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obitools:master obitools:push-wpwqvsqsrpwz obitools:push-yxknulsuqnvz obitools:push-pvunnvzrzslw obitools:push-kzmrqmplznrn obitools:push-snmwxkwkqxrm obitools:push-mvpuxnxoyypu obitools:push-uotrstkymowq obitools:push-uzpqqoqvpnxw obitools:V4.3 obitools:microasm obitools:taxonomy obitools:blackboard
obitools:Release_4.4.29 obitools:Release_4.4.28 obitools:Release_4.4.27 obitools:Release_4.4.26 obitools:Release_4.4.25 obitools:Release_4.4.24 obitools:Release_4.4.23 obitools:Release_4.4.22 obitools:Release_4.4.21 obitools:Release_4.4.20 obitools:Release_4.4.19 obitools:Release_4.4.18 obitools:Release_4.4.17 obitools:Release_4.4.16 obitools:Release_4.4.15 obitools:Release_4.4.14 obitools:Release_4.4.13 obitools:Release_4.4.12 obitools:Release_4.4.11 obitools:Release_4.4.10 obitools:Release_4.4.9 obitools:Release_4.4.8 obitools:Release_4.4.7 obitools:Release_4.4.6 obitools:Release_4.4.5 obitools:Release_4.4.0 obitools:Release_4.3.0
...
compare: obitools:Release_4.4.26
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obitools:master obitools:push-wpwqvsqsrpwz obitools:push-yxknulsuqnvz obitools:push-pvunnvzrzslw obitools:push-kzmrqmplznrn obitools:push-snmwxkwkqxrm obitools:push-mvpuxnxoyypu obitools:push-uotrstkymowq obitools:push-uzpqqoqvpnxw obitools:V4.3 obitools:microasm obitools:taxonomy obitools:blackboard
obitools:Release_4.4.29 obitools:Release_4.4.28 obitools:Release_4.4.27 obitools:Release_4.4.26 obitools:Release_4.4.25 obitools:Release_4.4.24 obitools:Release_4.4.23 obitools:Release_4.4.22 obitools:Release_4.4.21 obitools:Release_4.4.20 obitools:Release_4.4.19 obitools:Release_4.4.18 obitools:Release_4.4.17 obitools:Release_4.4.16 obitools:Release_4.4.15 obitools:Release_4.4.14 obitools:Release_4.4.13 obitools:Release_4.4.12 obitools:Release_4.4.11 obitools:Release_4.4.10 obitools:Release_4.4.9 obitools:Release_4.4.8 obitools:Release_4.4.7 obitools:Release_4.4.6 obitools:Release_4.4.5 obitools:Release_4.4.0 obitools:Release_4.3.0

14 Commits
Release_4. ... Release_4.

Author SHA1 Message Date
Eric Coissac
78e7933c6f 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.
 2026-03-13 19:30:37 +01:00
Eric Coissac
afc9ffda85 chore: bump version to 4.4.25 and fix CGO_CFLAGS for cross-compilation 
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.
 2026-03-13 19:30:29 +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
Eric Coissac
15d1f1fd80 Version 4.4.24 
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.
 2026-03-13 19:11:58 +01:00
Eric Coissac
8df2cbe22f Bump version to 4.4.23 and update release workflow 
- 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
 2026-03-13 19:11:55 +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
Eric Coissac
2f7be10b5d Build improvements and Go version update 
- Update Go version from 1.25.0 to 1.26.1 in go.mod and go.work
- Fix Makefile: quote LDFLAGS to handle spaces safely in -ldflags
- Improve build error handling: on failure, cat log then cleanup and exit with error code
- Update install_obitools.sh: properly set GOROOT, GOPATH, and GOTOOLCHAIN; ensure GOPATH directory is created
 2026-03-13 19:03:42 +01:00
Eric Coissac
43125f9f5e feat: add progress bar to curl downloads in install script 
Replace silent curl commands with --progress-bar option to provide visual feedback during Go and OBITools4 downloads, improving user experience without changing download logic.
 2026-03-13 16:40:55 +01:00
Eric Coissac
c23368e929 update dependencies and Go toolchain to 1.25.0 
Update go.mod and go.work to Go 1.25.0, bump several direct dependencies (e.g., go-getoptions, gval, regexp2, go-json, progressbar, logrus, testify), update indirect dependencies accordingly, and remove obsolete toolchain directive.
 2026-03-13 16:09:34 +01:00
coissac
6cb5a81685 Merge pull request #93 from metabarcoding/push-snmwxkwkqxrm 
Memory-aware Batching and Static Linux Builds
 2026-03-13 15:18:29 +01:00
Eric Coissac
94b0887069 Memory-aware Batching and Static Linux Builds 
### Memory-Aware Batching
- Replaced single batch size limits with configurable min/max bounds and memory limits for more precise control over resource usage.
- Added `--batch-mem` CLI option to enable adaptive batching based on estimated sequence memory footprint (e.g., 128K, 64M, 1G).
- Introduced `RebatchBySize()` with explicit support for both byte and count limits, flushing when either threshold is exceeded.
- Implemented conservative memory estimation via `BioSequence.MemorySize()` and enhanced garbage collection to trigger explicit cleanup after large batch discards.
- Updated internal batching logic across `batchiterator.go`, `fragment.go`, and `obirefidx.go` to consistently use 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.

