Merge pull request #183 from NeuroML/development

NeuroML 2.2 release

.github/workflows/ci.yml

@@ -5,18 +5,17 @@ name: Test commits
 
 on:
   push:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, documentation_update, osb* ]
   pull_request:
-    branches: [ master, development, experimental ]
-
+    branches: [ master, development, experimental, documentation_update, osb* ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java: [ 8, 11.0.x, 11.0.3, 12, 13 ]
+        java: [ 8, 11, 16, 17 ]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,6 +26,38 @@ jobs:
         java-version: ${{ matrix.java }}
         java-package: jdk
 
-    - name: Test build
+    - name: Install NeuroML 2 with Maven
       run: |
+        java -version
         mvn install
+
+    - name: Install jNeuroML
+      run: |
+        export main_repo_branch=${GITHUB_REF##*/}
+        if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi
+        echo Using branch $main_repo_branch
+        git clone https://github.com/NeuroML/jNeuroML.git
+        cd jNeuroML
+        git checkout $main_repo_branch
+        python getNeuroML.py $main_repo_branch  # will call mvn install on this & other repos
+        ls -alt
+        mvn dependency:tree
+        ./jnml -v
+        cd ..
+        
+    - name: Install OMV
+      run: |
+        pwd
+        echo $GITHUB_WORKSPACE
+        export PATH=$PATH:$GITHUB_WORKSPACE/jNeuroML
+        export JNML_HOME=$GITHUB_WORKSPACE/jNeuroML
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        omv list -V
+        env
+        pip freeze
+        
+    - name: Test examples using OMV
+      run: |
+        cd $GITHUB_WORKSPACE/NeuroML2/LEMSexamples
+        omv all -V  --engine=jNeuroML --ignore-non-py3
+        omv list -V

.gitignore

@@ -11,7 +11,6 @@ target
 
 *~
 *.pyc
-results
 build
 *.log
 *.xml0
@@ -64,3 +63,4 @@ examples/*.pov
 /LEMSexamples/report.txt
 /LEMSexamples/test/x86_64
 /LEMSexamples/report.ex*.txt
+/LEMSexamples/results/*.spikes

HISTORY.md

@@ -8,6 +8,20 @@ and [LEMS](https://github.com/LEMS/LEMS), but also the Python ([libNeuroML](http
 
 **Only contributors who are not [NeuroML Editors](https://neuroml.org/editors) are specifically pointed out below.**
 
+v2.2 / 2021-12-15
+--------------------
+
+* **Renamed the main Schema from NeuroML_v2.1.xsd to [NeuroML_v2.2.xsd](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.2).**
+
+* Significant updates to documentation in NeuroML LEMS XML definitions. Have been propagated to core documentation e.g. https://docs.neuroml.org/Userdocs/Schemas/Networks.html
+
+* Major changes to pyNeuroML & libNeuroML to aid usability. These updates have been reflected in the NeuroML user guides & other documentation, e.g.: https://docs.neuroml.org/Userdocs/GettingStarted.html
+
+* Updates to automated testing of Python & Java libraries: all moved to GitHub Actions (for overview see [here](https://github.com/NeuroML/.github/tree/main/testsheet)); updated to test on latest version of Python & Java and Windows/Mac.
+
+* Removed `ValueAcrossSegOrSegGroup` (https://github.com/NeuroML/NeuroML2/pull/165 that fixes https://github.com/NeuroML/NeuroML2/issues/162) and update any elements using it to directly include `Value` and `SegmentGroup` attributes. This allows their correct validation.
+
+
 v2.1 / 2021-03-22
 --------------------
 

LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml

@@ -0,0 +1 @@
+<Lems><!-- Example with Simple cell specifying segment details--><!-- This is a file which can be read and executed by the LEMS Interpreter.  It imports the LEMS definitions of the core NeuroML 2 Components, imports in "pure" NeuroML 2 and contains some LEMS elements for running a simulation --><Target component="sim1" reportFile="report.ex5.txt"/><Include file="Cells.xml"/><Include file="Networks.xml"/><Include file="Simulation.xml"/><!-- Including file with a <neuroml>root, a "real" NeuroML 2 file --><Include file="../examples/NML2_SingleCompHHCell.nml"/><Simulation id="sim1" length="300ms" step="0.01ms" target="net1"><Display id="d1" title="Ex5: HH cell with simple morphology: voltage" timeScale="1ms" xmin="0" xmax="300" ymin="-90" ymax="50"><Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#cccccc" timeScale="1ms"/><Line id="spiking" quantity="hhpop[0]/spiking" scale="0.1V"  color="#004040" timeScale="1ms"/><!--<Line id="l3" quantity="hhpop[0]/debugVal" scale="1V"  color="#999999" timeScale="1ms"/>--></Display><Display id="d2" title="Ex5: HH cell with simple morphology: rate variables" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1"><Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#000000" timeScale="1ms"/><Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#ff0000" timeScale="1ms"/><Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/></Display><Display id="d3" title="Ex5: HH cell with simple morphology: current densities" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1"><Line id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#000000" timeScale="1ms"/><Line id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ff0000" timeScale="1ms"/></Display><Display id="d4" title="Ex5: HH cell with simple morphology: conductance densities" timeScale="1ms" xmin="0" xmax="300" ymin="-50" ymax="350"><Line id="gna" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/gDensity" scale="1"  color="#000000" timeScale="1ms"/><Line id="gk" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/gDensity" scale="1"  color="#ff0000" timeScale="1ms"/></Display><OutputFile id="of0" fileName="results/ex5_v.dat"><OutputColumn id="v" quantity="hhpop[0]/v"/></OutputFile><OutputFile id="of1" fileName="results/ex5_vars.dat"><OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/><OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/><OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/></OutputFile></Simulation></Lems>

LEMSexamples/regression-tests/results/README

@@ -0,0 +1 @@
+Temporary folder for the results of simulations run with LEMS