Pxblat

Changes

Bug Fixes

- Fix 244 cauliyang

Miscellaneous Tasks

- Now the id of the query result will be a string concat the first 5 letters and the length of the sequence. for example, `TACCG_100`

:package: Dependencies

* build(deps): bump linkify-it-py from 2.0.2 to 2.0.3 (255) dependabot
* build(deps): bump pysimdjson from 5.0.2 to 6.0.2 (256) dependabot
* build(deps-dev): bump ruff from 0.2.0 to 0.2.1 (257) dependabot

Changes

* Benchmark (254) cauliyang

:package: Dependencies

* build(deps-dev): bump sphinx-autobuild from 2021.3.14 to 2024.2.4 (251) dependabot
* build(deps): bump pip from 23.3.2 to 24.0 in /.github/workflows (252) dependabot
* build(deps): bump linkify-it-py from 2.0.2 to 2.0.3 in /docs (253) dependabot

Changes

* fix 244: Simplify conditional statement in query_server() function (246) cauliyang

:package: Dependencies

* build(deps-dev): bump pytest-sugar from 0.9.7 to 1.0.0 (247) dependabot
* build(deps-dev): bump ruff from 0.1.15 to 0.2.0 (248) dependabot
* build(deps): bump release-drafter/release-drafter from 5.25.0 to 6.0.0 (249) dependabot
* build(deps): bump codecov/codecov-action from 3 to 4 (243) dependabot
* build(deps): bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (240) dependabot
* build(deps): bump urllib3 from 2.1.0 to 2.2.0 (241) dependabot
* build(deps-dev): bump cibuildwheel from 2.16.4 to 2.16.5 (242) dependabot
* build(deps-dev): bump ruff from 0.1.14 to 0.1.15 (239) dependabot
* build(deps): bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (235) dependabot
* build(deps-dev): bump cibuildwheel from 2.16.2 to 2.16.4 (236) dependabot
* build(deps): bump mashumaro from 3.11 to 3.12 (237) dependabot
* build(deps-dev): bump pytest from 7.4.4 to 8.0.0 (238) dependabot
* build(deps-dev): bump seaborn from 0.13.1 to 0.13.2 (234) dependabot
* build(deps-dev): bump psutil from 5.9.7 to 5.9.8 (232) dependabot
* build(deps-dev): bump ruff from 0.1.13 to 0.1.14 (233) dependabot
* build(deps): bump actions/cache from 3 to 4 (231) dependabot
* build(deps-dev): bump ruff from 0.1.12 to 0.1.13 (230) dependabot
* build(deps-dev): bump ruff from 0.1.11 to 0.1.12 (229) dependabot
* build(deps): bump biopython from 1.82 to 1.83 (227) dependabot
* build(deps): bump sphinxcontrib-bibtex from 2.6.1 to 2.6.2 (228) dependabot
* build(deps-dev): bump seaborn from 0.13.0 to 0.13.1 (225) dependabot
* build(deps-dev): bump pytest from 7.4.3 to 7.4.4 (224) dependabot
* build(deps-dev): bump ruff from 0.1.9 to 0.1.11 (226) dependabot
* build(deps): bump setuptools from 69.0.2 to 69.0.3 (222) dependabot
* build(deps): bump biopython from 1.81 to 1.82 (223) dependabot
* build(deps-dev): bump mypy from 1.7.1 to 1.8.0 (220) dependabot
* build(deps-dev): bump ruff from 0.1.8 to 0.1.9 (221) dependabot
* build(deps): bump pip from 23.3.1 to 23.3.2 in /.github/workflows (218) dependabot
* build(deps-dev): bump psutil from 5.9.6 to 5.9.7 (219) dependabot
* build(deps-dev): bump ruff from 0.1.7 to 0.1.8 (215) dependabot
* build(deps-dev): bump sphinx-immaterial from 0.11.9 to 0.11.10 (213) dependabot
* build(deps-dev): bump delocate from 0.10.6 to 0.10.7 (214) dependabot
* build(deps): bump actions/setup-python from 4 to 5 (212) dependabot