### Notes
- This release consolidates and improves batching behavior introduced in 4.4.20, with no breaking changes to the public API.
- All user-facing batching behavior is now governed by consistent memory and count constraints, improving predictability and stability during large dataset processing.
 2026-03-13 15:16:41 +01:00
9 changed files with 82 additions and 86 deletions
Expand all files Collapse all files

5
.github/workflows/release.yml vendored
View File

@@ -32,10 +32,12 @@ jobs:
goos: linux goos: linux
goarch: amd64 goarch: amd64
output_name: linux_amd64 output_name: linux_amd64
cgo_cflags: "-I/usr/include/x86_64-linux-gnu -I/usr/include"
- os: ubuntu-24.04-arm - os: ubuntu-24.04-arm
goos: linux goos: linux
goarch: arm64 goarch: arm64
output_name: linux_arm64 output_name: linux_arm64
cgo_cflags: "-I/usr/include/aarch64-linux-gnu -I/usr/include"
- os: macos-15-intel - os: macos-15-intel
goos: darwin goos: darwin
goarch: amd64 goarch: amd64
@@ -66,7 +68,7 @@ jobs:
if: runner.os == 'Linux' if: runner.os == 'Linux'
run: | run: |
sudo apt-get update -q sudo apt-get update -q
sudo apt-get install -y musl-tools sudo apt-get install -y musl-tools zlib1g-dev
- name: Install build tools (macOS) - name: Install build tools (macOS)
if: runner.os == 'macOS' if: runner.os == 'macOS'
@@ -81,6 +83,7 @@ jobs:
GOARCH: ${{ matrix.goarch }} GOARCH: ${{ matrix.goarch }}
VERSION: ${{ steps.get_version.outputs.version }} VERSION: ${{ steps.get_version.outputs.version }}
CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }} CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }}
CGO_CFLAGS: ${{ matrix.cgo_cflags || '' }}
run: | run: |
if [ "$GOOS" = "linux" ]; then if [ "$GOOS" = "linux" ]; then
make LDFLAGS='-linkmode=external -extldflags=-static' obitools make LDFLAGS='-linkmode=external -extldflags=-static' obitools

