Merge pull request #202 from DimitriPlotnikov/master

Restructure model artifacts. Increase development version.

docker/DockerfileRelease

@@ -36,7 +36,7 @@ ENV MAVEN_HOME /usr/share/maven
 
 # Define working directory.
 WORKDIR /data
-RUN wget https://github.com/nest/nestml/releases/download/0.0.4/nestml.jar
+RUN wget https://github.com/nest/nestml/releases/download/0.0.5/nestml.jar
 
 # create a non-root user named tester, 
 # give them the password "tester" put them in the sudo group

src/test/resources/codegeneration/iaf_neuron.nestml → models/iaf_neuron.nestml

@@ -1,4 +1,4 @@
-/* BeginDocumentation
+/*
 Name: iaf_neuron - Leaky integrate-and-fire neuron model.
 
 Description:

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>nestml</groupId>
     <artifactId>nestml-core</artifactId>
-    <version>0.0.5</version>
+    <version>0.1.0-SNAPSHOT</version>
 
     <properties>
         <!-- .. Libraries ..................................................... -->

src/main/java/org/nest/codegeneration/NESTCodeGenerator.java

@@ -218,37 +218,7 @@ private void generateModuleCodeForNeurons(
         cmakeModuleClass,
         neurons.get(0)); // an arbitrary AST to match the signature
 
-    final Path makefileFile = Paths.get("Makefile.am");
-    generator.generate(
-        "org.nest.nestml.module.Makefile",
-        makefileFile,
-        neurons.get(0)); // an arbitrary AST to match the signature
-
-    final Path bootstrappingFile = Paths.get("bootstrap.sh");
-    generator.generate(
-        "org.nest.nestml.module.Bootstrap",
-        bootstrappingFile,
-        neurons.get(0)); // an arbitrary AST to match the signature
-
-    final Path configureFile = Paths.get("configure.ac");
-    generator.generate(
-        "org.nest.nestml.module.Configure",
-        configureFile,
-        neurons.get(0)); // an arbitrary AST to match the signature
-
-    final Path moduleClass = Paths.get(moduleName + "Config.cpp");
-    generator.generate(
-        "org.nest.nestml.module.ModuleClass",
-        moduleClass,
-        neurons.get(0)); // an arbitrary AST to match the signature
-
-    final Path moduleHeader = Paths.get( moduleName + "Config.h");
-    generator.generate(
-        "org.nest.nestml.module.ModuleHeader",
-        moduleHeader,
-        neurons.get(0)); // an arbitrary AST to match the signature
-
-    final Path initSLI = Paths.get( moduleName + "-init.sli");
+    final Path initSLI = Paths.get("sli", moduleName + "-init.sli");
     generator.generate(
         "org.nest.nestml.module.SLI_Init",
         initSLI,

src/main/java/org/nest/codegeneration/converters/NESTReferenceConverter.java

@@ -84,7 +84,7 @@ public String convertFunctionCall(final ASTFunctionCall astFunctionCall) {
     if (functionName.contains(PredefinedFunctions.EMIT_SPIKE)) {
       return "set_spiketime(nest::Time::step(origin.get_steps()+lag+1));\n" +
           "nest::SpikeEvent se;\n" +
-          "network()->send(*this, se, lag);";
+          "nest::kernel().event_delivery_manager.send(*this, se, lag);";
     }
 
     final Optional<MethodSymbol> functionSymbol = NESTMLSymbols.resolveMethod(astFunctionCall);

src/main/java/org/nest/nestml/_cocos/UsesOnlyComponents.java

@@ -45,10 +45,13 @@ public void check(final ASTUSE_Stmt use) {
 
     final Optional<NeuronSymbol> neuronType = scope.resolve(typeName, NeuronSymbol.KIND);
 
-    if (neuronType.isPresent() && !neuronType.get().getType().equals(NeuronSymbol.Type.COMPONENT)) {
-      final String msg = errorStrings.getErrorMsgOnlyComponentsForComponents(this, typeName);
+    if (neuronType.isPresent()) {
+      if (!neuronType.get().getType().equals(NeuronSymbol.Type.COMPONENT)) {
+        final String msg = errorStrings.getErrorMsgOnlyComponentsForComponents(this, typeName);
+        Log.error(msg, use.get_SourcePositionStart());
+
+      }
 
