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

### Static Linux Builds
- Added `CGO_CFLAGS` environment variable to the release workflow for consistent static linking on Linux, ensuring portable, self-contained executables.
- Updated `go.work.sum` with the new dependency `golang.org/x/net v0.38.0`.
- Removed obsolete logs archive file from the distribution.

### Memory-Aware Batching (Introduced in 4.4.23, now stable)
- Users can now control batching behavior using `--batch-mem` to specify memory limits (e.g., `128K`, `64M`, `1G`), enabling adaptive batching based on sequence data size.
- Batching now respects both byte and record count limits, flushing batches when either threshold is exceeded.
- Conservative memory estimation for sequences (`BioSequence.MemorySize()`) and explicit garbage collection after large batch discards improve resource predictability.
- Default constraints remain non-breaking: minimum 1, maximum 2000 records per batch with a default memory limit of 128 MB.

### Build System Improvements
- Updated Go toolchain to 1.26.1 and bumped key dependencies for security and performance.
- Fixed Makefile quoting for `LDFLAGS` to safely handle paths containing spaces.
- Enhanced build failure handling: error logs are now displayed before cleanup, aiding diagnostics.
- The install script now correctly configures `GOROOT`, `GOPATH`, and `GOTOOLCHAIN`, creates the GOPATH directory, and shows a progress bar during downloads.

.github/workflows/release.yml

@@ -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
@@ -83,7 +81,7 @@ jobs:
           GOARCH: ${{ matrix.goarch }}
           VERSION: ${{ steps.get_version.outputs.version }}
           CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }}
-          CGO_CFLAGS: ${{ matrix.cgo_cflags || '' }}
+          CGO_CFLAGS: ${{ matrix.goos == 'linux' && '-I/usr/include' || '' }}
         run: |
           if [ "$GOOS" = "linux" ]; then
             make LDFLAGS='-linkmode=external -extldflags=-static' obitools

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 4.4.26"
+var _Version = "Release 4.4.25"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.26
+4.4.25