Merge branch 'master' of https://github.com/dmancilla85/java-mvn-laslo

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+- package-ecosystem: maven
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "09:00"
+  open-pull-requests-limit: 10

.github/workflows/maven.yml

@@ -0,0 +1,38 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: maven
+
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml
+
+    # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
+    - name: Update dependency graph
+      uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6

README.md

@@ -1,5 +1,11 @@
 # LoopMatcher (aka LASLO) v1.3.3 - README
 
+[![CodeQL](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/codeql-analysis.yml)
+[![Java CI with Maven](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/maven.yml/badge.svg)](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/maven.yml)
+
+[![Java CI with Maven](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/maven.yml/badge.svg)](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/maven.yml)
+[![CodeQL](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/dmancilla85/java-mvn-laslo/actions/workflows/codeql-analysis.yml)
+
 ## Introduction
 
 Multi-threaded application that searches for hairpin structures in cDNA / mRNA sequences (FASTA or GenBank) with specific consensus sequences in the loop. It implements RNAfold to predict the structure of the sequence, and UShuffle to generate random sequences with conservation of the k-nucleotide frequency.

pom.xml

@@ -14,15 +14,15 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>5.4.0</version>
+            <version>7.0.2</version>
         </dependency>
         <!-- other biojava jars as needed -->
         <!-- https://mvnrepository.com/artifact/com.opencsv/opencsv -->
         <!-- https://mvnrepository.com/artifact/org.netbeans.modules/org-netbeans-modules-web-inspect -->
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.3</version>
+            <version>5.8</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-io -->
         <dependency>
@@ -57,7 +57,7 @@
          <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-compiler-plugin</artifactId>
-            <version>3.8.1</version>
+            <version>3.11.0</version>
             <configuration>
                <debug>true</debug>
                <showDeprecation>true</showDeprecation>