[Biopython] Biopython 1.82 released

Tue Jan 9 09:12:46 EST 2024

Good question Mauricio ,

We did have some alpha releases before v1.0, and there were
some "d" suffixes back in the v0.9 days (I do not know what the
"d" meant). And there have been a couple of beta releases.
So in short, no good precedent to follow here.

I can see a case for 1.82.1 here, indeed I had been wondering if
1.82.post1 would be more sensible than 1.83, see
https://peps.python.org/pep-0440/

On balance though, I am inclined to keep it simple go for 1.83 here.

Peter

On Tue, Jan 9, 2024 at 1:17 PM Mauricio Herrera Cuadra
<mauricio at arareko.net> wrote:
>
> Hi Peter,
>
> Just out of curiosity, has there ever been patch releases, in semantic version style, for BioPython? Maybe 1.83 is the way to go due to historical reasons but I’m wondering if 1.82.1 for this specific revert could be appropriate?
>
> Mauricio
>
>
> On Mon, Jan 8, 2024 at 4:14 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> 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 <p.j.a.cock at googlemail.com> 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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