The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the how to help guide!
This guide is intended for maintaining non-core update sites by automating builds with GitHub Actions.
- The core update sites are updated manually or automatically. Automated update is performed with GitHub Actions.
- GitHub Actions is useful because it can freely build any open source project with minimal effort.
Requirements
- An open-source project hosted on GitHub
- An initialized upload password.
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:
- Create a fresh ImageJ2.app
- Build the update site’s repository and move the required artifacts (e.g.
.jars) to their intended locations in the ImageJ2.app - 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.zip
WIKI_USER: YOUR_USER_NAME
UPDATE_PASS: ${{ secrets.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 -O ${IJ_DOWNLOAD_URL}
unzip fiji-linux64.zip
./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
- 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.appwith 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/jarsor./Fiji.app/pluginsdirectory, 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 yourrelease.ymlto download your own update site into the base ImageJ2.app; only changes to the update site state will be uploaded. - 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.
- Using the Maven-based
release.ymlas 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.
