Merge pull request #13 from JonasSchaub/production

Bumped minimum required Java version to 11 and GH actions is now testing the Gradle build based on multiple Java versions

.github/workflows/gradle.yml

@@ -20,17 +20,22 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 11, 17, 21 ]
+    name: Java ${{ matrix.java }}
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 21
+    - name: Set up Java
       uses: actions/setup-java@v3
       with:
-        java-version: '21'
+        java-version: ${{ matrix.java }}
         distribution: 'temurin'
     - name: Change wrapper permissions
       run: chmod +x ./gradlew
     - name: Build with Gradle
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      uses: gradle/gradle-build-action@v2
       with:
+        gradle-version: 8.5
         arguments: build

.github/workflows/publish-javadoc.yml

@@ -21,5 +21,5 @@ jobs:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
           javadoc-branch: javadoc
           java-version: 21
-          target-folder: javadoc/1.2
+          target-folder: javadoc/1.2.1
           project: gradle

.github/workflows/publish-to-maven-central.yml

@@ -14,7 +14,7 @@ on:
   #push:
     #branches: [ "main" ]
   release:
-    types: [published]
+    types: [published] #alternatives: released, published, created
 jobs:
   publish:
     runs-on: ubuntu-latest

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: ErtlFunctionalGroupsFinder
-version: 1.2
+version: 1.2.1
 message: "If you use this software, please cite it as below and also cite the accompanying scientific publication referenced below."
 type: software
 authors:
@@ -20,7 +20,7 @@ authors:
     orcid: "https://orcid.org/0000-0003-0722-4229"
 url: "https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder"
 doi: "10.5281/zenodo.10391831"
-date-released: 2023-12-15
+date-released: 2024-01-08
 license: LGPL-2.1
 references:
   - authors:

Performance_Snapshot_App_jar/Performance usage instructions.txt

@@ -1,7 +1,7 @@
 --------------------------------------------------------------------------------
 Performance usage instructions with Java 21 (or higher)
 --------------------------------------------------------------------------------
-1. Install Java 21 (or higher) on your machine (if necessary)
+1. Install Java 11 (or higher) on your machine (if necessary)
 2. Copy the content of this sub-folder to a destination directory on your 
    machine with read/write access.
 3. Copy SD-file with your molecule library to the destination directory on your 
@@ -10,15 +10,15 @@ Performance usage instructions with Java 21 (or higher)
 To run a performance test from the command line, go to the destination directory 
 on your machine and type:
 
-java -jar "ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.0.0.jar" "sdFileName" numberOfThreads
+java -jar "ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.1.0.jar" "sdFileName" numberOfThreads
 
 sdFilePathname : Name of the SD-file with your molecule library to test (must be 
                  located in the same directory as 
-                 "ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.0.0.jar")
+                 "ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.1.0.jar")
 numberOfThreads: Number of parallel calculation threads (>= 1)
 
 You may wish to add additional JVM parameters in the command line (e.g. for 
 increased heap size to avoid an "out of memory" exception for large SD-files).
 
 Note: Sub-directory "src" contains the Java source code for 
-"ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.0.0.jar".
+"ErtlFunctionalGroupsFinder-PerformanceSnapshotApp-1.2.1.0.jar".

README.md

@@ -65,9 +65,9 @@ be pre-installed.
 
 ## Dependencies
 **Needs to be pre-installed:**
-* Java Development Kit (JDK) version 21
+* Java Development Kit (JDK) version 11+
     * [Adoptium OpenJDK](https://adoptium.net) (as one possible source of the JDK)
-* Gradle version 8.5
+* Gradle version 8.5+
     * [Gradle Build Tool](https://gradle.org)
 
 **Managed by Gradle:**

build.gradle

@@ -37,14 +37,14 @@ application {
 group = 'io.github.jonasschaub'
 archivesBaseName = 'ErtlFunctionalGroupsFinder'
 //see also version for publishing below! And do not forget to update CITATION.cff version as well!!!
-version = '1.2.0.0'
+version = '1.2.1.0'
 
-//sourceCompatibility = 1.21
+//sourceCompatibility = 1.11
 
 //Creates javadoc and sources jars
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(21)
+        languageVersion = JavaLanguageVersion.of(11)
     }
     withJavadocJar()
     withSourcesJar()
@@ -160,7 +160,7 @@ publishing {
 
             groupId = 'io.github.jonasschaub'
             artifactId = 'ErtlFunctionalGroupsFinder'
-            version = '1.2.0.0'
+            version = '1.2.1.0'
 
             from components.java
 

src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java

@@ -236,7 +236,7 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
             }
             tmpResultsPrintWriter.println(tmpExceptionsCounter + " molecules produced an exception.");
             tmpResultsPrintWriter.flush();
-            executor.close();
+            executor.shutdownNow();
             tmpResultsPrintWriter.println();
             tmpResultsPrintWriter.flush();
             tmpResultsPrintWriter.close();
@@ -248,7 +248,7 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
             }
         } finally {
             if (!Objects.isNull(executor)) {
-                executor.close();
+                executor.shutdownNow();
             }
             if (!Objects.isNull(tmpResultsPrintWriter)) {
                 tmpResultsPrintWriter.close();