-      Log.error(msg, use.get_SourcePositionStart());
     }
     // Undefined type of the name
   }

src/main/resources/org/nest/nestml/buffer/CurrentBufferFill.ftl

@@ -4,6 +4,6 @@
   @result TODO
 -->
 <#if ast.isCurrent()>
-get_${ast.getName()}().add_value(e.get_rel_delivery_steps( network()->get_slice_origin()),
+get_${ast.getName()}().add_value(e.get_rel_delivery_steps( nest::kernel().simulation_manager.get_slice_origin()),
            weight * current );
 </#if>

src/main/resources/org/nest/nestml/buffer/SpikeBufferFill.ftl

@@ -12,14 +12,14 @@
 -->
 <#if ast.isSpike()>
   // TODO do i need this?
-  //get_${ast.getName()}().add_value(e.get_rel_delivery_steps( network()->get_slice_origin()),
+  //get_${ast.getName()}().add_value(e.get_rel_delivery_steps( nest::kernel().simulation_manager.get_slice_origin()),
   //             weight * multiplicity );
   <#if bufferHelper.isVector(ast)>
   // 1
     for (size_t i=0; i < P_.${bufferHelper.vectorParameter(ast)}; i++)
     {
       if (B_.receptor_types_${ast.getName()}[i] == e.get_rport()) {
-      get_${ast.getName()}()[i].add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
+      get_${ast.getName()}()[i].add_value(e.get_rel_delivery_steps(nest::kernel().simulation_manager.get_slice_origin()),
       e.get_weight() * e.get_multiplicity());
       }
 
@@ -29,14 +29,14 @@
     <#if bufferHelper.isExcitatory(ast)>
     if ( weight >= 0.0 ) // excitatory
     {
-      get_${ast.getName()}().add_value(e.get_rel_delivery_steps( network()->get_slice_origin()),
+      get_${ast.getName()}().add_value(e.get_rel_delivery_steps( nest::kernel().simulation_manager.get_slice_origin()),
                    weight * multiplicity );
     }
     </#if>
     <#if bufferHelper.isInhibitory(ast)>
     if ( weight < 0.0 ) // inhibitory
     {
-      get_${ast.getName()}().add_value(e.get_rel_delivery_steps( network()->get_slice_origin()),
+      get_${ast.getName()}().add_value(e.get_rel_delivery_steps( nest::kernel().simulation_manager.get_slice_origin()),
                    weight * multiplicity );
     }
     </#if>

src/main/resources/org/nest/nestml/function/TimestepDynamics.ftl

@@ -1,7 +1,5 @@
 <#--Dynamics implements BodyElement = "dynamics" (MinDelay | TimeStep) "(" Parameter ")"
                                         BLOCK_OPEN! Block BLOCK_CLOSE!;-->
-assert(to >= 0 && (nest::delay) from < nest::Scheduler::get_min_delay());
-assert(from < to);
 
 double t;
 for ( nest::long_t lag = from ; lag < to ; ++lag ) {

src/main/resources/org/nest/nestml/module/CMakeLists.ftl

@@ -35,13 +35,13 @@ cmake_minimum_required( VERSION 2.8.12 )
 set( SHORT_NAME ${moduleName} )
 
 #    the complete module name is here:
-set( MODULE_NAME ${r"$"}{SHORT_NAME}module )
+set( MODULE_NAME ${r"$"}{SHORT_NAME} )
 
 # 2) Add all your sources here
 set( MODULE_SOURCES
     ${moduleName}.h ${moduleName}.cpp
     <#list neurons as neuron>
-      ${neuron.getName()}.cpp ${neuron.getName()}.h <#if neuron_has_next>\</#if>
+      ${neuron.getName()}.cpp ${neuron.getName()}.h <#if neuron_has_next> </#if>
     </#list>
     )
 

src/main/resources/org/nest/nestml/neuron/NeuronClass.ftl

@@ -20,19 +20,27 @@
 *
 */
 
+// C++ includes:
+#include <limits>
+
+// Includes from libnestutil:
+#include "numerics.h"
+
+// Includes from nestkernel:
 #include "exceptions.h"
-#include "network.h"
+#include "kernel_manager.h"
+#include "universal_data_logger_impl.h"
+
+// Includes from sli:
 #include "dict.h"
-#include "integerdatum.h"
-#include "doubledatum.h"
 #include "dictutils.h"
-#include "numerics.h"
-#include "universal_data_logger_impl.h"
+#include "doubledatum.h"
+#include "integerdatum.h"
+#include "lockptrdatum.h"
 
