Pxblat

- Bump ruff from 0.0.292 to 0.1.0
- Bump mypy from 1.6.0 to 1.6.1
- Bump black from 23.9.1 to 23.10.0
- Bump urllib3 from 2.0.4 to 2.0.7
- Update dependencies
- Bump ruff from 0.1.0 to 0.1.1
- Bump pybind11-stubgen from 2.3 to 2.3.4
- Bump pip from 23.3 to 23.3.1 in /.github/workflows
- Update pxblat version to 0.3.5

Styling

- Fix typo in README.md

- Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7
- Bump virtualenv in /.github/workflows
- Bump ruff from 0.0.276 to 0.0.277
- Bump numpy from 1.25.0 to 1.25.1
- Bump nox-poetry from 1.0.2 to 1.0.3
- Bump nox-poetry from 1.0.2 to 1.0.3 in /.github/workflows
- Bump black from 23.3.0 to 23.7.0
- Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8
- Bump virtualenv in /.github/workflows
- Bump pybind11 from 2.10.4 to 2.11.1
- Bump pybind11-stubgen from 0.16.1 to 0.16.2
- Bump pip from 23.1.2 to 23.2 in /.github/workflows
- Bump invoke from 2.1.3 to 2.2.0
- Bump ruff from 0.0.277 to 0.0.278
- Bump ruff from 0.0.278 to 0.0.280
- Bump pip from 23.2 to 23.2.1 in /.github/workflows
- Update pyproject.toml and remove unused timeout parameter
- Bump virtualenv in /.github/workflows
- Update lock files
- Upadte dependencies
- Add sphnix_click as dev dependency
- Bump gevent from 22.10.2 to 23.7.0
- Bump urllib3 from 2.0.3 to 2.0.4 (86)
- Bump gevent from 22.10.2 to 23.7.0
- Remove unused Signal class
- Update version to 0.3.0

Refactor

- Clean up pyproject.toml formatting and remove unused files
- Clean up and optimize client code
- Refactor query_server_by_file method
- Simplify query method and remove unnecessary code
- Split fas on single directory
- Fix typos and formatting in code and documentation
- Simplify error message handling
- Remove unnecessary logger.debug statements
- Remove unused function
- Rename copy function for clarity

Styling

- Fix formatting and spacing in README and installation.md
- Fix formatting and spacing in README and installation.md
- Fix typo in Makefile target name
- Update pre-commit hooks and remove commented code in utils.py
- Enbale more linter rules

Testing

- Add smoke test for set_state function
- Add smoke test for set_state function
- Add new test data
- Add benchmark tests for pxblat results and bpresult and bcresult tests
- Add failing tests
- Add test files to fix the bug about (open too many files)
- Remove unnecessary code
- Rename test_gevent.py to test_client.py

Build

- Update Ruff version to v0.0.276
- Update symbolic links for OpenSSL installation
- Update lock file
- Addd gevent
- Add py-spy dependency

Ci

- Fix ci error
- Make typing annotation to be compatible with py39
- Fix the ci errors of tests
- Fix ci error for tests

