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Automatic Update Site Uploads

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This guide is intended for maintaining non-core update sites by automating builds with GitHub Actions or Travis CI.

  • The core update sites are updated manually or automatically. Automated update is performed with GitHub Actions since July 2021, before that Travis CI was used.
  • GitHub Actions and Travis CI are useful because they can freely build any open source project with minimal effort.

GitHub Actions

Requirements

Additional resources

Automatic Uploads via GitHub Actions

GitHub Actions can be used to automatically build a repository in response to code changes. To ease the maintenance of ImageJ update sites, we can use GitHub Actions to automatically upload the latest version of a site. This is done by creating a .github/workflows/release.yml file in your update site’s GitHub repository that does the following:

  1. Create a fresh ImageJ2.app
  2. Build the update site’s repository and move the required artifacts (e.g. .jars) to their intended locations in the ImageJ2.app
  3. Upload the local update site state to your Wiki update site

As a starting point you can copy the following .github/workflows/release.yml :

name: Release to Update Site

on:
  push:
    branches: [master]  # Trigger the workflow on push to the master branch

jobs:
  build_release:
    runs-on: ubuntu-latest
    env:
      IJ_DOWNLOAD_URL: https://downloads.imagej.net/fiji/latest/fiji-linux64.tar.gz
      WIKI_USER: YOUR_USER_NAME
      UPDATE_PASS: $  # DO NOT WRITE your password here
      UPDATE_SITE: YOUR_UPDATE_SITE_NAME
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Build with Maven
        run: mvn -B package
      - name: Install ImageJ/Fiji
        run: |
          curl --silent ${IJ_DOWNLOAD_URL} | tar --extract --gzip
          ./Fiji.app/ImageJ-linux64 --headless --update edit-update-site ${UPDATE_SITE} https://sites.imagej.net/${UPDATE_SITE}/ "webdav:${WIKI_USER}:${UPDATE_PASS}" .
      - name: Install in ImageJ/Fiji (with Maven)
        run: mvn -B install -Dscijava.app.directory=./Fiji.app -Ddelete.other.versions=true -Dscijava.ignoreDependencies=true
      - name: Release to ImageJ update site
        run: |
          ./Fiji.app/ImageJ-linux64 --headless --update upload-complete-site --force ${UPDATE_SITE}

Don’t forget to replace the WIKI_USER and UPDATE_SITE variables by your informations.

Encrypting your password

To upload to your wiki update site, you will need to provide GitHub Actions with a UPDATE_PASS environment variable, which should evaluate to the upload password of the Wiki account performing the upload. To do so securely, follow the instructions on creating encrypted secrets for a repository.

Non-Mavenized Files

GitHub Actions is capable of building many languages besides Java. If you cannot use Maven with a scijava.app.directory then you need to replace the following line of your .github/workflows/release.yml:

mvn -B install -Dscijava.app.directory=./Fiji.app -Ddelete.other.versions=true -Dscijava.ignoreDependencies=true

with a sequence of commands that will move your build artifacts to the appropriate ./Fiji.app/jars or ./Fiji.app/plugins directory, as appropriate for your update site.

This is also true if you have custom scripts, macros, etc… if these files are not present in the correct locations of the local ImageJ2.app, they will appear to have been deleted.

Caveats

USE CAUTION HERE

  1. You are configuring GitHub Actions to upload the state of an ImageJ installation to your update site. The ImageJ2.app that will be uploaded is located at ./Fiji.app with respect to the current working directory of the virtual machine GitHub Actions is running on. If your build artifacts are not located in the ./Fiji.app/jars or ./Fiji.app/plugins directory, or you don’t manually copy scripts to the correct location, ImageJ will see these items as having been deleted—effectively removing all content from your update site. You can mitigate this danger by customizing your release.yml to download your own update site into the base ImageJ2.app; only changes to the update site state will be uploaded.
  2. By default—building the master branch of your repository—your update site will be updated with every change to the source code. Although we encourage the master branch to be “release ready”, a safer practice would be to configure GitHub Actions to only build specific events—and set it to build release versions only—e.g. with a release version integration branch.
  3. Using the Maven-based release.yml as suggested implies that you are conforming to the managed dependencies of the parent pom.xml. If you are not staying up-to-date with the ImageJ and Fiji update sites (by using the latest ImageJ or Fiji bill of materials) then this automation may break your own update site.