-#include <limits>
-<#assign stateSize = body.getEquations()?size>
 #include "${simpleNeuronName}.h"
 
+<#assign stateSize = body.getEquations()?size>
 /* ----------------------------------------------------------------
 * Recordables map
 * ---------------------------------------------------------------- */
@@ -318,7 +326,7 @@ ${simpleNeuronName}::handle(nest::SpikeEvent &e)
         if ( B_.receptor_types_${spikeBuffer.getName()}[ i ] == e.get_rport() )
         {
             B_.${spikeBuffer.getName()}[i].add_value(
-              e.get_rel_delivery_steps( network()->get_slice_origin() ),
+              e.get_rel_delivery_steps( nest::kernel().simulation_manager.get_slice_origin() ),
               e.get_weight() * e.get_multiplicity() );
         }
       }

src/main/resources/org/nest/nestml/neuron/NeuronHeader.ftl

@@ -43,11 +43,15 @@
 #include <gsl/gsl_odeiv.h>
 </#if>
 
-#include "nest.h"
-#include "event.h"
+// Includes from nestkernel:
 #include "archiving_node.h"
 #include "connection.h"
+#include "event.h"
+#include "nest_types.h"
+#include "ring_buffer.h"
 #include "universal_data_logger.h"
+
+// Includes from sli:
 #include "dictdatum.h"
 
 /* BeginDocumentation

src/test/java/org/nest/base/ModelbasedTest.java

@@ -33,7 +33,7 @@
  */
 public class ModelbasedTest {
   protected static final Path OUTPUT_FOLDER = Paths.get("target");
-  protected static final Path TEST_MODEL_PATH = Paths.get("src/test/resources/");
+  protected static final Path TEST_MODEL_PATH = Paths.get("models");
   protected final NESTMLParser parser = new NESTMLParser(TEST_MODEL_PATH);
   protected final NESTMLScopeCreator scopeCreator = new NESTMLScopeCreator(TEST_MODEL_PATH);
 

src/test/java/org/nest/codegeneration/NESTCodeGeneratorTest.java

@@ -30,9 +30,9 @@ public class NESTCodeGeneratorTest extends GenerationBasedTest {
   private static final Path OUTPUT_DIRECTORY = Paths.get("target", "build");
   private static final PSCMock pscMock = new PSCMock();
 
-  private static final String PSC_MODEL_WITH_ODE = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
+  private static final String PSC_MODEL_WITH_ODE = "models/iaf_psc_alpha.nestml";
   private static final String PSC_MODEL_IMPERATIVE = "src/test/resources/codegeneration/imperative/iaf_psc_alpha_imperative.nestml";
-  private static final String COND_MODEL_IMPLICIT = "src/test/resources/codegeneration/iaf_cond_alpha_implicit.nestml";
+  private static final String COND_MODEL_IMPLICIT = "models/iaf_cond_alpha_implicit.nestml";
 
   @Test
   public void testPSCModelWithoutOde() {

src/test/java/org/nest/codegeneration/helpers/AliasInverterTest.java

@@ -22,7 +22,7 @@
  * @author plotnikov
  */
 public class AliasInverterTest extends GenerationBasedTest {
-  private static final String PSC_MODEL_WITH_ODE = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
+  private static final String PSC_MODEL_WITH_ODE = "models/iaf_psc_alpha.nestml";
 
   @Test
   public void testComputationOfInverseFunction() {

src/test/java/org/nest/codegeneration/sympy/ExpressionFolderTest.java

@@ -28,10 +28,12 @@
 public class ExpressionFolderTest extends ModelbasedTest {
   private static final ExpressionsPrettyPrinter printer = new ExpressionsPrettyPrinter();
 
-  private static final String MODEL_FILE_PATH = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
-  private final static Path STATE_VARIABLES_FILE = Paths.get("src/test/resources/codegeneration/sympy/psc/",
+  private static final String MODEL_FILE_PATH = "models/iaf_psc_alpha.nestml";
+  private final static Path STATE_VARIABLES_FILE = Paths.get(
+      "src/test/resources/codegeneration/sympy/psc/",
       LinearSolutionTransformer.STATE_VARIABLES_FILE);
-  private final static Path STATE_UPDATE_STEPS_FILE = Paths.get("src/test/resources/codegeneration/sympy/psc/",
+  private final static Path STATE_UPDATE_STEPS_FILE = Paths.get(
+      "src/test/resources/codegeneration/sympy/psc/",
       LinearSolutionTransformer.STATE_VECTOR_UPDATE_STEPS_FILE);
 
