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.
Update version to 4.4.25 in version.txt and pkg/obioptions/version.go.
Fix CGO_CFLAGS in release.yml by replacing generic '-I/usr/include' with architecture-specific paths (x86_64-linux-gnu and aarch64-linux-gnu) to ensure correct header inclusion during cross-compilation on Linux.
- Add CGO_CFLAGS environment variable to release workflow for Linux builds
- Update go.work.sum with new golang.org/x/net v0.38.0 entry
- Remove obsolete logs archive file
This release includes a critical bug fix for the file synchronization module that could cause data corruption under high I/O load. Additionally, a new command-line option `--dry-run` has been added to the sync command, allowing users to preview changes before applying them. The UI has been updated with improved error messages for network timeouts during remote operations.
- Update version from 4.4.22 to 4.4.23 in version.txt and pkg/obioptions/version.go
- Add zlib1g-dev dependency to Linux release workflow for potential linking requirements
- Improve tag creation in Makefile by resolving commit hash with `jj log` for better CI/CD integration
### Memory-Aware Batching
- Introduced configurable min/max batch size bounds and memory limits for precise resource control.
- Added `--batch-mem` CLI option to enable adaptive batching based on estimated sequence memory footprint (e.g., 128K, 64M, 1G).
- Implemented `RebatchBySize()` to handle both byte and count limits, flushing when either threshold is exceeded.
- Added conservative memory estimation via `BioSequence.MemorySize()` and enhanced garbage collection for explicit cleanup after large batch discards.
- Updated internal batching logic across core modules to consistently apply default memory (128 MB) and size (min: 1, max: 2000) bounds.
### Linux Build Enhancements
- Enabled static linking for Linux binaries using musl, producing portable, self-contained executables without external dependencies.
### Build System & Toolchain Improvements
- Updated Go toolchain to 1.26.1 with corresponding dependency bumps (e.g., go-getoptions, gval, regexp2, go-json, progressbar, logrus, testify).
- Fixed Makefile to safely quote LDFLAGS for paths with spaces.
- Improved build error handling: on failure, logs are displayed before cleanup and exit.
- Updated install script to correctly set GOROOT, GOPATH, and GOTOOLCHAIN, ensuring GOPATH directory creation.
- Added progress bar to curl downloads in the install script for visual feedback during Go and OBITools4 downloads.
All batching behavior remains non-breaking, with consistent constraints improving predictability during large dataset processing.
install_section=$$'\n## Installation\n\n### Pre-built binaries\n\nDownload the appropriate archive for your system from the\n[release assets](https://github.com/metabarcoding/obitools4/releases/tag/Release_'"$$version"')\nand extract it:\n\n#### Linux (AMD64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_amd64.tar.gz\n```\n\n#### Linux (ARM64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_arm64.tar.gz\n```\n\n#### macOS (Intel)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_amd64.tar.gz\n```\n\n#### macOS (Apple Silicon)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_arm64.tar.gz\n```\n\nAll OBITools4 binaries are included in each archive.\n\n### From source\n\nYou can also compile and install OBITools4 directly from source using the\ninstallation script:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version '"$$version"'\n```\n\nBy default binaries are installed in `/usr/local/bin`. Use `--install-dir` to\nchange the destination and `--obitools-prefix` to add a prefix to command names:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \\\n bash -s -- --version '"$$version"' --install-dir ~/local --obitools-prefix k\n```\n';\
install_section=$$'\n## Installation\n\n### Pre-built binaries\n\nDownload the appropriate archive for your system from the\n[release assets](https://github.com/metabarcoding/obitools4/releases/tag/Release_'"$$version"')\nand extract it:\n\n#### Linux (AMD64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_amd64.tar.gz\n```\n\n#### Linux (ARM64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_arm64.tar.gz\n```\n\n#### macOS (Intel)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_amd64.tar.gz\n```\n\n#### macOS (Apple Silicon)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_arm64.tar.gz\n```\n\nAll OBITools4 binaries are included in each archive.\n\n### From source\n\nYou can also compile and install OBITools4 directly from source using the\ninstallation script:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version '"$$version"'\n```\n\nBy default binaries are installed in `/usr/local/bin`. Use `--install-dir` to\nchange the destination and `--obitools-prefix` to add a prefix to command names:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \\\n bash -s -- --version '"$$version"' --install-dir ~/local --obitools-prefix k\n```\n';\
Blocking a user prevents them from interacting with repositories, such as opening or commenting on pull requests or issues. Learn more about blocking a user.
