Merge pull request #2 from sanjayankur31/feat/neuroml-conversion

Feat/neuroml conversion
OpenSourceBrain · Jun 11, 2024 · 88ec6ef · 88ec6ef
2 parents df78373 + d72985e
commit 88ec6ef
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diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -0,0 +1,43 @@
+
+name: Continuous build using OMV
+
+on:
+  schedule:
+    - cron: "1 1 1 */2 *"
+  push:
+    branches: [ master, development, experimental ]
+  pull_request:
+    branches: [ master, development, experimental ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.8", "3.10"]
+        #engine: [ jNeuroML_validate, jNeuroML_NEURON ]
+        engine: [ jNeuroML_validate]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: Install OMV
+      run: |
+        pip install OSBModelValidation
+        pip install scipy sympy matplotlib cython pandas tables
+
+    - name: Run OMV tests on engine ${{ matrix.engine }}
+      run: |
+        omv all -V --engine=${{ matrix.engine }}
+
+    - name: OMV final version info
+      run: |
+        omv list -V # list installed engines
+        env
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,11 @@
+*.dat
+x86_64/
+/NeuroML2/*.mod
+*_nrn.py
+*_eden.py
+
+.mypy_cache/
+/NeuroML2/tests/arm64
+/NeuroML2/arm64
+
+__pycache__/
diff --git a/Purkinje19b972-1.nrn → NEURON/Purkinje19b972-1.nrn b/Purkinje19b972-1.nrn → NEURON/Purkinje19b972-1.nrn
diff --git a/cfdistrib.hoc → NEURON/cfdistrib.hoc b/cfdistrib.hoc → NEURON/cfdistrib.hoc
diff --git a/dendv_arnd21.ses → NEURON/dendv_arnd21.ses b/dendv_arnd21.ses → NEURON/dendv_arnd21.ses
diff --git a/distri.hoc → NEURON/distri.hoc b/distri.hoc → NEURON/distri.hoc
diff --git a/electrode.hoc → NEURON/electrode.hoc b/electrode.hoc → NEURON/electrode.hoc
diff --git a/mod/BK_Slow.mod → NEURON/mod/BK_Slow.mod b/mod/BK_Slow.mod → NEURON/mod/BK_Slow.mod
diff --git a/mod/CaP.mod → NEURON/mod/CaP.mod b/mod/CaP.mod → NEURON/mod/CaP.mod
diff --git a/mod/CaT.mod → NEURON/mod/CaT.mod b/mod/CaT.mod → NEURON/mod/CaT.mod
diff --git a/mod/Kv1.mod → NEURON/mod/Kv1.mod b/mod/Kv1.mod → NEURON/mod/Kv1.mod
diff --git a/mod/SK2.mod → NEURON/mod/SK2.mod b/mod/SK2.mod → NEURON/mod/SK2.mod
diff --git a/mod/capmax.mod → NEURON/mod/capmax.mod b/mod/capmax.mod → NEURON/mod/capmax.mod
diff --git a/mod/cdp_AIS.mod → NEURON/mod/cdp_AIS.mod b/mod/cdp_AIS.mod → NEURON/mod/cdp_AIS.mod
diff --git a/mod/cdp_smooth.mod → NEURON/mod/cdp_smooth.mod b/mod/cdp_smooth.mod → NEURON/mod/cdp_smooth.mod
diff --git a/mod/cdp_soma.mod → NEURON/mod/cdp_soma.mod b/mod/cdp_soma.mod → NEURON/mod/cdp_soma.mod
diff --git a/mod/cdp_spiny.mod → NEURON/mod/cdp_spiny.mod b/mod/cdp_spiny.mod → NEURON/mod/cdp_spiny.mod
diff --git a/mod/distr.mod → NEURON/mod/distr.mod b/mod/distr.mod → NEURON/mod/distr.mod
diff --git a/mod/ih.mod → NEURON/mod/ih.mod b/mod/ih.mod → NEURON/mod/ih.mod
diff --git a/mod/kv3.mod → NEURON/mod/kv3.mod b/mod/kv3.mod → NEURON/mod/kv3.mod
diff --git a/mod/kv4f.mod → NEURON/mod/kv4f.mod b/mod/kv4f.mod → NEURON/mod/kv4f.mod
diff --git a/mod/kv4s.mod → NEURON/mod/kv4s.mod b/mod/kv4s.mod → NEURON/mod/kv4s.mod
diff --git a/mod/mslo.mod → NEURON/mod/mslo.mod b/mod/mslo.mod → NEURON/mod/mslo.mod
diff --git a/mod/nap.mod → NEURON/mod/nap.mod b/mod/nap.mod → NEURON/mod/nap.mod
diff --git a/mod/narsg.mod → NEURON/mod/narsg.mod b/mod/narsg.mod → NEURON/mod/narsg.mod
diff --git a/mod/peak.mod → NEURON/mod/peak.mod b/mod/peak.mod → NEURON/mod/peak.mod
diff --git a/mod/pkjlk.mod → NEURON/mod/pkjlk.mod b/mod/pkjlk.mod → NEURON/mod/pkjlk.mod
diff --git a/mod/syn2.mod → NEURON/mod/syn2.mod b/mod/syn2.mod → NEURON/mod/syn2.mod
diff --git a/purkinje_demo.hoc → NEURON/purkinje_demo.hoc b/purkinje_demo.hoc → NEURON/purkinje_demo.hoc
diff --git a/readme → NEURON/readme b/readme → NEURON/readme
diff --git a/NeuroML2/.test.validate.omt b/NeuroML2/.test.validate.omt
@@ -0,0 +1,4 @@
+# Script for running automated tests, see https://github.com/OpenSourceBrain/osb-model-validation 
+# This test will validate MOST all of the NeuroML 2 files in the current directory
+target: "*.c*.nml"
+engine: jNeuroML_validate
diff --git a/NeuroML2/20240604170737_test_narsg_states_NEURON.png b/NeuroML2/20240604170737_test_narsg_states_NEURON.png
diff --git a/NeuroML2/20240605170054_test_SK2_ca_NEURON.png b/NeuroML2/20240605170054_test_SK2_ca_NEURON.png
diff --git a/NeuroML2/20240605170054_test_SK2_states_NEURON.png b/NeuroML2/20240605170054_test_SK2_states_NEURON.png
diff --git a/NeuroML2/20240605170054_test_sk2_ca_NML.png b/NeuroML2/20240605170054_test_sk2_ca_NML.png
diff --git a/NeuroML2/20240605170054_test_sk2_states_NML.png b/NeuroML2/20240605170054_test_sk2_states_NML.png
diff --git a/NeuroML2/20240607161612_test_narsg_states_NML.png b/NeuroML2/20240607161612_test_narsg_states_NML.png
diff --git a/NeuroML2/20240607181826_test_mslo_states_NEURON.png b/NeuroML2/20240607181826_test_mslo_states_NEURON.png
diff --git a/NeuroML2/Purkinje.morph.cell.nml b/NeuroML2/Purkinje.morph.cell.nml