   @Test

src/test/java/org/nest/codegeneration/sympy/LinearSolutionTransformerTest.java

@@ -62,7 +62,7 @@ public class LinearSolutionTransformerTest extends ModelbasedTest {
       LinearSolutionTransformer.STATE_VECTOR_TMP_BACK_ASSIGNMENTS_FILE);
 
   private static final String NEURON_NAME = "iaf_psc_alpha_nestml";
-  private static final String MODEL_FILE_PATH = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
+  private static final String MODEL_FILE_PATH = "models/iaf_psc_alpha.nestml";
 
   @Test
   public void testExactSolutionTransformation() {

src/test/java/org/nest/codegeneration/sympy/SympyScriptGeneratorTest.java

@@ -15,6 +15,7 @@
 import org.nest.ode._ast.ASTEquation;
 import org.nest.symboltable.predefined.PredefinedFunctions;
 import org.nest.utils.ASTUtils;
+import org.nest.utils.FilesHelper;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -32,14 +33,10 @@
  * @author plotnikov
  */
 public class SympyScriptGeneratorTest extends ModelbasedTest {
-  private static final String PATH_TO_PSC_MODEL
-      = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
-  private static final String PATH_TO_PSC_DELTA_MODEL
-      = "src/test/resources/codegeneration/iaf_psc_delta.nestml";
-  private static final String PATH_TO_COND_MODEL
-      = "src/test/resources/codegeneration/iaf_cond_alpha.nestml";
-  private static final String PATH_TO_COND_IMPLICIT_MODEL
-      = "src/test/resources/codegeneration/iaf_cond_alpha_implicit.nestml";
+  private static final String PATH_TO_PSC_MODEL = "models/iaf_psc_alpha.nestml";
+  private static final String PATH_TO_PSC_DELTA_MODEL = "models/iaf_psc_delta.nestml";
+  private static final String PATH_TO_COND_MODEL = "models/iaf_cond_alpha.nestml";
+  private static final String PATH_TO_COND_IMPLICIT_MODEL = "models/iaf_cond_alpha_implicit.nestml";
 
   private static final String OUTPUT_FOLDER = "target";
   private static final Path OUTPUT_SCRIPT_DIRECTORY = Paths.get(OUTPUT_FOLDER, "sympy");
@@ -92,6 +89,8 @@ private void generateAndCheck(final String pathToModel) throws IOException {
     final NESTMLScopeCreator nestmlScopeCreator = new NESTMLScopeCreator(TEST_MODEL_PATH);
     nestmlScopeCreator.runSymbolTableCreator(root.get());
 
+    FilesHelper.deleteFilesInFolder(OUTPUT_SCRIPT_DIRECTORY);
+
     final Optional<Path> generatedScript = generateSympyODEAnalyzer(
         root.get().getNeurons().get(0),
         OUTPUT_SCRIPT_DIRECTORY);

src/test/java/org/nest/integration/NESTCodeGeneratorIntegrationTest.java

@@ -23,17 +23,17 @@
 public class NESTCodeGeneratorIntegrationTest extends GenerationBasedTest {
 
   private final List<String> pscModelsWithOde = Lists.newArrayList(
-      "src/test/resources/codegeneration/iaf_neuron.nestml",
-      "src/test/resources/codegeneration/iaf_psc_alpha.nestml",
-      "src/test/resources/codegeneration/iaf_psc_exp.nestml",
-      "src/test/resources/codegeneration/iaf_tum_2000.nestml",
-      "src/test/resources/codegeneration/iaf_psc_delta.nestml",
-      "src/test/resources/codegeneration/mat2_psc_exp.nestml"
+      "models/iaf_neuron.nestml",
+      "models/iaf_psc_alpha.nestml",
+      "models/iaf_psc_exp.nestml",
+      "models/iaf_tum_2000.nestml",
+      "models/iaf_psc_delta.nestml",
+      "models/mat2_psc_exp.nestml"
   );
 
