pxblat -

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

:package: 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

- C
Published by github-actions[bot] almost 2 years ago

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

- C
Published by github-actions[bot] about 2 years ago

pxblat -

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

- C
Published by github-actions[bot] about 2 years ago

pxblat -

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

- C
Published by github-actions[bot] about 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat -

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 buildwheelslinux step
• Update pypa/cibuildwheel to v2.16.2
• Update buildwheelslinux and buildwheelsmacos 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

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat - v1.1.0

Changes

• feat : reduce htslib dependency (#180) @cauliyang

- C
Published by github-actions[bot] over 2 years ago

pxblat - v1.0.3

Changes

• No changes

- C
Published by github-actions[bot] over 2 years ago

pxblat - v1.0.0

Release Notes for Version v1.0.0

We are excited to announce the release of version v1.0.0 of our software. This release brings significant changes, including new features, documentation updates, and miscellaneous tasks. It's important to note that this version is not backward compatible with previous versions. We strongly recommend reviewing the changes and updates before upgrading.

Changes

:rocket: Features

• Pythonic Server (#178): We have introduced a more Pythonic way to interact with the server, enhancing the user experience and making integration with other Python tools and libraries smoother. Thanks to @cauliyang for this significant improvement.

```python

client = Client(
    host=host,
    port=port,
    seq_dir=seq_dir,
    min_score=20,  
    min_identity=90,  
)

with Server(host, port, two_bit, can_stop=True, step_size=5) as server:
    # work() assume work() is your own function that takes time to prepare something
    server.wait_ready()  
    result1 = client.query("ATCG")  

```

For more details please go to https://pxblat.readthedocs.io/en/latest/index.html

:books: Documentation

• Installation Guide and Compatibility Matrix Update (#179): The installation guide has been updated to reflect the latest changes, and the compatibility matrix has been revised for clarity and accuracy. Kudos to @cauliyang for these updates.
• Enhanced Tutorial: The tutorial has been completely rewritten and now includes code examples to provide a more comprehensive and user-friendly guide.

Miscellaneous Tasks

• New Test Data: Additional test data files have enhanced the tutorial experience.
• Configuration Updates: The pre-commit configuration has been updated to exclude tutorial.md from blacken-docs, ensuring the tutorial remains accessible and easy to follow.
• Exclusions Update in pyproject.toml: The pyproject.toml file has been updated to exclude new tutorial data files, keeping the project configuration tidy and well-organized.

:package: Dependencies

• Updated Dependencies: Several dependencies have been updated to their latest versions:
  • pypa/cibuildwheel has been bumped from 2.12.3 to 2.16.2 (#177). Thanks to @dependabot for this update.
  • docker/setup-qemu-action has been bumped from version 2 to 3 (#176). This update was also provided by @dependabot.
  • virtualenv has been bumped from 20.24.5 to 20.24.6 in .github/workflows (#174), and actions/checkout has been updated from version 3 to 4 (#175). Both of these updates were made possible thanks to @dependabot.

Important Notice on Backward Compatibility

This release includes changes that are not backward compatible with previous versions. We strongly recommend you review all the changes detailed in this release note and update your codebase accordingly to make sure you're able to transition smoothly to this new version.

We appreciate your continued support and are here to assist with any questions or issues you may have during the upgrade process. Thank you for being a part of our community!

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Release Notice: Important License Update for pxblat

Dear Users and Contributors,

We hope this message finds you well. We are reaching out to inform you of a significant update regarding the licensing terms of pxblat, a Python library that you have been using or contributing to. This change is crucial for the continued growth and sustainability of our project, and we believe it aligns more closely with our community's values and expectations.

Introduction of the New License:

pxblat is modified from blat, the license is the same as blat. The source code and ecutables are freely available for academic, nonprofit, and personal use. Commercial licensing information is available on the Kent Informatics website (https://kentinformatics.com/).

Effective as of 10/23/2023, all future releases of pxblat will be distributed under the terms of the new license. The adoption of this new license is a strategic decision aimed at respecting the license of blat.

Application to Previous Versions

To maintain consistency and transparency within our community, we have decided to retrospectively apply the new license to all previous versions of pxblat dating back to v0.0.1.

How Does This Affect You?

For Existing Users on Conda and PyPI: The license change affects all versions of pxblat, including those you have installed via Conda or PyPI. Please take a moment to review the new license terms to ensure your continued compliance with the software's usage terms.

For Contributors: We value and appreciate every contribution made to pxblat. Please be aware that this license change also applies retrospectively to past contributions. If you have any questions or concerns regarding this, do not hesitate to reach out to us.

