Init commit

.gitignore

+#N2S3 specific
+results/
+resource-cache/
+
+#SBT specific
+.cache/
+.history/
+.lib/
+dist/*
+target/
+lib_managed/
+src_managed/
+project/boot/
+project/plugins/project/
+
+# IntelliJ
+.idea/
+n2s3.iml
+
+# Scala IDE
+.project
+.settings/
+
+#Others
+.cache-main
+.cache-tests
+.classpath
\ No newline at end of file

.gitrepo

+; DO NOT EDIT (unless you know what you are doing)
+;
+; This subdirectory is a git "subrepo", and this file is maintained by the
+; git-subrepo command. See https://github.com/git-commands/git-subrepo#readme
+;
+[subrepo]
+	remote = git+ssh://git@git.renater.fr:2222/n2s3.git
+	branch = development
+	commit = f8a7382ccc0a54f641de0b7abe7ecbb624bdcf89
+	parent = 0fc67a1b92d3ab67aac48bf04b459be7ac289767
+	cmdver = 0.3.1

CHANGESLOG.md

+## Changes log v1.1
+
+N2S3 1.1 is a quality improvement release.
+The highlights of this version are the introduction of a new Domain Specific Language (DSL), a reorganization of the existing neuron models and lots of cleanups.
+
+###Core
+
+- Introduction of a DSL to simplify the task of creating a simulation.
+- The different models N2S3 supports have been reorganised:
+  - Neuron Models are now located in the `models.neurons` package. The featured models are:
+    - Izhikevich (http://www.izhikevich.org/publications/spikes.pdf)
+    - Leaky-Integrate-and-Fire (http://www.cns.nyu.edu/~eorhan/notes/lif-neuron.pdf)
+    - Spike-Response-Model (http://icwww.epfl.ch/~gerstner/SPNM/node27.html)
+  - Synapse Models are now located in the `models.synapses` package. The featured synapses are:
+    - Inhibitory Synapse
+    - Simplified STDP
+    - Stantard STDP
+    - Static Synapse
+    - Ternary Synapse
+    
+###Cleanups
+
+- Removal of lots of compilation warnings
+- Removal of unused classes from the support package, old inputs
+- Removal of the deprecated connections creation in ConnectionPolicy and subclasses
+- Removal and cleanup of commented code
+
+
+## Changes log v1.0
+
+N2S3 1.0 is mainly an infrastructure release oriented towards the ease of development and distribution. This version builds on version 0.2 with ~165 new commits! There are also some news in the core of the simulator and the documentation. Here you have the major changes:
+
+Infrastructure:
+  - N2S3 is now an SBT multi-project [1]
+  - Better integration with IntelliJ IDEA and Eclipse [2]
+  - Supporting the system's distribution:
+    - Clustering support
+    - Refactoring to support the dynamic deployment of actors in different cluster nodes.
+    - Two deployment strategies were implemented so far: Random and concrete node.
+    - Fixes in the core to make it distributable. E.g, fixed serialization of messages, global state.
+  - The Continuous Integration service was extended and enhanced [4]
+  - A new input mechanism was implemented [5, 6]
+
+Core:
+  - Preliminar version of supervised learning algorithm SpikeProp
+  - Preliminar version of Supervised Xor, an example of learning the Xor function with SpikeProp (Error-backpropagation in temporally encoded networks of spiking neurons)
+  - Added bio-inspired model i.e., a model with parameters similar to those in the nature.
+
+Examples:
+  - Examples of Mnist/Freeway/sevenSegment with the bio-inspired model.
+  - Example of Masquelier's experiment: Spike Timing Dependent Plasticity Finds the Start of Repeating Patterns in Continuous Spike Trains
+  - Preliminar version of an example of direction detection with reservoir computing (using supervised STDP and only 2 directions)
+
+Documentation:
+  - The core scaladocs were entirely revisited
+  - Technical documentation about the core implementation can be found in [7]
+
+[1] https://sourcesup.renater.fr/wiki/n2s3/environmentsetup#sbt_integration
+[2] https://sourcesup.renater.fr/wiki/n2s3/environmentsetup#ide_integration
+[3] https://sourcesup.renater.fr/wiki/n2s3/simulation_cluster
+[4] https://sourcesup.renater.fr/jenkins/job/N2S3/
+[5] https://sourcesup.renater.fr/wiki/n2s3/simulation_stimuli
+[6] https://sourcesup.renater.fr/wiki/n2s3/inputs
+[7] https://sourcesup.renater.fr/wiki/n2s3/devdocs
+
+## Changes log v0.2
+
+Infrastructural:
+ - all changes required to package and publish n2s3 as a library
+ - all tests are green
+
+Documentation:
+ - on the documentation side, scaladocs were added on the main classes that are needed to setup experiments
+
+Core:
+ - Added ternary synapse model

