {'model_name': 'soma_cm', 'x': [0.0],
+     'y': [0.0],
+     'z': [0.0],
+     'morphology': 'soma1',
+     'model_template': 'nml:soma_cm2.nml'}]
+
+bio_cells = bmtk.builder.NetworkBuilder("biophysical")
+for model_props in cell_models:
+    bio_cells.add_nodes(
+        model_type='biophysical',
+        **model_props)
+
+bio_cells.build()
+bio_cells.save_nodes(output_dir='../input/network')
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/.gitignore b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/.gitignore
new file mode 100644
index 0000000..1f57b97
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/.gitignore
@@ -0,0 +1 @@
+/output
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/run.sh b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/run.sh
new file mode 100755
index 0000000..275a227
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/run.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -e
+
+rm -rf output
+rm -rf __pycache__
+# python -m trace --trace ../shared_components/scripts/run_bionet.py ../input/config.json
+python ../shared_components/scripts/run_bionet.py ../input/config.json
+
+pytest -vvs
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/test_output.py b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/test_output.py
new file mode 100644
index 0000000..46548ee
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/test_output.py
@@ -0,0 +1,58 @@
+import os
+
+import numpy
+import h5py
+import pytest
+
+output_path = os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        'output'))
+
+dt = 0.025
+tstop = 60.0
+stim_start = 20.0
+stim_end = 50.0
+
+start_voltage = -80.0
+end_voltage = -20.0
+
+# Using as 'raw' code as possible here, so as not to depend on other code
+# that could contain errors
+
+
+def test_soma_voltage():
+    """Check soma voltages"""
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+
+    voltage = h5py.File(soma_voltage_path)['data'].value
+
+    assert len(voltage) == tstop / dt
+
+    time = numpy.arange(0, len(voltage)) * dt
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+    assert voltage[0] == pytest.approx(start_voltage)
+    assert numpy.mean(
+        voltage[
+            numpy.where(time < stim_start)]) == pytest.approx(start_voltage)
+    assert start_voltage < numpy.mean(voltage[numpy.where(
+        (time >= stim_start) & (time <= stim_end))]) < end_voltage
+    assert voltage[-1] == pytest.approx(end_voltage)
+
+
+def test_spikes():
+    """Check spike times"""
+
+    spikes_path = os.path.join(output_path, 'spikes.h5')
+
+    assert os.path.exists(spikes_path)
+
+    spikes = h5py.File(spikes_path)['spikes']['timestamps'].value
+
+    assert len(spikes) == 0
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/membrane_potential.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/membrane_potential.h5
new file mode 100644
index 0000000000000000000000000000000000000000..04c7302269766da24d4f4ddc85a96014375281c2
GIT binary patch
literal 33712
zcmeI52~<?azU~WDoDc_$5n~KdgA)$1n8%*!hNkJks5s(OfI&o21Y;5s4N*g!P-6ix
zIN?Oph%sV}`J8Y_fkvEARHBBcA;yRkPI-mGx$oqj`_8*>t@rM|@Ah7cuD$<NtN8lI
zSO2|t_3mPxUZZQ(qEib}w>4`<8k089cN<>*tlzfHei3OnZm5r`-*Kof=hl}S9AE4>
zkS3(Au48??O@06Fja~$H)yD@}wOS%uHuT?6)>o4iPA~SFH3aPCe=7odt<qfghKJU_
z>jpm^srOj}j7ejXlHwC%$@nqT#?-|ce5q(?@b4_!*8BCZzIG-GIaccWZ$_M@yHh4i
zO^%<O_`G#poDlctuMQ3`6g0?eDC;WgYMjY{`hJ|`els#@Ol<r(8Lu0Kf7g#ZuG?n5
z7^!lvfxz?dzj|?yz1Q{M(5m5m)OSkU>&MeS8+W(s2b|(x{RVsBzXO54jyrw*n^x5O
zr-4Ci{P^U${Rs&ZCQV43HadR%i<*Yxq{+{#Nqpk?38|x#CdVgEn=n;2nHE23LS4%j
zqvVC}>yB-vD2)SgtRH=Zq;{x_{@Yu_dEs3Bd8MJhzxw^(?&1H>8VBO^f^9tzhx&}r
zke3=bHI$7c@w)xG{PTjT;yIWm@~AHE=;-*oX*1bR-A*HiMJ~@9)VF@IPe{A^<GMD6
zeYb`alHO4DA6mZfRg=H@%I|Oa^dHM|uMg{6{^R<FXoLSMn>IxLaXFwqJk<Fg*Ed8J
z^*eE`8Y2I>%K!VmTJc}XSO0z<FUC(>_t3wMGq0A!>(Bc9^>2^2y#GxussEvd`DZ*D
zu7euNe}CTDP|u+*Q~k^KpEd9NGamJScJeRf|EWJx>$x;s`MqHCuetok`r}{zVs(2a
zMK*uFh5miK;i&R&@#iO>hOoV~6R;Do6R;Do6R;EbFGawCH2uqcY0u~S9bVjCl9=W%
z-cG~${;$W4>hC}Q>GgA?7r*9j_p6SLQv1E=dYhbItLy&xt=nI(kDQ7A`P6{}aUtzx
zlaw)2<Hw9mm@qnV%<~BgH#x6Ycja04^Frf`JHQ6Lb!BQ7`69O$vA@3_dr@P5wG*%t
zuoJKouoL+2MIcNaWqf{Kte?L5pU<0hBvSr@<6P^%1nh@)0(Js+0(Js+0(Js+0(Js+
z0(Js+0(Js+0(Jub=?T<5cUt#+U&C|W4Q2Wp|7+>n{9e>Iw5yxM|3}+^QGXw8XxA{$
z(D1z0-?y?K*$LPQ*a_GP*a_GP*a_GP{O2Sv2rqQmOFM@;0(KwRePH*2eH_^HfISb`
z^ME}M*z<rr57_g7JrCIPfISb`^ME}M*z<rr57_g7JrCIPfIScV*UkgqB^(#xi48N$
zS8`r!gRd@;vHLdM-5yM7jSXMDCKn94Z9`&ag%H&?^r_v<`3)PcPk4v1DjU|F45##}
z4P!$)5mITxYXvuisIZ};V-e@&Ht>(;GIqv>!FPsGT4sam=pKZeu;IiH_k|EPeCk)s
z`B59f*DYhL*oLO<CQy37hJ){U5ds@N__a}q*keP;&@#@8Y<PTdHDfz%*!AXAN(*h6
zzEVlZHX8=EY+E7<Z1{afCFdJ$D7dzjv3wiiE$>sh#s-hQCPMOTxZ1l*iO97f@3Y_J
z0wFexZ2TQ#%Wdd1C6m%D8_r&oOG_=XVQF}u5|L?x<(o&G&$Gd$`!U8cZ1`ajr*yUr
zbDze^C8%uBPV_4gvutoY+ccY}+3>ykEMqA)%-WVuX|fIeugY&8CE0L)p0-3J*id-C
zeKwD`A!*z-#+VI#PZUx*&W4*ovk8f@Vf{vHi5OwS_zqpOd9)3$&;En4!8Tm_9hBN^
z$QiMS5VH+KkB%-8MjKx8>7UIFHk@4jj4_=J3tN{`s<y#6>vKXBHZ;GHP$GhCD1Iv_
zoBP`^dw<JV=3|4R{{<>L#M7Kjgbc7@ce9x#!qbKs(+%0YmknN5I>s^&8~!j|r?i_5
zTfY5<5O*8i?)h<v=xjsJWrMT1n+-oZc*L>}Hmpv(N2#j~qc0qkUt+eQvwmrbaJHd*
z$GB|X+=k_^(^%$YgKdGM7j0xio5w%Ofn!5S?5Yy+#ESW+lCpWN6=6z6EW2+-<1MYd
zXpI&7I$f6jv*Nvvx0Hx#D+2Gno6T=n@h~PbmQ`8tbxCJ0dew@l0oBrfR`g&0ZHcI`
zqT2P7Y+i1~#`Iya?2Hxcw_aYf%!+QqYNh|Is4PBGB7_y6(-qnLs1?KVVq;mc6)(5)
z^`Zx?IF;t)Kw!n<s?*YcR+wz-vU!meEio;Y?X=>Er^bsGTJaHgbs*cUP&r+d{<GrG
zsoS&pMl1GQ{vej+Tajk8c+oXh_!PN2kUT4D-ncFOXT`Q9-^(RxteEuYf>^fPirxvM
zyl9pczntsqKo(iCR{K=?&x$eIMK+&jMVHrdV_Ak37e0C0i_W%U#lrvxl5WLY6Izst
zSyr?=SuXu&#qp4hu`I=k%+0A@G}#J6N4*0{vcl=3mrF&06$k#PlK!(Iebmla#;geb
z;Uh0P&WcCAZ#j?{E52FVy;O{_Vp`j~(tlRG`QCw8HrR?=H<x%(n-!afjCCMpE8-5m
zSt^WHyz!<(4mVhF<?|D<OlQRxE%Lmm+KLe~COZ&?6>ir;N=1+rXUr}++~10<?=DLJ
zSz+$|r5B}EwEAq80~uh&u|~#H;c3OkNw4JaURG!>-jx2c!XbRO7wu-n-ktLth`SZ<