For New Users: Whether you are installing pxblat via Conda or PyPI, all versions are now available under the terms of the new license. We welcome you to our community and encourage you to explore the library under these updated terms.

Acknowledgements

A heartfelt thank you to each and every member of the pxblat community. Your trust, support, and contributions have been pivotal to the growth of this project. We are committed to ensuring that pxblat remains a reliable, open, and thriving resource for everyone.

Thank you for being an essential part of our journey.

Warm regards, Yangyang Li

- C
Published by github-actions[bot] over 2 years ago

pxblat - V0.3.4

Changes

:rocket: Features

• Update virtualenv version from 20.24.3 to 20.24.4 in GitHub workflows (#124) @dependabot

:package: Dependencies

• chore(deps-dev): bump mypy from 1.5.1 to 1.6.0 (#161) @dependabot
• chore(deps-dev): bump pysam from 0.21.0 to 0.22.0 (#160) @dependabot
• chore(deps-dev): bump ipython from 8.15.0 to 8.16.1 (#155) @dependabot
• chore(deps-dev): bump ruff from 0.0.291 to 0.0.292 (#158) @dependabot
• chore(deps-dev): bump seaborn from 0.12.2 to 0.13.0 (#156) @dependabot
• chore(deps): bump rich from 13.5.3 to 13.6.0 (#157) @dependabot
• chore(deps-dev): bump sphinx-autoapi from 2.1.1 to 3.0.0 (#153) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 2.2.2 to 2.3 (#154) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 2.2.1 to 2.2.2 (#152) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 2.2 to 2.2.1 (#150) @dependabot
• chore(deps-dev): bump ruff from 0.0.290 to 0.0.291 (#151) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 2.1 to 2.2 (#149) @dependabot
• chore(deps-dev): bump ruff from 0.0.288 to 0.0.290 (#146) @dependabot
• chore(deps): bump rich from 13.5.2 to 13.5.3 (#147) @dependabot
• chore(deps): bump sphinx from 7.2.5 to 7.2.6 (#145) @dependabot
• chore(deps): bump setuptools from 68.2.1 to 68.2.2 (#143) @dependabot
• chore(deps): bump mashumaro from 3.9.1 to 3.10 (#140) @dependabot
• chore(deps-dev): bump ruff from 0.0.287 to 0.0.288 (#141) @dependabot
• chore(deps): bump virtualenv from 20.24.4 to 20.24.5 in /.github/workflows (#137) @dependabot
• chore(deps-dev): bump black from 23.7.0 to 23.9.1 (#138) @dependabot
• chore(deps): bump crazy-max/ghaction-github-labeler from 4.2.0 to 5.0.0 (#139) @dependabot
• chore(deps-dev): bump pytest from 7.4.1 to 7.4.2 (#136) @dependabot
• chore(deps): bump setuptools from 68.1.2 to 68.2.0 (#135) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 2.0.2 to 2.1 (#134) @dependabot
• chore(deps): bump actions/checkout from 3 to 4 (#132) @dependabot
• chore(deps): bump loguru from 0.7.0 to 0.7.1 (#133) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 1.2 to 2.0.2 (#128) @dependabot
• chore(deps-dev): bump pytest from 7.4.0 to 7.4.1 (#130) @dependabot
• chore(deps-dev): bump ruff from 0.0.286 to 0.0.287 (#131) @dependabot
• Update virtualenv version from 20.24.3 to 20.24.4 in GitHub workflows (#124) @dependabot

- C
Published by github-actions[bot] over 2 years ago

pxblat - V0.3.2

Changes

• refactor: Simplify code in client.py and server.py (#127) @cauliyang

:package: Dependencies

• chore(deps): bump crazy-max/ghaction-github-labeler from 4.1.0 to 4.2.0 (#125) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 1.1 to 1.2 (#126) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.16.2 to 1.1 (#122) @dependabot
• chore(deps): bump sphinx from 7.2.2 to 7.2.4 (#119) @dependabot
• chore(deps-dev): bump ruff from 0.0.285 to 0.0.286 (#120) @dependabot
• chore(deps): bump sphinxcontrib-bibtex from 2.5.0 to 2.6.1 (#121) @dependabot

- C
Published by github-actions[bot] over 2 years ago

pxblat - V0.3.1

Changes

• docs: enhance documentation (#99) @cauliyang
• feat: Add version information to CLI output (#98) @cauliyang

