Merge branch 'master' into dependabot/maven/algorithms/junit-junit-4.13.1

Author: cvaz

.github/workflows/test.yml

@@ -0,0 +1,51 @@
+name: phyloDB CI tests
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    services:
+      neo4j:
+        image: neo4j:5.13.0-community
+        env:
+          NEO4J_AUTH: neo4j/password
+          NEO4J_dbms_memory_pagecache_size: 1G
+          NEO4J_dbms.memory.heap.initial_size: 2G
+          NEO4J_dbms_memory_heap_max__size: 2G
+          NEO4J_dbms_security_procedures_unrestricted: apoc.*,algorithms.*
+          NEO4J_dbms_security_procedures_whitelist: apoc.*,algorithms.*
+          NEO4J_dbms_connector_bolt_advertised__address: localhost:7687
+          NEO4JLABS_PLUGINS: '["apoc", "apoc-extended"]'
+        volumes:
+          - /home/runner/work/phyloDB/instance/plugins:/var/lib/neo4j/plugins
+        ports:
+          - 7687:7687
+        options: --name neo4j
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+    - name: Build and test
+      run: |
+        cd algorithms
+        mvn -q package
+        sudo cp target/algorithms-1.0.jar /home/runner/work/phyloDB/instance/plugins
+        sudo ls -l /home/runner/work/phyloDB/instance/plugins
+        docker restart neo4j
+        mvn -q test
+        cd ../phylodb
+        ./gradlew test --tests pt.ist.meic.phylodb.unit*

.gitignore

@@ -2,6 +2,11 @@
 # Created by https://www.gitignore.io/api/java,gradle,maven,intellij
 # Edit at https://www.gitignore.io/?templates=java,gradle,maven,intellij
 
+
+# Project-specific.
+build.log
+instance1/*
+
 ### Intellij ###
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
@@ -48,6 +53,14 @@ cmake-build-*/
 # File-based project format
 *.iws
 
+# Visual Studio Code
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
 # IntelliJ
 out/