Merge pull request #216 from DimitriPlotnikov/master

Prepare release

models/ht_neuron.nestml

@@ -81,7 +81,7 @@ neuron ht_neuron_nestml:
     G_NMDA nS
     G_GABA_A nS
     G_GABA_B nS
-    IKNa_D pA
+    IKNa_D pA = KNa_D_EQ
     IT_m pA
     IT_h pA
     Ih_m pA
@@ -97,7 +97,7 @@ neuron ht_neuron_nestml:
 
     # The spike current is only activate immediately after a spike.
     # TODO const double_t I_spike = node.S_.g_spike_ ? -( V - node.P_.E_K ) / node.P_.Tau_spike : 0;
-    alias I_spike mV = 0
+    alias I_spike mV = (g_spike) ? -( V_m - E_K ) / Tau_spike : 0;
 
     # intrinsic currents
     # I_Na(p), m_inf^3 according to Compte et al, J Neurophysiol 2003 89:2707
@@ -188,7 +188,7 @@ neuron ht_neuron_nestml:
     T_E_rev mV = 0.0mV
     h_g_peak real = 1.0
     h_E_rev mV = -40.0mV
-    KNa_D_EQ real = 0.001;
+    KNa_D_EQ pA = 0.001pA;
   end
 
   internal:

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>nestml</groupId>
     <artifactId>nestml-core</artifactId>
-    <version>0.1.1-SNAPSHOT</version>
+    <version>0.1.1</version>
 
     <properties>
         <!-- .. Libraries ..................................................... -->

src/main/grammars/org/nest/Commons.mc4

@@ -50,6 +50,7 @@ grammar Commons extends de.monticore.types.Types {
          | logicalNot:["not"] Expr
          | left:Expr logicalAnd:["and"] right:Expr
          | left:Expr logicalOr:["or"] right:Expr
+         | condition:Expr "?" ifTure:Expr ":" ifNot:Expr
          | FunctionCall
          | BooleanLiteral // true & false;
          | NESTMLNumericLiteral

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

@@ -24,8 +24,13 @@
 public class GSLReferenceConverter implements IReferenceConverter {
 
   private static final String INDEX_VARIABLE_POSTFIX = "_INDEX";
+  private final boolean isUseUpperBound;
   private static final Double MAXIMAL_EXPONENT = 10.0;
 
+  public GSLReferenceConverter() {
+    isUseUpperBound = false; // TODO make it parametrizable
+  }
+
   @Override
   public String convertBinaryOperator(String binaryOperator) {
     if (binaryOperator.equals("**")) {
@@ -39,8 +44,17 @@ public String convertBinaryOperator(String binaryOperator) {
   @Override
   public String convertFunctionCall(final ASTFunctionCall astFunctionCall) {
     final String functionName = astFunctionCall.getCalleeName();
+
     if ("exp".equals(functionName)) {
-      return "std::exp(std::min(%s, " + MAXIMAL_EXPONENT + "))";
+
+      if (isUseUpperBound) {
+        return "std::exp(std::min(%s, " + MAXIMAL_EXPONENT + "))";
+      }
+      else {
+        return "std::exp(%s)";
+
+      }
+
     }
     if ("pow".equals(functionName)) {
       return "pow(%s)";
@@ -56,8 +70,7 @@ public String convertNameReference(final ASTVariable astVariable) {
     final Scope scope = astVariable.getEnclosingScope().get();
     final VariableSymbol variableSymbol = VariableSymbol.resolve(convertDevrivativeNameToSimpleName(astVariable), scope);
 
-    if (variableSymbol.getBlockType().equals(VariableSymbol.BlockType.STATE) &&
-        !variableSymbol.isAlias()) {
+    if (variableSymbol.definedByODE()) {
       return "y[" + variableName + INDEX_VARIABLE_POSTFIX + "]";
     }
     else {

src/main/java/org/nest/nestml/_ast/ASTBody.java

@@ -136,6 +136,14 @@ public List<ASTEquation> getEquations() {
     }
   }
 
+  @SuppressWarnings("unused") // used in freemarker templates
+  public List<VariableSymbol> variablesDefinedByODE() {
+    return getStateSymbols()
+        .stream()
+        .filter(VariableSymbol::definedByODE)
+        .collect(toList());
+  }
+
   private Optional<ASTEquations> findEquationsBlock() {
     final Optional<ASTBodyElement> equations = this.getBodyElements()
         .stream()
@@ -161,7 +169,12 @@ private String printBlockComment(final Optional<? extends ASTNode> block) {
 
