Merge pull request #181 from NeuroML/pg_updates

Updates for 2.3 release

.gitignore

@@ -28,3 +28,4 @@ NT_*/
 /source/Userdocs/NML2_examples/LEMS_Test_NaTa_t.xml
 /source/Userdocs/NML2_examples/LEMS_Test_SKv3_1.xml
 /source/Userdocs/NML2_examples/LEMS_iv_complex_cell.xml
+arm64

source/Devdocs/ReleaseProcess.md

@@ -3,7 +3,7 @@
 
 ## Overview
 
-In general, work is carried out in the **development** branches of the [main NeuroML repositories](https://github.com/NeuroML)
+In general, work is carried out in the **development** branches of the [main NeuroML repositories](https://github.com/NeuroML/.github/blob/main/testsheet/README.md)
 and these are merged to **master** branches on a new major release, e.g. move from NeuroML v2.1 to v2.2.
 
 A single page showing the **status of the automated test** as well as any **open Pull Requests** on all of the core NeuroML repositories can be found [here](https://github.com/NeuroML/.github/blob/main/testsheet/README.md).
@@ -14,30 +14,28 @@ These are the steps required for a new release of the NeuroML development tools.
 
 | Task | Version this was last done |
 | --- | --- |
-| Make releases (not just tag - generates DOI) previous development versions of individual repos | v2.2 |
-| Increment all version numbers - to distinguish release from previous development version | v2.2 |
-| Commit all work in development branches | v2.2 |
-| Test all development branches - rerun GitHub Actions at least once | v2.2 |
-| Recheck all READMEs & docs | v2.2 |
-| Run & check [test.py](https://github.com/NeuroML/NeuroML2/blob/master/test.py) in NeuroML2 repo | v2.2 |
-| Check through issues for closed & easily closable ones | v2.2 |
-| Update version in {ref}`documentation pages <userdocs:neuromlv2>` | v2.2 |
-| Update version on [COMBINE website](https://github.com/combine-org/combine-org.github.io/blob/master/content/authors/NeuroML/_index.md) | v2.2 |
-| Update NeuroML [milestones](https://github.com/NeuroML/NeuroML2/milestones) | v2.2 |
-| Update [HISTORY.md](https://github.com/NeuroML/NeuroML2/blob/master/HISTORY.md) in NeuroML2 | v2.2 |
-| pylems: Update README; Merge to master; Tag release; Release to pip | v2.2 |
-| libNeuroML:  Update README; Retest; Merge to master; Tag release; Release to pip; Check [installation docs](https://libneuroml.readthedocs.org/en/latest/install.html) | v2.2 |
-| pyNeuroML: Update Readme; Tag release; Release to pip | v2.2 |
-| NeuroMLlite: Update Readme; Tag release; Release to pip | v2.2 |
-| Java repositories ({ref}`jNeuroML <jNeuroML>`, org.neuroml.* etc.): Merge development to master; Tag releases | v2.2 |
-| Rebuild jNeuroML & commit to [jNeuroMLJar](https://sourceforge.net/p/neuroml/code/HEAD/tree/jNeuroMLJar/) and use latest for [jNeuroML for OMV](https://github.com/OpenSourceBrain/osb-model-validation/blob/master/omv/engines/getjnml.py#L8) | v2.2 |
-| Regenerate Cells.xml etc. on nml website & commit | v2.2 |
+| Commit final stable work in development branches | v2.3 |
+| Make releases (not just tag - generates DOI) previous development versions of individual repos | v2.3 |
+| Increment all version numbers - to distinguish release from previous development version | v2.3 |
+| Test all development branches - rerun GitHub Actions at least once | v2.3 |
+| Recheck all READMEs & docs | v2.3 |
+| Run & check [test.py](https://github.com/NeuroML/NeuroML2/blob/master/test.py) in NeuroML2 repo | v2.3 |
+| Check through issues for closed & easily closable ones | v2.3 |
+| Update version in {ref}`documentation pages <userdocs:neuromlv2>` | v2.3 |
+| Update [HISTORY.md](https://github.com/NeuroML/NeuroML2/blob/master/HISTORY.md) in NeuroML2 | v2.3 |
+| pylems: Update README; Merge to master; Tag release; Release to pip | v2.3 |
+| libNeuroML:  Update README; Retest; Merge to master; Tag release; Release to pip; Check [installation docs](https://libneuroml.readthedocs.org/en/latest/install.html) | v2.3 |
+| pyNeuroML: Update Readme; Tag release; Release to pip | v2.3 |
+| NeuroMLlite: Update Readme; Tag release; Release to pip | v2.3 |
+| Java repositories ({ref}`jNeuroML <jNeuroML>`, org.neuroml.* etc.): Merge development to master; Tag releases | v2.3 |
+| Rebuild jNeuroML & commit to [jNeuroMLJar](https://sourceforge.net/p/neuroml/code/HEAD/tree/jNeuroMLJar/) and use latest for [jNeuroML for OMV](https://github.com/OpenSourceBrain/osb-model-validation/blob/master/omv/engines/getjnml.py#L8) | v2.3 |
+| Add new binary release on [https://github.com/NeuroML/jNeuroML/releases](https://github.com/NeuroML/jNeuroML/releases) | v2.3 |
+| Update version used in [neuroConstruct](https://github.com/NeuralEnsemble/neuroConstruct) | v2.3 |
 | Update docs on [http://www.neuroml.org](https://www.neuroml.org) | v2.2 |
-| Add new binary release on [https://github.com/NeuroML/jNeuroML/releases](https://github.com/NeuroML/jNeuroML/releases) | v2.2 |
+| Update version on [COMBINE website](https://github.com/combine-org/combine-org.github.io/blob/master/content/authors/NeuroML/_index.md) | v2.2 |
 | ANNOUNCE (mailing list, Twitter) | v2.2 |
 | Increment version numbers in all development branches | v2.1 |
 | DOI on [Zenodo](https://doi.org/10.5281/zenodo.4627568) | v2.1 |
-| New milestone in issues | v2.1 |
-| Update version used in [neuroConstruct](https://github.com/NeuralEnsemble/neuroConstruct) | v2.2 |
+| Update NeuroML [milestones](https://github.com/NeuroML/NeuroML2/milestones) | v2.2 |
 | New release of neuroConstruct | v2.0 |
 | Test toolchain on Windows... | v2.0 |