7
Makefile
View File

@@ -12,7 +12,7 @@ NC := \033[0m
GOFLAGS= GOFLAGS=
LDFLAGS= LDFLAGS=
GOCMD=go GOCMD=go
GOBUILD=$(GOCMD) build $(GOFLAGS) $(if $(LDFLAGS),-ldflags='$(LDFLAGS)') GOBUILD=$(GOCMD) build $(GOFLAGS) $(if $(LDFLAGS),-ldflags="$(LDFLAGS)")
GOGENERATE=$(GOCMD) generate GOGENERATE=$(GOCMD) generate
GOCLEAN=$(GOCMD) clean GOCLEAN=$(GOCMD) clean
GOTEST=$(GOCMD) test GOTEST=$(GOCMD) test
@@ -51,7 +51,7 @@ $(OBITOOLS_PREFIX)$(notdir $(1)): $(BUILD_DIR) $(1) pkg/obioptions/version.go
@echo -n - Building obitool $(notdir $(1))... @echo -n - Building obitool $(notdir $(1))...
@$(GOBUILD) -o $(BUILD_DIR)/$(OBITOOLS_PREFIX)$(notdir $(1)) ./$(1) \ @$(GOBUILD) -o $(BUILD_DIR)/$(OBITOOLS_PREFIX)$(notdir $(1)) ./$(1) \
2> $(OBITOOLS_PREFIX)$(notdir $(1)).log \ 2> $(OBITOOLS_PREFIX)$(notdir $(1)).log \
|| cat $(OBITOOLS_PREFIX)$(notdir $(1)).log || { cat $(OBITOOLS_PREFIX)$(notdir $(1)).log; rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log; exit 1; }
@rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log @rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log
@echo Done. @echo Done.
endef endef
@@ -229,7 +229,8 @@ jjpush-tag:
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'; \
release_message="$$release_title"$$'\n\n'"$$release_body$$install_section"; \ release_message="$$release_title"$$'\n\n'"$$release_body$$install_section"; \
echo "$(BLUE)→ Creating tag $$tag_name...$(NC)"; \ echo "$(BLUE)→ Creating tag $$tag_name...$(NC)"; \
git tag -a "$$tag_name" -m "$$release_message" 2>/dev/null || echo "$(YELLOW)⚠ Tag $$tag_name already exists$(NC)"; \ commit_hash=$$(jj log -r @ --no-graph -T 'commit_id' 2>/dev/null); \
git tag -a "$$tag_name" $${commit_hash:+"$$commit_hash"} -m "$$release_message" 2>/dev/null || echo "$(YELLOW)⚠ Tag $$tag_name already exists$(NC)"; \
echo "$(BLUE)→ Pushing tag $$tag_name...$(NC)"; \ echo "$(BLUE)→ Pushing tag $$tag_name...$(NC)"; \
git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"; \ git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"; \
rm -f /tmp/obitools4-release-title.txt /tmp/obitools4-release-body.txt rm -f /tmp/obitools4-release-title.txt /tmp/obitools4-release-body.txt

41
go.mod
View File

@@ -1,35 +1,33 @@
module git.metabarcoding.org/obitools/obitools4/obitools4 module git.metabarcoding.org/obitools/obitools4/obitools4
go 1.23.4 go 1.26.1
toolchain go1.24.2
require ( require (
github.com/DavidGamba/go-getoptions v0.28.0 github.com/DavidGamba/go-getoptions v0.33.0
github.com/PaesslerAG/gval v1.2.2 github.com/PaesslerAG/gval v1.2.4
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df
github.com/buger/jsonparser v1.1.1 github.com/buger/jsonparser v1.1.1
github.com/chen3feng/stl4go v0.1.1 github.com/chen3feng/stl4go v0.1.1
github.com/dlclark/regexp2 v1.11.4 github.com/dlclark/regexp2 v1.11.5
github.com/goccy/go-json v0.10.3 github.com/goccy/go-json v0.10.6
github.com/klauspost/pgzip v1.2.6 github.com/klauspost/pgzip v1.2.6
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58
github.com/pelletier/go-toml/v2 v2.2.4 github.com/pelletier/go-toml/v2 v2.2.4
github.com/rrethy/ahocorasick v1.0.0 github.com/rrethy/ahocorasick v1.0.0
github.com/schollz/progressbar/v3 v3.13.1 github.com/schollz/progressbar/v3 v3.19.0
github.com/sirupsen/logrus v1.9.3 github.com/sirupsen/logrus v1.9.4
github.com/stretchr/testify v1.8.4 github.com/stretchr/testify v1.10.0
github.com/tevino/abool/v2 v2.1.0 github.com/tevino/abool/v2 v2.1.0
github.com/yuin/gopher-lua v1.1.1 github.com/yuin/gopher-lua v1.1.1
golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90
gonum.org/v1/gonum v0.14.0 gonum.org/v1/gonum v0.17.0
gopkg.in/yaml.v3 v3.0.1 gopkg.in/yaml.v3 v3.0.1
scientificgo.org/special v0.0.0 scientificgo.org/special v0.0.0
) )
require ( require (
github.com/davecgh/go-spew v1.1.1 // indirect github.com/davecgh/go-spew v1.1.1 // indirect
github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 // indirect github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9 // indirect
github.com/kr/pretty v0.3.1 // indirect github.com/kr/pretty v0.3.1 // indirect
github.com/kr/text v0.2.0 // indirect github.com/kr/text v0.2.0 // indirect
github.com/pmezard/go-difflib v1.0.0 // indirect github.com/pmezard/go-difflib v1.0.0 // indirect
@@ -38,16 +36,15 @@ require (
require ( require (
github.com/dsnet/compress v0.0.1 github.com/dsnet/compress v0.0.1
github.com/gabriel-vasile/mimetype v1.4.3 github.com/gabriel-vasile/mimetype v1.4.13
github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77 github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77
github.com/klauspost/compress v1.17.2 github.com/klauspost/compress v1.18.4
github.com/mattn/go-runewidth v0.0.15 // indirect github.com/mattn/go-runewidth v0.0.21 // indirect
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
github.com/rivo/uniseg v0.4.4 // indirect github.com/rivo/uniseg v0.4.7 // indirect
github.com/shopspring/decimal v1.3.1 // indirect github.com/shopspring/decimal v1.4.0 // indirect
github.com/ulikunitz/xz v0.5.11 github.com/ulikunitz/xz v0.5.15
golang.org/x/net v0.35.0 // indirect golang.org/x/sys v0.42.0 // indirect
golang.org/x/sys v0.30.0 // indirect golang.org/x/term v0.41.0 // indirect
golang.org/x/term v0.29.0 // indirect
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
) )

