Re: [Biopython] Biopython 1.82 released

Please note that the Biopython 1.82 release inadvertently removed
the .strand, .ref and .ref_db aliases from the SeqFeature object
(please use .location.strand etc instead) without a deprecation period.
Three people have reported this via GitHub, there are likely other
impacted. Our apologies.

We are looking at a quick Biopython 1.83 release to revert that
(restore the aliases as before) and start their formal deprecation.

See also https://biopython.org/wiki/Deprecation_policy

Peter

On Fri, Dec 22, 2023 at 3:21 PM Peter Cock <[email protected]> wrote:
>
> Dear Biopythoneers,
>
> Our second release of 2023 is now out, albeit way later than we'd all intended.
> The source code tar-ball and pre-compiled wheels for the major platforms
> are all live on PyPI:
>
> https://pypi.org/project/biopython/
>
> We would expect the release to be on conda-forge shortly too.
>
> This contains about 10 months worth of updates, so the NEWS file information
> is denser than usual:
>
> https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst
>
> Also, there have been more deprecations and removals of deprecated code
> than typical - see the DEPRECATED file too:
>
> https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst
>
> Many thanks to the Biopython developers and community for making this
> release possible, especially the following contributors:
>
> Alex Crocker (first contribution)
> Antonio Trande (first contribution)
> Arpan Sahoo (first contribution)
> Benedict Carling (first contribution)
> Cam McMenamie (first contribution)
> Ernesto Rodriguez (first contribution)
> Jacob Byerly (first contribution)
> João Rodrigues
> Joe Greener
> Manuel Lera Ramirez
> Michael R. Crusoe
> Michiel de Hoon
> Peter Cock
> Ricardas Ralys (first contribution)
> Rob Miller
> Thomas Holder
> Tom Eulenfeld (first contribution)
> Vladislav Kuznetsov (first contribution)
> Wibowo Arindrarto
> Yiming Qu (first contribution)
>
> Thank you all, and also those unnamed who have helped indirectly,
> though bug reports or otherwise.
>
> Kind regards,
>
> Peter
>
> --
>
> For reference, the checksum are as follows:
>
> $ md5sum biopython-1.82*
> cb9f9c3ad4929cb91da36bcef6551937
> biopython-1.82-cp310-cp310-macosx_10_9_x86_64.whl
> abe16fb7de1dcc31db2e5bab15bf9b7b
> biopython-1.82-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 38b629efd48c4ca7619ba9b305dad698 biopython-1.82-cp310-cp310-win32.whl
> 1bae03eda37a045f8fc1bb4be27ed7ac biopython-1.82-cp310-cp310-win_amd64.whl
> 7c691a79895a5e9c6b95bb9f778bc9c3
> biopython-1.82-cp311-cp311-macosx_10_9_x86_64.whl
> e2f292eb329f5d067a9d86bab40fe09f
> biopython-1.82-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 32b017abcb740e07aff09675e228ef4d biopython-1.82-cp311-cp311-win32.whl
> 2be8f44b2956e0c7a063a5621f3e6330 biopython-1.82-cp311-cp311-win_amd64.whl
> 1f67c9df8ee17c1af7d1afc53af4fb8c
> biopython-1.82-cp312-cp312-macosx_10_9_x86_64.whl
> 3869b9f3edf4f9719fa6938784778ba9
> biopython-1.82-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 886b20aa3123ed21d1746cd3b6c25f6a biopython-1.82-cp312-cp312-win32.whl
> 30a5171022f7afe00e999e147e82161b biopython-1.82-cp312-cp312-win_amd64.whl
> 449a29b9686122c0ddabedce25e60e6f biopython-1.82-cp38-cp38-macosx_10_9_x86_64.whl
> f9921cdf92a9cfc5cf4decf8267b9897
> biopython-1.82-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> dbf1904d8cfba5da3a4ff084bc685011
