v1.2.1

Changes

Bug Fixes

• Update sphinx-immaterial version to ^0.11.11

Features

• Add build_index function to generate precomputed index

Miscellaneous Tasks

• Remove pysam for dev dependencies
• Add workflow step for listing workflows folder

Styling

• Update pipx install commands in tests workflow
• Update Poetry and Nox installation commands
• Add type ignore to deprecated import

📦 Dependencies

• build(deps): bump sphinx-click from 5.1.0 to 5.2.2 (#328) @dependabot
• build(deps): bump virtualenv from 20.26.1 to 20.26.2 in /.github/workflows (#327) @dependabot
• build(deps): bump poetry from 1.8.2 to 1.8.3 in /.github/workflows (#323) @dependabot
• build(deps): bump mashumaro from 3.12 to 3.13 (#320) @dependabot
• build(deps): bump myst-parser from 3.0.0 to 3.0.1 (#321) @dependabot
• build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1 (#316) @dependabot
• build(deps-dev): bump pytest from 8.1.1 to 8.2.0 (#317) @dependabot
• build(deps): bump myst-parser from 3.0.0 to 3.0.1 in /docs (#318) @dependabot
• build(deps): bump virtualenv from 20.26.0 to 20.26.1 in /.github/workflows (#319) @dependabot
• build(deps-dev): bump ruff from 0.4.1 to 0.4.2 (#314) @dependabot
• build(deps-dev): bump mypy from 1.9.0 to 1.10.0 (#313) @dependabot
• build(deps): bump myst-parser from 2.0.0 to 3.0.0 (#310) @dependabot
• build(deps): bump myst-parser from 2.0.0 to 3.0.0 in /docs (#311) @dependabot
• build(deps): bump virtualenv from 20.25.3 to 20.26.0 in /.github/workflows (#312) @dependabot
• build(deps-dev): bump ruff from 0.4.0 to 0.4.1 (#309) @dependabot
• build(deps-dev): bump ruff from 0.3.7 to 0.4.0 (#307) @dependabot
• build(deps): bump sphinx from 7.3.6 to 7.3.7 (#308) @dependabot
• build(deps): bump virtualenv from 20.25.2 to 20.25.3 in /.github/workflows (#305) @dependabot
• build(deps): bump sphinx from 7.2.6 to 7.3.6 (#306) @dependabot
• build(deps): bump virtualenv from 20.25.1 to 20.25.2 in /.github/workflows (#302) @dependabot
• build(deps-dev): bump sphinx-autobuild from 2024.4.13 to 2024.4.16 (#303) @dependabot
• build(deps): bump nox from 2024.3.2 to 2024.4.15 in /.github/workflows (#300) @dependabot
• build(deps-dev): bump nox from 2024.3.2 to 2024.4.15 (#301) @dependabot
• build(deps): bump setuptools from 69.2.0 to 69.5.1 (#298) @dependabot
• build(deps-dev): bump ruff from 0.3.4 to 0.3.7 (#297) @dependabot
• build(deps-dev): bump sphinx-autobuild from 2024.2.4 to 2024.4.13 (#299) @dependabot
• build(deps): bump typer from 0.12.0 to 0.12.3 (#296) @dependabot
• build(deps): bump typer from 0.11.1 to 0.12.0 (#292) @dependabot
• build(deps): bump pybind11 from 2.11.1 to 2.12.0 (#289) @dependabot
• build(deps-dev): bump pybind11-stubgen from 2.5 to 2.5.1 (#290) @dependabot
• build(deps): bump typer from 0.11.0 to 0.11.1 (#291) @dependabot
• build(deps): bump typer from 0.10.0 to 0.11.0 (#288) @dependabot
• build(deps-dev): bump delocate from 0.10.7 to 0.11.0 (#286) @dependabot
• build(deps): bump typer from 0.9.0 to 0.10.0 (#287) @dependabot
• build(deps-dev): bump ruff from 0.3.3 to 0.3.4 (#285) @dependabot
• build(deps-dev): bump ruff from 0.3.2 to 0.3.3 (#284) @dependabot
• build(deps): bump setuptools from 69.1.1 to 69.2.0 (#283) @dependabot
• build(deps): bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#276) @dependabot
• build(deps): bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#281) @dependabot
• build(deps-dev): bump ruff from 0.3.0 to 0.3.1 (#275) @dependabot
• build(deps-dev): bump pybind11-stubgen from 2.4.2 to 2.5 (#274) @dependabot
• build(deps-dev): bump nox from 2023.4.22 to 2024.3.2 (#270) @dependabot
• build(deps-dev): bump pytest from 8.0.2 to 8.1.0 (#271) @dependabot
• build(deps): bump nox from 2023.4.22 to 2024.3.2 in /.github/workflows (#272) @dependabot
• build(deps): bump poetry from 1.8.1 to 1.8.2 in /.github/workflows (#273) @dependabot
• build(deps-dev): bump ruff from 0.2.2 to 0.3.0 (#269) @dependabot
• build(deps): bump poetry from 1.8.0 to 1.8.1 in /.github/workflows (#266) @dependabot
• build(deps): bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#267) @dependabot
• build(deps): bump rich from 13.7.0 to 13.7.1 (#268) @dependabot
• build(deps): bump setuptools from 69.1.0 to 69.1.1 (#263) @dependabot
• build(deps-dev): bump pytest from 8.0.1 to 8.0.2 (#264) @dependabot
• build(deps): bump poetry from 1.7.1 to 1.8.0 in /.github/workflows (#265) @dependabot
• build(deps): bump virtualenv from 20.25.0 to 20.25.1 in /.github/workflows (#262) @dependabot
• build(deps): bump urllib3 from 2.2.0 to 2.2.1 (#259) @dependabot
• build(deps-dev): bump pytest from 8.0.0 to 8.0.1 (#260) @dependabot
• build(deps-dev): bump ruff from 0.2.1 to 0.2.2 (#261) @dependabot
• build(deps): bump setuptools from 69.0.3 to 69.1.0 (#258) @dependabot

v1.1.20

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

📦 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

v1.1.19

Changes

• Benchmark (#254) @cauliyang

📦 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

v1.1.18

Changes

• fix #244: Simplify conditional statement in query_server() function (#246) @cauliyang

📦 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

v1.1.10

Changes

• No changes

v1.1.9

Changes

[1.1.9] - 2023-11-01

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

v1.1.8

Changes

• No changes

v1.1.7

Changes

• No changes

v1.1.5

Changes

• No changes

v1.1.2

Changes

• No changes