Merge pull request #86 from NeuroML/development

NeuroML 2.2 release

.github/workflows/ci.yml

@@ -0,0 +1,89 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches:  [ master, development, experimental, osb* ]
+  pull_request:
+    branches:  [ master, development, experimental, osb* ]
+
+jobs:
+  build_and_test:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        java: [ '8', '11', '16', '17' ]
+        runs-on: [ubuntu-latest, macos-11, windows-latest ]
+
+    name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK ${{ matrix.Java }}
+      uses: actions/setup-java@v2
+      with:
+        java-version: ${{ matrix.Java }}
+        distribution: 'adopt'
+
+    - name: Install using getNeuroML.py (non Win)
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        export main_repo_branch=${{env.main_repo_branch}}
+        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
+
+        python getNeuroML.py $main_repo_branch  -dont_switch_jneuroml_branch # will call mvn install on this & other repos
+        mvn dependency:tree
+        ./jnml -v
+
+    - name: Install using getNeuroML.py (Win)
+      if: ${{ matrix.runs-on == 'windows-latest' }}
+      run: |
+        $env:main_repo_branch=$env:GITHUB_REF_NAME
+        if ( $env:main_repo_branch -ne "master" -and $env:main_repo_branch -ne "development" -and $env:main_repo_branch -ne "experimental" -and $env:main_repo_branch -notlike '*osb*' ) { $env:main_repo_branch="development" }
+        echo "Using branch $env:main_repo_branch..."
+
+        python getNeuroML.py $env:main_repo_branch -dont_switch_jneuroml_branch # will call mvn install on this & other repos
+
+        mvn dependency:tree
+        .\jnml.bat -v
+
+    - name: Further tests (non Win)
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        pwd
+        ls -alt
+        mkdir results
+        ./jnml -validate ../NeuroML2/examples/NML2_FullNeuroML.nml # Test validate
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -nogui # Test running with jLEMS
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml -nogui
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -neuron
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -brian
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -sedml
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -cvode
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -matlab
+        ./jnml ../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -dlems
+        ./jnml ../NeuroML2/LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml -nogui
+        ./jnml ../NeuroML2/examples/NML2_SimpleMorphology.nml  -svg
+        ls -alt ../NeuroML2/examples
+        ls -alt ../NeuroML2/LEMSexamples
+
+    - name: Further tests (Win)
+      if: ${{ matrix.runs-on == 'windows-latest' }}
+      run: |
+        pwd
+        mkdir results
+        .\jnml.bat -validate ..\NeuroML2\examples\NML2_FullNeuroML.nml # Test validate
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -nogui # Test running with jLEMS
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex5_DetCell.xml -nogui
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -neuron
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -brian
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -sedml
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -cvode
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -matlab
+        .\jnml.bat ..\NeuroML2\LEMSexamples\LEMS_NML2_Ex9_FN.xml -dlems
+        .\jnml.bat ..\NeuroML2\LEMSexamples\regression-tests\LEMS_NML2_Ex5_DetCell_unformatted.xml -nogui
+        .\jnml.bat ..\NeuroML2\examples\NML2_SimpleMorphology.nml  -svg

.gitignore

@@ -11,3 +11,7 @@ src/main/java/META-INF/MANIFEST.MF
 .DS_Store
 *.*~
 *.log
+.classpath
+.factorypath
+.project
+.settings/

README.md

@@ -1,15 +1,18 @@
 jNeuroML
 ========
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4627568.svg)](https://doi.org/10.5281/zenodo.4627568)
+[![Java CI with Maven](https://github.com/NeuroML/jNeuroML/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/jNeuroML/actions/workflows/ci.yml)
 [![GitHub](https://img.shields.io/github/license/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/blob/master/LICENSE.lesser)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/pulls)
 [![GitHub issues](https://img.shields.io/github/issues/NeuroML/jNeuroML)](https://github.com/NeuroML/jNeuroML/issues)
 [![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
 [![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
+[![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 
-There are a number of repositories in active development under GitHub for handling [NeuroML](https://github.com/NeuroML) 
-and [LEMS](https://github.com/LEMS) with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation. 
+There are a number of repositories in active development under GitHub for handling [NeuroML](https://github.com/NeuroML)
+and [LEMS](https://github.com/LEMS) with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation.
 
