[Biopython] Planning the Biopython 1.84 release

[Peter Cock]

Nearly there, the Biopython 1.84 release is on PyPI now.

One open question, what should I call the new PDF for the archive here:
https://github.com/biopython/DIST/tree/gh-pages/docs/tutorial

Historically it was based on Tutorial.pdf and Tutorial.html, but now
we have Biopython_doc.pdf reflecting the fact this combines the old
"Tutorial and Cookbook" and the "API Documentation".

md5 checksums:

$ md5sum biopython-1.84.tar.gz biopython-1.84*.whl
92e639d2f3627759f12f0d000131c24d  biopython-1.84.tar.gz
2d121260dc6acc5d0abbd5f9f32bc70a
 biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl
6819b274d250b5a9d4dea7bdf40bf77b
 biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl
af78716df05afd11a550d92faf647cf5
 biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
4e81ecdff61d2fac377af1958bfbcdc5  biopython-1.84-cp310-cp310-win32.whl
dd6a434bf1c1c7af66ef890b0d43d398  biopython-1.84-cp310-cp310-win_amd64.whl
d471893df22b6198924f48b96c5c86fc
 biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl
54fe09ad0c76ed1d522369470456699b
 biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl
d47b8a1d0c5dc6fc66ba6c86773d02f9
 biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
1b9e7f5024a47bc17d1f122494bc4ec9  biopython-1.84-cp311-cp311-win32.whl
45c924f7245b1a136304d0a17b6e64f6  biopython-1.84-cp311-cp311-win_amd64.whl
2296549d1a73b86968bf8af049a3ffde
 biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl
c2b8d56c26ac5ef11dcf07097dbdf6da
 biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl
8ce75d3e2935829082c7e6fbe5e6eaab
 biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
a2fae5789c1d911948c55c63efe5b72c  biopython-1.84-cp312-cp312-win32.whl
1a72201772c299dd6a4c4f4e825ea829  biopython-1.84-cp312-cp312-win_amd64.whl
1e268eff35f32b7c0c829296a0527a45
 biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl
249a1c92cbed3a645cc17878564baacf
 biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl
a2bdc8f02dd45e6616b5385138d1b8ff
 biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
310b7676c7ad2528a6ee10f97471f9c0  biopython-1.84-cp39-cp39-win32.whl
76161614a81816de4d206b45aa02eb87  biopython-1.84-cp39-cp39-win_amd64.whl

And sha-256 checksums:

$ sha256sum  biopython-1.84.tar.gz biopython-1.84*.whl
60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4
 biopython-1.84.tar.gz
3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b
 biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl
b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4
 biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl
2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4
 biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad
 biopython-1.84-cp310-cp310-win32.whl
9e3f7476fd81f31e048965d7be2826f018686e870d96870f440b609002953954
 biopython-1.84-cp310-cp310-win_amd64.whl
2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4
 biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl
c792508988fc3ccf18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c
 biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl
894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a13e7585ff4
 biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f
 biopython-1.84-cp311-cp311-win32.whl
2cb8e839ab472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20
 biopython-1.84-cp311-cp311-win_amd64.whl
ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4f96d0059
 biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl
ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae
 biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl
61765b71f84814a1eeb55ab222f43330aa7ad3e55ab91e8b444706149c67a281
 biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
52b6098f47d6b90fc8a5e8579b81ee50047e9108f0976e69c891ae0c4817e42d
 biopython-1.84-cp312-cp312-win32.whl
ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c
 biopython-1.84-cp312-cp312-win_amd64.whl
f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c
 biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl
9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da7
 biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl
7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089
 biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
25f4ef193a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e
 biopython-1.84-cp39-cp39-win32.whl
b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b479118
 biopython-1.84-cp39-cp39-win_amd64.whl


On Fri, Jun 28, 2024 at 2:46 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> I am working on the release now, forgot I didn't have LaTeX on this machine
> which we still need for a PDF version of the Tutorial (this is the first
> release
> to use Sphinx and RST for the Tutorial, rather than LaTeX directly).
>
> Please don't update the master branch until the release is done.
>
> Peter
>
> On Wed, Jun 26, 2024 at 11:37 AM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> I've been working on this (as have Michiel, João, and others), and still
>> hope to do the release very soon.
>>
>> Touch wood the numpy 2.0.0 work is done. Right now I'm fixing a minor
>> regression with the new scipy 1.14.0 release, and hoping there are no more
>> surprises!
>>
>> Peter
>>
>> On Wed, May 22, 2024 at 9:39 PM Peter Cock <p.j.a.cock at googlemail.com>
>> wrote:
>>
>>> Hello all,
>>>
>>> I would have liked to tackle the release sooner, but things have been
>>> busy at work. However, I will be on leave soon and should be able to tackle
>>> the Biopython 1.84 in early June.
>>>
>>> That will be about six months worth of changes, including dropping
>>> Python 3.8 support and deprecating Python 3.9 support.
>>>
>>> It is worth noting this coincides with the release of NumPy 2.0. We have
>>> lots of code using NumPy, including C code, which was a major concern as
>>> there are C API breakages with NumPy 2.0. However, rather than the full
>>> NumPy C API, we're only using the buffer API designed for interoperability,
>>> so I believe that does not affect us. What does affect us are changes to
>>> the NumPy scalar repr output, which means a lot of the documentation tests
>>> in Biopython 1.63 fail. We have addressed those already, and the tests now
>>> pass on a recent NumPy v1 and on the v2 release candidate. i.e. I am not
>>> aware of any blocking issues relating to NumPy for our next release.
>>>
>>> Are there any outstanding issues which the community feels need to be
>>> addressed prior to our release?
>>>
>>> Thanks,
>>>
>>> Peter
>>>
>>
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