> biopython-1.82-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
> 8fb4ecebc37fa2ae3ddfea5ddadc9dc2 biopython-1.82-cp38-cp38-win32.whl
> 2330da915eb35444bf24ecb98ec65e27 biopython-1.82-cp38-cp38-win_amd64.whl
> e0aff6a47d8eea9fa229fb5fdf3d1ba1 biopython-1.82-cp39-cp39-macosx_10_9_x86_64.whl
> fe6f6e3f941be714ae7f8fdb86fe9fc4
> biopython-1.82-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 62c42cd250972b1add6a3b6100541914 biopython-1.82-cp39-cp39-win32.whl
> 3166c4ec614885bc43429850afda5451 biopython-1.82-cp39-cp39-win_amd64.whl
> f0900044ae4c97008992c4a36c66f8e2 biopython-1.82.tar.gz
> 4b9a8a48ff4630dca4a8667912f2ac88 biopython-1.82.zip
>
> $ shasum -a 256 biopython-1.82*
> 713be5e1e8571ea151864544dfcd2637eaf98c67a6e47b69781d325feb02f6b9
> biopython-1.82-cp310-cp310-macosx_10_9_x86_64.whl
> 5bc908e84278bf61ac901a0c1b695c85ce49491957e0ab07e1e2afc216882525
> biopython-1.82-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> f53aff30f01ac9a8aa1fd42dab347a96ee5312945098dfa38f9a5125f6e913fd
> biopython-1.82-cp310-cp310-win32.whl
> 0f3f685a2d85348b8c84c6eebe58a74cef7e1158ac52ae5aa91789436907f0e1
> biopython-1.82-cp310-cp310-win_amd64.whl
> c9bc080b7dc6cd6acbf2576766136e8e54acbcc6b7a29ad8075cb5a73f4cfb97
> biopython-1.82-cp311-cp311-macosx_10_9_x86_64.whl
> c7802b5033edaf34bd2fbd96b87f96999a6808caa0064c91087c7f1340624898
> biopython-1.82-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> ec35893b32458f6fa0c98d5f02d801a5fe76961ac66473455f51c0575562c594
> biopython-1.82-cp311-cp311-win32.whl
> 40297d418bb142a7ea1a47faedc24bbe21b0ba455f3805373264470e5cb6ec5c
> biopython-1.82-cp311-cp311-win_amd64.whl
> 96f77bd6540683c8958e4ebf55b58e8caa26d20db72891915d06670b783e9cdb
> biopython-1.82-cp312-cp312-macosx_10_9_x86_64.whl
> 49b829c2276a0711106663af632c7e203695a5cf082d488d6e10b8aca5ec63e4
> biopython-1.82-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 54a9b200d4960ed2a4ec85faac2124ffa278afa58d22e07e2d15ca7509219ea1
> biopython-1.82-cp312-cp312-win32.whl
> 762547037038d42c9ac98877fc32d4aeba798077129df7790cb178256171a4e5
> biopython-1.82-cp312-cp312-win_amd64.whl
> cb013256742d31e24fd5093d55511f58bc6a93b8ac723d2ca3b33c7904f1ca14
> biopython-1.82-cp38-cp38-macosx_10_9_x86_64.whl
> 16829760fab60ba17141b7a81494fed837c6f29ea28cdcfb3070764c8e8f2ff1
> biopython-1.82-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> c6af82894dd4f736d737fdea62008a19966251ba39aef39a0ce8b41321305ad5
> biopython-1.82-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
> a1ff583b2f8b314a4c2d612aad4f4b73827a5f741b391f3a834b0c192a4f1527
> biopython-1.82-cp38-cp38-win32.whl
> 0198f23776d9cb9d514a797e81a024f486adac973b252a2f4696995a5a163745
> biopython-1.82-cp38-cp38-win_amd64.whl
> c88e9f87d1b07958e7e1e25ff20efced4796daf650e5290692b5c3ff9aebf9d3
> biopython-1.82-cp39-cp39-macosx_10_9_x86_64.whl
> 8e2533db9275c3e1438151260844e7683f91308da320df02a4c28fb7053ea3a9
> biopython-1.82-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 80f48d220b92e747300281602f52e98ec6c537ddd4921b580d9a0368bae05ff5
> biopython-1.82-cp39-cp39-win32.whl
> 73d619611bd7cf9d2ad8b3217b08d3796acfabb765b0771ad2ff7ee2e46a59b0
> biopython-1.82-cp39-cp39-win_amd64.whl
> a9b10d959ae88a9744a91c6ce3601f4c86e7ec41679bc93c29f679218f6167bb
> biopython-1.82.tar.gz
> 05bbfc64b3fadf05c14a09f41c5fa870bbe2a13d352137a0e37216115bf99bd2
> biopython-1.82.zip
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