91
go.sum
View File

@@ -1,7 +1,7 @@
github.com/DavidGamba/go-getoptions v0.28.0 h1:18wgEvfZdrlfIhVDGEBO3Dl0fkOyXqXLa0tLMCKxM1c= github.com/DavidGamba/go-getoptions v0.33.0 h1:8xCPH87Yy5avYenygyHVlqqm8RpymH0YFe4a7IWlarE=
github.com/DavidGamba/go-getoptions v0.28.0/go.mod h1:zE97E3PR9P3BI/HKyNYgdMlYxodcuiC6W68KIgeYT84= github.com/DavidGamba/go-getoptions v0.33.0/go.mod h1:zE97E3PR9P3BI/HKyNYgdMlYxodcuiC6W68KIgeYT84=
github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E= github.com/PaesslerAG/gval v1.2.4 h1:rhX7MpjJlcxYwL2eTTYIOBUyEKZ+A96T9vQySWkVUiU=
github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac= github.com/PaesslerAG/gval v1.2.4/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI= github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8= github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0= github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
@@ -10,27 +10,32 @@ github.com/buger/jsonparser v1.1.1 h1:2PnMjfWD7wBILjqQbt530v576A/cAbQvEW9gGIpYMU
github.com/buger/jsonparser v1.1.1/go.mod h1:6RYKKt7H4d4+iWqouImQ9R2FZql3VbhNgx27UK13J/0= github.com/buger/jsonparser v1.1.1/go.mod h1:6RYKKt7H4d4+iWqouImQ9R2FZql3VbhNgx27UK13J/0=
github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q= github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU= github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU=
github.com/chengxilo/virtualterm v1.0.4 h1:Z6IpERbRVlfB8WkOmtbHiDbBANU7cimRIof7mk9/PwM=
github.com/chengxilo/virtualterm v1.0.4/go.mod h1:DyxxBZz/x1iqJjFxTFcr6/x+jSpqN0iwWCOK1q10rlY=
github.com/clipperhouse/uax29/v2 v2.2.0 h1:ChwIKnQN3kcZteTXMgb1wztSgaU+ZemkgWdohwgs8tY=
github.com/clipperhouse/uax29/v2 v2.2.0/go.mod h1:EFJ2TJMRUaplDxHKj1qAEhCtQPW2tJSwu5BF98AuoVM=
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github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
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github.com/dlclark/regexp2 v1.11.4/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8= github.com/dlclark/regexp2 v1.11.5/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8=
github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q= github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q=
github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo= github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo=
github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY= github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY=
github.com/gabriel-vasile/mimetype v1.4.3 h1:in2uUcidCuFcDKtdcBxlR0rJ1+fsokWf+uqxgUFjbI0= github.com/gabriel-vasile/mimetype v1.4.13 h1:46nXokslUBsAJE/wMsp5gtO500a4F3Nkz9Ufpk2AcUM=
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github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 h1:SajEQ6tktpF9SRIuzbiPOX9AEZZ53Bvw0k9Mzrts8Lg= github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419/go.mod h1:YKu81H3RSd1cFh0d7NhvUoTtUC9IY/vBX0WUQb1/o4Y= github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419/go.mod h1:YKu81H3RSd1cFh0d7NhvUoTtUC9IY/vBX0WUQb1/o4Y=
github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9 h1:vFjPvFavIiDY71bQ9HIxPQBANvNl1SmFC4fgg5xRkho=
github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9/go.mod h1:YKu81H3RSd1cFh0d7NhvUoTtUC9IY/vBX0WUQb1/o4Y=
github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77 h1:4dvq1tGHn1Y9KSRY0OZ24Khki4+4U+ZrA//YYsdUlJU= github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77 h1:4dvq1tGHn1Y9KSRY0OZ24Khki4+4U+ZrA//YYsdUlJU=
github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77/go.mod h1:HPelMYpOyy0XvglpBbmZ3krZpwaHmszj/vQNlnETPTM= github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77/go.mod h1:HPelMYpOyy0XvglpBbmZ3krZpwaHmszj/vQNlnETPTM=
github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213/go.mod h1:vNUNkEQ1e29fT/6vq2aBdFsgNPmy8qMdSay1npru+Sw=
github.com/klauspost/compress v1.4.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A= github.com/klauspost/compress v1.4.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A=
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github.com/klauspost/compress v1.17.2/go.mod h1:ntbaceVETuRiXiv4DpjP66DpAtAGkEQskQzEyD//IeE= github.com/klauspost/compress v1.18.4/go.mod h1:R0h/fSBs8DE4ENlcrlib3PsXS61voFxhIs2DeRhCvJ4=
