v0.14.0

Breaking Changes

• Dropped support for Python 3.8 .

Major Changes

• Added support for Python 3.14 .
• Updated list of wheels uploaded to PyPI:
  • dropped PyPy 3.9, PyPy 3.10, and all 32-bit Linux wheels
  • added PyPy 3.11, and free-threaded wheels for CPython 3.14

Other Changes

• Migrated from setup.cfg to pyproject.toml .
• Added testing with mypy.
• Fixed new black, ruff, flake8 and mypy errors.

Please report any bug you may encounter using these new free-threaded cp314t wheels!

Full Changelog: v0.13.0...v0.14.0

v0.13.0

Breaking Changes

• Remove psyco, it is only available for Python <= 2.6 by @mr-c and @tillea in #96
• Remove unused bx.cookbook.progress_bar module

Bug Fixes

• Fix import statement s/cookbook/bx.cookbook/ by @mr-c and @tillea in #95
• Decode C string to str. Fix galaxyproject/galaxy#18806 .

Other Changes

• Add support for Python 3.13
• Remove unneeded build-system requirement wheel
• Stop vendoring argparse and pyparsing
• Add linting with ruff and several ruff plugins

Full Changelog: v0.12.0...v0.13.0

v0.12.0

What's Changed

• Add pytest 8.x compatibility by @mr-c in #92
• Allow post install testing by @mr-c in #93
• Fix include for strlen() by @mr-c in #94
• Re-enable doctesting of C extension modules by @nsoranzo in 2e46af6
• Support NumPy 2.0 by @nsoranzo in 335ca02
• Build musllinux wheels for Python 3.9-3.11. Skip PyPy wheels on i686 by @nsoranzo in fba2c50

New Contributors

• @mr-c made their first contribution in #92

Full Changelog: v0.11.0...v0.12.0

v0.11.0

Breaking Changes

• Added support for Python 3.12.
• Dropped support for Python 3.7.

Other Changes

• Added musllinux wheels for Python 3.12.
• Restore docs building on https://bx-python.readthedocs.io/

v0.10.0

Breaking Changes

• Added support for Python 3.11.
• Added arm64 macOS wheels. Dropped PyPy 3.7 Linux wheels and all PyPy 3.8 wheels.

Deprecations

• Support for Python 3.7 is deprecated.

Other Changes

• From NumPy 1.24.0 np.float is deprecated by @lldelisle in #90
• Fix exception message by @lldelisle in #89
• Fix compilation with Cython 3 by @mvdbeek in #91

Full Changelog: v0.9.0...v0.10.0

v0.9.0

Breaking Changes

• Index TwoBitFile sequences by str not bytes by @nsoranzo in #85
• Skip building also other musllinux wheels by @nsoranzo in #86

Other Changes

• Fix new E275 linting error by @nsoranzo in #84
• Upgrade GitHub Actions by @cclauss in #83
• Format Python code with black and isort by @nsoranzo in #87

New Contributors

• @cclauss made their first contribution in #83

Full Changelog: v0.8.13...v0.9.0

v0.8.13

What's Changed

• Improve MAF handling by @lldelisle in #77
• Drop support for Python 3.6, add 3.10 by @nsoranzo in 1283016

New Contributors

• @lldelisle made their first contribution in #77

Full Changelog: v0.8.12...v0.8.13

v0.8.12

• Fix .so files not being copied to build and therefore not installed by python setup.py install .
• Distribute aarch64 wheels

v0.8.11

• Build wheels using oldest-supported-numpy instead of the latest numpy. In this way, the generated wheels will be forward-compatible with newer numpy versions
• Remove runtime dependency on setuptools

Other packaging and testing changes:

• Use pyproject.toml to specify build requirements
• Execute build_ext when running sdist.
• Use PyPA build package to build the sdist.
• Move most metadata from setup.py to setup.cfg .
• Test built packages by importing

v0.8.10

• Fix lzop_build_offset_table.py and maf_build_index.py scripts under Python 3. Pull Request #70
• Drop support for Python 2 and 3.5, add 3.9
• Add tox configuration for testing
• Move Continuous Integration from TravisCI to GitHub workflows