zbc-$(ovrX&)H8>>S#j^l1L;32w#Og#qOMj<KC@hYk=_bVH7ga)R@~U?ox_`3k>9yV
z9CNZ_+`LoLe^$8PUn3vgv*O~|<Wlj(g6!j}9A0a|kf3&P?7ju<H~u93XTgszedR!I
zTd?56^iol6LB#J-IsAqN%|^Ty$EqwibmW%wp9LR!?{y%R7KE<;v{Y1B@Wf?g4llQ$
z=pD~EcE*B~>yM@XETC`w;6P4TaC={NsSp-?*>7SFKWf3m9RE00Y(bA^&AsUX3$9H&
zC;ex^s-M=Eiai#LGR?^0MHamBtuBu3wBTHi4&JoTf@Mp8mj1KA>hN``D6pV);+!15
z(E@Sa7RT}}m>1T~o361yx8siVp9PIx-(M<nEx@OXb2zu)-A6HTY`Fyiu>-tmmIV*W
z{*?Z+V29#(smQco%9ks1_&f{xbxMq585aDS5$sK8Td<+V*^#7MFd?Qw`p<%{C7W}2
zngy5r--%->7UbrKd(&hKqFp;Vk|YZ{q~DPKv!JYcR}PQ2U{UnkIL0i9EFR)b$63&V
z_HZOI799TKzVx33bDWEFc(et|v}JK@um#V49`8+U7JO^<awKL8QonC>To^6z_AHbB
zv*6B()p1N`!PX{Iy{X!QgsDnLqOhRX<u=DfkOfr{mC}C}tl70Sj`>&+^Tzw$lv?oW
z5|bktV8QukuO1hk7JT;hZ_<Aj3_7<bj(J$nR-5TfyID~B)o@4RZowyA`WzRXEzp1R
zNczu$CJ&Fsu?`mOAJ4t1s|D}>7$+B*v>+(N@3?TbpmtN!T;AM*oiCr2{<9!?PQEv7
zWWj(xrpu+uEck7t_PBUr#-?NKb9t>9vA)-&|IFyVw$Pi_nDJAa*^cD487tql9v9VS
z48Qq$F27+$$02`6|Cw?60KDl{GnNck<VY&bi28i=aZzE0bBq4DyxfeVDbJ+;%*eP}
z;!VrUP@6w@Bqz)u&rkejeAg=|mmf7_=JJ;Dtk?|SMi-?2%(y#wlOur{Usa?X7kkV|
zG#GMukr{n<c8q5`&A8t6y7ZqJ>lS|FNVb_V_DRNZQDDYv@q=^uMl&i-zY)*!&ETqg
z(tl<Q-g?lH<eA~xdFgSHYsQJW<8nDS<I{Ts<JodE!pA!L&@3~W9{<siEHdL@;Hu*y
z(~J)`B<1pXW`w+?h-VpQJpQ1y51nnsu3ML+|IC;^e9Lh$%Z!0X-p%D{X8i6I8P8J8
zC|K3mhbEg5?@}%OXNJc+-yRnUW?cPcelCwUBX7{Kc*e{axv!TG9cM<TeznqnW}MAF
za$JlsV`<YBxjfno%e2^dHrNc8pL~3%&5R!+of;9d8FP1^mi{wC+hbiWH<;nLbXq*q
znejc*_)xVOvnIJVA__D7&tH-LGvmH)doK4kqp<LUc;;h9lDox+QZxE~Dp#%^V8+eb
z-=+V|SkJ!C<-N=pU$!8gd6@CKVw4Z<X2zw0zKw{x898oGrT@$rnjvzzn;9?F<ixWM
zW}F=TwhwhRW1$F;OW&Dc^lx!OIGfQtzg+syjN*11<C&8gv)@nkp^eN?RENo>;mmmS
zRlhu58-;0~l=#z{DBK#KP$sIQ5Es&N603^Bm6ta;k;*8H_(Pw^%cF4S*f0LHEDGke
z8D&C5;n=%xOk%}R&<r`~L=c6&1IFd?qA2*aa15Y@QP_SpuS^s~!SlP&Ni07K`O7ak
zk-R9lC%v1;c@(k@odalA6xw(DwoGJ3VZoE=Nh~7@&CWb@BI!~1aO-DzJS_@O=K2KC
z<S3+!JzXXeqHsHK+9bxJF!3eVrX(f`*KU24$D^Y#>WDdj+M;l7)$e7(7zOJ)3nnpL
z6vUvuO^G53x_%;$`$qvy-wvQO3IRVgKP5b)uw(azNz5Y({g#F`CGJt!FsUk!yG5aE
z*hc}>H43@z-A@VUD0FzVe-d+w!lJS<a%IjawD^*&;<YBs$@n6G)|l{YbjT@DZ9=O5
zMaj>EJMCsQC6y*5RCij%%T1^{R1`qVOo;hn=qVvgIG_4J@-tzOb$L?)6H5Ddui`}}
z=$o99{7l$?Y3eCaU_#KYwuvm?gq@4GH6?i_40t<g73U^w(%h2#Oz7U_(^DeTgq08a
zB(e+>I{tX9DM>eB$)@;KJk12>In4rTvI!X@*PjvzCXnYB`X<b5^Rwh<!rdFQSMg{Q
z5)X6@q&5?-=k7Ztj3$gtiAiKS6Dp$ql>AH>+-v13?r*{g$KXIpO$e{JAo-ba@avh0
z%)^9`g>KD=y9vAEcCF%WCJa;!38bzj6ufd@@-xBX-qJ+oWI|pkm5<Du&}qX-$uAO1
zKbR6oYa-z?yv=D*9f`SKTN7DTBph8#%}8Y=X8lqv`9<PBJ_)2{kx0t!eOib}+)O^2
z$ciH|J~FNuK_o7DG+oV$A~BTY2hzewoGjOz76p+o7G9P7B2k?AVKb5!2?cw7HRqAo
z9g0Aj6$vl5(WgabB(~gnD)~jCr^sza(j&2YUEpe-7KzU9pO^e1v3zLSX^{|#HUm3O
zW-Jo(TYl4w#6+U;&u^{f(UEv>?_J3+5)VJiIxUQmm^x+PWTuNmb@-3Xh$0fKd(vv|
zABoDRE<uz=V%XU)PYcgToZ4ob%se7tn*Xch7l|X|=C9^%kx&Kq3Zkx&*wf+2Y2h3R
zpWAFQbBe^aqfO+BMv>^fX6<TTYsA`F>L6NUM3=!=BtIio^#5Qot1_ZpbNA+?(um9}
zdsp*vBb@e(45DR5q%V6S`5EyjF=sL>He#ASpgDmNw_Y!o{EUcuJR^t}8gb=RhclwU
zh!I=9p3L%%IP>wK<|NMu^OzdR&xm6IOM+;Y5t{aIo)MWw?EUTdWR_us-{HjOB;APZ
zd9Bv)G$TA`76j2`Bl2w#XGDS#?tO1cenw<F&1+6#jA&okV-1fsVnI=H5VaZ6ENj9U
zVKm~ygvLosXT%fjn&w1dM9OQbHQe8b+Yc)xKO-ideE*E_G~(LkE=kP8h*2MX*POT;
zac<OzHQdbztKVbE&j`^r`;2flLiej*5_2*F2hU1=Mg*)(S;K21uw%wc!L%j<{VY4q
zi0TMz=xs}4RT1dg_>SZkf!vFW*6{KOboi!!FfEI~qD7@=gor?kiIb98aRlb5om&t@
z;92L*Yj{xvQtumrX<-EJ9KSC4MId40$4M+d0#zS+v><sAh#7Hc4d)R!?>#=4W<_97
z>qciqW&}#FuS#MW5zy~fv>@pb*q?J*@{2&w^!I{kas+moUOg)kA~2xmo+QR1u*qR~
z3lbB7?iXq$zX+_{u_Bn-BG7Sx?^$7tz>?TAl3xUzmD5`gMFcWBwO`BqBS4<t;74F)
ziRG;DjKJOe+mc@d64Mv9Anp;k9^G#(cZ<MSS`tiMBT(U-a8@`+U~pB7Da<JXC%)e(
zS2~VBIM=V`wc$88^%u!693jSxv!Xg2yWV(X3abjoz&{VPAeG@LI5&1JFAs;uc83sJ
z7LL46^3Dnoj!qLor?BF1EDgCN`Gv!!<GX8lQ8?!Q@k$6S42R<nyU&V(aLig8J%#0m
z<Nmu3CBJYa4f$*>=i#_Hz$b)eg=2h+(~@5}E?rHY!ZN}!^t*N~NqRU=F8^vRPYZ`J
z$s9tH!%=MbUGfWuqT7NgjD=(O6VH|;CLCU8ept(+!?9)S#1Lu=N6&f9&k18VR*&5<
zh3Uf4IVh|pQG{dpOI4CzINJO^Cxp^)%s<lYobU`s<JJ48FpqG&_s*D>#627j2a$E$
zEgVz(eGx)k!%^Kd<eYF02m7f)@(V}h?sw!0(BT-iw9`6XYrv^VMIp4t08`k|bE4XS
zBkm6*KLb>cmbE062J9*GTF1)`@cFV#@-tvt#?*5{7|=VW?NnB5z*_%pEeQ<h;u^J%
z7a6dk`ZvkXfOf^1=R|=4nP2po%JL0xN;}q)<Qb4|jbF#P0gw7L3#C~GOlz|KoX9lb
z)+Oy!mSI5Lu4|H?0aq5!UdPi681Z)3P?~JO8O^?PBEbN2mzb%H8F1{uGs({Y&5xh2
z<Ix7}-4ql`Z3g(wxghx&uzlprsZ3{pr>~p*7Y7F9x7oFh`y1eXb8sl724o+&C;1uB
z{_~|%nTG)jQm8X=H=vpMq~vG7hrOnRQda|>IJPMl&IY7ZY?;cO47mMuq+IdZfQbvM
zB|kl`#eEV=YxEeU>Rm3X^*Hy+(W$IT59_^HXHuz$D0Rx`<$CBgtP7=Odf)?1xe$5;
z48JP*>9ND>LuUd#`nkNG&x`cf@XPn1v`~+(`$m<E0zGoGpGtmubeNXwO!D+t6d9P$
zxgITgoR|Fcm_yRaMW!Cl%3n@q8G57^?sO*Udfdr;E1#$7k-+XsetJ}eW|fNsJ!0Gj
zCNrkT`8y|^NsJzY#N>P)tw-rP7X`KHp@09&a$(eC|4?Hx)9Dd3@K?!CkDV>&=W~BO
z2K?MpL8%^__8u-5o_cg&!IGJW9xJCbX+_-i=oqm!pS$U?q`O){UG;E&_LJnNN5<Lo
zWagv?c|NhH$ISVA^LcF;?v5L&pfzDg41OZ{h2eUKoMcuNhOxK(Tan5zR2)4g`GsNd
zni&dO7KRhEI-D0G4B>;nPG-enIM{zsD}peDG_R5T!m#VgVg)S>!@xZQ&WnOD6f8TQ
z%<{wFF*&gn$qPfCzSVlp!_cW~fr4g*Vd>-W^CB}0E~jrueqorqWo|2y9tOv`J=XKI
zFw7cLtf0wZxF0a#yhsQ`Qv1f!7z@MA-&VIGF<}^gSh=1@hv8CQrQ{cep)=n<FN|S0
zY3nkL>B3;_`&}!d2t%>ci1pk*42sG}l3y5h7xDALGYno?e$$vo7`7ywmHficQ<t)y
zyM<x(YcDCOYZyA$7M>T*VOW0BI*mDnp-sUba$+<L^FLa&p4aNocyxayt<m8<ztZ!f
zT8D>iCrx8jI!yhwr3<Olq59ya^}JjMw$h-aWja*OxGwqWFwFAtG*+y`soowg1Ui@+
zA6n0gbU1QxoRSvmp!&w~f+)~o&!Sb+SiTNE6BRBbPls*l%aWfCy<dG#NwaiVd%yDq
zk*PzM6W>l_89J=kILw8l>(Fj?t>mXe=7<$anyiD9kM9MMphJ4=Gm@VUkFHO1Au&2k
z+wZ!8N9%AaXS<Txbcma7xgd->Tru62{B#)6bD;}S=y1lN-v;ilgZY9`QmVtT9dBO{
zo;qk2w3yC3bl4la(S^9{;HT7Y;BGo>@AQl0r-SF+k1hyj9r8=MPiIa#xUWCpLWmC8
z>0>wWS}ocSb5PM5Ef&zc3!++!X01Y}vnnk<thy-qY4POySsQq{7AgD{6)n@^_SD@M
zgwSH5F?u>H*5cY54<$b>M*X>b1259z+&OO*E!4ug{gmXVh4>_SI?LBWH=$i?lBWei
zzS_XK76Bd2Dw?Imjz4Zmep>YV;nV3XLyHY-JzJA>ExNw<!v>zFMedM^Dw?cChc}y7
zhy*Pbwb(G7F)dnL)3qisTFm+GXUR{CXUpfPs7;I1q;3_$sKp(_{^?AoMMAeRt%*X5
zswaO+ep<wwS*fB_i}PE9D}<*OgXUF8ep-}{eWx{X*FqoEX(M;jV*g7;D(b35(C<Sk
zgtHbqkKC91v>32@nOwn2i%su%ZRE8YbbqT%^3z~tzo`|XT7!<w+NQ874VL`0wKb{K
z!1-I#MqaK##?s#;KMlz934IM_hV@Bd#TwjoKh~N+gTzO18+nli*UOr!X`u#Vzs#=?