github.com/klauspost/cpuid v1.2.0/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgoMS4s3ek= github.com/klauspost/cpuid v1.2.0/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgoMS4s3ek=
github.com/klauspost/pgzip v1.2.6 h1:8RXeL5crjEUFnR2/Sn6GJNWtSQ3Dk8pq4CL3jvdDyjU= github.com/klauspost/pgzip v1.2.6 h1:8RXeL5crjEUFnR2/Sn6GJNWtSQ3Dk8pq4CL3jvdDyjU=
github.com/klauspost/pgzip v1.2.6/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= github.com/klauspost/pgzip v1.2.6/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
@@ -41,10 +46,8 @@ github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI= github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY= github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE= github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
github.com/mattn/go-isatty v0.0.17/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM= github.com/mattn/go-runewidth v0.0.21 h1:jJKAZiQH+2mIinzCJIaIG9Be1+0NR+5sz/lYEEjdM8w=
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github.com/mattn/go-runewidth v0.0.15/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ= github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw= github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 h1:onHthvaw9LFnH4t2DcNVpwGmV9E1BkGknEliJkfwQj0= github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 h1:onHthvaw9LFnH4t2DcNVpwGmV9E1BkGknEliJkfwQj0=
@@ -54,50 +57,40 @@ github.com/pelletier/go-toml/v2 v2.2.4/go.mod h1:2gIqNv+qfxSVS7cM2xJQKtLSTLUE9V8
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github.com/ulikunitz/xz v0.5.11/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14= github.com/ulikunitz/xz v0.5.15/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
github.com/yuin/gopher-lua v1.1.1 h1:kYKnWBjvbNP4XLT3+bPEwAXJx262OhaHDWDVOPjL46M= github.com/yuin/gopher-lua v1.1.1 h1:kYKnWBjvbNP4XLT3+bPEwAXJx262OhaHDWDVOPjL46M=
github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw= github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw=
golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa h1:FRnLl4eNAQl8hwxVVC17teOw8kdjVDVAiFMtgUdTSRQ= golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90 h1:jiDhWWeC7jfWqR9c/uplMOqJ0sbNlNWv0UkzE0vX1MA=
golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa/go.mod h1:zk2irFbV9DP96SEBUUAy67IdHUaZuSnrz1n472HUCLE= golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90/go.mod h1:xE1HEv6b+1SCZ5/uscMRjUBKtIxworgEcEi+/n9NQDQ=
golang.org/x/net v0.35.0 h1:T5GQRQb2y08kTAByq9L4/bz8cipCdA8FbRTXewonqY8= golang.org/x/sys v0.42.0 h1:omrd2nAlyT5ESRdCLYdm3+fMfNFE/+Rf4bDIQImRJeo=
golang.org/x/net v0.35.0/go.mod h1:EglIi67kWsHKlRzzVMUD93VMSWGFOMSZgxFjparz1Qk= golang.org/x/sys v0.42.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/term v0.41.0 h1:QCgPso/Q3RTJx2Th4bDLqML4W6iJiaXFq2/ftQF13YU=
golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/term v0.41.0/go.mod h1:3pfBgksrReYfZ5lvYM0kSO0LIkAl4Yl2bXOkKP7Ec2A=
golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= gonum.org/v1/gonum v0.17.0 h1:VbpOemQlsSMrYmn7T2OUvQ4dqxQXU+ouZFQsZOx50z4=
golang.org/x/sys v0.30.0 h1:QjkSwP/36a20jFYWkSue1YwXzLmsV5Gfq7Eiy72C1uc= gonum.org/v1/gonum v0.17.0/go.mod h1:El3tOrEuMpv2UdMrbNlKEh9vd86bmQ6vqIcDwxEOc1E=
golang.org/x/sys v0.30.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
golang.org/x/term v0.6.0/go.mod h1:m6U89DPEgQRMq3DNkDClhWw02AUbt2daBVO4cn4Hv9U=
golang.org/x/term v0.29.0 h1:L6pJp37ocefwRRtYPKSWOWzOtWSxVajvz2ldH/xi3iU=
golang.org/x/term v0.29.0/go.mod h1:6bl4lRlvVuDgSf3179VpIxBF0o10JUpXWOnI7nErv7s=
gonum.org/v1/gonum v0.14.0 h1:2NiG67LD1tEH0D7kM+ps2V+fXmsAnpUeec7n8tcr4S0=
gonum.org/v1/gonum v0.14.0/go.mod h1:AoWeoz0becf9QMWtE8iWXNXc27fK4fNeHNf/oMejGfU=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk= gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q= gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA= gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
scientificgo.org/special v0.0.0 h1:P6WJkECo6tgtvZAEfNXl+KEB9ReAatjKAeX8U07mjSc= scientificgo.org/special v0.0.0 h1:P6WJkECo6tgtvZAEfNXl+KEB9ReAatjKAeX8U07mjSc=

