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Fix moose gh install #9

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merged 5 commits into from
May 15, 2024
Merged

Fix moose gh install #9

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d14b66b
Update full cell nml example
pgleeson May 14, 2024
4c64d0d
Try pip install
pgleeson May 14, 2024
2f77e90
Test more py versions
pgleeson May 15, 2024
d318edc
Test apt-get install libhdf5-dev
pgleeson May 15, 2024
9ff34b1
More reqs
pgleeson May 15, 2024
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11 changes: 9 additions & 2 deletions .github/workflows/build-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [ "3.8", "3.9" ]
python-version: [ "3.8", "3.9", "3.10", "3.11" ]

steps:
- uses: actions/checkout@v4
Expand All @@ -38,10 +38,17 @@ jobs:
pip install jupyter_packaging
pip install scipy
pip install pyneuroml
pip install pybind11[global]
pip install python-libsbml

python setup.py install
sudo apt-get install libhdf5-dev

pip install .

pip list

echo "MOOSE version:"
python -c "import moose; print(moose.__version__)"

- name: Test Moose files
run: |
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17 changes: 9 additions & 8 deletions NeuroML2/test_files/NML2_FullCell.nml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,21 @@

<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xi="http://www.w3.org/2001/XInclude"
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
id="NML2_FullCell">


<!-- Example of a multicompartmental cell with biophysics in NeuroML 2 -->

<!-- This is a "pure" NeuroML 2 file. It cannot currently used for simulations with
jLEMS/jNeuroML however, as jLEMS does not yet support multicompartmental cells -->
<!-- This is a "pure" NeuroML 2 file. It cannot currently used for simulations with
jLEMS/jNeuroML however, as jLEMS does not yet support multicompartmental cells -->

<include href="SimpleIonChannel.xml"/> <!-- Contains ionChannel NaConductance -->

<ionChannel type="ionChannelPassive" id="pas" conductance="10pS"/> <!--For use in example cell below-->

<!-- Note, no <cells> element... -->

<cell id="SpikingCell" metaid="HippoCA1Cell">

<notes>A Simple Spiking cell for testing purposes</notes>
Expand Down Expand Up @@ -54,7 +53,7 @@
<parent segment="1"/>
<distal x="30" y="0" z="0" diameter="1"/>
</segment>

<segment id ="3" name="Spine1">
<parent segment="2" fractionAlong="0.5"/>
<proximal x="25" y="0" z="0" diameter="0.1"/>
Expand All @@ -63,7 +62,7 @@

<!-- segmentGroups follow -->

<segmentGroup id="soma_group" neuroLexId="sao1044911821"> <!-- Points to category "Neuronal Cell Body" in NeuroLex -->
<segmentGroup id="soma_group" neuroLexId="sao1044911821"> <!-- Points to category "Neuronal Cell Body" in NeuroLex -->
<member segment="0"/>
</segmentGroup>

Expand All @@ -81,14 +80,16 @@

<biophysicalProperties id="bio_cell">

<membraneProperties>
<membraneProperties>

<channelPopulation id="naChansDend" ionChannel="NaConductance" segment="2" number="120000" erev="50mV" ion="na"/> <!-- Use population instead of density -->

<channelDensity id="pasChans" ionChannel="pas" condDensity="3.0 S_per_m2" erev="-70mV" ion="non_specific"/> <!-- no segmentGroup => all segments! -->

<channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2" erev="50mV" ion="na"/>

<spikeThresh value="0mV"/>

<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>

<specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>
Expand Down