README.md

+# N2S3 a Neural Network Simulator
+
+Thank you for downloading N2S3. 
+
+The aim of this simulator is to simulate different physical neural networks topology with different Synapses/Neurons models. 
+
+# Installation and testing
+
+To use N2S3 in your project just declare a dependency as follows in your sbt file:
+
+```scala
+libraryDependencies ++= Seq(
+  "fr.univ-lille.cristal" %% "n2s3" % "1.0" exclude("net.sf", "jaer_2.11"),
+  "net.sf" %% "jaer" % "1.0" from "https://sourcesup.renater.fr/frs/download.php/file/5047/jaer.jar"
+)
+```
+
+If you want to compile the code in this repository you can execute:
+
+```bash
+$ sbt compile
+```
+
+Similarly, you can run the tests:
+
+```bash
+$ sbt test
+```
+
+Check the docs: https://sourcesup.renater.fr/wiki/n2s3/
+  
+# Changes Log
+
+## v1.1
+
+N2S3 1.1 is a quality improvement release.
+The highlights of this version are the introduction of a new Domain Specific Language (DSL), a reorganization of the existing neuron models and lots of cleanups.
+
+###Infrastructure
+
+- Update XChart version
+
+###Core
+
+- Introduction of a DSL to simplify the task of creating a simulation//TODO: introduce link to the documentation.
+- The different models N2S3 supports have been reorganised:
+  - Neuron Models are now located in the `models.neurons` package. The featured models are:
+    - Izhikevich (http://www.izhikevich.org/publications/spikes.pdf)
+    - Leaky-Integrate-and-Fire (http://www.cns.nyu.edu/~eorhan/notes/lif-neuron.pdf)
+    - Spike-Response-Model (http://icwww.epfl.ch/~gerstner/SPNM/node27.html)
+  - Synapse Models are now located in the `models.synapses` package. The featured synapses are:
+    - Inhibitory Synapse
+    - Simplified STDP (http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6033439)
+    - Stantard STDP (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431193/)
+    - Static Synapse
+    - Ternary Synapse
+  - Improve the usage of Squant units
+  - There is no more `defaultSynapse` method in neuron model, therefore synapse model need to be given explicitly
+  - Modification in the synapses identifications. All incoming synapses have an local unique identifier
+    - Synapse weight graph require an explicit list of `NeuronConnection` in order to display then in the right order
+    
+###Support
+ 
+ - Add a Resource manager that aims to automatically download and unzip used datasets. Removal of datasets in the code repertory
+ 
+###Cleanups
+
+- Removal of lots of compilation warnings
+- Removal of unused classes from the support package, old inputs
+- Removal of the deprecated connections creation in ConnectionPolicy and subclasses
+- Removal and cleanup of commented code
+
+###Documentation
+
+- Updated tutorial for version 1.1 https://sourcesup.renater.fr/wiki/n2s3/tutorial
+- Updated download page https://sourcesup.renater.fr/wiki/n2s3/installation
+- //TODO make page on DSL
+- //TODO doc about models
+
+## v1.0
+
+N2S3 is now feature complete, well tested and fully documented. External users are welcome!
+
+N2S3 1.0 is mainly an infrastructure release oriented towards the ease of development and distribution. This version builds on version 0.2 with ~165 new commits! There are also some news in the core of the simulator and the documentation. Here you have the major changes:
+
+###Infrastructure
+
+- N2S3 is now an SBT multi-project [1]
+- Better integration with IntelliJ IDEA and Eclipse [2]
+- Supporting the system's distribution:
+  - Clustering support
+  - Refactoring to support the dynamic deployment of actors in different cluster nodes.
+  - Two deployment strategies were implemented so far: Random and concrete node.
+  - Fixes in the core to make it distributable. E.g, fixed serialization of messages, global state.
+- The Continuous Integration service was extended and enhanced [4]
+- A new input mechanism was implemented [5, 6]
+
+###Core
+
+- Preliminar version of supervised learning algorithm SpikeProp
+- Preliminar version of Supervised Xor, an example of learning the Xor function with SpikeProp (Error-backpropagation in temporally encoded networks of spiking neurons)
+- Added bio-inspired model i.e., a model with parameters similar to those in the nature.
+
+###Examples
+
+- Examples of Mnist/Freeway/sevenSegment with the bio-inspired model.
+- Example of Masquelier's experiment: Spike Timing Dependent Plasticity Finds the Start of Repeating Patterns in Continuous Spike Trains
+- Preliminar version of an example of direction detection with reservoir computing (using supervised STDP and only 2 directions)
+
+###Documentation
+
+- The core scaladocs were entirely revisited
+- Technical documentation about the core implementation can be found in [7]
+
+We are waiting for your contributions, And do not hesitate to share!
+
+The N2S3 team
+
+[1] https://sourcesup.renater.fr/wiki/n2s3/environmentsetup#sbt_integration
+
+[2] https://sourcesup.renater.fr/wiki/n2s3/environmentsetup#ide_integration
+
+[3] https://sourcesup.renater.fr/wiki/n2s3/simulation_cluster
+
+[4] https://sourcesup.renater.fr/jenkins/job/N2S3/
+
+[5] https://sourcesup.renater.fr/wiki/n2s3/simulation_stimuli
+
+[6] https://sourcesup.renater.fr/wiki/n2s3/inputs
+
+[7] https://sourcesup.renater.fr/wiki/n2s3/devdocs
+
+## v0.2
+
+### Infrastructural
+ - all changes required to package and publish n2s3 as a library
+ - all tests are green
+
+### Documentation
+ - on the documentation side, scaladocs were added on the main classes that are needed to setup experiments
+
+### Core
+ - Added ternary synapse model
\ No newline at end of file