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

Build

- Bump setuptools from 69.0.3 to 69.1.0
- Bump ruff from 0.2.1 to 0.2.2
- Bump pytest from 8.0.0 to 8.0.1
- Bump urllib3 from 2.2.0 to 2.2.1
- Bump virtualenv in /.github/workflows
- Bump poetry from 1.7.1 to 1.8.0 in /.github/workflows
- Bump pytest from 8.0.1 to 8.0.2
- Bump setuptools from 69.1.0 to 69.1.1
- Bump rich from 13.7.0 to 13.7.1
- Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12
- Bump poetry from 1.8.0 to 1.8.1 in /.github/workflows
- Bump ruff from 0.2.2 to 0.3.0
- Bump poetry from 1.8.1 to 1.8.2 in /.github/workflows
- Bump nox from 2023.4.22 to 2024.3.2 in /.github/workflows
- Bump pytest from 8.0.2 to 8.1.0
- Bump nox from 2023.4.22 to 2024.3.2
- Bump pybind11-stubgen from 2.4.2 to 2.5
- Bump ruff from 0.3.0 to 0.3.1
- Bump pypa/cibuildwheel from 2.16.5 to 2.17.0
- Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14
- Bump setuptools from 69.1.1 to 69.2.0
- Bump ruff from 0.3.2 to 0.3.3
- Bump ruff from 0.3.3 to 0.3.4
- Bump typer from 0.9.0 to 0.10.0
- Bump delocate from 0.10.7 to 0.11.0 (286)
- Bump typer from 0.10.0 to 0.11.0
- Bump typer from 0.11.0 to 0.11.1
- Bump pybind11-stubgen from 2.5 to 2.5.1
- Bump pybind11 from 2.11.1 to 2.12.0
- Bump typer from 0.11.1 to 0.12.0
- Bump typer from 0.12.0 to 0.12.3
- Bump sphinx-autobuild from 2024.2.4 to 2024.4.13
- Bump ruff from 0.3.4 to 0.3.7
- Bump setuptools from 69.2.0 to 69.5.1
- Bump nox from 2024.3.2 to 2024.4.15
- Bump nox from 2024.3.2 to 2024.4.15 in /.github/workflows
- Bump sphinx-autobuild from 2024.4.13 to 2024.4.16
- Bump virtualenv in /.github/workflows
- Bump sphinx from 7.2.6 to 7.3.6
- Bump virtualenv in /.github/workflows
- Bump sphinx from 7.3.6 to 7.3.7
- Bump ruff from 0.3.7 to 0.4.0
- Bump ruff from 0.4.0 to 0.4.1
- Bump virtualenv in /.github/workflows
- Bump myst-parser from 2.0.0 to 3.0.0 in /docs
- Bump myst-parser from 2.0.0 to 3.0.0
- Bump mypy from 1.9.0 to 1.10.0
- Bump ruff from 0.4.1 to 0.4.2
- Bump virtualenv in /.github/workflows
- Bump myst-parser from 3.0.0 to 3.0.1 in /docs
- Bump pytest from 8.1.1 to 8.2.0
- Bump pytest-xdist from 3.5.0 to 3.6.1
- Bump myst-parser from 3.0.0 to 3.0.1
- Bump mashumaro from 3.12 to 3.13
- Bump poetry from 1.8.2 to 1.8.3 in /.github/workflows
- Bump virtualenv in /.github/workflows
- Bump sphinx-click from 5.1.0 to 5.2.2
- Update pre-commit hooks and dependencies

Ci

- Add step to check current directory

Bug Fixes

- Fix import error in fa2twobit.py

Documentation

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

Features

- Update version to 1.1.2
- Add skip test for macOS arm64 in CI workflow
- Add script to find library path
- Use setuppy
- Install cibuildwheel and build wheels
- Remove setuppy

Miscellaneous Tasks

- Comment out dependency installation step
- Remove unused code
- 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
- Bump version to 1.1.3
- Update Python version requirement
- Bump version to 1.1.4
- Bump version to 1.1.5
- Update version to 1.1.6
- Update version to 1.1.7
- 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 file
- Update release.yml to remove unnecessary code
- Update release.yml file
- Update version to 1.1.9

Refactor

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

Styling

- Update code style badge
- Import fix

Build

- Add DYLD_LIBRARY_PATH to delocate commands
- Remove unnecessary build configurations
- Remove numpy dependency
- Update manylinux images for macOS job
- Update cibw_build options and delocate-wheel command
- Update macOS deployment target to 12.0
- Add delocate as a dependency for cibuildwheel
- Update macOS version and architecture for cibuildwheel
- Configure Homebrew and Install Dependencies
- Install openssl3 using Homebrew

Build_wheels_macos

- Enable build_wheels_macos_arm64

Features

- Add find_openssl_libs() function

Miscellaneous Tasks

- Update version to 1.1.1

Styling

- Remove unused library "z"

Ci

- Update release workflow to skip if no tag

Bug Fixes

- Uncomment "hts" external library

Features

- Update version to 1.1.0

Miscellaneous Tasks

- Remove unused external library
- Remove unnecessary installation of htslib and update OpenSSL dependencies

Refactor

- Comment out unused code in build.py and linefile.c

Build

- Update package dependencies and installation