Merge pull request #94 from phenopackets/release_v0.4.5

Release v0.4.5

.github/workflows/main.yaml

@@ -1,17 +1,29 @@
 name: Java CI
 
-on: [push]
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop, main ]
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    env:
+      JDK_VERSION: ${{ matrix.jdk }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ windows-latest, macOS-latest, ubuntu-latest ]
+        jdk: [ 17 ]
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v2
         with:
-          java-version: '11'
+          java-version: '17'
           distribution: 'adopt'
       - name: Build with Maven
         run: mvn --batch-mode --update-snapshots verify

.github/workflows/pages.yml

@@ -0,0 +1,44 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: [ "0.4.5" ]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+    - name: Set up Python 3.
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: pip install sphinx
+
+    - name: Build documentation
+      run: | 
+        mkdir gh-pages
+        touch gh-pages/.nojekyll
+        cd docs/ 
+        sphinx-build -b html . _build
+        cp -r _build/* ../gh-pages/
+
+    - name: Deploy documentation.
+      if: ${{ github.event_name == 'push' }}
+      uses: JamesIves/github-pages-deploy-action@v4.3.0
+      with:
+        branch: gh-pages
+        force: true
+        folder: gh-pages
+
+

.gitignore

@@ -12,6 +12,7 @@
 
 # Package Files #
 *.jar
+!maven-wrapper.jar
 *.war
 *.nar
 *.ear
@@ -26,28 +27,9 @@ hs_err_pid*
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
 
-# User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
-
-# Generated files
-.idea/**/contentModel.xml
-
-# Sensitive or high-churn files
-.idea/**/dataSources/
-.idea/**/dataSources.ids
-.idea/**/dataSources.local.xml
-.idea/**/sqlDataSources.xml
-.idea/**/dynamic.xml
-.idea/**/uiDesigner.xml
-.idea/**/dbnavigator.xml
-
-# Gradle
-.idea/**/gradle.xml
-.idea/**/libraries
+.idea
+*.iml
+modules.xml
 
 # Maven
 target/
@@ -59,22 +41,10 @@ release.properties
 dependency-reduced-pom.xml
 buildNumber.properties
 .mvn/timing.properties
-# https://github.com/takari/maven-wrapper#usage-without-binary-jar
-.mvn/wrapper/maven-wrapper.jar
-
-# Gradle and Maven with auto-import
-# When using Gradle or Maven with auto-import, you should exclude module files,
-# since they will be recreated, and may cause churn.  Uncomment if using
-# auto-import.
-.idea/modules.xml
-.idea/*.iml
-.idea/modules
 
 # CMake
 cmake-build-*/
 
-# Mongo Explorer plugin
-.idea/**/mongoSettings.xml
 
 # File-based project format
 *.iws
@@ -88,34 +58,15 @@ out/
 # JIRA plugin
 atlassian-ide-plugin.xml
 
-# Cursive Clojure plugin
-.idea/replstate.xml
-
 # Crashlytics plugin (for Android Studio and IntelliJ)
 com_crashlytics_export_strings.xml
 crashlytics.properties
 crashlytics-build.properties
 fabric.properties
 
-# Editor-based Rest Client
-.idea/httpRequests
-
-# Android studio 3.1+ serialized cache file
-.idea/caches/build_file_checksums.ser
-
-# JetBrains templates
-**___jb_tmp___
-
-*.iml
-modules.xml
-.idea/misc.xml
-*.ipr
-
-# Sonarlint plugin
-.idea/sonarlint
-
 # Mac
 *.DS_Store
 /*.json
 /*.yml
 /examples/
+/docs/_build/