Add GitHub Actions CI/CD for Multi-Platform Native Library Builds

[NicoKiaru]

Overview

This PR changes the build infrastructure by adding automated GitHub Actions workflows to build native libraries (clFFT and clij2-fft) across all supported platforms. The JAR now includes natives for all platforms, eliminating the need for manual native builds.

Key Changes

GitHub Actions CI/CD Pipeline

• New workflow: .github/workflows/build-and-deploy.yml
• Matrix builds for 4 platforms:
  • Linux x86_64 (ubuntu-latest)
  • Windows x86_64 (windows-latest)
  • macOS x86_64 (macos-13)
  • macOS ARM64 (macos-14)
• Smart trigger system: Natives rebuild only when commit contains [build natives] or on manual dispatch
• Automatic commit-back: Native libraries automatically committed to repository with [skip ci] to prevent infinite loops

Platform-Specific Build Setup

Linux GH build:

• Builds clFFT from source (no package manager support)
• Dependencies: build-essential, cmake, ocl-icd-opencl-dev, opencl-headers
• CMake version patched from 2.8 → 3.5 for compatibility

macOS (Intel & ARM64) GH build:

• Builds clFFT from source (removed from Homebrew)
• Uses built-in OpenCL framework
• Platform-specific install paths: /usr/local (Intel), /opt/homebrew (ARM)
• Dynamic library paths fixed with install_name_tool

Windows GH build:

• Uses pre-built clFFT binaries (v2.12.2)
• Downloads OpenCL SDK components
• MSVC environment setup via ilammy/msvc-dev-cmd action

Maven Build Improvements

• Updated parent POM: pom-scijava 37.0.0 → 43.0.0
• New platform profiles: Updated folder naming to match JavaCPP conventions:
  • win64 → windows-x86_64
  • linux64 → linux-x86_64
  • macosx → macosx-x86_64
  • macosx-arm64 (unchanged)
• Maven resources plugin: Automatically copies all platform natives into JAR during packaging
• Local builds with mvn clean package -Dgpg.skip=true -Djavacpp.skip=true now produce multi-platform JARs
• Dependency versions: Moved to properties for easier maintenance
• CI management: Specified as GitHub Actions

Repository Structure Changes

• Native libraries now committed to repository at lib/{platform}/
• Updated .github/workflows/ with new build pipeline

Documentation Updates

• README updated with relative paths
• Documented new CI-based native build process
• Removed references to manual Fiji native builds (natives now bundled in JAR)
• Added mention of clijx-deconvolution update site in main README

Testing

• All 4 platform builds succeed
• Natives correctly packaged in JAR at expected paths
• JAR loads and runs (tested on windows only)
• Commit-back mechanism works without infinite loops

Breaking Changes

None - this is purely additive infrastructure. Existing local build workflows remain compatible.

[Copilot]

Pull request overview

This PR modernizes the build infrastructure by introducing a GitHub Actions CI/CD pipeline that automatically builds native libraries (clFFT and clij2-fft) for all supported platforms. The key improvement is that the JAR now bundles natives for all platforms, eliminating manual build requirements for most users.

Key Changes:

• Automated multi-platform native builds via GitHub Actions with smart triggers ([build natives] commit message or manual dispatch)
• Updated Maven configuration with corrected platform naming conventions (e.g., win64 → windows-x86_64) and resource plugin to package all natives in JAR
• Comprehensive documentation updates with relative paths and updated build instructions reflecting the new CI-based workflow

Reviewed changes

Copilot reviewed 9 out of 44 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.github/workflows/build-and-deploy.yml	New CI/CD workflow for matrix builds across 4 platforms with automatic commit-back
pom.xml	Updated parent POM to 43.0.0, fixed platform profile naming, added maven-resources-plugin for multi-platform JAR packaging
native/clij2fft/cppbuild.sh	Updated folder paths to match new naming conventions (linux64→linux-x86_64, win64→windows-x86_64, macosx→macosx-x86_64)
native/clij2fft/CMakeLists.txt	Removed trailing whitespace from Python command
mvn_with_options.sh	Fixed typo in comment
lib/windows-x86_64/*	New Windows native binaries (DLLs and libs) for x86_64
docs/buildlibs/build.md	Restructured to prioritize GitHub Actions workflow over local builds
README.md	Updated with relative paths and references to new CI infrastructure
docs/python/clij-fft-python.md	Converted absolute URLs to relative paths
docs/fiji/test_installation.md	Removed manual native lib verification section (now bundled in JAR)
docs/deconvolution/RichardsonLucy.md	Fixed duplicate regularization link
docs/releaselog.md	Added release note for version 2.2.0.19

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