source/Userdocs/NML2_examples/LEMS_HH_single_compartment_example_sim.xml

@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
 
      -->
 

source/Userdocs/NML2_examples/LEMS_example-single-izhikevich2007cell-sim.xml

@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
 
      -->
 

source/Userdocs/NML2_examples/LEMS_example_izhikevich2007network_sim.xml

@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
 
      -->
 

source/Userdocs/NML2_examples/LEMS_olm_example_sim.xml

@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
 
      -->
 

source/Userdocs/NML2_examples/olm.cell.nml

@@ -15,7 +15,7 @@
                 <distal x="0.0" y="20.0" z="0.0" diameter="10.0"/>
             </segment>
             <segment id="2" name="Seg0_axon_0">
-                <parent segment="0" fractionAlong="0."/>
+                <parent segment="0" fractionAlong="0.0"/>
                 <proximal x="0.0" y="0.0" z="0.0" diameter="1.5"/>
                 <distal x="0.0" y="-75.0" z="0.0" diameter="1.5"/>
             </segment>
@@ -77,10 +77,11 @@
                 <include segmentGroup="dend_1"/>
             </segmentGroup>
             <segmentGroup id="all">
-                <include segmentGroup="soma_0"/>
+                <notes>Default segment group for all segments in the cell</notes>
                 <include segmentGroup="axon_0"/>
                 <include segmentGroup="dend_0"/>
                 <include segmentGroup="dend_1"/>
+                <include segmentGroup="soma_0"/>
             </segmentGroup>
         </morphology>
         <biophysicalProperties id="biophys">

source/Userdocs/NML2_examples/olm.hoc

@@ -39,7 +39,7 @@
     "sections" : [ "dend_0", "dend_1" ]
   }, {
     "name" : "all",
-    "sections" : [ "soma_0", "soma_0", "axon_0", "axon_0", "dend_0", "dend_0", "dend_1", "dend_1" ]
+    "sections" : [ "soma_0", "axon_0", "dend_0", "dend_1" ]
   } ],
   "specificCapacitance" : [ {
     "group" : "all",
@@ -160,7 +160,7 @@ objref soma_group
 objref axon_group
 // Group: {name=dendrite_group, groups=[], sections=[dend_0, dend_1]}
 objref dendrite_group
-// Group: {name=all, sections=[soma_0, soma_0, axon_0, axon_0, dend_0, dend_0, dend_1, dend_1]}
+// Group: {name=all, sections=[soma_0, axon_0, dend_0, dend_1]}
 objref all
 
 objref synlist
@@ -238,15 +238,11 @@ proc subsets() { local i
     dend_0 dendrite_group.append()
     dend_1 dendrite_group.append()
 
-    // Group: {name=all, sections=[soma_0, soma_0, axon_0, axon_0, dend_0, dend_0, dend_1, dend_1]}
+    // Group: {name=all, sections=[soma_0, axon_0, dend_0, dend_1]}
     all = new SectionList()
     soma_0 all.append()
-    soma_0 all.append()
-    axon_0 all.append()
     axon_0 all.append()
     dend_0 all.append()
-    dend_0 all.append()
-    dend_1 all.append()
     dend_1 all.append()
 
 }

source/Userdocs/NML2_examples/olm_example_net.nml

@@ -8,7 +8,7 @@
         <population id="pop0" component="olm" size="1" type="populationList">
             <notes>A population for our cell</notes>
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <explicitInput target="pop0[0]" input="pg_olm"/>

source/Userdocs/NeuroMLv2.md

@@ -1,9 +1,8 @@
 (userdocs:neuromlv2)=
 # NeuroML v2
 
-
-The current stable version of NeuroML is v2.2, and the schema for this can be seen [here](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.2.xsd).
-The following figure, taken from Cannon et al. 2014 ({cite}`Cannon2014`) shows some of the elements defined in NeuroML version 2 (note: these core elements haven't changed since that publication).
+The current stable version of NeuroML is v2.3, and the XSD Schema for this can be found [here](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.3.xsd).
+The following figure, taken from Cannon et al. 2014 ({cite}`Cannon2014`) shows some of the core elements defined in NeuroML version 2 (note: these key elements haven't changed since that publication).
 
 ```{figure} ../images/Figure6a.png
 :alt: Elements defined in the NeuroML schema, version 2.