 jNeuroML can:
 
@@ -51,8 +54,8 @@ Typing *./jnml* (or *jnml.bat* on Windows) will list the options available. Some
     ./jnml MyLEMS.xml -graph                    (generate png of structure of LEMS model using GraphViz)
     ./jnml MyLEMS.xml -neuron                   (generate code to run on the NEURON simulator)
 
-Export and import features for [NEURON](http://www.neuron.yale.edu/neuron/), [SBML](http://sbml.org), 
-[Brian](http://www.briansimulator.org/) etc. are under active development (see https://github.com/NeuroML/org.neuroml.export 
+Export and import features for [NEURON](http://www.neuron.yale.edu/neuron/), [SBML](http://sbml.org),
+[Brian](http://www.briansimulator.org/) etc. are under active development (see https://github.com/NeuroML/org.neuroml.export
 and https://github.com/NeuroML/org.neuroml.import).
 
 **Note:**
@@ -63,35 +66,34 @@ Adding the environment variable *JNML_HOME*, pointing to the *jNeuroML* folder,
 Getting the source for jNeuroML
 -------------------------------
 
-If you prefer to clone all of the individual repositories and build the jNeuroML application yourself, 
+If you prefer to clone all of the individual repositories and build the jNeuroML application yourself,
 use the [getNeuroML.py](https://github.com/NeuroML/jNeuroML/blob/master/getNeuroML.py) utility in the jNeuroML repo:
 
     git clone git://github.com/NeuroML/jNeuroML.git neuroml_dev/jNeuroML
     cd neuroml_dev/jNeuroML
     python getNeuroML.py
 
-This will clone ~11 repos for NML2 & LEMS (including Python based libraries) into *neuroml_dev/* and compile 
+This will clone ~11 repos for NML2 & LEMS (including Python based libraries) into *neuroml_dev/* and compile
 the Java based ones using Maven (download [here](http://maven.apache.org/) or use package managers for Linux (e.g. apt-get install maven) or Mac (brew install maven)). The full process may take 5-10 mins on first installation, but subsequently running:
 
     git pull
     python getNeuroML.py
 
-in the jNeuroML folder will get the stable version of each repo & compile using Maven if necessary. 
+in the jNeuroML folder will get the stable version of each repo & compile using Maven if necessary.
 
 **To access the very latest version** (the [development](https://github.com/NeuroML/jNeuroML/tree/development) branches of the GitHub repos) use:
 
     python getNeuroML.py clean
     python getNeuroML.py development
 
-Use of Maven is a great way to manage versions of applications being developed in distributed repositories, 
-and will make it easy to use selected parts of this for different Java applications. For example, these packages 
+Use of Maven is a great way to manage versions of applications being developed in distributed repositories,
+and will make it easy to use selected parts of this for different Java applications. For example, these packages
 will be used in various ways to provide NeuroML/LEMS support in [neuroConstruct](http://www.neuroConstruct.org) and for handling NeuroML on the [Open Source Brain website](http://www.OpenSourceBrain.org).
 
 Prefer Python?
 --------------
 
 If you prefer using/installing/coding in Python, try out [pyNeuroML](https://github.com/NeuroML/pyNeuroML). Much of the functionality of jNeuroML is bundled inside pyNeuroML and can be accessed with a command line utility (*pynml*) with similar usage as *jnml*.
 
-[![Build Status](https://travis-ci.com/NeuroML/jNeuroML.png?branch=master)](https://travis-ci.com/NeuroML/jNeuroML)
 
 This code is distributed under the terms of the GNU Lesser General Public License.