Pxblat

Documentation

- Remove unnecessary section in README.md

Miscellaneous Tasks

- Update version to 0.3.4
- Update dependencies
- Bump pip from 23.2.1 to 23.3 in /.github/workflows
- Bump psutil from 5.9.5 to 5.9.6
- Update dependencies

Features

- Add pr_agent.yml workflow for pull requests and comments

Miscellaneous Tasks

- Remove unnecessary lines from README.md
- Bump virtualenv in /.github/workflows
- Bump ruff from 0.0.286 to 0.0.287
- Bump pytest from 7.4.0 to 7.4.1
- Bump pybind11-stubgen from 1.2 to 2.0.2 (128)
- Bump loguru from 0.7.0 to 0.7.1
- Bump actions/checkout from 3 to 4
- Bump pybind11-stubgen from 2.0.2 to 2.1
- Bump setuptools from 68.1.2 to 68.2.0
- Bump pytest from 7.4.1 to 7.4.2
- Bump crazy-max/ghaction-github-labeler from 4.2.0 to 5.0.0
- Bump black from 23.7.0 to 23.9.1
- Bump virtualenv in /.github/workflows
- Bump ruff from 0.0.287 to 0.0.288
- Bump mashumaro from 3.9.1 to 3.10
- Bump setuptools from 68.2.1 to 68.2.2
- Bump sphinx from 7.2.5 to 7.2.6
- Bump rich from 13.5.2 to 13.5.3
- Bump ruff from 0.0.288 to 0.0.290
- Bump pybind11-stubgen from 2.1 to 2.2
- Bump ruff from 0.0.290 to 0.0.291
- Bump pybind11-stubgen from 2.2 to 2.2.1
- Bump pybind11-stubgen from 2.2.1 to 2.2.2
- Bump pybind11-stubgen from 2.2.2 to 2.3
- Bump sphinx-autoapi from 2.1.1 to 3.0.0 (153)
- Bump rich from 13.5.3 to 13.6.0
- Bump seaborn from 0.12.2 to 0.13.0 (156)
- Bump ruff from 0.0.291 to 0.0.292
- Bump ipython from 8.15.0 to 8.16.1
- Bump pysam from 0.21.0 to 0.22.0
- Update version to 0.3.3
- Bump mypy from 1.5.1 to 1.6.0
- Update dependencies and version numbers

Miscellaneous Tasks

- Bump sphinxcontrib-bibtex from 2.5.0 to 2.6.1
- Bump ruff from 0.0.285 to 0.0.286
- Bump sphinx from 7.2.2 to 7.2.4
- Bump pybind11-stubgen from 0.16.2 to 1.1
- Bump pybind11-stubgen from 1.1 to 1.2
- Bump crazy-max/ghaction-github-labeler from 4.1.0 to 4.2.0
- Update version to 0.3.2

Refactor

- Simplify code in client.py and server.py
- Simplify nested loop for printing hsps in client query

Build

- Update pre-commit and typos dependencies

Documentation

- Update docuemnt for CLIs
- Add FAQ for installing PxBLAT on MacOS Arm
- Update citation link in README.md
- Update README.md
- Update contributors and pre-commit config versions
- Add documentation for `create_client_option` function
- Add example files for users to try
- Update README.md with more detailed explanation

Features

- Add version information to CLI output
- Update version to 0.3.1

Miscellaneous Tasks

- Update lock file
- Update sys.path in conf.py
- Cerate figures for paper
- Bump rich from 13.4.2 to 13.5.0
- Bump ruff from 0.0.280 to 0.0.281
- Bump numpy from 1.25.1 to 1.25.2
- Bump rich from 13.5.0 to 13.5.1
- Bump ruff from 0.0.281 to 0.0.282
- Bump rich from 13.5.0 to 13.5.2 (95)
- Bump mashumaro from 3.8.1 to 3.9
- Update repository link in README.md
- Bump ruff from 0.0.282 to 0.0.283
- Bump ruff from 0.0.283 to 0.0.284
- Bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10
- Bump mypy from 1.4.1 to 1.5.0
- Bump virtualenv in /.github/workflows
- Bump setuptools from 68.0.0 to 68.1.0
- Bump mypy from 1.5.0 to 1.5.1
- Bump sphinx-click from 4.4.0 to 5.0.1
- Bump ruff from 0.0.284 to 0.0.285 (109)
- Bump sphinx-immaterial from 0.11.6 to 0.11.7
- Bump setuptools from 68.1.0 to 68.1.2
- Bump sphinx-click from 4.4.0 to 5.0.1 in /docs
- Cache pip packages and Poetry virtual environment
- Remove Docker workflow configuration
- Update pre-commit hooks versions
- Bump poetry from 1.5.1 to 1.6.0 in /.github/workflows
- Bump poetry from 1.6.0 to 1.6.1 in /.github/workflows
- Update test workflow configuration
- Bump sphinx from 7.1.2 to 7.2.2

Refactor

- Remove unnecessary import statement
- Assign version info to query result

Styling

- Simplify code formatting and remove unnecessary lines
- Change port number in tutorial code example

