4.4.26: Static Linux Builds, Memory-Aware Batching & Cross-Compilation Fixes

This release includes critical build system improvements and enhanced batching capabilities for more predictable resource usage.

### Cross-Compilation & Static Builds
- Fixed cross-compilation for Linux by introducing architecture-specific `CGO_CFLAGS` (x86_64-linux-gnu and aarch64-linux-gnu), ensuring correct header resolution during static linking.
- Enabled fully static Linux binaries using musl, producing self-contained executables with no external runtime dependencies.

### Memory-Aware Batching (New Feature)
- Added `--batch-mem` CLI option to control batching based on estimated memory usage (e.g., 128K, 64M, 1G), in addition to size-based limits.
- Introduced configurable min/max batch sizes and memory thresholds, with conservative memory estimation per sequence to avoid over-allocation.
- Implemented intelligent flushing logic that triggers when *either* byte or record count limits are exceeded, ensuring predictable memory behavior.
- Improved garbage collection after large batch discards to reduce memory pressure during large-scale processing.

### Build & Toolchain Improvements
- Updated Go toolchain to 1.26.1 and bumped key dependencies (e.g., golang.org/x/net v0.38.0).
- Enhanced build error reporting: logs are now displayed before cleanup on failure.
- Fixed Makefile quoting for `LDFLAGS` containing spaces.
- Updated install script to properly configure GOROOT, GOPATH, and GOTOOLCHAIN, with added progress feedback for downloads.

All batching behavior is backward-compatible and uses sensible defaults (128 MB memory, min: 1 record, max: 2000 records) to ensure smooth upgrades.

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Setup Go
         uses: actions/setup-go@v5
         with:
-          go-version: "1.26"
+          go-version: "1.23"
       - name: Checkout obitools4 project
         uses: actions/checkout@v4
       - name: Run tests
@@ -32,10 +32,12 @@ 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
@@ -54,7 +56,7 @@ jobs:
       - name: Setup Go
         uses: actions/setup-go@v5
         with:
-          go-version: "1.26"
+          go-version: "1.23"
 
       - name: Extract version from tag
         id: get_version
@@ -62,6 +64,12 @@ 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: |
@@ -69,30 +77,21 @@ jobs:
           xcode-select --install 2>/dev/null || true
           xcode-select -p
 
-      - name: Build binaries (Linux)
+      - name: Build binaries
-        if: runner.os == 'Linux'
-        env:
-          VERSION: ${{ steps.get_version.outputs.version }}
-        run: |
-          docker run --rm \
-            -v "$(pwd):/src" \
-            -w /src \
-            -e VERSION="${VERSION}" \
-            golang:1.26-alpine \
-            sh -c "apk add --no-cache gcc musl-dev zlib-dev make && \
-                   make LDFLAGS='-linkmode=external -extldflags=-static' obitools"
-          mkdir -p artifacts
-          tar -czf artifacts/obitools4_${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: ${{ matrix.cgo_cflags || '' }}
         run: |
-          make obitools
+          if [ "$GOOS" = "linux" ]; then
+            make LDFLAGS='-linkmode=external -extldflags=-static' obitools
+          else
+            make obitools
+          fi
           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 4.4.27"
+var _Version = "Release 4.4.26"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.27
+4.4.26