:books: Documentation

• chore: Update pre-commit hooks versions (#112) @cauliyang

:package: Dependencies

• chore(deps): bump sphinx from 7.1.2 to 7.2.2 (#113) @dependabot
• chore(deps): bump poetry from 1.6.0 to 1.6.1 in /.github/workflows (#115) @dependabot
• chore(deps): bump poetry from 1.5.1 to 1.6.0 in /.github/workflows (#114) @dependabot
• chore(deps): bump sphinx-click from 4.4.0 to 5.0.1 in /docs (#107) @dependabot
• chore(deps): bump setuptools from 68.1.0 to 68.1.2 (#111) @dependabot
• chore(deps-dev): bump sphinx-immaterial from 0.11.6 to 0.11.7 (#108) @dependabot
• chore(deps-dev): bump ruff from 0.0.284 to 0.0.285 (#109) @dependabot
• chore(deps): bump sphinx-click from 4.4.0 to 5.0.1 (#110) @dependabot
• chore(deps-dev): bump mypy from 1.5.0 to 1.5.1 (#106) @dependabot
• chore(deps): bump setuptools from 68.0.0 to 68.1.0 (#105) @dependabot
• chore(deps): bump virtualenv from 20.24.2 to 20.24.3 in /.github/workflows (#104) @dependabot
• chore(deps-dev): bump mypy from 1.4.1 to 1.5.0 (#102) @dependabot
• chore(deps): bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10 (#103) @dependabot
• chore(deps-dev): bump ruff from 0.0.283 to 0.0.284 (#101) @dependabot
• chore(deps-dev): bump ruff from 0.0.282 to 0.0.283 (#100) @dependabot
• chore(deps): bump mashumaro from 3.8.1 to 3.9 (#97) @dependabot
• chore(deps): bump rich from 13.5.0 to 13.5.2 (#95) @dependabot
• chore(deps-dev): bump ruff from 0.0.281 to 0.0.282 (#96) @dependabot
• chore(deps): bump rich from 13.5.0 to 13.5.1 (#92) @dependabot
• chore(deps): bump numpy from 1.25.1 to 1.25.2 (#93) @dependabot
• chore(deps-dev): bump ruff from 0.0.280 to 0.0.281 (#94) @dependabot
• chore(deps): bump rich from 13.4.2 to 13.5.0 (#91) @dependabot

- C
Published by github-actions[bot] over 2 years ago

pxblat - V0.3.0

Changes

• docs: add mencian as a contributor for infra (#80) @allcontributors
• build: Update symbolic links for OpenSSL installation (#63) @cauliyang

:rocket: Features

• build(poetry.lock): addd gevent (#64) @cauliyang

:books: Documentation

• Enhance Documents (#88) @cauliyang
• Docs: Update api docs (#40) @cauliyang

:package: Dependencies

• chore(deps): bump gevent from 22.10.2 to 23.7.0 (#89) @dependabot
• chore(deps): bump urllib3 from 2.0.3 to 2.0.4 (#86) @dependabot
• chore(deps): bump gevent from 22.10.2 to 23.7.0 (#87) @dependabot
• chore(deps): bump virtualenv from 20.24.1 to 20.24.2 in /.github/workflows (#84) @dependabot
• chore(deps): bump pip from 23.2 to 23.2.1 in /.github/workflows (#81) @dependabot
• chore(deps-dev): bump ruff from 0.0.278 to 0.0.280 (#82) @dependabot
• chore(deps-dev): bump ruff from 0.0.277 to 0.0.278 (#72) @dependabot
• chore(deps-dev): bump invoke from 2.1.3 to 2.2.0 (#73) @dependabot
• chore(deps): bump pip from 23.1.2 to 23.2 in /.github/workflows (#77) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.16.1 to 0.16.2 (#74) @dependabot
• chore(deps): bump pybind11 from 2.10.4 to 2.11.1 (#78) @dependabot
• chore(deps): bump virtualenv from 20.23.1 to 20.24.1 in /.github/workflows (#79) @dependabot
• chore(deps): bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8 (#71) @dependabot
• chore(deps-dev): bump black from 23.3.0 to 23.7.0 (#70) @dependabot
• chore(deps): bump nox-poetry from 1.0.2 to 1.0.3 in /.github/workflows (#67) @dependabot
• chore(deps-dev): bump nox-poetry from 1.0.2 to 1.0.3 (#68) @dependabot
• chore(deps): bump numpy from 1.25.0 to 1.25.1 (#69) @dependabot
• chore(deps-dev): bump ruff from 0.0.276 to 0.0.277 (#65) @dependabot
• chore(deps): bump virtualenv from 20.23.0 to 20.23.1 in /.github/workflows (#47) @dependabot
• chore(deps): bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 (#56) @dependabot
• chore(deps): bump release-drafter/release-drafter from 5.23.0 to 5.24.0 (#58) @dependabot
• chore(deps-dev): bump sphinx-immaterial from 0.11.4 to 0.11.5 (#59) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.15.1 to 0.16.1 (#60) @dependabot
• chore(deps-dev): bump ruff from 0.0.275 to 0.0.276 (#61) @dependabot
• chore(deps-dev): bump pytest from 7.3.2 to 7.4.0 (#54) @dependabot
• chore(deps): bump mashumaro from 3.8 to 3.8.1 (#55) @dependabot
• chore(deps): bump mashumaro from 3.7 to 3.8 (#52) @dependabot
• chore(deps-dev): bump ruff from 0.0.274 to 0.0.275 (#53) @dependabot
• chore(deps-dev): bump invoke from 2.1.2 to 2.1.3 (#45) @dependabot
• chore(deps): bump setuptools from 67.8.0 to 68.0.0 (#49) @dependabot
• chore(deps-dev): bump ruff from 0.0.272 to 0.0.274 (#50) @dependabot
• chore(deps): bump myst-parser from 1.0.0 to 2.0.0 in /docs (#43) @dependabot
• chore(deps): bump myst-parser from 1.0.0 to 2.0.0 (#41) @dependabot