   // STATE variables handling
   public List<VariableSymbol> getStateSymbols() {
-    return getVariableSymbols(getDeclarationsFromBlock(ASTVar_Block::isState), getEnclosingScope().get());
+    return this.getEnclosingScope().get().resolveLocally(VariableSymbol.KIND)
+        .stream()
+        .map(stateSymbol -> (VariableSymbol) stateSymbol)
+        .filter(VariableSymbol::isState)
+        .collect(toList());
+
   }
 
   public List<VariableSymbol> getStateAliasSymbols() {

src/main/java/org/nest/nestml/_symboltable/NESTMLSymbolTableCreator.java

@@ -164,8 +164,8 @@ private void addDerivedVariable(final ASTEquation ode) {
 
   private void assignOdeToVariables(final ASTBody astBody) {
     if (astBody.getODEBlock().isPresent()) {
-      astBody.getODEBlock().get().getODEs()
-          .stream()
+      astBody.getODEBlock().get()
+          .getODEs()
           .forEach(this::addOdeToVariable);
 
     }
@@ -174,8 +174,8 @@ private void assignOdeToVariables(final ASTBody astBody) {
 
   private void addOdeToVariable(final ASTEquation ode) {
     checkState(this.currentScope().isPresent());
-
     final Scope scope = currentScope().get();
+
     final String variableName = convertToSimpleName(ode.getLhs());
     final Optional<VariableSymbol> stateVariable = scope.resolve(variableName, VariableSymbol.KIND);
 

src/main/java/org/nest/spl/prettyprinter/ExpressionsPrettyPrinter.java

@@ -133,8 +133,14 @@ else if (expr.isLogicalOr() || expr.isLogicalAnd()) {
     else if (expr.isLogicalNot()) {
       return "not " + print(expr.getExpr().get());
     }
+    else if (expr.getCondition().isPresent()) {
+      final String condition = print(expr.getCondition().get());
+      final String ifTrue = print(expr.getIfTure().get()); // guaranteed by grammar
+      final String ifNot = print(expr.getIfNot().get()); // guaranteed by grammar
+      return "(" + condition + ")?(" + ifTrue + "):(" + ifNot + ")";
+    }
 
-    final String errorMsg = "Unsupported grammar element. PrettyPrinter must be fixed " + expr.get_SourcePositionStart() + "}";
+    final String errorMsg = "Unsupported grammar element:  PrettyPrinter must be fixed " + expr.get_SourcePositionStart();
 
     throw new RuntimeException(errorMsg);
   }

src/main/java/org/nest/spl/symboltable/typechecking/ExpressionTypeCalculator.java

@@ -396,6 +396,30 @@ else if (expr.isLogicalAnd() || expr.isLogicalOr()) {
       }
 
     }
+    else if (expr.getCondition().isPresent()) {
+
+      final Either<TypeSymbol, String> condition = computeType(expr.getCondition().get());
+      final Either<TypeSymbol, String> ifTrue = computeType(expr.getIfTure().get()); // guaranteed by the grammar
+      final Either<TypeSymbol, String> ifNot = computeType(expr.getIfNot().get()); // guaranteed by the grammar
+
+      if (condition.isError()) {
+        return condition;
+      }
+      if (ifTrue.isError()) {
+        return ifTrue;
+      }
+
+      if (ifNot.isError()) {
+        return ifNot;
+      }
+      if (!condition.getValue().equals(getBooleanType())) {
+        return Either.error("The ternary operator condition must be a boolean: " + ASTUtils.toString(expr) + ".  And not a: " + condition.getValue());
+      }
+      if (!isCompatible(ifTrue.getValue(), (ifNot.getValue()))) {
+        return Either.error("The ternary operator results must be of the same type: " + ASTUtils.toString(expr) + ".  And not: " + ifTrue.getValue() + " and " + ifNot.getValue());
+      }
+      return ifTrue;
+    }
 
     final String errorMsg = "This operation for expressions is not supported yet.";
 

