Re: [Biopython] Planning the Biopython 1.84 release

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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=E2=80=AFAM Peter Cock <[email protected]=
om>
wrote:

> I am working on the release now, forgot I didn't have LaTeX on this machi=
ne
> 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=E2=80=AFAM Peter Cock <p.j.a.cock@googlemai=
l.com>
> wrote:
>
>> I've been working on this (as have Michiel, Jo=C3=A3o, 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 mo=
re
>> surprises!
>>
>> Peter
>>
>> On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock <p.j.a.cock@googlemai=
l.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 ta=
ckle
>>> 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 hav=
e
>>> lots of code using NumPy, including C code, which was a major concern a=
s
>>> 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 interoperabil=
ity,
>>> so I believe that does not affect us. What does affect us are changes t=
o
>>> the NumPy scalar repr output, which means a lot of the documentation te=
sts
>>> 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 no=
t
>>> 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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<div dir=3D"ltr"><div>Nearly there, the Biopython 1.84 release is on PyPI n=
ow.</div><div><br></div><div>One open question, what should I call the new =
PDF for the archive here:</div><div><a href=3D"https://github.com/biopython=
/DIST/tree/gh-pages/docs/tutorial">https://github.com/biopython/DIST/tree/g=
h-pages/docs/tutorial</a></div><div><br></div><div>Historically it was base=
d on Tutorial.pdf and Tutorial.html, but now</div><div>we have Biopython_do=
c.pdf reflecting the fact this combines the old</div><div>&quot;Tutorial an=
d Cookbook&quot; and the &quot;API Documentation&quot;.<br></div><div><br><=
/div><div>md5 checksums:</div><div><br></div><div>$ md5sum biopython-1.84.t=
ar.gz biopython-1.84*.whl<br>92e639d2f3627759f12f0d000131c24d =C2=A0biopyth=
on-1.84.tar.gz<br>2d121260dc6acc5d0abbd5f9f32bc70a =C2=A0biopython-1.84-cp3=
10-cp310-macosx_10_9_x86_64.whl<br>6819b274d250b5a9d4dea7bdf40bf77b =C2=A0b=
iopython-1.84-cp310-cp310-macosx_11_0_arm64.whl<br>af78716df05afd11a550d92f=
af647cf5 =C2=A0biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux20=
14_x86_64.whl<br>4e81ecdff61d2fac377af1958bfbcdc5 =C2=A0biopython-1.84-cp31=
0-cp310-win32.whl<br>dd6a434bf1c1c7af66ef890b0d43d398 =C2=A0biopython-1.84-=
cp310-cp310-win_amd64.whl<br>d471893df22b6198924f48b96c5c86fc =C2=A0biopyth=
on-1.84-cp311-cp311-macosx_10_9_x86_64.whl<br>54fe09ad0c76ed1d5223694704566=
99b =C2=A0biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl<br>d47b8a1d0c5dc=
6fc66ba6c86773d02f9 =C2=A0biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.=
manylinux2014_x86_64.whl<br>1b9e7f5024a47bc17d1f122494bc4ec9 =C2=A0biopytho=
n-1.84-cp311-cp311-win32.whl<br>45c924f7245b1a136304d0a17b6e64f6 =C2=A0biop=
ython-1.84-cp311-cp311-win_amd64.whl<br>2296549d1a73b86968bf8af049a3ffde =
=C2=A0biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl<br>c2b8d56c26ac5ef1=
1dcf07097dbdf6da =C2=A0biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl<br>=
8ce75d3e2935829082c7e6fbe5e6eaab =C2=A0biopython-1.84-cp312-cp312-manylinux=
_2_17_x86_64.manylinux2014_x86_64.whl<br>a2fae5789c1d911948c55c63efe5b72c =
=C2=A0biopython-1.84-cp312-cp312-win32.whl<br>1a72201772c299dd6a4c4f4e825ea=
829 =C2=A0biopython-1.84-cp312-cp312-win_amd64.whl<br>1e268eff35f32b7c0c829=
296a0527a45 =C2=A0biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl<br>249a1c=
92cbed3a645cc17878564baacf =C2=A0biopython-1.84-cp39-cp39-macosx_11_0_arm64=
.whl<br>a2bdc8f02dd45e6616b5385138d1b8ff =C2=A0biopython-1.84-cp39-cp39-man=
ylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>310b7676c7ad2528a6ee10f97471=
f9c0 =C2=A0biopython-1.84-cp39-cp39-win32.whl<br>76161614a81816de4d206b45aa=
02eb87 =C2=A0biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br></div><di=
v>And sha-256 checksums:</div><div><br></div><div>$ sha256sum =C2=A0biopyth=
on-1.84.tar.gz biopython-1.84*.whl<br>60fbe6f996e8a6866a42698c17e552127d99a=
9aab3259d6249fbaabd0e0cc7b4 =C2=A0biopython-1.84.tar.gz<br>3c8beded38884aba=
e4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b =C2=A0biopython-1.84-cp310=
-cp310-macosx_10_9_x86_64.whl<br>b51ef31bfb79872a182a85b4113625e1b553c024bb=
1586c72ac98b479f8d8fe4 =C2=A0biopython-1.84-cp310-cp310-macosx_11_0_arm64.w=
hl<br>2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4 =C2=
=A0biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l<br>4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad =C2=
=A0biopython-1.84-cp310-cp310-win32.whl<br>9e3f7476fd81f31e048965d7be2826f0=
18686e870d96870f440b609002953954 =C2=A0biopython-1.84-cp310-cp310-win_amd64=
.whl<br>2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4 =