Testing

- Add benchmark result for hsp compared to BLAT

Build

- Add caching for macOS dependencies

Ci

- Update crate-ci/typos to v1.16.8

Bug Fixes

- Find free port in specified range
- Fix file existence check in query method

Documentation

- Update Sphinx configuration and requirements
- Remove autodoc2 and update API generation groups
- Use ruff docs
- Remove d417
- Add rst prolog and python highlighting
- Add references and annotations to conf.py and tutorial.md
- Update Sphinx configuration and requirements
- Remove autodoc2 and update API generation groups
- Use ruff docs
- Remove d417
- Add rst prolog and python highlighting
- Add references and annotations to conf.py and tutorial.md
- Update README.md [skip ci]
- Update .all-contributorsrc [skip ci]
- Fix the error of docs build
- Update API example in README.md
- Draft a tutorial

Features

- Add test_gevent.py
- Implemt new client and add tests
- Change query api to be more friendly and use gevent to implement query
- Make `__repr__` equals to `__str__`
- Add fa_to_two_bit function and update tutorial.md
- Add static method create_option()

Miscellaneous Tasks

- Remove obsolete test_pickle file
- Remove obsolete test_pickle file
- Add/update pre-commit and commitizen config
- Add commitizen and update pre-commit hooks
- Bump myst-parser from 1.0.0 to 2.0.0
- Bump myst-parser from 1.0.0 to 2.0.0 in /docs
- Update version to v0.2.0 and add example in README
- Bump ruff from 0.0.272 to 0.0.274
- Bump setuptools from 67.8.0 to 68.0.0
- Bump invoke from 2.1.2 to 2.1.3
- Bump ruff from 0.0.274 to 0.0.275
- Bump mashumaro from 3.7 to 3.8
- Bump mashumaro from 3.8 to 3.8.1
- Bump pytest from 7.3.2 to 7.4.0
- Update lock file
- Remove unnecessary MACHTYPE variable assignment
- Bump ruff from 0.0.275 to 0.0.276
- Bump pybind11-stubgen from 0.15.1 to 0.16.1 (60)
- Bump sphinx-immaterial from 0.11.4 to 0.11.5 (59)

Bug Fixes

- Update urllib3 version to 1.26.9

Documentation

- Add logo
- Update contact information in epilog
- Add installation guide for prerequisites
- Add tutorial and CLI usage to docs
- Update CLI list in usage.md
- Add installation instructions for pxblat
- Update README.md [skip ci]
- Create .all-contributorsrc [skip ci]
- Add tutorial and CLI usage to docs
- Update CLI list in usage.md
- Add installation instructions for pxblat
- Update CLI usage and add completion command
- Update FAQ heading in installation.md

Features

- Add twoBitToFa conversion function
- Draft new features
- Finish cpp implementation
- Add twobit2fa.py script and CLI arguments
- Add linkcheck to build docs
- Finish twobit2fa cpp
- Add twoBitToFa module and bind it in \_extc.cpp
- Add PXBLATLIB macro to escape unused code
- Add support for twobittofa command
- Add twoBitToFa conversion function
- Draft new features
- Finish cpp implementation
- Add twobit2fa.py script and CLI arguments
- Add linkcheck to build docs
- Finish twobit2fa cpp
- Add twoBitToFa module and bind it in \_extc.cpp
- Add PXBLATLIB macro to escape unused code
- Add support for twobittofa command

Miscellaneous Tasks

- Update aicommits to use conventional type
- Bump deprecated from 1.2.13 to 1.2.14
- Bump urllib3 from 1.26.9 to 2.0.2
- Bump pybind11-stubgen from 0.14.0 to 0.15.0 (15)
- Bump poetry from 1.5.0 to 1.5.1 in /.github/workflows
- Bump scienceplots from 2.0.1 to 2.1.0
- Bump rich from 13.3.5 to 13.4.1
- Bump sphinx-immaterial from 0.11.3 to 0.11.4
- Bump ipython from 8.13.2 to 8.14.0
- Update pull_request configuration and remove empty line
- Add search_source to Makefile commands
- Bump urllib3 from 1.26.9 to 2.0.2
- Bump ruff from 0.0.270 to 0.0.271 (32)
- Bump ruff from 0.0.271 to 0.0.272
- Bump urllib3 from 2.0.2 to 2.0.3 (34)
- Remove 2to3 binary on macOS build workflow
- Rename directories and update tasks
- Remove unnecessary file for macos-latest build
- Update lock file
- Remove unnecessary file in Install Dependencies script
- Remove unused code and update comments
- Remove unused Python IDLE3 binary
- Update installation.md and tests.yml files
- Update tests.yml and README.md
- Bump pybind11-stubgen from 0.15.0 to 0.15.1 (38)
- Bump pytest from 7.3.1 to 7.3.2 (37)
- Bump sphinx-autoapi from 2.1.0 to 2.1.1 (36)
- Remove urllib3 dependency
- Update version to 0.2.0 and change log

Refactor

- Add udcDir option to twoBitToFa() function
- Add udcDir option to twoBitToFa() function
- Rename gfClientOption to ClientOption
- Rename gfServerOption to ServerOption
- Throw exceptions instead of aborting
- Remove unnecessary horizontal lines and update installation instructions in README.md

Styling

- Remove commented code in twoBitToFa.hpp
- Update file path in test_server.py
- Remove commented code in twoBitToFa.hpp
- Update file path in test_server.py
- Remove blank line in README.md
- Fix capitalization of executable names
- Remove comments and emphasize headings in installation.md
- Remove unnecessary commented lines and update dependencies in tests.yml, fix a typo in tutorial.md
- Update macOS dependencies installation command and update README features section
- Update font weights in CSS file

Testing

- Add test for twobit2fa
- Add test for twobit2fa
- Add blat suit as benchmark
- Test correct result with blat suit

Ci

- Fix peotry