Release v2.0.4

.editorconfig

@@ -1,5 +1,6 @@
 [*]
 indent_style = space
 indent_size = 2
+max_line_length = 120
 trim_trailing_whitespace = true
 insert_final_newline = true

CHANGELOG.rst

@@ -6,6 +6,18 @@ Changelog
 latest
 ------
 
+-----
+2.0.4
+-----
+
+Minor release, no breaking changes.
+
+- Fix broken implementation of `MinimalOntology.subOntology` method.
+- Simplify implementation of CSR adjacency matrix that backs `OntologyGraph` by default.
+- Improve `OntologyGraph` test coverage.
+- Add microbenchmark to benchmark the ontology loading.
+- Update dependencies, remove Guava usage.
+
 ------
 2.0.3
 ------

README.md

@@ -14,7 +14,7 @@ associate phenotype annotation files.
 
 - **Language/Platform:** Java >=11
 - **License:** BSD 3-Clause Clear
-- **Version:** 2.0.3
+- **Version:** 2.0.4
 - **Authors:**
     - Sebastian Bauer
     - Peter N. Robinson
@@ -39,7 +39,7 @@ We recommend indicating the phenol version in the `properties` section of the po
 ```
 <properties>
   (...)
-  <phenol.version>2.0.3</phenol.version>
+  <phenol.version>2.0.4</phenol.version>
 </properties>
 ```
 

docs/conf.py

@@ -12,7 +12,7 @@
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.3'
+release = '2.0.4'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

phenol-analysis/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.3</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-analysis</artifactId>

phenol-annotations/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.3</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-annotations</artifactId>

phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/formats/mpo/MpAnnotationTest.java

@@ -1,7 +1,6 @@
 package org.monarchinitiative.phenol.annotations.formats.mpo;
 
 
-import com.google.common.collect.ImmutableSet;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
@@ -15,7 +14,7 @@ public class MpAnnotationTest {
   @Test
   public void testAnnotationTypeString() {
     TermId mpId = TermId.of("MP:123");
-    Set<String> pmids = ImmutableSet.of();
+    Set<String> pmids = Set.of();
     MpAnnotation.Builder builder = new MpAnnotation.Builder(mpId,pmids).sexSpecific(MpSex.FEMALE);
     MpAnnotation annot = builder.build();
     String expected = "MP:123FEMALE_SPECIFIC_ABNORMAL";

phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/hpo/HpoAnnotationFileParserTest.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.phenol.annotations.hpo;
 
-import com.google.common.collect.ImmutableSet;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -84,14 +83,14 @@ void testNumberOfAnnotationsPostmerge() {
     }
     assertNotNull(anophthalmiaEntry);
     assertEquals(expectedFrequency,anophthalmiaEntry.getFrequencyModifier());
-    Set<String> expectedBiocuration= ImmutableSet.of("HP:probinson[2018-05-28]","HP:probinson[2019-05-28]");
+    Set<String> expectedBiocuration= Set.of("HP:probinson[2018-05-28]","HP:probinson[2019-05-28]");
     String actualBiocuration=anophthalmiaEntry.getBiocuration();
     String[] bioc=actualBiocuration.split(";");
     for (String biocurationItem : bioc) {
       assertTrue(expectedBiocuration.contains(biocurationItem));
     }
 
-    Set<String> expectedPublication=ImmutableSet.of("PMID:3214","PMID:1234");
+    Set<String> expectedPublication=Set.of("PMID:3214","PMID:1234");
     String actualPub=anophthalmiaEntry.getPublication();
     String []pubs=actualPub.split(";");
     for (String pub:pubs) {

phenol-cli/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.3</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-cli</artifactId>

phenol-cli/src/main/java/org/monarchinitiative/phenol/cli/Main.java

@@ -9,7 +9,7 @@
 
 @CommandLine.Command(name = "phenol demo",
   mixinStandardHelpOptions = true,
-  version = "2.0.3",
+  version = "2.0.4",
   description = "phenol demo programs")
 public class Main implements Callable<Integer> {
   private static final Logger LOGGER = LoggerFactory.getLogger(Main.class);

phenol-core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.3</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-core</artifactId>

phenol-core/src/main/java/org/monarchinitiative/phenol/graph/OntologyGraph.java

@@ -189,6 +189,11 @@ default boolean isDescendantOf(T subject, T object) {
     return runQuery(t -> getDescendants(t, false), subject, object);
   }
 
+  /**
+   * Get the subgraph with {@code subRoot} as the new root node.
+   */
+  OntologyGraph<T> extractSubgraph(T subRoot);
+
   /**
    * Get the number of nodes in the graph.
    *

phenol-core/src/main/java/org/monarchinitiative/phenol/graph/OntologyGraphBuilders.java

@@ -1,7 +1,8 @@
 package org.monarchinitiative.phenol.graph;
 
 
-import org.monarchinitiative.phenol.graph.csr.CsrOntologyGraphBuilder;
+import org.monarchinitiative.phenol.graph.csr.mono.CsrMonoOntologyGraphBuilder;
+import org.monarchinitiative.phenol.graph.csr.poly.CsrPolyOntologyGraphBuilder;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
 /**
@@ -31,7 +32,15 @@ private OntologyGraphBuilders(){}
    *
    */
   public static <E> OntologyGraphBuilder<TermId> csrBuilder(Class<E> clz) {
-    return CsrOntologyGraphBuilder.builder(clz);
+    return CsrPolyOntologyGraphBuilder.builder(clz);
+  }
+
+  /**
+   * Get an {@link OntologyGraphBuilder} for building a simple graph with one edge type backed by a CSR-like
+   * data structure.
+   */
+  public static OntologyGraphBuilder<TermId> monoCsrBuilder() {
+    return CsrMonoOntologyGraphBuilder.builder();
   }
 
 }