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

@@ -6,9 +6,10 @@
 <#assign ODEs = ast.getEquations()>
 <#assign index = 0>
 <#assign indexPostfix = "INDEX">
-<#list ast.getStateNonAliasSymbols() as stateVariable>
-const int ${stateVariable.getName()}_${indexPostfix} = ${index};
- <#assign index = index + 1>
+
+<#list ast.variablesDefinedByODE() as odeVariable>
+const int ${odeVariable.getName()}_${indexPostfix} = ${index};
+<#assign index = index + 1>
 </#list>
 
 extern "C" inline int

src/main/resources/org/nest/spl/ODEDeclaration.ftl

@@ -8,23 +8,21 @@
   @param stateSize number of the step variables
   @result TODO
 -->
-<#assign stateSize = body.getStateNonAliasSymbols()?size>
+<#assign stateSize = body.getEquations()?size>
 <#assign indexPostfix = "INDEX">
 
 double step_ = nest::Time::get_resolution().get_ms();
 double IntegrationStep_ = nest::Time::get_resolution().get_ms();
 double t = 0;
 
-while ( t < step_ )
-{
-
 double stateVector[${stateSize}];
 <#assign index = 0>
-<#list body.getStateNonAliasSymbols() as stateVariable>
-  stateVector[${stateVariable.getName()}_${indexPostfix}] = S_.${stateVariable.getName()};
+<#list body.variablesDefinedByODE() as odeVariable>
+  stateVector[${odeVariable.getName()}_${indexPostfix}] = S_.${odeVariable.getName()};
   <#assign index = index + 1>
 </#list>
-
+while ( t < step_ )
+{
   const int status = gsl_odeiv_evolve_apply( B_.e_,
   B_.c_,
   B_.s_,
@@ -34,8 +32,9 @@ double stateVector[${stateSize}];
   &IntegrationStep_, // integration step size
   stateVector );               // neuronal state
 <#assign index = 0>
-<#list body.getStateNonAliasSymbols() as stateVariable>
-  S_.${stateVariable.getName()} = stateVector[${stateVariable.getName()}_${indexPostfix}];
+
+}
+<#list body.variablesDefinedByODE() as odeVariable>
+  S_.${odeVariable.getName()} = stateVector[${odeVariable.getName()}_${indexPostfix}];
   <#assign index = index + 1>
-</#list>
-}
+</#list>

src/test/java/org/nest/nestml/symboltable/NESTMLSymbolTableTest.java

@@ -8,6 +8,7 @@
 import com.google.common.collect.Lists;
 import de.monticore.symboltable.Scope;
 import de.monticore.symboltable.ScopeSpanningSymbol;
+import de.monticore.symboltable.Symbol;
 import org.junit.Test;
 import org.nest.base.ModelbasedTest;
 import org.nest.nestml._ast.*;
@@ -55,12 +56,24 @@ public void testCreationOfSymtabAndResolvingOfSymbols() throws IOException {
     Collection<TypeSymbol> nestmlTypes = modelScope.resolveLocally(NeuronSymbol.KIND);
     assertEquals(2, nestmlTypes.size());
 
-    final Optional<TypeSymbol> neuronTypeOptional = modelScope.resolve(
+    final Optional<NeuronSymbol> neuronTypeOptional = modelScope.resolve(
         "iaf_neuron",
         NeuronSymbol.KIND);
     assertTrue(neuronTypeOptional.isPresent());
+    final Optional<VariableSymbol> y0TVariable = neuronTypeOptional.get().getSpannedScope().resolve("y0", VariableSymbol.KIND);
+    final Optional<VariableSymbol> y1Varialbe = neuronTypeOptional.get().getSpannedScope().resolve("y1", VariableSymbol.KIND);
+    assertTrue(y0TVariable.isPresent());
+    assertTrue(y0TVariable.get().definedByODE());
 
-    final Optional<TypeSymbol> testComponentOptional = modelScope.resolve(
+    assertTrue(y1Varialbe.isPresent());
+    assertFalse(y1Varialbe.get().definedByODE());
+
+    // Checks that the derived variable is also resolvable
+    final Optional<VariableSymbol> Dy0Varialbe = neuronTypeOptional.get().getSpannedScope().resolve("__Dy0", VariableSymbol.KIND);
+    assertTrue(Dy0Varialbe.isPresent());
+    assertTrue(Dy0Varialbe.get().definedByODE());
+
+    final Optional<NeuronSymbol> testComponentOptional = modelScope.resolve(
         "TestComponent",
         NeuronSymbol.KIND);
     assertTrue(testComponentOptional.isPresent());

src/test/java/org/nest/spl/parsing/SPLParserTest.java

@@ -32,7 +32,7 @@ public class SPLParserTest extends ModelbasedTest {
 
   @Test
   public void testParsableModels() throws IOException {
-    final List<Path> filenames = collectSPLModelFilenames(TEST_MODEL_PATH);
+    final List<Path> filenames = collectSPLModelFilenames(Paths.get("src/test/resources/org/nest/spl"));
 