z1sYUjXj53e27_a+Nq!of@SnYra}B~>yQ*oH1_!HAAu=@xDIT4|GBnur#WTrIgMn$E
zZ{%qj6j+1QG+6@=&kK^D26;_prZA>Kr^_ANkQfb??)qjUkJi9t$zV0LX)yQgdy=09
zj@qRuOsB!DF0>6%XmJ0*j~lta21!3AsVUXq=BCycg{KDN=WIz~9vWO48QF%oYcSNe
zTJqE2WSdXa)KvrH&0ZIUvj)Wnj-)Ur4HTcp%9X-2*q!3EiPx&(WnQPIHEL|>rMW1o
z)#%yis^q7}>WUBAkV-W=?{we9%hg!E@Ow2aQ=?7%sEb0VF<<pm@>8R6=iD{~YP@$Z
zU=uG=<6&vJ<fq2e4XGDJfg05xygY;DtHFlvY(w(YsPuYk6X$9SbGa+|sd4I;B^O1e
z8m4`3&R`j89LYY>hNP>Znl^b8Pg7%0q>F|otKrk*%ZnmGjcvp@gE2LFpT8;jsj;?j
z-X<QcMwd@}YN$<(73}auVN|1?g3Vw$H8S0rv?U5PoNCr=;{Ix+3zbHGP=H74ev<su
znD&194CbN6t)Z{ACGKj(4cxnlyQy)d<wy;6Rb#}@k0n1f&g{*e!JO1Eukde6h#JSH
zoRj=i&_vA8&>9u?cJFXWRIA|kY{v{%rNZ{Jwzi~F1<$YUNPa5h&tI&eWh%IjA8<(s
z6|#em&tSzWw0}9VErALPZaZ)0MJhBqwpl|9RrqjC_$5)G!joAyBtI2W2G4Cv@>ICp
zzlZ!FN`;Bdi#0S$g=<&FUlN%rjM~#Em1U@KZrSR#BwYpTWaVa_rh?E{N`5Nny1su&
zB&dMLuck7lLcr-gZApv@JGKnp%%fH4H}{d`r^1FY{E{%L&^6F6mFZN-ZGTqsQ=!AH
z>6^K~3X2Z6*HWrNi&ce}gr^E~W?EC3hYHVZe@K2Rr1o93nY*cQ$Em-Tx~h;+S#n7@
zt58*xkjk7?h{<Z%jt~{jCv4ixYn2$JGiYgz5~Z(Qm;98_*Jh-$Dkb)xe4`zyR3fP0
z;AUQ~#Lkb#X=#}f14cVu7D9<leydVhu@c?eDcTVzvGUhTlAjVC5523Ug-R@0+4-_4
zP{KL&+f<gXM22NpJCdgadHzA35;GgG(9$d=?q2k{EHafy{N}Xer^NL|)7p`ACB{y4
zE#PTNRH(OWX|fW7U$tBo2}+!}|GVU;MEHpX?MRFg2RHUD;L%Ei%obW|Q)1VMw=WB$
z5(9l&q%oZm1+6!>BMK!vZiE$Ze<kwvS4n<KbjtncvhY-5>GbYt%tHy6r~~bYyApGI
zjxFGBO2~f?qob}$%)0Q!W#O#E{T(4`%t?u)1s5ehC2q#fD&VyWj90#*qcsX#>a_c^
zs8(R;-Jxl$N`aFl4<tVYjO&*d@Nxx;)4g@HOaaBPQ<9$oyJ>P7D^|d(RXbM#1-4Xe
zE8s;6^hA`77Amls-;(?k=$!m%8p~H;xzW>=<SEd`<A(yy6`22LypCom(73!=rN~s^
zz3uDMScU=*Khe38bOokP_*wE(pgLrZjwUO>I(DlR2?|vHu`i7=1%~|)<4R%_IJNdq
z$xi{(dn<L+rofRQ!Ii?Ofa=W($xnejE#7e@3I%+wxqZp~71;LOE*+%`^!{u}rSMc>
zZPI<oPk}Ds%Up@O0xP<CeaYPvX!rD_<flO9nJJaRSplbQZDukj1=8njb(J3wqUKQU
zFj^Ces?_tJvZ_#&_vyHgmxn@Jdh4zbq4<7rRu6(uY}foaj24Ds-2;~eEI$-0HW~ME
z9*R#!&c7=%L-AglBRxoZD5e}}GMpxdVtk5v0b`*U((8kLJUUd)6Yae#jG+i#_@oC>
zgkpdyU^u0r=yq?$0_G8l4jaDS$K68Fe0a@W;T(!5t={ZONGN_s;&56Mf-A`d3s_YM
zPJ7&x`a*D|yvIEuLhx<ogq{Q;*b=&CI4umpsymfZUkH}2>$0Eo5PUpz#66K2f|)I|
zdy@1JOxk-^>I*^4l$RDV76My$+kPG$0^Qj~_k=M7{_{(F5=96+gPliE8iLnu8x}H;
z5VTwK@qX?Wf+m9x-4o6sc-X8_FG51_>$i##v?dsr65m_Ms)F(3>wEU|@?ac1RV(!c
z<C~9tdl3X<Q^52Qv@jT-|F(T0%MZq)yxUS=FlO8O-4~g`NO4N&Mbd*2U$k)qO%BG0
zgkPk-U_`z4#sMB34Asf8_k}SS-XG=lB8p)2^t&YW1>==pUs=RFg5k0<`T%zehJ)p^
z`@%UGcN?9S`hxMx&UPbdO%Tq<n-{UFAe3}oaDbNw0mth;fDc09hs}Ev1R>u$Y$PoV
z0>3_I5z7xkX3qWtoCo236L}yqgD}-0q&G<q!h{{~jHJmy7#dr&h_N6<bb2851tFxw
z>wz!^;m!1^y@?_S-RZWGlm_ADs^6r(Ahh6p4sy33JdKEdAe@76`&oW(LV|Ght7}qU
zAkK{Mx|mf3;^@mU2YGoQ_8j~Cfe?Y%`tAj(FA%E-xQ(KPfmn8R@M4x9h`Gy`9^^a_
z?-))>eSt`P(z*{x55$<Qk)vpGAO?;7WHDob2z%-1K^`55fFn*1g)tC)-_i6Tia@yc
z`*0McfpGol`^C&75Kc><N_~N-)dfBj&Vi_|P3=QSATAf|97Ssa<ox<wsV@MB+6_F!
z%LB0M(By|g1YmROmwgBVu(HpuQeOZTU+TGp<p*HSVs?o00L;*=eJC;mF!8}pQeOZ@
zZhCDrO%8y0<j5tA1wh><=Maw$fX{(*QeOairF8HliU4%(HE1-Y0cc&ZcnR|efaAjB
zhqzk+?kQW<3g-Y^zZ>pJNB}OZpF5h?_@i`K@e)?$kA1Bg7xQv|?0~XX2!E_ke&3V8
zAK4z?ji!bE__X|y)aQ@%%(@3J{E-}*QY$k3!R{1#l5~GWulqyl^M`S0|18G*5!!N6
zF^~3#yd0<%Mt{69<+{}8kB;3vVkq@T%d_LMn1?@}&0AH>-Td)K&}FI5AJ=~G+?No4
zoLxOEhSvDu*jp>ISd|~XYj#HJ^TW1pT^|YIhc$_oz65^q`GAEnw9pUpPKhj*?}u3*
zw>ZqXA0`LrABjvqjQ#DSz9iibZ{;0`p~-&G+Z>iM=7&J1(8E015B-W}JrYJgyq>VT
zFH!iR{c8`UK0h=)>AjSB_~Fr<<ip&}55M_-^+-7Tq4MS}sm~8(pL>p>HNGe|Ph85X
zd{NYB!(m?Ti-Mg$OMSlhBEDNc0$(iYJZ20n^u<TVS1x7wzDWJBLhAFy+uofXi%egP
zx;~^IN%w^%XW1B<><f*lOzQK6uS44-JlYq%cbFavqc2{K&Fn`MzG&0w*ceKE(Ws>9
zGUnln`|oRya5rDv7&!Z}aP~#T&*(>pFOIKxCiVGXe?-tSR^@}QpQRn)<v!T()i;lY
z@IlV_ds3ed7Q9Ty(n246a4cyV%lE;wcefnj+y}7(s--?347=K^KS}pN<nq|DG}#9V
zL)`;6KA=yoNPRx=*y{d77=7S2c2s|&@PYG7xnn8y!JmiAr9L0rnfdZj?&gD^`@Z!=
zIQ!sS<&yq{_~3`E6Ju$OH}>jWma{5vd{rB9l$U#BZNa=JLU`k|(TDpJcw>IMCgW(K
zH{Ly@TF&ylk(8Q#lyh&4>$CTX$n?hGOOK^KZx|N)kE6-n2-3`0&X_m)KiF}UM|-2|
zraMxfH(nY!U;t5gqgk88ag=)F@&3)rnTI!SO}`=adE=*^J)R0@Z=AX?egGlfIJ{u>
zI9lU{-O5U-&kJAPef1bG_d?$K;ZKF|Le?-ofWQkGt<Fk)UPwdx&se?}5|XXQIQPP6
zk3~;KrWdT`B?Cyh7qpoz$J1ml_=OriW6TSE?qnR}(O&4X?%-2l^g`RAj&Bl$7aF%z
zjHlEK559Z%Gv?uin@Qgu<8EHK*sWIT^TLTUK5r6YFYO%cKCq7idmgao0ec>>=K*^j
Ru;&4L9<b+u|95%de*jU4-rN8H

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/spikes.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2/expected_output/spikes.h5
new file mode 100644
index 0000000000000000000000000000000000000000..a4c6a361dc1f4f34997381d637272c354c864f99
GIT binary patch
literal 7112
zcmeHL%}xSA4DK$X8^j34gWzQ!!2<_xu2B>dqeeZLc!4M(8^cdnVvHw_`UXCNkHFO%
zkHFC<@D+4AZ4Frsq8^CSNtkxqPG{!Zwq$!>+TK}6<x_ye^I!%tmX+z1M}L(h@+|r?