   private final List<String> multisynapseModels = Lists.newArrayList(
-      "src/test/resources/codegeneration/iaf_psc_alpha_multisynapse.nestml",
-      "src/test/resources/codegeneration/iaf_psc_exp_multisynapse.nestml"
+      "models/iaf_psc_alpha_multisynapse.nestml",
+      "models/iaf_psc_exp_multisynapse.nestml"
   );
 
   private final List<String> imperativeModels = Lists.newArrayList(
@@ -47,15 +47,15 @@ public class NESTCodeGeneratorIntegrationTest extends GenerationBasedTest {
   );
 
   private final List<String> nestmlCondModels = Lists.newArrayList(
-      "src/test/resources/codegeneration/iaf_cond_alpha.nestml"
+      "models/iaf_cond_alpha.nestml"
   );
 
   private final List<String> nestmlCondImplicitModels = Lists.newArrayList(
-      "src/test/resources/codegeneration/iaf_cond_alpha_implicit.nestml",
-      "src/test/resources/codegeneration/iaf_cond_exp_implicit.nestml",
-      "src/test/resources/codegeneration/aeif_cond_alpha_implicit.nestml",
-      "src/test/resources/codegeneration/aeif_cond_exp_implicit.nestml",
-      "src/test/resources/codegeneration/hh_psc_alpha.nestml"
+      "models/iaf_cond_alpha_implicit.nestml",
+      "models/iaf_cond_exp_implicit.nestml",
+      "models/aeif_cond_alpha_implicit.nestml",
+      "models/aeif_cond_exp_implicit.nestml",
+      "models/hh_psc_alpha.nestml"
 
   );
 
@@ -152,7 +152,7 @@ public void testGlifModel() {
 
   @Test
   public void testIzhikevich() {
-    final List<String> modelName = Lists.newArrayList("src/test/resources/codegeneration/izhikevich.nestml");
+    final List<String> modelName = Lists.newArrayList("models/izhikevich.nestml");
     modelName.forEach(this::checkCocos);
     modelName.forEach(this::invokeCodeGenerator);
     final List<ASTNESTMLCompilationUnit> roots = modelName.stream()
@@ -164,7 +164,7 @@ public void testIzhikevich() {
   @Ignore("Don't run this tests on github")
   @Test
   public void testManually() {
-    final List<String> modelName = Lists.newArrayList("src/test/resources/codegeneration/iaf_cond_exp_implicit.nestml");
+    final List<String> modelName = Lists.newArrayList("models/iaf_cond_exp_implicit.nestml");
     modelName.forEach(this::checkCocos);
     modelName.forEach(this::invokeCodeGenerator);
     final List<ASTNESTMLCompilationUnit> roots = modelName.stream()

src/test/java/org/nest/integration/ODEProcessorTest.java

@@ -28,9 +28,9 @@
  * @author plotnikov
  */
 public class ODEProcessorTest extends ModelbasedTest {
-  private static final String COND_MODEL_FILE = "src/test/resources/codegeneration/iaf_cond_alpha.nestml";
-  private static final String PSC_MODEL_FILE = "src/test/resources/codegeneration/iaf_neuron.nestml";
-  private static final String PSC_DELTA_MODEL_FILE = "src/test/resources/codegeneration/iaf_psc_delta.nestml";
+  private static final String COND_MODEL_FILE = "models/iaf_cond_alpha.nestml";
+  private static final String PSC_MODEL_FILE = "models/iaf_neuron.nestml";
+  private static final String PSC_DELTA_MODEL_FILE = "models/iaf_psc_delta.nestml";
   private static final String PSC_NEURON_NAME = "iaf_neuron_nestml";
 
   private final ODEProcessor testant = new ODEProcessor();
@@ -68,7 +68,7 @@ private Scope processModel(final String pathToModel) {
     final ASTNESTMLCompilationUnit modelRoot = parseNESTMLModel(pathToModel);
     scopeCreator.runSymbolTableCreator(modelRoot);
     final String modelFolder = modelRoot.getFullName();
-    final Path outputBase = Paths.get(OUTPUT_FOLDER.toString(), Names.getPathFromQualifiedName(modelFolder));
+    final Path outputBase = Paths.get(OUTPUT_FOLDER.toString(), Names.getPathFromQualifiedName(pathToModel.toString()));
     FilesHelper.deleteFilesInFolder(outputBase);
 
     testant.solveODE(modelRoot.getNeurons().get(0), outputBase);