     filenames.forEach(this::parseAndCheck);
   }

src/test/java/org/nest/spl/prettyprinter/SPLPrettyPrinterTest.java

@@ -1 +1 @@
-/* * Copyright (c) 2015 RWTH Aachen. All rights reserved. * * http://www.se-rwth.de/ */package org.nest.spl.prettyprinter;import org.junit.Test;import org.nest.base.ModelbasedTest;import org.nest.spl._ast.ASTSPLFile;import org.nest.spl._parser.SPLParser;import org.nest.spl._symboltable.SPLLanguage;import java.io.IOException;import java.io.StringReader;import java.nio.file.Path;import java.nio.file.Paths;import java.util.List;import java.util.Optional;import static org.junit.Assert.assertTrue;import static org.nest.utils.FilesHelper.collectFiles;/** * Checks that the pretty printed result can be parsed again. * * @author plotnikov */public class SPLPrettyPrinterTest extends ModelbasedTest {  private final SPLParser splFileParser = new SPLParser();  private final ExpressionsPrettyPrinter prettyPrinter = new ExpressionsPrettyPrinter();  private Optional<ASTSPLFile> parseStringAsSPLFile(final String fileAsString) throws IOException {    return splFileParser.parse(new StringReader(fileAsString));  }  @Test  public void testThatPrettyPrinterProducesParsableOutput() throws IOException {    final SPLPrettyPrinter splPrettyPrinter = new SPLPrettyPrinter(prettyPrinter);    final Optional<ASTSPLFile> root = splFileParser.parse        //("src/test/resources/org/nest/spl/parsing/modelContainingAllLanguageElements.simple");        ("src/test/resources/org/nest/spl/parsing/complexExpressions.simple");    assertTrue(root.isPresent());    root.get().accept(splPrettyPrinter); // starts prettyPrinter    Optional<ASTSPLFile> prettyPrintedRoot = parseStringAsSPLFile(splPrettyPrinter.getResult());    assertTrue(prettyPrintedRoot.isPresent());    System.out.println(splPrettyPrinter.getResult());  }  @Test  public void testAllModelsForParser() throws IOException {    parseAndCheckSPLModelsFromFolder("src/test/resources/org/nest/spl/parsing");  }  @Test  public void testAllModelsForCocos() throws IOException {    parseAndCheckSPLModelsFromFolder("src/test/resources/org/nest/spl/_cocos");  }  private void parseAndCheckSPLModelsFromFolder(final String folderPath) throws IOException {    final List<Path> splFiles = collectFiles(        Paths.get(folderPath),        model -> model.endsWith(SPLLanguage.FILE_ENDING));    for (final Path splModelFile : splFiles) {      System.out.println("Handles the model: " + splModelFile);      final SPLPrettyPrinter splPrettyPrinter = new SPLPrettyPrinter(prettyPrinter);      final Optional<ASTSPLFile> splModelRoot = splFileParser.parse(splModelFile.toString());      assertTrue("Cannot parse the model: " + splModelFile, splModelRoot.isPresent());      splModelRoot.get().accept(splPrettyPrinter);      //System.out.println(splPrettyPrinter.getResult());      Optional<ASTSPLFile> prettyPrintedRoot = parseStringAsSPLFile(splPrettyPrinter.getResult());      assertTrue(prettyPrintedRoot.isPresent());    }  }}
+/* * Copyright (c) 2015 RWTH Aachen. All rights reserved. * * http://www.se-rwth.de/ */package org.nest.spl.prettyprinter;import org.junit.Test;import org.nest.base.ModelbasedTest;import org.nest.spl._ast.ASTSPLFile;import org.nest.spl._parser.SPLParser;import org.nest.spl._symboltable.SPLLanguage;import java.io.IOException;import java.io.StringReader;import java.nio.file.Path;import java.nio.file.Paths;import java.util.List;import java.util.Optional;import static org.junit.Assert.assertTrue;import static org.nest.utils.FilesHelper.collectFiles;/** * Checks that the pretty printed result can be parsed again. * * @author plotnikov */public class SPLPrettyPrinterTest extends ModelbasedTest {  private final SPLParser splFileParser = new SPLParser();  private final ExpressionsPrettyPrinter prettyPrinter = new ExpressionsPrettyPrinter();  private Optional<ASTSPLFile> parseStringAsSPLFile(final String fileAsString) throws IOException {    return splFileParser.parse(new StringReader(fileAsString));  }  @Test  public void testThatPrettyPrinterProducesParsableOutput() throws IOException {    final SPLPrettyPrinter splPrettyPrinter = new SPLPrettyPrinter(prettyPrinter);    final Optional<ASTSPLFile> root = splFileParser.parse        //("src/test/resources/org/nest/spl/parsing/modelContainingAllLanguageElements.simple");        ("src/test/resources/org/nest/spl/parsing/complexExpressions.simple");    assertTrue(root.isPresent());    root.get().accept(splPrettyPrinter); // starts prettyPrinter    Optional<ASTSPLFile> prettyPrintedRoot = parseStringAsSPLFile(splPrettyPrinter.getResult());    assertTrue(prettyPrintedRoot.isPresent());    System.out.println(splPrettyPrinter.getResult());  }  @Test  public void testAllModelsForParser() throws IOException {    parseAndCheckSPLModelsFromFolder("src/test/resources/org/nest/spl");  }  private void parseAndCheckSPLModelsFromFolder(final String folderPath) throws IOException {    final List<Path> splFiles = collectFiles(        Paths.get(folderPath),        model -> model.endsWith(SPLLanguage.FILE_ENDING));    for (final Path splModelFile : splFiles) {      System.out.println("Handles the model: " + splModelFile);      final SPLPrettyPrinter splPrettyPrinter = new SPLPrettyPrinter(prettyPrinter);      final Optional<ASTSPLFile> splModelRoot = splFileParser.parse(splModelFile.toString());      assertTrue("Cannot parse the model: " + splModelFile, splModelRoot.isPresent());      splModelRoot.get().accept(splPrettyPrinter);      //System.out.println(splPrettyPrinter.getResult());      Optional<ASTSPLFile> prettyPrintedRoot = parseStringAsSPLFile(splPrettyPrinter.getResult());      assertTrue(prettyPrintedRoot.isPresent());    }  }}

