Re: [Biopython] Biopython 1.82 released

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Peter Cock reacted via Gmail
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On Tue, Jan 9, 2024 at 2:53 PM Mauricio Herrera Cuadra <[email protected]>
wrote:

> I’m definitely more inclined towards keeping it simple as you mention. I’d
> think changing the way versioning is done can only be worthy of a separate
> conversation if people that are more involved in the project think it is.
>
> Thanks,
> Mauricio
>
> On Tue, Jan 9, 2024 at 3:12 PM Peter Cock <[email protected]>
> wrote:
>
>> 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
>> <[email protected]> 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 <[email protected]>
>> 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 <[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
>> >> _______________________________________________
>> >> Biopython mailing list  -  [email protected]
>> >> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>

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