4.4.28: Static Linux Builds, Memory-Aware Batching, and Build Stability

This release focuses on improving build reliability, memory efficiency for large datasets, and portability of Linux binaries.

### Static Linux Binaries
- Linux binaries are now built with static linking using musl, eliminating external runtime dependencies and ensuring portability across distributions.

### Memory-Aware Batching
- Users can now control memory usage during processing with the new `--batch-mem` option, specifying limits such as 128K, 64M, or 1G.
- Batching logic now respects both size and memory constraints: batches are flushed when either threshold is exceeded.
- Conservative memory estimation for sequences helps avoid over-allocation, and explicit garbage collection after large batch discards reduces memory spikes.

### Build System Improvements
- Upgraded to Go 1.26 for improved performance and toolchain stability.
- Fixed cross-compilation issues by replacing generic include paths with architecture-specific ones (x86_64-linux-gnu and aarch64-linux-gnu).
- Streamlined macOS builds by removing special flags, using standard `make` targets.
- Enhanced error reporting during build failures: logs are now shown before cleanup and exit.
- Updated install script to correctly configure GOROOT, GOPATH, and GOTOOLCHAIN, with visual progress feedback for downloads.

All batching behavior is non-breaking and maintains backward compatibility while offering more predictable resource usage on large datasets.

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Setup Go
         uses: actions/setup-go@v5
         with:
-          go-version: "1.23"
+          go-version: "1.26"
       - name: Checkout obitools4 project
         uses: actions/checkout@v4
       - name: Run tests
@@ -32,12 +32,10 @@ jobs:
             goos: linux
             goarch: amd64
             output_name: linux_amd64
-            cgo_cflags: "-I/usr/include/x86_64-linux-gnu -I/usr/include"
           - os: ubuntu-24.04-arm
             goos: linux
             goarch: arm64
             output_name: linux_arm64
-            cgo_cflags: "-I/usr/include/aarch64-linux-gnu -I/usr/include"
           - os: macos-15-intel
             goos: darwin
             goarch: amd64
@@ -56,7 +54,7 @@ jobs:
       - name: Setup Go
         uses: actions/setup-go@v5
         with:
-          go-version: "1.23"
+          go-version: "1.26"
 
       - name: Extract version from tag
         id: get_version
@@ -64,12 +62,6 @@ jobs:
           TAG=${GITHUB_REF#refs/tags/Release_}
           echo "version=$TAG" >> $GITHUB_OUTPUT
 
-      - name: Install build tools (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update -q
-          sudo apt-get install -y musl-tools zlib1g-dev
-
       - name: Install build tools (macOS)
         if: runner.os == 'macOS'
         run: |
@@ -77,21 +69,30 @@ jobs:
           xcode-select --install 2>/dev/null || true
           xcode-select -p
 
-      - name: Build binaries
+      - name: Build binaries (Linux)
+        if: runner.os == 'Linux'
+        env:
+          VERSION: ${{ steps.get_version.outputs.version }}
+        run: |
+          docker run --rm \
+            -v "$(pwd):/src" \
+            -w /src \
+            -e VERSION="${VERSION}" \
+            golang:1.26-alpine \
+            sh -c "apk add --no-cache gcc musl-dev zlib-dev zlib-static make && \
+                   make LDFLAGS='-linkmode=external -extldflags=-static' obitools"
+          mkdir -p artifacts
+          tar -czf artifacts/obitools4_${VERSION}_${{ matrix.output_name }}.tar.gz -C build .
+
+      - name: Build binaries (macOS)
+        if: runner.os == 'macOS'
         env:
           GOOS: ${{ matrix.goos }}
           GOARCH: ${{ matrix.goarch }}
           VERSION: ${{ steps.get_version.outputs.version }}
-          CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }}
-          CGO_CFLAGS: ${{ matrix.cgo_cflags || '' }}
         run: |
-          if [ "$GOOS" = "linux" ]; then
-            make LDFLAGS='-linkmode=external -extldflags=-static' obitools
-          else
-            make obitools
-          fi
+          make obitools
           mkdir -p artifacts
-          # Create a single tar.gz with all binaries for this platform
           tar -czf artifacts/obitools4_${VERSION}_${{ matrix.output_name }}.tar.gz -C build .
 
       - name: Upload artifacts

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.25"
+var _Version = "Release 4.4.28"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.25
+4.4.28