src/test/java/org/nest/spl/symboltable/typechecking/ExpressionTypeCalculatorTest.java

@@ -121,6 +121,12 @@ public void testTypeCalculation() throws IOException {
 
     // n boolean = not true
     assertType("n", declarations, getBooleanType());
+
+    // o1 real = true? 13:14
+    assertType("o1", declarations, getIntegerType());
+
+    // o2 string = true?"test1":"test"
+    assertType("o2", declarations, getStringType());
   }
 
   private void assertType(final String variableName, List<ASTDeclaration> declarations, final TypeSymbol expectedType) {
@@ -159,6 +165,11 @@ public void testNegativeExamples() throws IOException {
     // n boolean = not 1
     assertInvaidType("n", declarations);
 
+    //o1 real = 12? 13:14
+    assertInvaidType("o1", declarations);
+
+    //o2 real = true?13:"test"
+    assertInvaidType("o2", declarations);
 
   }
 

src/test/resources/org/nest/nestml/symboltable/iaf_neuron.nestml

@@ -14,6 +14,11 @@ neuron iaf_neuron:
     alias V_m mV = y3 + E_L
   end
 
+  equations:
+    y0' = y0 + 1
+    y0'' = y0' + 1
+  end
+
   parameter:
     # Capacity of the membrane
     C_m       pF = 250

src/test/resources/org/nest/spl/_cocos/invalid/mathExpressions.simple

@@ -3,4 +3,6 @@ a real = ((( 1.0 | (-3+6%2) & ~(0x4fa) | 0x23 ^ 12) >> 2) << 2)
 k integer = ~1.0
 m real = 1 ** "a"
 m1 boolean = "a" and k != 0.0
-n boolean = not 1
+n boolean = not 1
+o1 real = 12? 13:14
+o2 real = true?13:"test"

src/test/resources/org/nest/spl/_cocos/valid/mathExpressions.simple

@@ -12,3 +12,5 @@ P11ex real = pow(1.0, 1.0) # TODO **,h / pow(E, (-h / tau_syn_ex))
 tmp string = ("")
 m boolean = true and l != 0.0
 n boolean = not true
+o1 real = true? 13:14
+o2 string = true?"test1":"test"

src/test/resources/org/nest/spl/parsing/complexExpressions.simple

@@ -11,3 +11,4 @@ RefractoryCounts integer = steps(t_ref)
 # it is a pre-comment 1
 print("" + ((( C_m | (-3+6%2) & ~(0x4fa) | 0x23) >> 2) << 2)) # it is a post comment 1
 # it is a post commet 2
+tmp real = (11 > 12)?13:14