Merge pull request #494 from ModECI/nml_examples

Regenerated neuroml examples
ModECI · Feb 1, 2024 · 48c7518 · 48c7518
2 parents fca26bf + 0892259
commit 48c7518
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Showing 14 changed files with 39 additions and 42 deletions.
diff --git a/examples/NeuroML/LEMS_SimABCD.xml b/examples/NeuroML/LEMS_SimABCD.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.8 (libNeuroML v0.5.7)
 
      -->
 
@@ -19,7 +19,6 @@
     <Include file="ABCD__lems.xml"/>
 
     <Simulation id="SimABCD" length="5000.0ms" step="100.0ms" target="ABCD" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-
         <Display id="A_0_OUTPUT" title="Plots of A_0_OUTPUT" timeScale="1ms" xmin="-500.0" xmax="5500.0" ymin="-1" ymax="1">
             <Line id="A_0_a_OUTPUT" quantity="A/0/a/OUTPUT" scale="1" color="#d54f33" timeScale="1ms"/>
         </Display>

diff --git a/examples/NeuroML/LEMS_SimFN.xml b/examples/NeuroML/LEMS_SimFN.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.8 (libNeuroML v0.5.7)
 
      -->
 
@@ -19,7 +19,6 @@
     <Include file="FN__lems.xml"/>
 
     <Simulation id="SimFN" length="100.0ms" step="0.05ms" target="FN" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-
         <Display id="FNpop_0_V" title="Plots of FNpop_0_V" timeScale="1ms" xmin="-10.0" xmax="110.00000000000001" ymin="-1" ymax="1">
             <Line id="FNpop_0_fn_V" quantity="FNpop/0/fn/V" scale="1" color="#d54f33" timeScale="1ms"/>
         </Display>

diff --git a/examples/NeuroML/LEMS_SimIzhikevichTest.xml b/examples/NeuroML/LEMS_SimIzhikevichTest.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.8 (libNeuroML v0.5.7)
 
      -->
 
@@ -18,7 +18,6 @@
     <Include file="IzhikevichTest.net.nml"/>
 
     <Simulation id="SimIzhikevichTest" length="700.0ms" step="0.025ms" target="IzhikevichTest" seed="5678">  <!-- Note seed: ensures same random numbers used every run -->
-
         <Display id="izhPop_0_u" title="Plots of izhPop_0_u" timeScale="1ms" xmin="-70.0" xmax="770.0000000000001" ymin="-1" ymax="1">
             <Line id="izhPop_0__u" quantity="izhPop[0]/u" scale="1" color="#d54f33" timeScale="1ms"/>
         </Display>

diff --git a/examples/NeuroML/PyNN/HH.mdf.yaml b/examples/NeuroML/PyNN/HH.mdf.yaml
@@ -135,10 +135,10 @@ HH:
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: HH_cond_exp,\n   parameters:\
                         \ {'cm': '0.2', 'i_offset': 0.05, 'tau_syn_E': '0.2', 'tau_syn_I':\
-                        \ '2.', 'v_init': '-65.', 'v_offset': '-63.', 'e_rev_E': '0.',\
-                        \ 'e_rev_I': '-80.', 'e_rev_K': '-90.', 'e_rev_Na': '50.',\
-                        \ 'e_rev_leak': '-65.', 'g_leak': '0.01', 'gbar_K': '6.',\
-                        \ 'gbar_Na': '20.'}\n   parent: None\n"
+                        \ '2.0', 'v_init': '-65.0', 'v_offset': '-63.0', 'e_rev_E':\
+                        \ '0.0', 'e_rev_I': '-80.0', 'e_rev_K': '-90.0', 'e_rev_Na':\
+                        \ '50.0', 'e_rev_leak': '-65.0', 'g_leak': '0.01', 'gbar_K':\
+                        \ '6.0', 'gbar_Na': '20.0'}\n   parent: None\n"
                 InputList_stim:
                     parameters:
                         delay:

diff --git a/examples/NeuroML/PyNN/HH.net.nml b/examples/NeuroML/PyNN/HH.net.nml
@@ -5,8 +5,8 @@
     NeuroMLlite parameters:
         input_amp = 0</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.0nA"/>
-    <HH_cond_exp id="testcell" cm="0.2" i_offset="0.05" tau_syn_E="0.2" tau_syn_I="2." v_init="-65." v_offset="-63." e_rev_E="0." e_rev_I="-80." e_rev_K="-90." e_rev_Na="50." e_rev_leak="-65." g_leak="0.01" gbar_K="6." gbar_Na="20."/>
-    <alphaCurrSynapse id="ampaSyn" tau_syn="20."/>
+    <HH_cond_exp id="testcell" cm="0.2" i_offset="0.05" tau_syn_E="0.2" tau_syn_I="2.0" v_init="-65.0" v_offset="-63.0" e_rev_E="0.0" e_rev_I="-80.0" e_rev_K="-90.0" e_rev_Na="50.0" e_rev_leak="-65.0" g_leak="0.01" gbar_K="6.0" gbar_Na="20.0"/>
+    <alphaCurrSynapse id="ampaSyn" tau_syn="20.0"/>
     <network id="HH">
         <notes>Example: HH</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/examples/NeuroML/PyNN/InputWeights.mdf.yaml b/examples/NeuroML/PyNN/InputWeights.mdf.yaml
@@ -185,9 +185,9 @@ InputWeights:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '0.5', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '0.5', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 InputList_stim:
                     parameters:

diff --git a/examples/NeuroML/PyNN/InputWeights.net.nml b/examples/NeuroML/PyNN/InputWeights.net.nml
@@ -5,8 +5,8 @@
     NeuroMLlite parameters:
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_curr_alpha id="testcell" cm="1." i_offset="0." tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50."/>
-    <alphaCurrSynapse id="ampaSyn" tau_syn="20."/>
+    <IF_curr_alpha id="testcell" cm="1.0" i_offset="0.0" tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
+    <alphaCurrSynapse id="ampaSyn" tau_syn="20.0"/>
     <network id="InputWeights">
         <notes>Example: InputWeights</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/examples/NeuroML/PyNN/Net1.mdf.yaml b/examples/NeuroML/PyNN/Net1.mdf.yaml
@@ -153,9 +153,9 @@ Net1:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '20.', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '20.0', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 pop1:
                     metadata:
@@ -322,9 +322,9 @@ Net1:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '20.', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '20.0', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 proj0_ampaSyn:
                     parameters:

diff --git a/examples/NeuroML/PyNN/Net1.net.nml b/examples/NeuroML/PyNN/Net1.net.nml
@@ -5,8 +5,8 @@
     NeuroMLlite parameters:
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_curr_alpha id="testcell" cm="1." i_offset="0." tau_syn_E="20." tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50."/>
-    <alphaCurrSynapse id="ampaSyn" tau_syn="20."/>
+    <IF_curr_alpha id="testcell" cm="1.0" i_offset="0.0" tau_syn_E="20.0" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
+    <alphaCurrSynapse id="ampaSyn" tau_syn="20.0"/>
     <network id="Net1">
         <notes>Example: Net1</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/examples/NeuroML/PyNN/OneCell.mdf.yaml b/examples/NeuroML/PyNN/OneCell.mdf.yaml
@@ -137,9 +137,9 @@ OneCell:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '0.5', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '0.5', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 InputList_stim:
                     parameters:

diff --git a/examples/NeuroML/PyNN/OneCell.net.nml b/examples/NeuroML/PyNN/OneCell.net.nml
@@ -5,8 +5,8 @@
     NeuroMLlite parameters:
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_curr_alpha id="testcell" cm="1." i_offset="0." tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50."/>
-    <alphaCurrSynapse id="ampaSyn" tau_syn="20."/>
+    <IF_curr_alpha id="testcell" cm="1.0" i_offset="0.0" tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
+    <alphaCurrSynapse id="ampaSyn" tau_syn="20.0"/>
     <network id="OneCell">
         <notes>Example: OneCell</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/examples/NeuroML/PyNN/SimpleNet.mdf.yaml b/examples/NeuroML/PyNN/SimpleNet.mdf.yaml
@@ -137,9 +137,9 @@ SimpleNet:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '20.', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '20.0', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 pop1:
                     metadata:
@@ -274,9 +274,9 @@ SimpleNet:
                         \ neuroml2_cell=None, pynn_cell='IF_curr_alpha', arbor_cell=None,\
                         \ bindsnet_node=None)] is defined in None and in Lems is:\
                         \ Component, id: testcell, type: IF_curr_alpha,\n   parameters:\
-                        \ {'cm': '1.', 'i_offset': 0.0, 'tau_syn_E': '20.', 'tau_syn_I':\
-                        \ '0.5', 'v_init': '-65.', 'tau_m': '20.', 'tau_refrac': 5,\
-                        \ 'v_reset': '-65.', 'v_rest': '-65.', 'v_thresh': '-50.'}\n\
+                        \ {'cm': '1.0', 'i_offset': 0.0, 'tau_syn_E': '20.0', 'tau_syn_I':\
+                        \ '0.5', 'v_init': '-65.0', 'tau_m': '20.0', 'tau_refrac':\
+                        \ 5, 'v_reset': '-65.0', 'v_rest': '-65.0', 'v_thresh': '-50.0'}\n\
                         \   parent: None\n"
                 proj0_ampaSyn:
                     parameters:

diff --git a/examples/NeuroML/PyNN/SimpleNet.net.nml b/examples/NeuroML/PyNN/SimpleNet.net.nml
@@ -5,8 +5,8 @@
     NeuroMLlite parameters:
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_curr_alpha id="testcell" cm="1." i_offset="0." tau_syn_E="20." tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50."/>
-    <alphaCurrSynapse id="ampaSyn" tau_syn="20."/>
+    <IF_curr_alpha id="testcell" cm="1.0" i_offset="0.0" tau_syn_E="20.0" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
+    <alphaCurrSynapse id="ampaSyn" tau_syn="20.0"/>
     <network id="SimpleNet">
         <notes>Example: SimpleNet</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/setup.cfg b/setup.cfg
@@ -16,16 +16,16 @@ classifiers =
     License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
     Natural Language :: English
     Operating System :: OS Independent
-    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.8
     Topic :: Scientific/Engineering
     Intended Audience :: Science/Research
     Programming Language :: Python
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Scientific/Engineering
     Topic :: Software Development
     Typing :: Typed
@@ -35,7 +35,7 @@ packages = find:
 install_requires =
     typing_compat;python_version<'3.8'
     dataclasses;python_version<'3.7'
-    graph_scheduler>=1.1.1
+    graph_scheduler<1.2.0,>=1.1.1
     numpy
     matplotlib
     graphviz
@@ -89,7 +89,7 @@ optional =
     Jinja2<3.1
     torchviz
     netron
-    torch>=1.11.0
+    torch<2.2.0,>=1.11.0
     torchvision
     h5py