refactor(language): module and node declarations

* New default file extension: .refinery (.problem is also supported).
* Add module keyword for self-contained modules.
* Rename indiv declarations to atom declaration.
* Add node and multi declarations for explicitly declared nodes and
  multi-objects, respectively.

4 files changed, 28 insertions, 26 deletions

diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
index 72d57f54..17ae5fbb 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
@@ -42,7 +42,7 @@ class ProblemParsingTest {
                                 error invalidTaxStatus(Person p) <->
                                         taxStatus(p, CHILD), children(p, _q).
 
-                                indiv family.
+                                atom family.
                                 Family(family).
                                 members(family, anne): true.
                                 members(family, bob).
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
index f688d970..4a15f9de 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
@@ -183,8 +183,8 @@ class ProblemFormatterTest {
         }
 
         @Test
-        void individualDeclarationTest() {
-                testFormatter("  indiv  a  ,  b  .  ", "indiv a, b.\n");
+        void atomDeclarationTest() {
+                testFormatter("  atom  a  ,  b  .  ", "atom a, b.\n");
         }
 
         @Test
@@ -194,7 +194,7 @@ class ProblemFormatterTest {
                                 pred foo(node a).
                                 class Foo.
                                 foo(n1, n2).
-                                indiv i1.
+                                atom i1.
                                 !foo(i1, n1).
                                 pred bar(node a, node b).
                                 pred quux().
@@ -207,7 +207,7 @@ class ProblemFormatterTest {
                                 class Foo.
 
                                 foo(n1, n2).
-                                indiv i1.
+                                atom i1.
                                 !foo(i1, n1).
 
                                 pred bar(node a, node b).
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
index e76d2993..bc0320a6 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
@@ -69,35 +69,35 @@ class NodeScopingTest {
         }
 
         @ParameterizedTest
-        @MethodSource("individualNodeReferenceSource")
-        void individualNodeInAssertionTest(String qualifiedNamePrefix, boolean namedProblem) {
+        @MethodSource("atomNodeReferenceSource")
+        void atomNodeInAssertionTest(String qualifiedNamePrefix, boolean namedProblem) {
                 var problem = parse("""
-                                indiv a, b.
+                                atom a, b.
                                 pred predicate(node x, node y) <-> node(x).
                                 predicate({PARAM}a, {PARAM}a).
                                 ?predicate({PARAM}a, {PARAM}b).
                                 """, qualifiedNamePrefix, namedProblem);
                 assertThat(problem.getResourceErrors(), empty());
                 assertThat(problem.nodeNames(), empty());
-                assertThat(problem.assertion(0).arg(0).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(0).arg(1).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(1).arg(0).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(1).arg(1).node(), equalTo(problem.individualNode("b")));
+                assertThat(problem.assertion(0).arg(0).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(0).arg(1).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(1).arg(0).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(1).arg(1).node(), equalTo(problem.atomNode("b")));
         }
 
         @ParameterizedTest
-        @MethodSource("individualNodeReferenceSource")
-        void individualNodeInPredicateTest(String qualifiedNamePrefix, boolean namedProblem) {
+        @MethodSource("atomNodeReferenceSource")
+        void atomNodeInPredicateTest(String qualifiedNamePrefix, boolean namedProblem) {
                 var problem = parse("""
-                                indiv b.
+                                atom b.
                                 pred predicate(node a) <-> node({PARAM}b).
-                                """);
+                                """, qualifiedNamePrefix, namedProblem);
                 assertThat(problem.getResourceErrors(), empty());
                 assertThat(problem.nodeNames(), empty());
-                assertThat(problem.pred("predicate").conj(0).lit(0).arg(0).node(), equalTo(problem.individualNode("b")));
+                assertThat(problem.pred("predicate").conj(0).lit(0).arg(0).node(), equalTo(problem.atomNode("b")));
         }
 
-        static Stream<Arguments> individualNodeReferenceSource() {
+        static Stream<Arguments> atomNodeReferenceSource() {
                 return Stream.of(Arguments.of("", false), Arguments.of("", true), Arguments.of("test::", true));
         }
 
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
index 65675b6b..ad583f8e 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
@@ -56,15 +56,16 @@ class ProblemSerializerTest {
                 var pred = createPred();
                 var node = ProblemFactory.eINSTANCE.createNode();
                 node.setName("a");
-                var individualDeclaration = ProblemFactory.eINSTANCE.createIndividualDeclaration();
-                individualDeclaration.getNodes().add(node);
-                problem.getStatements().add(individualDeclaration);
+                var atomDeclaration = ProblemFactory.eINSTANCE.createNodeDeclaration();
+                atomDeclaration.setKind(NodeKind.ATOM);
+                atomDeclaration.getNodes().add(node);
+                problem.getStatements().add(atomDeclaration);
                 createAssertion(pred, node, value);
 
                 assertSerializedResult("""
                                 pred foo(node p).
 
-                                indiv a.
+                                atom a.
                                 """ + serializedAssertion + "\n");
         }
 
@@ -79,15 +80,16 @@ class ProblemSerializerTest {
                 var pred = createPred();
                 var node = ProblemFactory.eINSTANCE.createNode();
                 node.setName("a");
-                var individualDeclaration = ProblemFactory.eINSTANCE.createIndividualDeclaration();
-                individualDeclaration.getNodes().add(node);
-                problem.getStatements().add(individualDeclaration);
+                var atomDeclaration = ProblemFactory.eINSTANCE.createNodeDeclaration();
+                atomDeclaration.setKind(NodeKind.ATOM);
+                atomDeclaration.getNodes().add(node);
+                problem.getStatements().add(atomDeclaration);
                 createAssertion(pred, node, value, true);
 
                 assertSerializedResult("""
                                 pred foo(node p).
 
-                                indiv a.
+                                atom a.
                                 default\040""" + serializedAssertion + "\n");
         }