zGY-=`rjIT$4kQ6}D=g2je?LKj9?MUUi$yS&;$JAM;bE3IPXtP*3V~8_^9V0|#<!Lz
z?Q@(77*Q*{szw+|G)kiQA<c5U#^X8-YbIB4pIJzQ2lYxVyfDvrE|dfKc9wJ8Qid7Z
zfY*73UxDjtI|`ePkLw&-Dc2K<PDvvfWw-e-Ic68M6D!HP=Q%R%@`|tWu9YK0%{vBc
z%1Au#e7=9c^;qEOg!O9FsnlC0_i)t0OUp_8uakJ}`Q+em+c6O=aW~-q3-QNE27c@u
zV{b4ehEl)ccn#N~WrK3mY<I#&4RWULU=70`VNGv9aL3wK=9fY;sW6`dy1R9_Z|%5X
z5BtFt7&pT!2aCf`$}0kjfFhs>C<2OrBA^H;0*Zhlpa>`eiojn$0Q;l%o1Z`Y9qvdv
z+~1TtNWVW}^k|y(H@No`Kw%yVuiXDh8Y$}C1iAItU&3|81-3e*Z3Iiq;+nmumvev{
x*>WP3`daRLU$&PYeGIusd32j)w3C0R{eE0!Y`|a}iZBf<D!-4XuJtqN=?%(ShDrbc

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/circuit_config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/circuit_config.json
new file mode 100755
index 0000000..ffd4224
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/circuit_config.json
@@ -0,0 +1,20 @@
+{
+  "manifest": {
+    "$NETWORK_DIR": "../input/network",
+    "$COMPONENT_DIR": "../shared_components"
+  },
+
+  "components": {
+    "morphologies_dir": "$COMPONENT_DIR/morphologies",
+    "biophysical_neuron_models_dir": "$COMPONENT_DIR/templates/nml"
+  },
+
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_DIR/biophysical_nodes.h5",
+        "node_types_file": "$NETWORK_DIR/biophysical_node_types.csv"
+      }
+    ]
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/config.json
new file mode 120000
index 0000000..a7569e2
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/config.json
@@ -0,0 +1 @@
+../shared_components/configs/config.json
\ No newline at end of file
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_node_types.csv b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_node_types.csv
new file mode 100644
index 0000000..4c42dc5
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_node_types.csv
@@ -0,0 +1,2 @@
+node_type_id model_type model_template morphology model_name
+100 biophysical nml:soma_cm2.nml soma1 soma_cm
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_nodes.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_nodes.h5
new file mode 100644
index 0000000000000000000000000000000000000000..c49819b49a122ec597a8edc143fbca0d7bc0f9fc
GIT binary patch
literal 8536
zcmeHMJ8u&~5T3JfI3<phpa={EaYz)DE>fh+A;st_uz<o61rD(lP6FGC1H!2&p`uMm
zNlBTXz)wh-k`hs+3p+dCSa9ZI8{){1-D2mlb91|&XJ_ZuAEV6&i}N?;iJR}!C0eqq
zcBg2SJEBop$E#pG&<~(rGQxP2BOWV2zXbn5RuqTOKYd&(k+D?&N-<0abHe$maCD{+
zh)Va%yx<B}tx@_7ai(B2nzee{2pW%(4*VlsM!Y8DI!{HjSNJ`1lqa8FZ|%g}M&^03
zo+z-r&SPJ8n6VA<oNxF7y{+%I<7T7xIZvL{<tb&SGNL=mzNV-1j1}9dm97JmqX7G<
z-@f~ddAohr1My5KlKW2MDMb7z2ruGh>t&}MZ*RS_DvkS44Thvo9zNRS2-dhe!g-;7
zlW{zx`<XFM%LC@9x9uMGcfUMvvLg1HcV`Abw@{0K=7F!kqYPSH9W6k~JaBwj-lusW
z8ONiY&E$ILI>llJ;5<|Y9_kFmQ)$*zB+T=EmsAnj#pjH~`b;KcO?~5snXGq`w+7ve
zEz%XpY_sv{=QE=BGB756ZA|9jrr{892si{B0uBL(z~~W>x-v%*Ue&rTj4f&mdjR?H
zrsxA9RK5l#g%qK$>W6ZQoqpGTUq~^4n(Hra;Z>pI){nlfq(xb?A|}$f)|LN*$M5%s
z>2<abJj7b#VH)um?7JgBVe#?zd)Z{Z>31LV<CgsLebS7Ehoe)5fZoScu&w~~2<Me9
zw*%%K=su{PbL(n2B<25Ep2sz^bg$F0g7IPHo!#b}7LWcZH)?gAhWYnIn$DvN`Mk;S
z`B?5VmV=G%y~o-Dt)1fjIXy40448+y5S;f?2l6L%58v)cTfcqwV|wZy_qpdQz)cjK
W?QdE}FD|ZDCnByc4v)JNfyXc9iM&(*

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/node_sets.json b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/node_sets.json
new file mode 100644
index 0000000..2ebb09c
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/node_sets.json
@@ -0,0 +1,5 @@
+{
+  "soma_cm2": {
+    "model_type": "biophysical"
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/input/simulation_config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/simulation_config.json
new file mode 100755
index 0000000..c34a77a
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/input/simulation_config.json
@@ -0,0 +1,55 @@
+{
+  "manifest": {
+    "$OUTPUT_DIR": "./output",
+    "$INPUT_DIR": "../input"
+  },
+
+  "run": {
+    "tstop": 60.0,
+    "dt": 0.025,
+    "dL": 20.0,
+    "spike_threshold": -15,
+    "nsteps_block": 5000
+  },
+
+  "target_simulator":"NEURON",
+
+  "network": "$INPUT_DIR/circuit_config.json",
+
+  "conditions": {
+    "celsius": 34.0,
+    "v_init": -80
+  },
+
+  "node_sets_file": "$INPUT_DIR/node_sets.json", 
+
+  "mechanisms_dir": "../shared_components_mechanisms",
+  
+  
+  "inputs": {
+   "current_clamp_1": {
+     "input_type": "current_clamp",
+     "module": "IClamp",
+     "node_set": "soma_cm2",
+     "amp": 0.0001256637,
+     "delay": 20.0,
+     "duration": 30.0
+   }
+  },
+
+  "output": {
+    "log_file": "log.txt",
+    "output_dir": "$OUTPUT_DIR",
+    "spikes_file": "spikes.h5",
+    "spikes_sort_order": "time"
+  },
+
+  "reports": {
+    "membrane_potential": {
+      "cells": "soma_cm2",
+      "variable_name": "v",
+      "module": "membrane_report",
+      "sections": "soma"
+    }
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/pytest.ini b/examples/sim_tests/biophysical/one_cell/soma_cm2/pytest.ini
new file mode 100644
index 0000000..3d8fe4a
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::FutureWarning
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2/shared_components b/examples/sim_tests/biophysical/one_cell/soma_cm2/shared_components
new file mode 120000
index 0000000..d3ced13
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2/shared_components
@@ -0,0 +1 @@
+../../../shared_components
\ No newline at end of file
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_build/build_network.py b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_build/build_network.py
new file mode 100755
index 0000000..a53aebb
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_build/build_network.py
@@ -0,0 +1,24 @@
+#!/bin/env python
+
+# Sonata Simulator Test Suite
+# 1-cell circuit, single soma, only cm, 1 step current
+
+# Authors: Werner Van Geit @ BBP
+
+import bmtk.builder
+