RELEASING.md

+# N2S3's release process so far is the following
+
+During development,
+  * development of version [X] is done in branch dev-[X], e.g. dev-0.2
+  * version numbers in build.sbt is [X]-SNAPSHOT, e.g., 0.2-SNAPSHOT
+  * regularly, SNAPSHOT versions are published in https://oss.sonatype.org/content/repositories/snapshots/fr/univ-lille/cristal/n2s3_2.11/
+At release time
+  1) branch dev-[X] is merged into master
+  2) version numbers in build.sbt are set to [X]
+  3) a fixed version is staged/published in https://oss.sonatype.org/
+  4) a tag v[X] is created
+  5) a new development branch dev-[X+1] is started
+     * and a new development cycle starts

build.sbt

+import com.typesafe.sbt.SbtMultiJvm
+import com.typesafe.sbt.SbtMultiJvm.MultiJvmKeys.{MultiJvm, scalatestOptions}
+
+lazy val commonSettings = Seq(
+  version          := "1.1",
+  organization     := "fr.univ-lille.cristal",
+  scalaVersion     := "2.11.6",
+  scalacOptions    := Seq("-unchecked", "-deprecation", "-encoding", "utf8", "-language:postfixOps"),
+
+ /********************************************************************************************************************
+  * Dependecy information
+  ******************************************************************************************************************/
+  resolvers += "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/releases",
+
+  /********************************************************************************************************************
+    * Publishing options
+    ******************************************************************************************************************/
+  publishTo := {
+    val nexus = "https://oss.sonatype.org/"
+    if (isSnapshot.value)
+      Some("snapshots" at nexus + "content/repositories/snapshots")
+    else
+      Some("releases"  at nexus + "service/local/staging/deploy/maven2")
+  },
+  credentials += Credentials(Path.userHome / ".ivy2" / ".credentials"),
+
+  publishMavenStyle := true,
+  publishArtifact in Test := false,
+  pomIncludeRepository := { x => false },
+  pomExtra := <url>https://sourcesup.renater.fr/projects/n2s3/</url>
+    <licenses>
+      <license>
+        <name>CeCILL-B Version 1</name>
+        <url>http://www.cecill.info/licences/Licence_CeCILL-B_V1-fr.html</url>
+        <distribution>repo</distribution>
+      </license>
+    </licenses>
+    <scm>
+      <connection>scm:git://git.renater.fr/n2s3.git</connection>
+      <developerConnection>scm:git:ssh://git@git.renater.fr:2222/n2s3.git</developerConnection>
+      <url>https://sourcesup.renater.fr/scm/?group_id=2343</url>
+    </scm>
+    <developers>
+      <developer>
+        <id>emeraude-team</id>
+        <name>Emeraude Team</name>
+        <email>n2s3-dev@univ-lille1.fr</email>
+      </developer>
+    </developers>
+)
+
+lazy val root = (project in file(".")).
+  aggregate(n2s3, n2s3_cluster, examples, daemon)
+
+lazy val n2s3 = (project in file("n2s3")).
+  settings(commonSettings: _*)
+
+lazy val n2s3_cluster = (project in file("n2s3_cluster")).
+  settings(commonSettings: _*).
+  dependsOn(n2s3)
+
+lazy val examples = (project in file("n2s3_examples")).
+  settings(commonSettings: _*).
+  dependsOn(n2s3, n2s3_cluster)
+
+lazy val daemon = (project in file("n2s3_daemon")).
+  settings(commonSettings: _*).
+  dependsOn(n2s3)
+
+lazy val integration_tests = (project in file("n2s3_integration_tests")).
+  settings(SbtMultiJvm.multiJvmSettings: _*).
+  settings(commonSettings: _*).
+  configs(MultiJvm).
+  dependsOn(n2s3, n2s3_cluster)