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Changelog

All notable changes to this project will be documented in this file.

[1.2.0] - 2024-05-15

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

[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

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 openssl@3 using Homebrew

Build_wheels_macos

  • Enable build_wheels_macos_arm64

[1.1.1] - 2023-10-27

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

[1.1.0] - 2023-10-27

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

[1.0.3] - 2023-10-27

Documentation

  • Update README.md with documentation links and instructions
  • Update URLs in README and pyproject.toml
  • Update changelog for v1.0.1

Miscellaneous Tasks

  • Update upload_to_test_pypi step
  • Add update command in Makefile
  • Add concurrency settings for workflows
  • Update version to 1.0.1
  • Update version to 1.0.2
  • Update version to 1.0.2
  • Update version to 1.0.3

Styling

  • Update ruff-pre-commit to v0.1.3

Build

  • Remove depdendency

[1.0.0] - 2023-10-25

Bug Fixes

  • Validate two_bit file before starting server
  • Fix logic bug in _cpsl function

Documentation

  • Update version number to v0.3.10
  • Update installation guide and compatibility matrix
  • Rewrite toturial
  • Update tutorial and conf.py
  • Add code example for turorial
  • Update README.md
  • Polish tutorial
  • Update link in tutorial
  • Update tutorial.md with proper Python script execution and comments
  • Add CLI documentation link to tutorial.md

Features

  • Add optional parameters to Server constructor
  • Add new options for starting the server
  • Add server option 'can stop' and 'step size'
  • Add documentation for Client class and methods
  • Add Pure Python BLAT code for creating our own BLAT

Miscellaneous Tasks

  • Bump actions/checkout from 3 to 4
  • Bump virtualenv in /.github/workflows
  • Bump docker/setup-qemu-action from 2 to 3
  • Bump pypa/cibuildwheel from 2.12.3 to 2.16.2
  • Update .pre-commit-config.yaml and pyproject.toml
  • Add platform badge to README.md
  • Remove unused code and properties
  • Update release workflow configuration
  • Update version to 1.0.0

Styling

  • Remove unnecessary parentheses and simplify code
  • Update code style badge URL

Build

  • Update python dependencies

Chroe

  • Update dependencies

[0.3.10] - 2023-10-24

Features

  • Update version to 0.3.10

[0.3.9] - 2023-10-24

Features

  • Update version to 0.3.9

Miscellaneous Tasks

  • Update version to 0.3.8

[0.3.7] - 2023-10-24

Features

  • Add tests for Python 3.11 and 3.12 on macOS
  • Update supported Python versions

Miscellaneous Tasks

  • Remove unnecessary OS Independent classifier
  • Update release workflow and dependencies
  • Update CIBW_BEFORE_ALL command in release.yml
  • Update package installation command
  • Update build dependencies
  • Update cibw_build and cibw_archs configurations
  • Update CIBW_BEFORE_ALL command
  • Update release.yml and pyproject.toml configurations
  • Update manylinux x86_64 image version
  • Update cibw_build and cibw_archs values
  • Remove commented out code and unused steps
  • Update test command in release.yml
  • Update release workflow
  • Update tests.yml configuration
  • Update Python version range
  • Update python dependency
  • Update version to 0.3.7

Refactor

  • Update python version requirement and add numpy dependency

Testing

  • Importing tests

Build

  • Add sdist artifact to release workflow
  • Update CIBW_BEFORE_ALL command
  • Update build dependencies
  • Use manylinux1 image and skip musllinux builds
  • Add Homebrew dependencies and configure
  • Update setuptools requirement
  • Update python version

Ci

  • Upgrade Python version to 3.11

[0.3.6] - 2023-10-23

Styling

  • Update pyproject.toml version and license

Build

  • Remove numpy dependency

[0.3.5] - 2023-10-23

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
  • Bump release-drafter/release-drafter from 5.24.0 to 5.25.0
  • 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

[0.3.4] - 2023-10-11

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

[0.3.2] - 2023-09-01

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

[0.3.1] - 2023-08-22

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

[0.3.0] - 2023-07-27

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)
  • Bump release-drafter/release-drafter from 5.23.0 to 5.24.0
  • 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

[0.2.0] - 2023-06-13

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

[0.1.6] - 2023-05-27

Bug Fixes

  • Add path

Documentation

  • Customiza document

[0.1.5] - 2023-05-26

Documentation

  • Add doc draft

Miscellaneous Tasks

  • Bump sphinx-click from 4.3.0 to 4.4.0 in /docs
  • Bump pybind11-stubgen from 0.13.0 to 0.14.0

[0.1.4] - 2023-05-26

Features

  • Fallback to use source code

Miscellaneous Tasks

  • Bump sphinx from 5.3.0 to 7.0.1 in /docs
  • Bump linkify-it-py from 2.0.0 to 2.0.2 in /docs
  • Bump sphinx-click from 4.3.0 to 4.4.0 in /docs (#9)
  • Bump myst-parser from 0.18.1 to 1.0.0 in /docs (#8)
  • Bump pybind11-stubgen from 0.13.0 to 0.14.0
  • Bump ruff from 0.0.263 to 0.0.270 (#5)
  • Bump invoke from 2.1.1 to 2.1.2 (#6)
  • Bump setuptools from 67.7.2 to 67.8.0 (#4)
  • Bump actions/checkout from 2 to 3
  • Bump docker/build-push-action from 3 to 4
  • Update changelog, bump version to 0.1.4 in pyproject.toml

Build

  • Refactor build script

[0.1.3] - 2023-05-25

Bug Fixes

  • Fix the bug that make result consistent with c
  • It is optional to output file when client
  • Use strong type for status and add test

Documentation

  • Add descriptions to the make targets

Features

  • Complie for gfClient and gfServer
  • Complie for blat
  • Rename directory
  • Add py binding
  • Add header guide for cpp
  • Add binging for gfServer
  • Implement cpp gfserver
  • Refactor gfserver binding
  • Create static lib
  • Fix c code error from cxx compiler
  • Add start sever in cpp
  • Add test for python
  • Use invoke
  • Add more ruff rule
  • Do not abort when check status
  • Add bindings
  • Add native python for client
  • Change client binding
  • Foramt files
  • Avoide global variable
  • Pass extra parameter
  • Add debug printer
  • Add boolean parameter to dynamicServerQuery and errorSafeQuery functions
  • Use binder
  • Add docker for binder
  • Use binder
  • Update binding
  • Add Signal class to init.pyi
  • Use thread pool for every client
  • Rename macro round to cround
  • Splite handle client func
  • Finish one-thread-per-client mode
  • Rename pyblat to pxblat
  • Create cli application
  • Creat cli application
  • Refactor cli
  • Refactor cli
  • Add benchmark data
  • Use sequences as client input
  • Add test for fatotwobit
  • Implement server
  • Add test for client and server
  • Finish test and add bencharmk
  • Refactor server
  • Refactor test
  • Improve buffer size for client to hold more content
  • Add plot script
  • Test for performance
  • Prepare to public
  • Add binder code
  • Add docs draft

Miscellaneous Tasks

  • Comment out removal of binder files
  • Add git add . command to commit target in Makefile
  • Update TODO list with new tasks and mark parser gfclient result as completed

Refactor

  • Add options for gfserver
  • Add cpp binding
  • Comment out unused logInfo calls and replace uglyf calls with dbg calls