+cell_models = [
+    {'model_name': 'soma_cm', 'x': [0.0],
+     'y': [0.0],
+     'z': [0.0],
+     'morphology': 'soma1',
+     'model_template': 'nml:soma_cm2_hh.nml'}]
+
+bio_cells = bmtk.builder.NetworkBuilder("biophysical")
+for model_props in cell_models:
+    bio_cells.add_nodes(
+        model_type='biophysical',
+        **model_props)
+
+bio_cells.build()
+bio_cells.save_nodes(output_dir='../input/network')
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/.gitignore b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/.gitignore
new file mode 100644
index 0000000..1f57b97
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/.gitignore
@@ -0,0 +1 @@
+/output
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/run.sh b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/run.sh
new file mode 100755
index 0000000..5c5107d
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/run.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+rm -rf output
+rm -rf __pycache__
+# python -m trace --trace ../shared_components/scripts/run_bionet.py ../input/config.json
+python ../shared_components/scripts/run_bionet.py ../input/config.json
+
+pytest -vvs
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/test_output.py b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/test_output.py
new file mode 100644
index 0000000..3e16989
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/test_output.py
@@ -0,0 +1,66 @@
+import os
+
+import numpy
+import h5py
+import pytest
+
+output_path = os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        'output'))
+
+# TBD
+
+'''
+dt = 0.025
+tstop = 60.0
+stim_start = 20.0
+stim_end = 50.0
+
+start_voltage = -80.0
+end_voltage = -20.0
+
+# Using as 'raw' code as possible here, so as not to depend on other code
+# that could contain errors
+
+
+def test_soma_voltage():
+    """Check soma voltages"""
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+
+    voltage = h5py.File(soma_voltage_path)['data'].value
+
+    assert len(voltage) == tstop / dt
+
+    time = numpy.arange(0, len(voltage)) * dt
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    import matplotlib.pyplot as plt
+    plt.plot(voltage)
+    plt.show()
+
+    assert os.path.exists(soma_voltage_path)
+    assert voltage[0] == pytest.approx(start_voltage)
+    assert numpy.mean(
+        voltage[
+            numpy.where(time < stim_start)]) == pytest.approx(start_voltage)
+    assert start_voltage < numpy.mean(voltage[numpy.where(
+        (time >= stim_start) & (time <= stim_end))]) < end_voltage
+    assert voltage[-1] == pytest.approx(end_voltage)
+
+
+def test_spikes():
+    """Check spike times"""
+
+    spikes_path = os.path.join(output_path, 'spikes.h5')
+
+    assert os.path.exists(spikes_path)
+
+    spikes = h5py.File(spikes_path)['spikes']['timestamps'].value
+
+    assert len(spikes) == 0
+'''
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/membrane_potential.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/membrane_potential.h5
new file mode 100644
index 0000000000000000000000000000000000000000..04c7302269766da24d4f4ddc85a96014375281c2
GIT binary patch
literal 33712
zcmeI52~<?azU~WDoDc_$5n~KdgA)$1n8%*!hNkJks5s(OfI&o21Y;5s4N*g!P-6ix
zIN?Oph%sV}`J8Y_fkvEARHBBcA;yRkPI-mGx$oqj`_8*>t@rM|@Ah7cuD$<NtN8lI
zSO2|t_3mPxUZZQ(qEib}w>4`<8k089cN<>*tlzfHei3OnZm5r`-*Kof=hl}S9AE4>
zkS3(Au48??O@06Fja~$H)yD@}wOS%uHuT?6)>o4iPA~SFH3aPCe=7odt<qfghKJU_
z>jpm^srOj}j7ejXlHwC%$@nqT#?-|ce5q(?@b4_!*8BCZzIG-GIaccWZ$_M@yHh4i
zO^%<O_`G#poDlctuMQ3`6g0?eDC;WgYMjY{`hJ|`els#@Ol<r(8Lu0Kf7g#ZuG?n5
z7^!lvfxz?dzj|?yz1Q{M(5m5m)OSkU>&MeS8+W(s2b|(x{RVsBzXO54jyrw*n^x5O
zr-4Ci{P^U${Rs&ZCQV43HadR%i<*Yxq{+{#Nqpk?38|x#CdVgEn=n;2nHE23LS4%j
zqvVC}>yB-vD2)SgtRH=Zq;{x_{@Yu_dEs3Bd8MJhzxw^(?&1H>8VBO^f^9tzhx&}r
zke3=bHI$7c@w)xG{PTjT;yIWm@~AHE=;-*oX*1bR-A*HiMJ~@9)VF@IPe{A^<GMD6
zeYb`alHO4DA6mZfRg=H@%I|Oa^dHM|uMg{6{^R<FXoLSMn>IxLaXFwqJk<Fg*Ed8J
z^*eE`8Y2I>%K!VmTJc}XSO0z<FUC(>_t3wMGq0A!>(Bc9^>2^2y#GxussEvd`DZ*D
zu7euNe}CTDP|u+*Q~k^KpEd9NGamJScJeRf|EWJx>$x;s`MqHCuetok`r}{zVs(2a
zMK*uFh5miK;i&R&@#iO>hOoV~6R;Do6R;Do6R;EbFGawCH2uqcY0u~S9bVjCl9=W%
z-cG~${;$W4>hC}Q>GgA?7r*9j_p6SLQv1E=dYhbItLy&xt=nI(kDQ7A`P6{}aUtzx
zlaw)2<Hw9mm@qnV%<~BgH#x6Ycja04^Frf`JHQ6Lb!BQ7`69O$vA@3_dr@P5wG*%t
zuoJKouoL+2MIcNaWqf{Kte?L5pU<0hBvSr@<6P^%1nh@)0(Js+0(Js+0(Js+0(Js+
z0(Js+0(Js+0(Jub=?T<5cUt#+U&C|W4Q2Wp|7+>n{9e>Iw5yxM|3}+^QGXw8XxA{$
z(D1z0-?y?K*$LPQ*a_GP*a_GP*a_GP{O2Sv2rqQmOFM@;0(KwRePH*2eH_^HfISb`
z^ME}M*z<rr57_g7JrCIPfISb`^ME}M*z<rr57_g7JrCIPfIScV*UkgqB^(#xi48N$
zS8`r!gRd@;vHLdM-5yM7jSXMDCKn94Z9`&ag%H&?^r_v<`3)PcPk4v1DjU|F45##}
z4P!$)5mITxYXvuisIZ};V-e@&Ht>(;GIqv>!FPsGT4sam=pKZeu;IiH_k|EPeCk)s
z`B59f*DYhL*oLO<CQy37hJ){U5ds@N__a}q*keP;&@#@8Y<PTdHDfz%*!AXAN(*h6
zzEVlZHX8=EY+E7<Z1{afCFdJ$D7dzjv3wiiE$>sh#s-hQCPMOTxZ1l*iO97f@3Y_J
z0wFexZ2TQ#%Wdd1C6m%D8_r&oOG_=XVQF}u5|L?x<(o&G&$Gd$`!U8cZ1`ajr*yUr
zbDze^C8%uBPV_4gvutoY+ccY}+3>ykEMqA)%-WVuX|fIeugY&8CE0L)p0-3J*id-C
zeKwD`A!*z-#+VI#PZUx*&W4*ovk8f@Vf{vHi5OwS_zqpOd9)3$&;En4!8Tm_9hBN^
z$QiMS5VH+KkB%-8MjKx8>7UIFHk@4jj4_=J3tN{`s<y#6>vKXBHZ;GHP$GhCD1Iv_
zoBP`^dw<JV=3|4R{{<>L#M7Kjgbc7@ce9x#!qbKs(+%0YmknN5I>s^&8~!j|r?i_5
zTfY5<5O*8i?)h<v=xjsJWrMT1n+-oZc*L>}Hmpv(N2#j~qc0qkUt+eQvwmrbaJHd*
z$GB|X+=k_^(^%$YgKdGM7j0xio5w%Ofn!5S?5Yy+#ESW+lCpWN6=6z6EW2+-<1MYd
zXpI&7I$f6jv*Nvvx0Hx#D+2Gno6T=n@h~PbmQ`8tbxCJ0dew@l0oBrfR`g&0ZHcI`
zqT2P7Y+i1~#`Iya?2Hxcw_aYf%!+QqYNh|Is4PBGB7_y6(-qnLs1?KVVq;mc6)(5)
z^`Zx?IF;t)Kw!n<s?*YcR+wz-vU!meEio;Y?X=>Er^bsGTJaHgbs*cUP&r+d{<GrG
zsoS&pMl1GQ{vej+Tajk8c+oXh_!PN2kUT4D-ncFOXT`Q9-^(RxteEuYf>^fPirxvM
zyl9pczntsqKo(iCR{K=?&x$eIMK+&jMVHrdV_Ak37e0C0i_W%U#lrvxl5WLY6Izst
zSyr?=SuXu&#qp4hu`I=k%+0A@G}#J6N4*0{vcl=3mrF&06$k#PlK!(Iebmla#;geb
z;Uh0P&WcCAZ#j?{E52FVy;O{_Vp`j~(tlRG`QCw8HrR?=H<x%(n-!afjCCMpE8-5m
