Tags: talmolab/sleap
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Fix Linux Qt library conflicts with system/OpenCV-bundled Qt (#2604) * Fix Linux Qt library conflicts with system/OpenCV-bundled Qt On Linux systems with system Qt 6 packages (e.g., Debian 12 ships Qt 6.4), PySide6's bundled Qt libraries can conflict with the system versions, causing ImportError with undefined symbols like _ZN14QObjectPrivateC2Ei. Additionally, opencv-python bundles its own Qt plugins which can hijack QT_PLUGIN_PATH. This adds a startup fix in app.py (matching the existing macOS DYLD_LIBRARY_PATH pattern) that prepends PySide6's bundled Qt lib and plugin paths to LD_LIBRARY_PATH and QT_PLUGIN_PATH, then re-execs the process so the dynamic linker resolves all Qt symbols from the same version. The fix runs on all Linux systems and can be disabled with SLEAP_SKIP_QT_FIX=1. Also adds Display/GUI troubleshooting entries to help.md covering: - Qt library version mismatch errors - xcb platform plugin failures (libxcb-cursor0 + OpenCV conflict) - SSH/X11 forwarding setup checklist Co-Authored-By: Claude Opus 4.6 <[email protected]> * Add --video-backend CLI option and preference Expose sleap-io's video backend plugin system through: 1. `sleap label --video-backend FFMPEG` CLI option 2. `"default video backend"` persistent preference in prefs.yaml 3. Wiring in app.py that applies the backend before any videos are loaded Priority: CLI flag > saved preference > auto-detect (opencv → FFMPEG → pyav). This allows users to work around OpenCV h264 codec failures (e.g., when LD_LIBRARY_PATH changes cause OpenCV to pick up wrong ffmpeg libraries) by switching to imageio-ffmpeg or pyav backends. Co-Authored-By: Claude Opus 4.6 <[email protected]> * Persist --video-backend flag to preferences When the user explicitly passes --video-backend, save it to preferences so subsequent launches use the same backend without the flag. Co-Authored-By: Claude Opus 4.6 <[email protected]> * Fix line length lint errors in Qt fix comments Co-Authored-By: Claude Opus 4.6 <[email protected]> * Route flags to default subcommand in CLI group When the first argument is a flag (e.g. `sleap --video-backend ffmpeg`), insert the default subcommand name so it routes to `label` instead of being misinterpreted. Excludes --help and --version which belong to the group itself. Co-Authored-By: Claude Opus 4.6 <[email protected]> * Add --video-backend to CLI docs and fix flag routing Update CLI reference docs with --video-backend option. Also fixes routing so `sleap --video-backend ffmpeg` works the same as `sleap label --video-backend ffmpeg` by detecting flags as the first argument and inserting the default subcommand. Co-Authored-By: Claude Opus 4.6 <[email protected]> * Add h264/OpenCV codec failure troubleshooting to help docs Include the specific error strings (Could not open codec h264, Failed initializing scaling graph, swscaler) so users can find the entry when searching for these errors. Co-Authored-By: Claude Opus 4.6 <[email protected]> --------- Co-authored-by: Claude Opus 4.6 <[email protected]>
Bump version to v1.6.0a3, sleap-nn to 0.1.0a4 (#2580) - Update SLEAP version from 1.6.0a2 to 1.6.0a3 - Bump sleap-nn minimum from 0.1.0a3 to 0.1.0a4 - sleap-io minimum remains at 0.6.3 (already updated in #2573) - Update all version references in installation docs Co-authored-by: Claude Opus 4.5 <[email protected]>
Bump version to 1.6.0a1 (#2561) * Bump version to 1.6.0a1 - Update __version__ to 1.6.0a1 - Bump sleap-nn minimum to >=0.1.0a1 - sleap-io minimum already at >=0.6.1 Co-Authored-By: Claude Opus 4.5 <[email protected]> * Fix lint errors (line length, unused imports) - Break long line in video.py:617 - Remove unused pytest imports in test_qc.py and test_config.py - Break long line in test_detector.py:200 Co-Authored-By: Claude Opus 4.5 <[email protected]> * Apply ruff format to QC module files Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Claude Opus 4.5 <[email protected]>
Add pre-release installation documentation (#2548) - Add "Pre-release Versions" section with install commands for alpha/beta/RC - Add navigation link "Test new features before release" - Add "Install Latest Pre-release" with --prerelease allow flag - Add "Install a Specific Version" for version pinning - Add "Pin Dependency Versions" with --with flag for sleap-io/sleap-nn - Add version compatibility table (SLEAP, sleap-io, sleap-nn) - Add "Rollback to Stable" instructions - Add CUDA 13.0 support documentation - Update "Update to latest version" to clarify "stable" version - Add "Check installed version" with sleap doctor command Co-authored-by: Claude Opus 4.5 <[email protected]>
Bump version to 1.5.2 and update dependencies (#2451) - Bump package version to 1.5.2 - Update minimum sleap-io version to 0.5.7 - Update minimum sleap-nn version to 0.0.4 - Add --python 3.13 flag to uv tool install commands to prevent Python 3.14 issues - Consolidate repetitive installation documentation (reduce by 55 lines) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude <[email protected]>
Migrate to `mkdocs` for sleap documentation (#2367) * Modify mkdocs.yml and docs.yml * Change docs to mkdocs * Change docs workflow to uv * Remove path filters * Fix docs.yml * Fix docs.yml * Add branches * Run with uv * Fix links * Fix redirect links * Fix docs sleap.ai links * Add API references * Modify CLI docs * Modify colab to use sleap-nn and sleap-io * change: uv installation integration * change: remove unnecessary warning * change: comment out conda related setup * change: remove conda setup steps & replace w/ uv * fix: add tip to copy entire instance * fix: additional reminder for pip installation * fix: add help flag shortcut to train/track * fix: include yaml config format * change: add `uv run` reminder & remove deprecated sleap-render args * Update guides and learnings * change: update features to include nn and io & uv quick install * fix: remove deprecated CLI feature desc. from sleap-inspect * fix: ruff error * Add note to point to sleap-nn cli * Update training notebooks * change: update uv installation instructions for uv tool install/uvx/uv sync * fix: change quick install to quick start and use uvx * Add what's new section * change: typos and moving around info boxes * change: uv installation steps revamp (platform-specific/installation verification * Update model evaluation notebook * fix: reformat tip about uv pip * fix: highlight use of YAML config * fix: highlight that uvx is only invocation, not installation --------- Co-authored-by: AmickL <[email protected]> Co-authored-by: AmickL <[email protected]> Co-authored-by: Talmo Pereira <[email protected]>
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