4
go.work
View File

@@ -1,5 +1,3 @@
go 1.23.4 go 1.26.1
toolchain go1.24.2
use . use .

2
go.work.sum
View File

@@ -52,6 +52,8 @@ 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 h1:I/DsJXRlw/8l/0c24sM9yb0T4z9liZTduXvdAWYiysY=
golang.org/x/mod v0.13.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c= 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/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/sync v0.0.0-20220722155255-886fb9371eb4 h1:uVc8UZUe6tr40fFVnUP5Oj+veunVezqYl9z7DYw9xzw=
golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k= golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k=
golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE= golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE=

14
install_obitools.sh
View File

@@ -183,22 +183,24 @@ GOURL=$(curl -s "${URL}${GOFILE}" \
echo "Installing Go from: $GOURL" 1>&2 echo "Installing Go from: $GOURL" 1>&2
curl -s "$GOURL" | tar zxf - curl --progress-bar "$GOURL" | tar zxf -
PATH="$(pwd)/go/bin:$PATH" export GOROOT="$(pwd)/go"
PATH="${GOROOT}/bin:$PATH"
export PATH export PATH
GOPATH="$(pwd)/go" export GOPATH="$(pwd)/gopath"
export GOPATH
export GOCACHE="$(pwd)/cache" export GOCACHE="$(pwd)/cache"
export GOTOOLCHAIN=local
echo "GOROOT=$GOROOT" 1>&2
echo "GOCACHE=$GOCACHE" 1>&2 echo "GOCACHE=$GOCACHE" 1>&2
mkdir -p "$GOCACHE" mkdir -p "$GOPATH" "$GOCACHE"
# Download OBITools4 source # Download OBITools4 source
echo "Downloading OBITools4 v${VERSION}..." 1>&2 echo "Downloading OBITools4 v${VERSION}..." 1>&2
echo "Source URL: $OBIURL4" 1>&2 echo "Source URL: $OBIURL4" 1>&2
if ! curl -sL "$OBIURL4" > obitools4.zip; then if ! curl --progress-bar -L "$OBIURL4" > obitools4.zip; then
echo "Error: Could not download OBITools4 version ${VERSION}" 1>&2 echo "Error: Could not download OBITools4 version ${VERSION}" 1>&2
echo "Please check that this version exists with: $0 --list" 1>&2 echo "Please check that this version exists with: $0 --list" 1>&2
exit 1 exit 1

2
pkg/obioptions/version.go
View File

@@ -3,7 +3,7 @@ package obioptions
// Version is automatically updated by the Makefile from version.txt // Version is automatically updated by the Makefile from version.txt
// The patch number (third digit) is incremented on each push to the repository // The patch number (third digit) is incremented on each push to the repository
var _Version = "Release 4.4.21" var _Version = "Release 4.4.26"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.
// //

2
version.txt
View File

@@ -1 +1 @@
4.4.21 4.4.26