Mass++ 4

How to develop

This repository requires Maven to build.

First of all, please prepare your GitHub access token. Go to https://github.com/settings/tokens and click Generate new token -> Generate new token (classic). This token should have at least the read:packages scope assigned. (In my case, granting the write:packages scope provided sufficient permissions.)

Next, create a Maven settings file (~/.m2/settings.xml) in your local environment as follows:

<?xml version="1.0" encoding="UTF-8"?>
<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd">
  <servers>
    <server>
      <id>github</id>
      <username>YOUR_GITHUB_ACCOUNT_NAME</username>
      <password>YOUR_ACCESS_TOKEN</password>
    </server>
  </servers>
</settings>

You are now ready to build. You can build the source code as follows.

# Install `mspp4-core` first
$ cd mspp4-core
$ mvn install

$ cd ../

$ cd mspp4-desktop
$ mvn package

How to run

Once mspp4-core is installed and dependencies are resolved, the desktop application can be launched directly from Maven via the javafx-maven-plugin.

# Compile changed sources and run the application (typical dev cycle)
$ mvn compile javafx:run

Tips for faster iteration:

• Skip dependency resolution once everything is cached:

  $ mvn -o compile javafx:run

• A full clean build is rarely needed during development; use it only when switching branches or after dependency changes:

  $ mvn clean package -DskipTests

• To re-run without recompilation (e.g. after editing only resources):

  $ mvn javafx:run

Optional: Docker for vendor file conversion

Opening Thermo .raw or Sciex .wiff files (via File > Open > MS Data... or File > Convert > mzML...) requires Docker Desktop to be running. The application launches the chambm/pwiz-skyline-i-agree-to-the-vendor-licenses image to invoke ProteoWizard msconvert for the conversion. Reading .mzML files does not require Docker.