- C
Published by github-actions[bot] over 2 years ago

pxblat - Refactor

Changes

• test: add blat suit as benchmark (#31) @cauliyang
• Fix CI Error in linux (#30) @cauliyang
• docs: add cauliyang as a contributor for maintenance (#18) @allcontributors

:rocket: Features

• test: test correct result with blat suit (#39) @cauliyang
• docs: Add tutorial and CLI usage to docs (feat #24) (#29) @cauliyang

:package: Dependencies

• chore(deps-dev): bump sphinx-autoapi from 2.1.0 to 2.1.1 (#36) @dependabot
• chore(deps-dev): bump pytest from 7.3.1 to 7.3.2 (#37) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.15.0 to 0.15.1 (#38) @dependabot
• chore(deps-dev): bump urllib3 from 2.0.2 to 2.0.3 (#34) @dependabot
• chore(deps-dev): bump ruff from 0.0.271 to 0.0.272 (#35) @dependabot
• chore(deps-dev): bump ruff from 0.0.270 to 0.0.271 (#32) @dependabot
• chore(deps-dev): bump urllib3 from 1.26.9 to 2.0.2 (#33) @dependabot
• chore(deps-dev): bump ipython from 8.13.2 to 8.14.0 (#23) @dependabot
• chore(deps-dev): bump sphinx-immaterial from 0.11.3 to 0.11.4 (#22) @dependabot
• chore(deps): bump rich from 13.3.5 to 13.4.1 (#21) @dependabot
• chore(deps-dev): bump scienceplots from 2.0.1 to 2.1.0 (#20) @dependabot
• chore(deps): bump poetry from 1.5.0 to 1.5.1 in /.github/workflows (#19) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.14.0 to 0.15.0 (#15) @dependabot
• chore(deps-dev): bump urllib3 from 1.26.9 to 2.0.2 (#16) @dependabot
• chore(deps): bump deprecated from 1.2.13 to 1.2.14 (#17) @dependabot

- C
Published by github-actions[bot] over 2 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] almost 3 years ago

pxblat - Documentation

Changes

:package: Dependencies

• chore(deps-dev): bump pybind11-stubgen from 0.13.0 to 0.14.0 (#13) @dependabot
• chore(deps): bump sphinx-click from 4.3.0 to 4.4.0 in /docs (#12) @dependabot

- C
Published by github-actions[bot] almost 3 years ago

pxblat -

Changes

:package: Dependencies

• chore(deps): bump docker/build-push-action from 3 to 4 (#2) @dependabot
• chore(deps): bump actions/checkout from 2 to 3 (#1) @dependabot
• chore(deps): bump setuptools from 67.7.2 to 67.8.0 (#4) @dependabot
• chore(deps-dev): bump invoke from 2.1.1 to 2.1.2 (#6) @dependabot
• chore(deps-dev): bump ruff from 0.0.263 to 0.0.270 (#5) @dependabot
• chore(deps-dev): bump pybind11-stubgen from 0.13.0 to 0.14.0 (#3) @dependabot
• chore(deps): bump myst-parser from 0.18.1 to 1.0.0 in /docs (#8) @dependabot
• chore(deps): bump sphinx-click from 4.3.0 to 4.4.0 in /docs (#9) @dependabot
• chore(deps): bump linkify-it-py from 2.0.0 to 2.0.2 in /docs (#10) @dependabot
• chore(deps): bump sphinx from 5.3.0 to 7.0.1 in /docs (#11) @dependabot

- C
Published by github-actions[bot] almost 3 years ago

pxblat -

Changes

• No changes

- C
Published by github-actions[bot] almost 3 years ago