Travis CI

Requirements

Additional resources

Automatic Uploads via Travis CI

Travis CI can be used to automatically build a repository in response to code changes. To ease the maintenance of ImageJ update sites, we can use Travis to automatically upload the latest version of a site. This is done by creating a .travis.yml file in your update site’s GitHub repository that does the following:

  1. Create a fresh ImageJ2.app
  2. Build the update site’s repository and move the required artifacts (e.g. .jars) to their intended locations in the ImageJ2.app
  3. Upload the local update site state to your Wiki update site

As a starting point you can copy the following .travis.yml :

language: java
sudo: false

cache:
  directories:
        - $HOME/.m2/

install:
      - mvn package

script:
      - ./.travis-deploy.sh

branches:
  only:
        - master

and this script .travis-deploy.sh :

#!/usr/bin/env sh
set -e

# Define some variables
export USER="Username"
export UPDATE_SITE="/update-sites"

export IJ_PATH="$HOME/Fiji.app"
export URL="http://sites.imagej.net/$UPDATE_SITE/"
export IJ_LAUNCHER="$IJ_PATH/ImageJ-linux64"
export PATH="$IJ_PATH:$PATH"

# Install ImageJ
mkdir -p $IJ_PATH/
cd $HOME/
wget --no-check-certificate https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
unzip fiji-linux64.zip

# Install the package
cd $TRAVIS_BUILD_DIR/
mvn clean install -Dscijava.app.directory=$IJ_PATH -Ddelete.other.versions=true

# Deploy the package
# Deploy the package
$IJ_LAUNCHER --update edit-update-site $UPDATE_SITE $URL "webdav:$USER:$WIKI_UPLOAD_PASS" .
$IJ_LAUNCHER --update update
$IJ_LAUNCHER --update upload --update-site $UPDATE_SITE --force-shadow jars/YOUR-FILE.jar

Don’t forget to replace

export USER="Username"
export UPDATE_SITE="/update-sites"

by your informations.

Encrypting your password

To upload to your wiki update site, you will need to provide Travis CI with a WIKI_UPLOAD_PASS environment variable, which should evaluate to the upload password of the Wiki account performing the upload. To do so securely, follow the instructions on the encrypting environment variables.

Note that when you run:

$ travis encrypt WIKI_UPLOAD_PASS=super_secret --add env.matrix

in your repository, the .travis.yml will automatically be updated appropriately. You can simply commit and push the changes.

Non-Mavenized Files

Travis CI is capable of building many languages besides Java. If you cannot use Maven with a scijava.app.directory then you need to replace the following line of your .travis.yml:

mvn clean install -Dscijava.app.directory="$(pwd)" -Ddelete.other.versions=true

with a sequence of commands that will move your build artifacts to the appropriate /jars or /plugins directory, as appropriate for your update site.

This is also true if you have custom scripts, macros, etc… if these files are not present in the correct locations of the local ImageJ2.app, they will appear to have been deleted.

Caveats

USE CAUTION HERE

  1. You are configuring Travis CI to upload the state of an ImageJ2 installation to your update site. The current working directory IS the ImageJ2.app that will be uploaded. If your build artifacts are not located in the jars or plugins directory, or you don’t manually copy scripts to the correct location, ImageJ will see these items as having been deleted—effectively removing all content from your update site. You can mitigate this danger by customizing your .travis-deploy.sh to download your own update site into the base ImageJ2.app; only changes to the update site state will be uploaded.
  2. By default—building the master branch of your repository—your update site will be updated with every change to the source code. Although we encourage the master branch to be “release ready”, a safer practice would be to configure Travis CI to only build specific branches—and set it to build release versions only—e.g. with a release version integration branch.
  3. Using the Maven-based .travis.yml as suggested implies that you are conforming to the managed dependencies of the parent pom.xml. If you are not staying up-to-date with the ImageJ and Fiji update sites (by using the latest ImageJ or Fiji bill of materials) then this automation may break your own update site.

See Also