=C2=A0biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl<br>c792508988fc3ccf=
18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c =C2=A0biopython-1.84-cp311=
-cp311-macosx_11_0_arm64.whl<br>894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2=
170753d101a13e7585ff4 =C2=A0biopython-1.84-cp311-cp311-manylinux_2_17_x86_6=
4.manylinux2014_x86_64.whl<br>7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b=
2fbab26e9467706603f =C2=A0biopython-1.84-cp311-cp311-win32.whl<br>2cb8e839a=
b472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20 =C2=A0biopython-1.8=
4-cp311-cp311-win_amd64.whl<br>ba58a6d76288333c5f178a426116953fa68204bd0cfc=
401694087dd4f96d0059 =C2=A0biopython-1.84-cp312-cp312-macosx_10_9_x86_64.wh=
l<br>ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae =C2=
=A0biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl<br>61765b71f84814a1eeb5=
5ab222f43330aa7ad3e55ab91e8b444706149c67a281 =C2=A0biopython-1.84-cp312-cp3=
12-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>52b6098f47d6b90fc8a5e8=
579b81ee50047e9108f0976e69c891ae0c4817e42d =C2=A0biopython-1.84-cp312-cp312=
-win32.whl<br>ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f73=
96c =C2=A0biopython-1.84-cp312-cp312-win_amd64.whl<br>f4c1c9ad7da9eaf8d8f45=
15bf931a7f6548a468e7ef29b8429e31aaff2d95f4c =C2=A0biopython-1.84-cp39-cp39-=
macosx_10_9_x86_64.whl<br>9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce562=
6ffa8976d170da7 =C2=A0biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl<br>7b6=
9d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089 =C2=A0biopyth=
on-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>25f4ef1=
93a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e =C2=A0biopython-1=
.84-cp39-cp39-win32.whl<br>b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4=
813376855b479118 =C2=A0biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br=
></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail=
_attr">On Fri, Jun 28, 2024 at 2:46=E2=80=AFAM Peter Cock &lt;<a href=3D"ma=
ilto:[email protected]">[email protected]</a>&gt; wrote:<br=
></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;=
border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><=
div>I am working on the release now, forgot I didn&#39;t have LaTeX on this=
 machine</div><div>which we still need for a PDF version of the Tutorial (t=
his is the first release</div><div>to use Sphinx and RST for the Tutorial, =
rather than LaTeX directly).</div><div><br></div><div>Please don&#39;t upda=
te the master branch until the release is done.<br></div><div><br></div><di=
v>Peter<br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" clas=
s=3D"gmail_attr">On Wed, Jun 26, 2024 at 11:37=E2=80=AFAM Peter Cock &lt;<a=
 href=3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock@goo=
glemail.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=
=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding=
-left:1ex"><div dir=3D"ltr"><div>I&#39;ve been working on this (as have Mic=
hiel,=C2=A0Jo=C3=A3o,  and others), and still hope to do the release very s=
oon.</div><div><br></div><div>Touch wood the numpy 2.0.0 work is done. Righ=
t now I&#39;m fixing a minor regression with the new scipy 1.14.0 release, =
and hoping there are no more surprises!<br></div><div><br></div><div>Peter<=
br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gma=
il_attr">On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock &lt;<a href=3D"=
mailto:[email protected]" target=3D"_blank">[email protected]=
om</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margi=
n:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex=
"><div dir=3D"ltr"><div>Hello all,</div><div><br></div><div>I would have li=
ked to tackle the release sooner, but things have been busy at work. Howeve=
r, I will be on leave soon and should be able to tackle the Biopython 1.84 =
in early June.</div><div><br></div><div>That will be about six months worth=
 of changes, including dropping Python 3.8 support and deprecating Python 3=
.9 support.<br></div><div><br></div><div>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&#39;re only using the buf=
fer 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 me=
ans a lot of the documentation tests in Biopython 1.63 fail. We have addres=
sed those already, and the tests now pass on a recent NumPy v1 and on the v=
2 release candidate. i.e. I am not aware of any blocking issues relating to=
 NumPy for our next release.</div><div><br></div><div>Are there any outstan=
ding issues which the community feels need to be addressed prior to our rel=
ease?</div><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div></d=
iv>
</blockquote></div>
</blockquote></div>
</blockquote></div>

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Biopython mailing list  -  [email protected]
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