Add compatibility with Java 13

.gitignore

@@ -15,3 +15,5 @@ canvases
 .idea
 *.iml
 *.class
+*.java-version
+*dockerfile

.travis.yml

@@ -1,6 +1,8 @@
 language: java
-jdk: oraclejdk8
-dist: trusty
+jdk: openjdk13
+dist: focal
+services:
+  - xvfb
 branches:
   only:
   - master

README.md

@@ -16,51 +16,19 @@ Paintera is a general visualization tool for 3D volumetric data and proof-readin
 
 ## Installation and Usage
 
-Paintera is available for installation through [conda](#conda) and the [Python Package Index](#pip). Alternatively, you can use [jgo](#jgo) to run Paintera from an existing Maven artifact on the [SciJava Maven repository](https://maven.scijava.org) or your local maven repository, typically located at `$HOME/.m2` on your computer. For all of these options, Java 8 with JavaFX and Apache Maven are requirement. Efforts to create a standalone app have not been successful so far ([#253](https://github.com/saalfeldlab/paintera/issues/253)).
+Paintera is available for installation through [conda](#conda) and the [Python Package Index](#pip). Alternatively, you can use [jgo](#jgo) to run Paintera from an existing Maven artifact on the [SciJava Maven repository](https://maven.scijava.org) or your local maven repository, typically located at `$HOME/.m2` on your computer. For all of these options, Java 11 and Apache Maven are required. Efforts to create a standalone app have not been successful so far ([#253](https://github.com/saalfeldlab/paintera/issues/253)).
 
 ### Dependencies
 
-Java 8 (through [OpenJDK](https://openjdk.java.net/)), JavaFX, and Apache Maven are available for [installation on many Linux distributions](#installation-on-linux).
-
-On Windows and macOS the use of [Oracle Java 8](https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html) (comes with JavaFX) is recommended and [Apache Maven needs to be downloaded and installed](https://maven.apache.org) manually. Make sure that both Java and Maven are available on the `PATH` after installation. Note that our experience with Windows and macOS installations is very limited and there may be better ways to install Java 8 with JavaFX and Maven on these operating systems. If you are aware of any, please create a pull request to add these to this README.
-
-Alternatively, OpenJDK and Maven are available through the default (`pkgs/main`) and `conda-forge` channels on [conda](https://conda.io), respectively.
+OpenJDK and Maven are available through the default (`pkgs/main`) and `conda-forge` channels on [conda](https://conda.io), respectively.
 ```sh
 conda install -c pkgs/main openjdk
 conda install -c conda-forge maven
 ```
-Note that OpenJDK on the `conda-forge` channels does not ship with JavaFX and cannot be used.
-
-
-#### Installation on Linux
-
-##### Arch Linux
-```shell
-pacman -S jdk8-openjdk
-pacman -S java8-openjfx
-pacman -S maven
-```
-
-##### Ubuntu
-```shell
-sudo apt install default-jre default-jdk
-sudo apt install maven
-sudo apt install openjfx
-```
 
-On Ubuntu 18.04, you will have to install OpenJFX 8 explicitly and then immediately pin this version:
-
-```shell
-sudo apt install openjfx=8u161-b12-1ubuntu2 libopenjfx-java=8u161-b12-1ubuntu2 libopenjfx-jni=8u161-b12-1ubuntu2
-sudo apt-mark hold openjfx libopenjfx-java libopenjfx-jni
-```
+Alternatively, you can install Java 11 and Maven manually. Java 11 (through [OpenJDK](https://openjdk.java.net/)) and Apache Maven are available for [installation on many Linux distributions](#installation-on-linux).
 
-If you are on 18.10 or newer, add the bionic repositories following instruction on https://bugs.launchpad.net/ubuntu/+source/openjfx/+bug/1799946:
-```shell
-sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3B4FE6ACC0B21F32
-sudo apt-add-repository 'deb http://de.archive.ubuntu.com/ubuntu/ bionic main'
-sudo apt-add-repository 'deb http://de.archive.ubuntu.com/ubuntu/ bionic universe'
-```
+On Windows and macOS the use of [Oracle Java 11](https://www.oracle.com/java/technologies/javase-jdk11-downloads.html) is recommended and [Apache Maven needs to be downloaded and installed](https://maven.apache.org) manually. Make sure that both Java and Maven are available on the `PATH` after installation. Note that our experience with Windows and macOS installations is very limited and there may be better ways to install Java 11 and Maven on these operating systems. If you are aware of any, please create a pull request to add these to this README.
 
