v1.1.1

Changes

• No changes

v1.1.0

Changes

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

v1.0.3

Changes

• No changes

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

🚀 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.

    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

📚 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.

📦 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!

v0.3.10

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