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.
fix: add CGO_CFLAGS for static Linux builds and update go.work.sum
2026-03-25 13:30:52 +00:00 · 2026-03-13 19:24:26 +01:00 · 2026-03-13 19:24:18 +01:00 · 2026-03-13 19:13:02 +01:00 · 2026-03-13 19:12:49 +01:00 · 2026-03-13 19:04:15 +01:00
5 changed files with 4 additions and 2 deletions
--- a/.github/workflows/release.yml
+++ b/.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
--- a/go.work.sum
+++ b/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=
--- a/logs_60531881222.zip
+++ b/logs_60531881222.zip
--- a/pkg/obioptions/version.go
+++ b/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.
 //
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-4.4.24
+4.4.25
Author	SHA1	Message	Date
Eric Coissac	3cd4944fd8	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.	2026-03-13 19:24:26 +01:00
Eric Coissac	fdd972bbd2	fix: add CGO_CFLAGS for static Linux builds and update go.work.sum - 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	2026-03-13 19:24:18 +01:00
coissac	76f595e1fe	Merge pull request #95 from metabarcoding/push-kzmrqmplznrn Version 4.4.24	2026-03-13 19:13:02 +01:00
coissac	1e1e5443e3	Merge branch 'master' into push-kzmrqmplznrn	2026-03-13 19:12:49 +01:00
coissac	58d685926b	Merge pull request #94 from metabarcoding/push-lxxxlurqmqrt 4.4.23: Memory-aware batching, static Linux builds, and build improvements	2026-03-13 19:04:15 +01:00
Eric Coissac	e9f24426df	4.4.23: Memory-aware batching, static Linux builds, and build improvements ### 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.	2026-03-13 19:03:50 +01:00
@@ -1 +1 @@
 .4.24
 .4.25