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

@@ -81,6 +81,7 @@ jobs:
           GOARCH: ${{ matrix.goarch }}
           VERSION: ${{ steps.get_version.outputs.version }}
           CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }}
+          CGO_CFLAGS: ${{ matrix.goos == 'linux' && '-I/usr/include' || '' }}
         run: |
           if [ "$GOOS" = "linux" ]; then
             make LDFLAGS='-linkmode=external -extldflags=-static' obitools

go.work.sum

@@ -52,6 +52,7 @@ golang.org/x/image v0.6.0/go.mod h1:MXLdDR43H7cDJq5GEGXEVeeNhPgi+YYEQ2pC1byI1x0=
 golang.org/x/mod v0.13.0 h1:I/DsJXRlw/8l/0c24sM9yb0T4z9liZTduXvdAWYiysY=
 golang.org/x/mod v0.13.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
 golang.org/x/mod v0.14.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
+golang.org/x/net v0.38.0/go.mod h1:ivrbrMbzFq5J41QOQh0siUuly180yBYtLp+CKbEaFx8=
 golang.org/x/net v0.52.0/go.mod h1:R1MAz7uMZxVMualyPXb+VaqGSa3LIaUqk0eEt3w36Sw=
 golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4 h1:uVc8UZUe6tr40fFVnUP5Oj+veunVezqYl9z7DYw9xzw=
 golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k=

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 4.4.24"
+var _Version = "Release 4.4.25"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.24
+4.4.25