Releases | Open Source Science

Breaking Changes

Remove psyco, it is only available for Python <= 2.6 by @mr-c and @tillea in https://github.com/bxlab/bx-python/pull/96
Remove unused bx.cookbook.progress_bar module

Bug Fixes

Fix import statement s/cookbook/bx.cookbook/ by @mr-c and @tillea in https://github.com/bxlab/bx-python/pull/95
Decode C string to str. Fix https://github.com/galaxyproject/galaxy/issues/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: https://github.com/bxlab/bx-python/compare/v0.12.0...v0.13.0

- Python
Published by nsoranzo almost 2 years ago

What's Changed

Add pytest 8.x compatibility by @mr-c in https://github.com/bxlab/bx-python/pull/92
Allow post install testing by @mr-c in https://github.com/bxlab/bx-python/pull/93
Fix include for strlen() by @mr-c in https://github.com/bxlab/bx-python/pull/94
Re-enable doctesting of C extension modules by @nsoranzo in https://github.com/bxlab/bx-python/commit/2e46af6b2954fec38ad1bc85839d812a2dd0919d
Support NumPy 2.0 by @nsoranzo in https://github.com/bxlab/bx-python/commit/335ca029d000d3f030f45ffe8a4e3c4a4b8f729c
Build musllinux wheels for Python 3.9-3.11. Skip PyPy wheels on i686 by @nsoranzo in https://github.com/bxlab/bx-python/commit/fba2c50c7b1d2dcb3f9619c50951f63783ec7b02

New Contributors

@mr-c made their first contribution in https://github.com/bxlab/bx-python/pull/92

Full Changelog: https://github.com/bxlab/bx-python/compare/v0.11.0...v0.12.0

- Python
Published by nsoranzo almost 2 years ago

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/

- Python
Published by nsoranzo over 2 years ago

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 https://github.com/bxlab/bx-python/pull/90
Fix exception message by @lldelisle in https://github.com/bxlab/bx-python/pull/89
Fix compilation with Cython 3 by @mvdbeek in https://github.com/bxlab/bx-python/pull/91

Full Changelog: https://github.com/bxlab/bx-python/compare/v0.9.0...v0.10.0

- Python
Published by nsoranzo almost 3 years ago

Breaking Changes

Index TwoBitFile sequences by str not bytes by @nsoranzo in https://github.com/bxlab/bx-python/pull/85
Skip building also other musslinux wheels by @nsoranzo in https://github.com/bxlab/bx-python/pull/86

Other Changes

Fix new E275 linting error by @nsoranzo in https://github.com/bxlab/bx-python/pull/84
Upgrade GitHub Actions by @cclauss in https://github.com/bxlab/bx-python/pull/83
Format Python code with black and isort by @nsoranzo in https://github.com/bxlab/bx-python/pull/87

New Contributors

@cclauss made their first contribution in https://github.com/bxlab/bx-python/pull/83

Full Changelog: https://github.com/bxlab/bx-python/compare/v0.8.13...v0.9.0

- Python
Published by nsoranzo almost 4 years ago

What's Changed

Improve MAF handling by @lldelisle in https://github.com/bxlab/bx-python/pull/77
Drop support for Python 3.6, add 3.10 by @nsoranzo in https://github.com/bxlab/bx-python/commit/1283016a55ac4e8ced6dc623215ea6d19a18d0a2

New Contributors

@lldelisle made their first contribution in https://github.com/bxlab/bx-python/pull/77

Full Changelog: https://github.com/bxlab/bx-python/compare/v0.8.12...v0.8.13

- Python
Published by nsoranzo over 4 years ago

bx-python - v0.8.12

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

- Python
Published by nsoranzo over 4 years ago

bx-python - 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

- Python
Published by nsoranzo over 5 years ago

bx-python - 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

- Python
Published by nsoranzo over 5 years ago