 ### Conda
 Installation through conda requires an [installation of the conda package manager](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).
@@ -87,11 +55,13 @@ PAINTERA_SLF4J_BINDING=ch.qos.logback:logback-classic paintera
 ```
 
 ### Pip
+Note: If installing via pip, it will be necessary to have Java 11 and Maven installed manually.
+
 Paintera is [available on the Python Package Index](https://pypi.org/project/paintera) and can be installed through pip ([`Python >= 3.6`](https://www.python.org) required):
 ```sh
 pip install paintera
 ```
-Generally, it is adivsable to install packages into user space with pip, i.e.
+Generally, it is advisable to install packages into user space with pip, i.e.
 ```sh
 pip install --user paintera
 ```
@@ -116,9 +86,13 @@ PAINTERA_SLF4J_BINDING=ch.qos.logback:logback-classic paintera
 ### Jgo
 You can use [jgo](https://github.com/scijava/jgo) to run Paintera from an existing Maven artifact on the [SciJava Maven repository](https://maven.scijava.org) or your local maven repository, typically located at `$HOME/.m2` on your computer. Jgo is available through PyPI and conda. Please follow the instructions on the [jgo GitHub repository](https://github.com/scijava/jgo#the-python-module) for installation.
 
+When using jgo manually, it is necessary to specify certain javafx specific JGO arguments manually. An example of running paintera via jgo on linux is shows below.
 ```sh
+PLATFORM=linux # set to 'win' if Windows and 'mac' if MacOS
+JAVAFX_JGO_ARGS="--module-dependencies org.openjfx:javafx-base:13.0.1 org.openjfx:javafx-base:13.0.1:${PLATFORM} org.openjfx:javafx-controls:13.0.1 org.openjfx:javafx-controls:13.0.1:${PLATFORM} org.openjfx:javafx-fxml:13.0.1 org.openjfx:javafx-fxml:13.0.1:${PLATFORM} org.openjfx:javafx-media:13.0.1 org.openjfx:javafx-media:13.0.1:${PLATFORM} org.openjfx:javafx-swing:13.0.1 org.openjfx:javafx-swing:13.0.1:${PLATFORM} org.openjfx:javafx-web:13.0.1 org.openjfx:javafx-web:13.0.1:${PLATFORM} org.openjfx:javafx-graphics:13.0.1 org.openjfx:javafx-graphics:13.0.1:${PLATFORM} --illegal-access=permit --add-opens=javafx.base/javafx.util=ALL-UNNAMED --add-opens=javafx.base/javafx.event=ALL-UNNAMED --add-opens=javafx.base/javafx.beans.property=ALL-UNNAMED --add-opens=javafx.base/com.sun.javafx.binding=ALL-UNNAMED --add-opens=javafx.base/com.sun.javafx.event=ALL-UNNAMED --add-opens=javafx.graphics/javafx.scene=ALL-UNNAMED --add-opens=javafx.graphics/javafx.stage=ALL-UNNAMED --add-opens=javafx.graphics/javafx.geometry=ALL-UNNAMED --add-opens=javafx.graphics/javafx.animation=ALL-UNNAMED --add-opens=javafx.graphics/javafx.scene.input=ALL-UNNAMED --add-opens=javafx.graphics/javafx.scene.image=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.prism=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.geom=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.image=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.scene=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.stage=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.perf=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.cursor=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.tk=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.scene.traversal=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.geom.transform=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.scenario.animation=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.scenario.animation.shared=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.scenario.effect=ALL-UNNAMED --add-opens=javafx.graphics/com.sun.javafx.sg.prism=ALL-UNNAMED --add-modules javafx.base,javafx.controls,javafx.fxml,javafx.media,javafx.swing,javafx.web,javafx.graphics"
 jgo \
-    [JGO ARG...] [JVM ARG...] \
+    [JVM ARGS...] [ADDITIONAL JGO ARGS...] \
+    ${JAVAFX_JGO_ARGS} -- \
     -r scijava.public=https://maven.scijava.org/content/groups/public \
     org.janelia.saalfeldlab:paintera[:$VERSION][+org.slf4j:slf4j-simple:1.7.25]
 ```
@@ -133,7 +107,8 @@ git checkout <branch-name>
 mvn clean install
 # maven will log the version it installs. Replace <VERSION> below with that version
 jgo \
-    [JGO ARG...] [JVM ARG...] \
+    [JVM ARGS...] [ADDITIONAL JGO ARGS...] \
+    ${JAVAFX_JGO_ARGS} -- \
     org.janelia.saalfeldlab:paintera:<VERSION>+org.slf4j:slf4j-simple:1.7.25
 ```
 The `-r` flag can be ommitted here because Paintera is available in the local maven repository.

create-changelog.kts

@@ -22,11 +22,10 @@ data class Change(
 		val author: String,
 		val message: String,
 		val date: String) {
-	constructor(commit: JSONObject) : this(
-			sha = commit.getString("sha"),
-			author = (commit["author"] as JSONObject).getString("login"),
-			message = (commit["commit"] as JSONObject).getString("message"),
-			date = (((commit["commit"] as JSONObject)["author"] as JSONObject)).getString("date"))
+	constructor(commit: JSONObject) : this(sha = commit.getString("sha"),
+        author = if (commit.isNull("author")) "NULL" else (commit["author"] as JSONObject).getString("login"),
+        message = (commit["commit"] as JSONObject).getString("message"),
+        date = if (commit.isNull("author")) "NULL" else (((commit["commit"] as JSONObject)["author"] as JSONObject)).getString("date"))
 }
 
 fun versionFromString(str: String): Version {