zSt^WHyz!<(4mVhF<?|D<OlQRxE%Lmm+KLe~COZ&?6>ir;N=1+rXUr}++~10<?=DLJ
zSz+$|r5B}EwEAq80~uh&u|~#H;c3OkNw4JaURG!>-jx2c!XbRO7wu-n-ktLth`SZ<
zbc-$(ovrX&)H8>>S#j^l1L;32w#Og#qOMj<KC@hYk=_bVH7ga)R@~U?ox_`3k>9yV
z9CNZ_+`LoLe^$8PUn3vgv*O~|<Wlj(g6!j}9A0a|kf3&P?7ju<H~u93XTgszedR!I
zTd?56^iol6LB#J-IsAqN%|^Ty$EqwibmW%wp9LR!?{y%R7KE<;v{Y1B@Wf?g4llQ$
z=pD~EcE*B~>yM@XETC`w;6P4TaC={NsSp-?*>7SFKWf3m9RE00Y(bA^&AsUX3$9H&
zC;ex^s-M=Eiai#LGR?^0MHamBtuBu3wBTHi4&JoTf@Mp8mj1KA>hN``D6pV);+!15
z(E@Sa7RT}}m>1T~o361yx8siVp9PIx-(M<nEx@OXb2zu)-A6HTY`Fyiu>-tmmIV*W
z{*?Z+V29#(smQco%9ks1_&f{xbxMq585aDS5$sK8Td<+V*^#7MFd?Qw`p<%{C7W}2
zngy5r--%->7UbrKd(&hKqFp;Vk|YZ{q~DPKv!JYcR}PQ2U{UnkIL0i9EFR)b$63&V
z_HZOI799TKzVx33bDWEFc(et|v}JK@um#V49`8+U7JO^<awKL8QonC>To^6z_AHbB
zv*6B()p1N`!PX{Iy{X!QgsDnLqOhRX<u=DfkOfr{mC}C}tl70Sj`>&+^Tzw$lv?oW
z5|bktV8QukuO1hk7JT;hZ_<Aj3_7<bj(J$nR-5TfyID~B)o@4RZowyA`WzRXEzp1R
zNczu$CJ&Fsu?`mOAJ4t1s|D}>7$+B*v>+(N@3?TbpmtN!T;AM*oiCr2{<9!?PQEv7
zWWj(xrpu+uEck7t_PBUr#-?NKb9t>9vA)-&|IFyVw$Pi_nDJAa*^cD487tql9v9VS
z48Qq$F27+$$02`6|Cw?60KDl{GnNck<VY&bi28i=aZzE0bBq4DyxfeVDbJ+;%*eP}
z;!VrUP@6w@Bqz)u&rkejeAg=|mmf7_=JJ;Dtk?|SMi-?2%(y#wlOur{Usa?X7kkV|
zG#GMukr{n<c8q5`&A8t6y7ZqJ>lS|FNVb_V_DRNZQDDYv@q=^uMl&i-zY)*!&ETqg
z(tl<Q-g?lH<eA~xdFgSHYsQJW<8nDS<I{Ts<JodE!pA!L&@3~W9{<siEHdL@;Hu*y
z(~J)`B<1pXW`w+?h-VpQJpQ1y51nnsu3ML+|IC;^e9Lh$%Z!0X-p%D{X8i6I8P8J8
zC|K3mhbEg5?@}%OXNJc+-yRnUW?cPcelCwUBX7{Kc*e{axv!TG9cM<TeznqnW}MAF
za$JlsV`<YBxjfno%e2^dHrNc8pL~3%&5R!+of;9d8FP1^mi{wC+hbiWH<;nLbXq*q
znejc*_)xVOvnIJVA__D7&tH-LGvmH)doK4kqp<LUc;;h9lDox+QZxE~Dp#%^V8+eb
z-=+V|SkJ!C<-N=pU$!8gd6@CKVw4Z<X2zw0zKw{x898oGrT@$rnjvzzn;9?F<ixWM
zW}F=TwhwhRW1$F;OW&Dc^lx!OIGfQtzg+syjN*11<C&8gv)@nkp^eN?RENo>;mmmS
zRlhu58-;0~l=#z{DBK#KP$sIQ5Es&N603^Bm6ta;k;*8H_(Pw^%cF4S*f0LHEDGke
z8D&C5;n=%xOk%}R&<r`~L=c6&1IFd?qA2*aa15Y@QP_SpuS^s~!SlP&Ni07K`O7ak
zk-R9lC%v1;c@(k@odalA6xw(DwoGJ3VZoE=Nh~7@&CWb@BI!~1aO-DzJS_@O=K2KC
z<S3+!JzXXeqHsHK+9bxJF!3eVrX(f`*KU24$D^Y#>WDdj+M;l7)$e7(7zOJ)3nnpL
z6vUvuO^G53x_%;$`$qvy-wvQO3IRVgKP5b)uw(azNz5Y({g#F`CGJt!FsUk!yG5aE
z*hc}>H43@z-A@VUD0FzVe-d+w!lJS<a%IjawD^*&;<YBs$@n6G)|l{YbjT@DZ9=O5
zMaj>EJMCsQC6y*5RCij%%T1^{R1`qVOo;hn=qVvgIG_4J@-tzOb$L?)6H5Ddui`}}
z=$o99{7l$?Y3eCaU_#KYwuvm?gq@4GH6?i_40t<g73U^w(%h2#Oz7U_(^DeTgq08a
zB(e+>I{tX9DM>eB$)@;KJk12>In4rTvI!X@*PjvzCXnYB`X<b5^Rwh<!rdFQSMg{Q
z5)X6@q&5?-=k7Ztj3$gtiAiKS6Dp$ql>AH>+-v13?r*{g$KXIpO$e{JAo-ba@avh0
z%)^9`g>KD=y9vAEcCF%WCJa;!38bzj6ufd@@-xBX-qJ+oWI|pkm5<Du&}qX-$uAO1
zKbR6oYa-z?yv=D*9f`SKTN7DTBph8#%}8Y=X8lqv`9<PBJ_)2{kx0t!eOib}+)O^2
z$ciH|J~FNuK_o7DG+oV$A~BTY2hzewoGjOz76p+o7G9P7B2k?AVKb5!2?cw7HRqAo
z9g0Aj6$vl5(WgabB(~gnD)~jCr^sza(j&2YUEpe-7KzU9pO^e1v3zLSX^{|#HUm3O
zW-Jo(TYl4w#6+U;&u^{f(UEv>?_J3+5)VJiIxUQmm^x+PWTuNmb@-3Xh$0fKd(vv|
zABoDRE<uz=V%XU)PYcgToZ4ob%se7tn*Xch7l|X|=C9^%kx&Kq3Zkx&*wf+2Y2h3R
zpWAFQbBe^aqfO+BMv>^fX6<TTYsA`F>L6NUM3=!=BtIio^#5Qot1_ZpbNA+?(um9}
zdsp*vBb@e(45DR5q%V6S`5EyjF=sL>He#ASpgDmNw_Y!o{EUcuJR^t}8gb=RhclwU
zh!I=9p3L%%IP>wK<|NMu^OzdR&xm6IOM+;Y5t{aIo)MWw?EUTdWR_us-{HjOB;APZ
zd9Bv)G$TA`76j2`Bl2w#XGDS#?tO1cenw<F&1+6#jA&okV-1fsVnI=H5VaZ6ENj9U
zVKm~ygvLosXT%fjn&w1dM9OQbHQe8b+Yc)xKO-ideE*E_G~(LkE=kP8h*2MX*POT;
zac<OzHQdbztKVbE&j`^r`;2flLiej*5_2*F2hU1=Mg*)(S;K21uw%wc!L%j<{VY4q
zi0TMz=xs}4RT1dg_>SZkf!vFW*6{KOboi!!FfEI~qD7@=gor?kiIb98aRlb5om&t@
z;92L*Yj{xvQtumrX<-EJ9KSC4MId40$4M+d0#zS+v><sAh#7Hc4d)R!?>#=4W<_97
z>qciqW&}#FuS#MW5zy~fv>@pb*q?J*@{2&w^!I{kas+moUOg)kA~2xmo+QR1u*qR~
z3lbB7?iXq$zX+_{u_Bn-BG7Sx?^$7tz>?TAl3xUzmD5`gMFcWBwO`BqBS4<t;74F)
ziRG;DjKJOe+mc@d64Mv9Anp;k9^G#(cZ<MSS`tiMBT(U-a8@`+U~pB7Da<JXC%)e(
zS2~VBIM=V`wc$88^%u!693jSxv!Xg2yWV(X3abjoz&{VPAeG@LI5&1JFAs;uc83sJ
z7LL46^3Dnoj!qLor?BF1EDgCN`Gv!!<GX8lQ8?!Q@k$6S42R<nyU&V(aLig8J%#0m
z<Nmu3CBJYa4f$*>=i#_Hz$b)eg=2h+(~@5}E?rHY!ZN}!^t*N~NqRU=F8^vRPYZ`J
z$s9tH!%=MbUGfWuqT7NgjD=(O6VH|;CLCU8ept(+!?9)S#1Lu=N6&f9&k18VR*&5<
zh3Uf4IVh|pQG{dpOI4CzINJO^Cxp^)%s<lYobU`s<JJ48FpqG&_s*D>#627j2a$E$
zEgVz(eGx)k!%^Kd<eYF02m7f)@(V}h?sw!0(BT-iw9`6XYrv^VMIp4t08`k|bE4XS
zBkm6*KLb>cmbE062J9*GTF1)`@cFV#@-tvt#?*5{7|=VW?NnB5z*_%pEeQ<h;u^J%
z7a6dk`ZvkXfOf^1=R|=4nP2po%JL0xN;}q)<Qb4|jbF#P0gw7L3#C~GOlz|KoX9lb
z)+Oy!mSI5Lu4|H?0aq5!UdPi681Z)3P?~JO8O^?PBEbN2mzb%H8F1{uGs({Y&5xh2
z<Ix7}-4ql`Z3g(wxghx&uzlprsZ3{pr>~p*7Y7F9x7oFh`y1eXb8sl724o+&C;1uB
z{_~|%nTG)jQm8X=H=vpMq~vG7hrOnRQda|>IJPMl&IY7ZY?;cO47mMuq+IdZfQbvM
zB|kl`#eEV=YxEeU>Rm3X^*Hy+(W$IT59_^HXHuz$D0Rx`<$CBgtP7=Odf)?1xe$5;
z48JP*>9ND>LuUd#`nkNG&x`cf@XPn1v`~+(`$m<E0zGoGpGtmubeNXwO!D+t6d9P$
zxgITgoR|Fcm_yRaMW!Cl%3n@q8G57^?sO*Udfdr;E1#$7k-+XsetJ}eW|fNsJ!0Gj
zCNrkT`8y|^NsJzY#N>P)tw-rP7X`KHp@09&a$(eC|4?Hx)9Dd3@K?!CkDV>&=W~BO
z2K?MpL8%^__8u-5o_cg&!IGJW9xJCbX+_-i=oqm!pS$U?q`O){UG;E&_LJnNN5<Lo
zWagv?c|NhH$ISVA^LcF;?v5L&pfzDg41OZ{h2eUKoMcuNhOxK(Tan5zR2)4g`GsNd
zni&dO7KRhEI-D0G4B>;nPG-enIM{zsD}peDG_R5T!m#VgVg)S>!@xZQ&WnOD6f8TQ
z%<{wFF*&gn$qPfCzSVlp!_cW~fr4g*Vd>-W^CB}0E~jrueqorqWo|2y9tOv`J=XKI
zFw7cLtf0wZxF0a#yhsQ`Qv1f!7z@MA-&VIGF<}^gSh=1@hv8CQrQ{cep)=n<FN|S0
zY3nkL>B3;_`&}!d2t%>ci1pk*42sG}l3y5h7xDALGYno?e$$vo7`7ywmHficQ<t)y
zyM<x(YcDCOYZyA$7M>T*VOW0BI*mDnp-sUba$+<L^FLa&p4aNocyxayt<m8<ztZ!f
zT8D>iCrx8jI!yhwr3<Olq59ya^}JjMw$h-aWja*OxGwqWFwFAtG*+y`soowg1Ui@+
zA6n0gbU1QxoRSvmp!&w~f+)~o&!Sb+SiTNE6BRBbPls*l%aWfCy<dG#NwaiVd%yDq
zk*PzM6W>l_89J=kILw8l>(Fj?t>mXe=7<$anyiD9kM9MMphJ4=Gm@VUkFHO1Au&2k
z+wZ!8N9%AaXS<Txbcma7xgd->Tru62{B#)6bD;}S=y1lN-v;ilgZY9`QmVtT9dBO{
zo;qk2w3yC3bl4la(S^9{;HT7Y;BGo>@AQl0r-SF+k1hyj9r8=MPiIa#xUWCpLWmC8
z>0>wWS}ocSb5PM5Ef&zc3!++!X01Y}vnnk<thy-qY4POySsQq{7AgD{6)n@^_SD@M
zgwSH5F?u>H*5cY54<$b>M*X>b1259z+&OO*E!4ug{gmXVh4>_SI?LBWH=$i?lBWei
zzS_XK76Bd2Dw?Imjz4Zmep>YV;nV3XLyHY-JzJA>ExNw<!v>zFMedM^Dw?cChc}y7
zhy*Pbwb(G7F)dnL)3qisTFm+GXUR{CXUpfPs7;I1q;3_$sKp(_{^?AoMMAeRt%*X5
zswaO+ep<wwS*fB_i}PE9D}<*OgXUF8ep-}{eWx{X*FqoEX(M;jV*g7;D(b35(C<Sk
zgtHbqkKC91v>32@nOwn2i%su%ZRE8YbbqT%^3z~tzo`|XT7!<w+NQ874VL`0wKb{K
z!1-I#MqaK##?s#;KMlz934IM_hV@Bd#TwjoKh~N+gTzO18+nli*UOr!X`u#Vzs#=?
