Merge branch 'experimental' into development

OpenSourceBrain · May 2, 2024 · 7b5b4cb · 7b5b4cb
2 parents 0c83616 + 3090f5b
commit 7b5b4cb
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Showing 9 changed files with 21 additions and 13 deletions.
diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
@@ -13,17 +13,22 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.8, 3.9, "3.10" ]
+        python-version: [ 3.9, "3.10" ]
         runs-on: [ ubuntu-latest, macos-latest ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 
+    - name: Install HDF5 for pytables on macos-latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -17,11 +17,12 @@ jobs:
         engine: [ NetPyNE, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
+
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
@@ -32,6 +33,7 @@ jobs:
     - 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

diff --git a/NeuroML2/.test.exGJ.jnmleden.omt b/NeuroML2/.test.exGJ.jnmleden.omt
@@ -14,7 +14,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: -69.5
-        tolerance: 0.00034498419085947374
+        tolerance: 0.0003449267030756095
   cell1:
     observables:
       spike times:

diff --git a/NeuroML2/.test.exIzh.jnmleden.omt b/NeuroML2/.test.exIzh.jnmleden.omt
@@ -13,4 +13,4 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 0.00014888369126089628
+        tolerance: 0.00014884116521364865
diff --git a/NeuroML2/.test.hh.jnmleden.omt b/NeuroML2/.test.hh.jnmleden.omt
@@ -13,7 +13,7 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 0.00011745994437245375
+        tolerance: 0.0001175226231050635
   v1:
     observables:
       spike times:
@@ -23,7 +23,7 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 0.0001244750601708972
+        tolerance: 0.00012449165905872983
   v2:
     observables:
       spike times:

diff --git a/NeuroML2/.test.hhsim.jnmleden.omt b/NeuroML2/.test.hhsim.jnmleden.omt
@@ -13,4 +13,4 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 0.0007232195903184108
+        tolerance: 0.0007232712525507523
diff --git a/NeuroML2/.test.hyizh.jnmleden.omt b/NeuroML2/.test.hyizh.jnmleden.omt
@@ -13,4 +13,4 @@ experiments:
           scaling: [1000, 1000]
         spike detection:
           method: threshold
-        tolerance: 3.66282906798275e-05
+        tolerance: 3.6664955635370336e-05
diff --git a/NeuroML2/TwoCells/.test.two.jnmleden.omt b/NeuroML2/TwoCells/.test.two.jnmleden.omt
@@ -15,7 +15,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.017343922603342065
+        tolerance: 0.01734388742304312
   bask0:
     observables:
       spike times:
@@ -26,4 +26,4 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.0017869092394359062
+        tolerance: 0.001786960295444412
diff --git a/README.md b/README.md
@@ -7,3 +7,4 @@ See also info about [NetPyNE on OSBv2](https://docs.opensourcebrain.org/OSBv2/Ne
 [![Continuous builds](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/omv-ci.yml) [![Regenerate files](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/non-omv.yml/badge.svg)](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/non-omv.yml)
 
 
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,3 +7,4 @@ See also info about [NetPyNE on OSBv2](https://docs.opensourcebrain.org/OSBv2/Ne
		[![Continuous builds](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/omv-ci.yml) [![Regenerate files](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/non-omv.yml/badge.svg)](https://github.com/OpenSourceBrain/NetPyNEShowcase/actions/workflows/non-omv.yml)