Merge pull request #231 from NeuroML/development

Changes for NeuroML v2.3.1 release

.github/workflows/ci.yml

@@ -3,27 +3,27 @@ name: Build all NML Java
 
 on:
   push:
-    branches: [ master, development, experimental, documentation_update, osb* ]
+    branches: [ master, development, experimental, documentation_update, osb*, update* ]
   pull_request:
-    branches: [ master, development, experimental, documentation_update, osb* ]
+    branches: [ master, development, experimental, documentation_update, osb*, update* ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '19' ]
+        java: [ '8', '11', '16', '17', '19', '21' ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up JDK ${{ matrix.java }}
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.java }}
         java-package: jdk
-        distribution: 'adopt'
+        distribution: 'temurin'
 
     - name: Install NeuroML 2 with Maven
       run: |

.github/workflows/omv-ci.yml

@@ -2,9 +2,9 @@ name: Run OMV tests
 
 on:
   push:
-    branches: [ master, development, experimental, documentation_update, osb* ]
+    branches: [ master, development, experimental, documentation_update, osb*, update* ]
   pull_request:
-    branches: [ master, development, experimental, documentation_update, osb* ]
+    branches: [ master, development, experimental, documentation_update, osb*, update* ]
 
 jobs:
   build:
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9 ]
+        python-version: [ "3.9" ]
         engine:
           - jNeuroML
           - jNeuroML_Brian2
@@ -25,10 +25,10 @@ jobs:
           - PyLEMS_NeuroML2
 
     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 }}
 

.gitignore

@@ -68,3 +68,15 @@ examples/*.pov
 /LEMSexamples/tmp
 arm64
 /examples/NML2_SingleCompHHCell.nml__flattened.xml
+/LEMSexamples/morphologies/*.mod
+/LEMSexamples/morphologies/*.c
+/LEMSexamples/morphologies/*.so
+*eden.py
+*netpyne.py
+*nrn.py
+/LEMSexamples/morphologies/*.dat
+/LEMSexamples/morphologies/*.hoc
+/LEMSexamples/morphologies/NET_m_in_b_in.net.nml
+/LEMSexamples/morphologies/simulator.props
+/LEMSexamples/morphologies/NET_m_in_b_out.net.nml
+/LEMSexamples/morphologies/NET_m_out_b_in.net.nml

HISTORY.md

@@ -8,6 +8,32 @@ and [LEMS](https://github.com/LEMS/LEMS), but also the Python ([libNeuroML](http
 
 **Only contributors who are not [NeuroML Editors](https://docs.neuroml.org/NeuroMLOrg/Board.html) are specifically pointed out below.**
 
+v2.3.1 / 2024-08-25
+--------------------
+
+* **Renamed the main Schema from NeuroML_v2.3.xsd to [NeuroML_v2.3.1.xsd](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.3.1).**
+
+* Adds support for external <morphology>/<biophysicalProperties> in cell element. Also simulator mappings for NEURON/NetPyNE support this. See [here](https://docs.neuroml.org/Userdocs/ImportingMorphologyFiles.html#neuroml2) for more details. Multiple examples of NeuroML2/LEMS files using this feature can be found [here](https://github.com/NeuroML/NeuroML2/tree/development/LEMSexamples/morphologies). 
+
+* pyNeuroML analysis feature updates: better support for analysing kinetic scheme based channels in `pynml-channelanalysis`; better support for plotting generated spike trains with `pynml-plotspikes`.
+
+* Improved testing of Java based libraries on latest versions of Java and recent Mac OS versions. 
+
+* Improved support for adding RDF annotations to NeuroML files.
+
+* Added ability to load (a subset of) XPPAUT files with `pynml-xpp` and export the model to LEMS or back to XPPAUT.
+
+* Improvements to handling of SBML and SED-ML files - added to pynml ability to validate both formats, or run SED-ML files which refer to SBML models using simulator tellurium.
+
+* Added option to archive NeuroML models as COMBINE Archives with `pynml-archive`.
+
+* Initial support for sending archived NeuroML models to Biosimulations.org for simulation.
+
+* Improved ability for pynml and related tools to detect the correct file type (NeuroML or LEMS) for the appropriate export/simulation option, and give advice when an incorrect file is provided. 
+
+* Updates to `pynml-plotmorph` for plotting morphologies in 2D, and in 3D with VisPy.
+
+
 v2.3 / 2023-09-20
 --------------------
 

LEMSexamples/morphologies/.test.jnml.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.004018425953151025

LEMSexamples/morphologies/.test.jnmleden.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+

LEMSexamples/morphologies/.test.jnmleden.multi.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+

LEMSexamples/morphologies/.test.jnmleden.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445

LEMSexamples/morphologies/.test.jnmleden.out.omt

@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445

LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+

LEMSexamples/morphologies/.test.jnmlnrn.multi.omt

@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NEURON
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+