z1sYUjXj53e27_a+Nq!of@SnYra}B~>yQ*oH1_!HAAu=@xDIT4|GBnur#WTrIgMn$E
zZ{%qj6j+1QG+6@=&kK^D26;_prZA>Kr^_ANkQfb??)qjUkJi9t$zV0LX)yQgdy=09
zj@qRuOsB!DF0>6%XmJ0*j~lta21!3AsVUXq=BCycg{KDN=WIz~9vWO48QF%oYcSNe
zTJqE2WSdXa)KvrH&0ZIUvj)Wnj-)Ur4HTcp%9X-2*q!3EiPx&(WnQPIHEL|>rMW1o
z)#%yis^q7}>WUBAkV-W=?{we9%hg!E@Ow2aQ=?7%sEb0VF<<pm@>8R6=iD{~YP@$Z
zU=uG=<6&vJ<fq2e4XGDJfg05xygY;DtHFlvY(w(YsPuYk6X$9SbGa+|sd4I;B^O1e
z8m4`3&R`j89LYY>hNP>Znl^b8Pg7%0q>F|otKrk*%ZnmGjcvp@gE2LFpT8;jsj;?j
z-X<QcMwd@}YN$<(73}auVN|1?g3Vw$H8S0rv?U5PoNCr=;{Ix+3zbHGP=H74ev<su
znD&194CbN6t)Z{ACGKj(4cxnlyQy)d<wy;6Rb#}@k0n1f&g{*e!JO1Eukde6h#JSH
zoRj=i&_vA8&>9u?cJFXWRIA|kY{v{%rNZ{Jwzi~F1<$YUNPa5h&tI&eWh%IjA8<(s
z6|#em&tSzWw0}9VErALPZaZ)0MJhBqwpl|9RrqjC_$5)G!joAyBtI2W2G4Cv@>ICp
zzlZ!FN`;Bdi#0S$g=<&FUlN%rjM~#Em1U@KZrSR#BwYpTWaVa_rh?E{N`5Nny1su&
zB&dMLuck7lLcr-gZApv@JGKnp%%fH4H}{d`r^1FY{E{%L&^6F6mFZN-ZGTqsQ=!AH
z>6^K~3X2Z6*HWrNi&ce}gr^E~W?EC3hYHVZe@K2Rr1o93nY*cQ$Em-Tx~h;+S#n7@
zt58*xkjk7?h{<Z%jt~{jCv4ixYn2$JGiYgz5~Z(Qm;98_*Jh-$Dkb)xe4`zyR3fP0
z;AUQ~#Lkb#X=#}f14cVu7D9<leydVhu@c?eDcTVzvGUhTlAjVC5523Ug-R@0+4-_4
zP{KL&+f<gXM22NpJCdgadHzA35;GgG(9$d=?q2k{EHafy{N}Xer^NL|)7p`ACB{y4
zE#PTNRH(OWX|fW7U$tBo2}+!}|GVU;MEHpX?MRFg2RHUD;L%Ei%obW|Q)1VMw=WB$
z5(9l&q%oZm1+6!>BMK!vZiE$Ze<kwvS4n<KbjtncvhY-5>GbYt%tHy6r~~bYyApGI
zjxFGBO2~f?qob}$%)0Q!W#O#E{T(4`%t?u)1s5ehC2q#fD&VyWj90#*qcsX#>a_c^
zs8(R;-Jxl$N`aFl4<tVYjO&*d@Nxx;)4g@HOaaBPQ<9$oyJ>P7D^|d(RXbM#1-4Xe
zE8s;6^hA`77Amls-;(?k=$!m%8p~H;xzW>=<SEd`<A(yy6`22LypCom(73!=rN~s^
zz3uDMScU=*Khe38bOokP_*wE(pgLrZjwUO>I(DlR2?|vHu`i7=1%~|)<4R%_IJNdq
z$xi{(dn<L+rofRQ!Ii?Ofa=W($xnejE#7e@3I%+wxqZp~71;LOE*+%`^!{u}rSMc>
zZPI<oPk}Ds%Up@O0xP<CeaYPvX!rD_<flO9nJJaRSplbQZDukj1=8njb(J3wqUKQU
zFj^Ces?_tJvZ_#&_vyHgmxn@Jdh4zbq4<7rRu6(uY}foaj24Ds-2;~eEI$-0HW~ME
z9*R#!&c7=%L-AglBRxoZD5e}}GMpxdVtk5v0b`*U((8kLJUUd)6Yae#jG+i#_@oC>
zgkpdyU^u0r=yq?$0_G8l4jaDS$K68Fe0a@W;T(!5t={ZONGN_s;&56Mf-A`d3s_YM
zPJ7&x`a*D|yvIEuLhx<ogq{Q;*b=&CI4umpsymfZUkH}2>$0Eo5PUpz#66K2f|)I|
zdy@1JOxk-^>I*^4l$RDV76My$+kPG$0^Qj~_k=M7{_{(F5=96+gPliE8iLnu8x}H;
z5VTwK@qX?Wf+m9x-4o6sc-X8_FG51_>$i##v?dsr65m_Ms)F(3>wEU|@?ac1RV(!c
z<C~9tdl3X<Q^52Qv@jT-|F(T0%MZq)yxUS=FlO8O-4~g`NO4N&Mbd*2U$k)qO%BG0
zgkPk-U_`z4#sMB34Asf8_k}SS-XG=lB8p)2^t&YW1>==pUs=RFg5k0<`T%zehJ)p^
z`@%UGcN?9S`hxMx&UPbdO%Tq<n-{UFAe3}oaDbNw0mth;fDc09hs}Ev1R>u$Y$PoV
z0>3_I5z7xkX3qWtoCo236L}yqgD}-0q&G<q!h{{~jHJmy7#dr&h_N6<bb2851tFxw
z>wz!^;m!1^y@?_S-RZWGlm_ADs^6r(Ahh6p4sy33JdKEdAe@76`&oW(LV|Ght7}qU
zAkK{Mx|mf3;^@mU2YGoQ_8j~Cfe?Y%`tAj(FA%E-xQ(KPfmn8R@M4x9h`Gy`9^^a_
z?-))>eSt`P(z*{x55$<Qk)vpGAO?;7WHDob2z%-1K^`55fFn*1g)tC)-_i6Tia@yc
z`*0McfpGol`^C&75Kc><N_~N-)dfBj&Vi_|P3=QSATAf|97Ssa<ox<wsV@MB+6_F!
z%LB0M(By|g1YmROmwgBVu(HpuQeOZTU+TGp<p*HSVs?o00L;*=eJC;mF!8}pQeOZ@
zZhCDrO%8y0<j5tA1wh><=Maw$fX{(*QeOairF8HliU4%(HE1-Y0cc&ZcnR|efaAjB
zhqzk+?kQW<3g-Y^zZ>pJNB}OZpF5h?_@i`K@e)?$kA1Bg7xQv|?0~XX2!E_ke&3V8
zAK4z?ji!bE__X|y)aQ@%%(@3J{E-}*QY$k3!R{1#l5~GWulqyl^M`S0|18G*5!!N6
zF^~3#yd0<%Mt{69<+{}8kB;3vVkq@T%d_LMn1?@}&0AH>-Td)K&}FI5AJ=~G+?No4
zoLxOEhSvDu*jp>ISd|~XYj#HJ^TW1pT^|YIhc$_oz65^q`GAEnw9pUpPKhj*?}u3*
zw>ZqXA0`LrABjvqjQ#DSz9iibZ{;0`p~-&G+Z>iM=7&J1(8E015B-W}JrYJgyq>VT
zFH!iR{c8`UK0h=)>AjSB_~Fr<<ip&}55M_-^+-7Tq4MS}sm~8(pL>p>HNGe|Ph85X
zd{NYB!(m?Ti-Mg$OMSlhBEDNc0$(iYJZ20n^u<TVS1x7wzDWJBLhAFy+uofXi%egP
zx;~^IN%w^%XW1B<><f*lOzQK6uS44-JlYq%cbFavqc2{K&Fn`MzG&0w*ceKE(Ws>9
zGUnln`|oRya5rDv7&!Z}aP~#T&*(>pFOIKxCiVGXe?-tSR^@}QpQRn)<v!T()i;lY
z@IlV_ds3ed7Q9Ty(n246a4cyV%lE;wcefnj+y}7(s--?347=K^KS}pN<nq|DG}#9V
zL)`;6KA=yoNPRx=*y{d77=7S2c2s|&@PYG7xnn8y!JmiAr9L0rnfdZj?&gD^`@Z!=
zIQ!sS<&yq{_~3`E6Ju$OH}>jWma{5vd{rB9l$U#BZNa=JLU`k|(TDpJcw>IMCgW(K
zH{Ly@TF&ylk(8Q#lyh&4>$CTX$n?hGOOK^KZx|N)kE6-n2-3`0&X_m)KiF}UM|-2|
zraMxfH(nY!U;t5gqgk88ag=)F@&3)rnTI!SO}`=adE=*^J)R0@Z=AX?egGlfIJ{u>
zI9lU{-O5U-&kJAPef1bG_d?$K;ZKF|Le?-ofWQkGt<Fk)UPwdx&se?}5|XXQIQPP6
zk3~;KrWdT`B?Cyh7qpoz$J1ml_=OriW6TSE?qnR}(O&4X?%-2l^g`RAj&Bl$7aF%z
zjHlEK559Z%Gv?uin@Qgu<8EHK*sWIT^TLTUK5r6YFYO%cKCq7idmgao0ec>>=K*^j
Ru;&4L9<b+u|95%de*jU4-rN8H

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/spikes.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/expected_output/spikes.h5
new file mode 100644
index 0000000000000000000000000000000000000000..a4c6a361dc1f4f34997381d637272c354c864f99
GIT binary patch
literal 7112
zcmeHL%}xSA4DK$X8^j34gWzQ!!2<_xu2B>dqeeZLc!4M(8^cdnVvHw_`UXCNkHFO%
zkHFC<@D+4AZ4Frsq8^CSNtkxqPG{!Zwq$!>+TK}6<x_ye^I!%tmX+z1M}L(h@+|r?