* build(deps-dev): bump ruff from 0.1.6 to 0.1.7 (211) dependabot
* build(deps): bump virtualenv from 20.24.7 to 20.25.0 in /.github/workflows (210) dependabot
* build(deps): bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (209) dependabot
* build(deps-dev): bump scienceplots from 2.1.0 to 2.1.1 (206) dependabot
* build(deps): bump sphinx-autodoc2 from 0.4.2 to 0.5.0 (207) dependabot
* build(deps-dev): bump pybind11-stubgen from 2.4 to 2.4.2 (208) dependabot
* build(deps): bump mashumaro from 3.10 to 3.11 (204) dependabot
* build(deps-dev): bump mypy from 1.7.0 to 1.7.1 (205) dependabot
* build(deps): bump sphinx-click from 5.0.1 to 5.1.0 (203) dependabot
* build(deps): bump virtualenv from 20.24.6 to 20.24.7 in /.github/workflows (196) dependabot
* build(deps-dev): bump delocate from 0.10.5 to 0.10.6 (198) dependabot
* build(deps): bump setuptools from 69.0.0 to 69.0.2 (199) dependabot
* build(deps-dev): bump pytest-xdist from 3.4.0 to 3.5.0 (200) dependabot
* build(deps-dev): bump pybind11-stubgen from 2.3.7 to 2.4 (201) dependabot
* build(deps): bump sphinx-click from 5.0.1 to 5.1.0 (202) dependabot
* build(deps-dev): bump pybind11-stubgen from 2.3.6 to 2.3.7 (193) dependabot
* build(deps-dev): bump ruff from 0.1.5 to 0.1.6 (194) dependabot
* build(deps): bump setuptools from 68.2.2 to 69.0.0 (195) dependabot
* build(deps): bump poetry from 1.7.0 to 1.7.1 in /.github/workflows (192) dependabot
* build(deps-dev): bump delocate from 0.10.4 to 0.10.5 (190) dependabot
* build(deps): bump urllib3 from 2.0.7 to 2.1.0 (188) dependabot
* build(deps-dev): bump sphinx-immaterial from 0.11.8 to 0.11.9 (189) dependabot
* build(deps-dev): bump ruff from 0.1.4 to 0.1.5 (187) dependabot
* build(deps-dev): bump black from 23.10.1 to 23.11.0 (186) dependabot
* build(deps): bump poetry from 1.6.1 to 1.7.0 in /.github/workflows (184) dependabot
* build(deps-dev): bump ruff from 0.1.3 to 0.1.4 (185) dependabot

Changes

* No changes

Bug Fixes

- Fix import error in fa2twobit.py

Documentation

- Update installation.md with bug reporting information
- Update tutorial.md and pyproject.toml files

Miscellaneous Tasks

- Comment out dependency installation step
- Remove unnecessary steps
- Update release.yml and pyproject.toml files
- Update Python version requirements
- Add Python 3.8 to python_versions
- Update Python version and import annotations
- Update test matrix
- Update release and test workflow
- Update Python version requirement
- Comment out unnecessary code in release.yml
- Remove build_wheels_linux step
- Update pypa/cibuildwheel to v2.16.2
- Update build_wheels_linux and build_wheels_macos configurations
- Update version to 1.1.8
- Update Python versions and dependencies
- Update release workflow
- Update find_lib.py script
- Update release.yml to remove unnecessary code

Refactor

- Remove unnecessary code and add RAISE_ERROR flag
- Remove unused variables and print statements
- Refactor setup.py code
- Comment out unnecessary code lines

Styling

- Update code style badge
- Import fix

Build

- Remove unnecessary build configurations
- Remove numpy dependency
- Remove htsliib dependency
- Update many Linux images for the macOS job

Changes

* No changes