zGY-=`rjIT$4kQ6}D=g2je?LKj9?MUUi$yS&;$JAM;bE3IPXtP*3V~8_^9V0|#<!Lz
z?Q@(77*Q*{szw+|G)kiQA<c5U#^X8-YbIB4pIJzQ2lYxVyfDvrE|dfKc9wJ8Qid7Z
zfY*73UxDjtI|`ePkLw&-Dc2K<PDvvfWw-e-Ic68M6D!HP=Q%R%@`|tWu9YK0%{vBc
z%1Au#e7=9c^;qEOg!O9FsnlC0_i)t0OUp_8uakJ}`Q+em+c6O=aW~-q3-QNE27c@u
zV{b4ehEl)ccn#N~WrK3mY<I#&4RWULU=70`VNGv9aL3wK=9fY;sW6`dy1R9_Z|%5X
z5BtFt7&pT!2aCf`$}0kjfFhs>C<2OrBA^H;0*Zhlpa>`eiojn$0Q;l%o1Z`Y9qvdv
z+~1TtNWVW}^k|y(H@No`Kw%yVuiXDh8Y$}C1iAItU&3|81-3e*Z3Iiq;+nmumvev{
x*>WP3`daRLU$&PYeGIusd32j)w3C0R{eE0!Y`|a}iZBf<D!-4XuJtqN=?%(ShDrbc

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/circuit_config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/circuit_config.json
new file mode 100755
index 0000000..ffd4224
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/circuit_config.json
@@ -0,0 +1,20 @@
+{
+  "manifest": {
+    "$NETWORK_DIR": "../input/network",
+    "$COMPONENT_DIR": "../shared_components"
+  },
+
+  "components": {
+    "morphologies_dir": "$COMPONENT_DIR/morphologies",
+    "biophysical_neuron_models_dir": "$COMPONENT_DIR/templates/nml"
+  },
+
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_DIR/biophysical_nodes.h5",
+        "node_types_file": "$NETWORK_DIR/biophysical_node_types.csv"
+      }
+    ]
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/config.json
new file mode 120000
index 0000000..a7569e2
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/config.json
@@ -0,0 +1 @@
+../shared_components/configs/config.json
\ No newline at end of file
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_node_types.csv b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_node_types.csv
new file mode 100644
index 0000000..5be64ca
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_node_types.csv
@@ -0,0 +1,2 @@
+node_type_id model_type model_template morphology model_name
+100 biophysical nml:soma_cm2_hh.nml soma1 soma_cm
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_nodes.h5 b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_nodes.h5
new file mode 100644
index 0000000000000000000000000000000000000000..3a6e422ed58113a89ba1c1bb5e5b31304a0530fa
GIT binary patch
literal 8536
zcmeHMy>1gh5T3Jfa!MR2K@k`T;*cmPU8G3IA;st_uz<o61rD(lEP-vsfN-jm@CGR<
zsSsrzfk#N0k`hs+3p+dWS#aiZHpG#Cc8i^#otxYJJUctL{upgOSX#KgK-_$vF43}O
z(Vc3m+!hUFj8~QMlzve9IU|fmIpVQ`>X+4jkQK$D>YqL?mB?7aKd27V!JKeD6pqdm
z0#WIHnHOBqRU=BjX`BI!W~)~37y<DZVc;L>ipFa^uJcqhdxhUKM|tw;_0~>f+sHgG
z))NJ`$2|6AhZ);YpYsi0pm+7%PNUWAf6kL9u{=<ADkIoY_BDN-XRO!`R#=Bljso3J
zY5VSz&fD#~K8R;R5#M)+r%>YuAiQX_+Aq7E#`e}Lt3up|Fc^|PdH86PBN%aaq~`_v
z#^ZQM_cLRjln2aFZ`)nn-)VW^WL4~ucV`Abw@`}!^1xTcqpY;JHd=t<dEj_n-iJI8
zkK@tKW^%oAonkRl;5@AiJgqZ;Cur7GB+T=EmsAnj#pjH~`b;KcO?~5snXGq`w+6k8
zEz)I`*{1yE=QE;x85onkHYW3M({Knl1RMem0f&G?VDtz`U74duU)8=Qj4f&md!X{+
z4bcZesC-qK1X5Ie6(7n8cKELSzL;R3YOcSyg;#`*TR-}`l9pu6Kun}@tt<ZrkKgYN
zlk03>@epgo!!+VC*mp;M!s6ra_p<SPlXf5T<EH%bDQO1b;pmhhfcuz=t}9S_q~{fu
z+g0Yh(mka(=QdzCB<25Eo;PY_>6>ob3dV<(cXnHE+dTTG+^p3x4fF4bG|Z!_@_Cct
z^Re7#tOWOZ_a5tuw0^4h&&hdtb-+B-gW$ZEI*>o9d-!%o+QzN3AH%78oN~`sP&ZL<
Xw!di^y|}nqn~1o&I6Ur51RlQtOqIQ)

literal 0
HcmV?d00001

diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/node_sets.json b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/node_sets.json
new file mode 100644
index 0000000..2ebb09c
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/node_sets.json
@@ -0,0 +1,5 @@
+{
+  "soma_cm2": {
+    "model_type": "biophysical"
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/simulation_config.json b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/simulation_config.json
new file mode 100755
index 0000000..d8d5f03
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/simulation_config.json
@@ -0,0 +1,55 @@
+{
+  "manifest": {
+    "$OUTPUT_DIR": "./output",
+    "$INPUT_DIR": "../input"
+  },
+
+  "run": {
+    "tstop": 60.0,
+    "dt": 0.025,
+    "dL": 20.0,
+    "spike_threshold": -15,
+    "nsteps_block": 5000
+  },
+
+  "target_simulator":"NEURON",
+
+  "network": "$INPUT_DIR/circuit_config.json",
+
+  "conditions": {
+    "celsius": 34.0,
+    "v_init": -80
+  },
+
+  "node_sets_file": "$INPUT_DIR/node_sets.json", 
+
+  "mechanisms_dir": "../shared_components_mechanisms",
+  
+  
+  "inputs": {
+   "current_clamp_1": {
+     "input_type": "current_clamp",
+     "module": "IClamp",
+     "node_set": "soma_cm2",
+     "amp": 0.002,
+     "delay": 20.0,
+     "duration": 30.0
+   }
+  },
+
+  "output": {
+    "log_file": "log.txt",
+    "output_dir": "$OUTPUT_DIR",
+    "spikes_file": "spikes.h5",
+    "spikes_sort_order": "time"
+  },
+
+  "reports": {
+    "membrane_potential": {
+      "cells": "soma_cm2",
+      "variable_name": "v",
+      "module": "membrane_report",
+      "sections": "soma"
+    }
+  }
+}
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/pytest.ini b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/pytest.ini
new file mode 100644
index 0000000..3d8fe4a
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::FutureWarning
diff --git a/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/shared_components b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/shared_components
new file mode 120000
index 0000000..d3ced13
--- /dev/null
+++ b/examples/sim_tests/biophysical/one_cell/soma_cm2_hh/shared_components
@@ -0,0 +1 @@
+../../../shared_components
\ No newline at end of file
diff --git a/examples/sim_tests/shared_components/configs/config.json b/examples/sim_tests/shared_components/configs/config.json
new file mode 100755
index 0000000..890caa3
--- /dev/null
+++ b/examples/sim_tests/shared_components/configs/config.json
@@ -0,0 +1,4 @@
+{
+  "network": "./circuit_config.json",
+  "simulation": "./simulation_config.json"
+}
diff --git a/examples/sim_tests/shared_components/morphologies/soma1.swc b/examples/sim_tests/shared_components/morphologies/soma1.swc
new file mode 100644
index 0000000..fa8360a
--- /dev/null
+++ b/examples/sim_tests/shared_components/morphologies/soma1.swc
@@ -0,0 +1,5 @@
+# 3-point soma with diameter of 1
+# id,type,x,y,z,r,pid
+1 1 0.0 0.0 0.0 0.5 -1
+2 1 0.0 -0.5 0.0 0.5 1
+3 1 0.0 0.5 0.0 0.5 1
diff --git a/examples/sim_tests/shared_components/scripts/run_bionet.py b/examples/sim_tests/shared_components/scripts/run_bionet.py
new file mode 100755
index 0000000..b7f65d2
--- /dev/null
+++ b/examples/sim_tests/shared_components/scripts/run_bionet.py
@@ -0,0 +1,19 @@
+#!/bin/env python
+
+import sys
+from bmtk.simulator import bionet
+
+
+def run(config_file):
+    conf = bionet.Config.from_json(config_file, validate=True)
+    conf.build_env()
+    net = bionet.BioNetwork.from_config(conf)
+    sim = bionet.BioSimulator.from_config(conf, network=net)
+    sim.run()
+
+
+if __name__ == '__main__':
+    if __file__ != sys.argv[-1]:
+        run(sys.argv[-1])
+    else:
+        run('config.json')
diff --git a/examples/sim_tests/shared_components/templates/nml/soma_cm2.nml b/examples/sim_tests/shared_components/templates/nml/soma_cm2.nml
new file mode 100755
index 0000000..46c8595
--- /dev/null
+++ b/examples/sim_tests/shared_components/templates/nml/soma_cm2.nml
@@ -0,0 +1,9 @@
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="NeuroML2_file_exported_from_NEURON">
+    <cell id="soma">
+        <biophysicalProperties id="biophys">
+            <membraneProperties>
+                <specificCapacitance segmentGroup="soma" value="2 uF_per_cm2"/>
+            </membraneProperties>
+        </biophysicalProperties>
+    </cell>
+</neuroml>
diff --git a/examples/sim_tests/shared_components/templates/nml/soma_cm2_hh.nml b/examples/sim_tests/shared_components/templates/nml/soma_cm2_hh.nml
new file mode 100755
index 0000000..9bf5c55
--- /dev/null
+++ b/examples/sim_tests/shared_components/templates/nml/soma_cm2_hh.nml
@@ -0,0 +1,13 @@
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="NeuroML2_file_exported_from_NEURON">
+    <cell id="soma">
+        <biophysicalProperties id="biophys">
+            <membraneProperties>
+                <specificCapacitance segmentGroup="soma" value="1 uF_per_cm2"/>
+                <channelDensity id="gnabar_hh" segmentGroup="soma" ion="na" ionChannel="hh" erev="50 mV" condDensity="0.0 S_per_cm2"/>
+                <channelDensity id="gkbar_hh" segmentGroup="soma" ion="k" ionChannel="hh" erev="-85 mV" condDensity="0.00 S_per_cm2"/>
+                <channelDensity id="gl_hh" segmentGroup="soma" ion="non_specific" ionChannel="hh" erev="-80 mV" condDensity="0.005 S_per_cm2"/>
+                <channelDensity id="el_hh" segmentGroup="soma" ion="non_specific" ionChannel="hh" erev="-80 mV" condDensity="-80"/>
+            </membraneProperties>
+        </biophysicalProperties>
+    </cell>
+</neuroml>