Build wheels for Python 3.12

[peterjc]

Would like to make Python 3.12 wheels for Biopyton 1.81

See also biopython/biopython#4312 which will also need this.

[peterjc]

Hmm. Good news, Windows OK although not trying Python 3.12 yet:

10 wheels produced in 12 minutes:
  biopython-1.81-cp310-cp310-win32.whl       2,623 kB
  biopython-1.81-cp310-cp310-win_amd64.whl   2,657 kB
  biopython-1.81-cp311-cp311-win32.whl       2,623 kB
  biopython-1.81-cp311-cp311-win_amd64.whl   2,657 kB
  biopython-1.81-cp37-cp37m-win32.whl        2,623 kB
  biopython-1.81-cp37-cp37m-win_amd64.whl    2,656 kB
  biopython-1.81-cp38-cp38-win32.whl         2,623 kB
  biopython-1.81-cp38-cp38-win_amd64.whl     2,657 kB
  biopython-1.81-cp39-cp39-win32.whl         2,623 kB
  biopython-1.81-cp39-cp39-win_amd64.whl     2,657 kB
creating virtual environment...

Bad news, Linux breaking on testing cp39-manylinux_i686 wheel when it appears to try to install numpy-1.26.1.tar.gz from source (!)

Worse news, this isn't targetting Python 3.12 - cross reference #17, suspect we would have to update cibuildwheel and drop Python 3.7 support (which we're doing anyway in Biopython 1.82)

[peterjc]

Python 3.12 will probably want cibuildwheel v2.16.2 https://cibuildwheel.readthedocs.io/en/stable/changelog/ (latest release from earlier this month) if targetting the final release.

Note v2.14.0 dropped support for running under Python 3.7, but still should be able to build it (how?)

[peterjc]

OK, not as many i686 as before but passes:

7 wheels produced in 12 minutes:
  biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                 3,011 kB
  biopython-1.81-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                 3,021 kB
  biopython-1.81-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                  2,974 kB
  biopython-1.81-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl   2,940 kB
  biopython-1.81-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                   3,020 kB
  biopython-1.81-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl    2,985 kB
  biopython-1.81-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                   3,010 kB

 10 wheels produced in 13 minutes:
  biopython-1.81-cp310-cp310-win32.whl       2,623 kB
  biopython-1.81-cp310-cp310-win_amd64.whl   2,657 kB
  biopython-1.81-cp311-cp311-win32.whl       2,623 kB
  biopython-1.81-cp311-cp311-win_amd64.whl   2,657 kB
  biopython-1.81-cp37-cp37m-win32.whl        2,623 kB
  biopython-1.81-cp37-cp37m-win_amd64.whl    2,656 kB
  biopython-1.81-cp38-cp38-win32.whl         2,623 kB
  biopython-1.81-cp38-cp38-win_amd64.whl     2,657 kB
  biopython-1.81-cp39-cp39-win32.whl         2,623 kB
  biopython-1.81-cp39-cp39-win_amd64.whl     2,657 kB

5 wheels produced in 13 minutes:
  biopython-1.81-cp310-cp310-macosx_10_9_x86_64.whl   2,621 kB
  biopython-1.81-cp311-cp311-macosx_10_9_x86_64.whl   2,621 kB
  biopython-1.81-cp37-cp37m-macosx_10_9_x86_64.whl    2,620 kB
  biopython-1.81-cp38-cp38-macosx_10_9_x86_64.whl     2,621 kB
  biopython-1.81-cp39-cp39-macosx_10_9_x86_64.whl     2,621 kB

Not actually any more useful though ;)

[peterjc]

Good, will merge this and update PyPI shortly:

8 wheels produced in 10 minutes:
  biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                 3,011 kB
  biopython-1.81-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                 3,021 kB
  biopython-1.81-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                 3,034 kB
  biopython-1.81-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                  2,974 kB
  biopython-1.81-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl   2,940 kB
  biopython-1.81-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                   3,020 kB
  biopython-1.81-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl    2,985 kB
  biopython-1.81-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl                                   3,010 kB

etc.

i.e. We've gained some Python 3.12 wheels, but 32-bit Linux Python 3.9 wheels no longer build.

[peterjc]

Red cross shown here as I cancelled the redundant push run (the PR run worked).

Anyway, post merging https://github.com/biopython/biopython-wheels/actions/runs/6631252001/job/18014368302 worked fine. Artifact downloaded, unzipped, and and new wheels uploaded:

$ twine upload --skip-existing biopython-1.81-*
Uploading distributions to https://upload.pypi.org/legacy/
WARNING  Skipping biopython-1.81-cp310-cp310-macosx_10_9_x86_64.whl because it appears to already exist       
WARNING  Skipping biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl because it appears
         to already exist                                                                                     
WARNING  Skipping biopython-1.81-cp310-cp310-win32.whl because it appears to already exist                    
WARNING  Skipping biopython-1.81-cp310-cp310-win_amd64.whl because it appears to already exist                
WARNING  Skipping biopython-1.81-cp311-cp311-macosx_10_9_x86_64.whl because it appears to already exist       
WARNING  Skipping biopython-1.81-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl because it appears
         to already exist                                                                                     
WARNING  Skipping biopython-1.81-cp311-cp311-win32.whl because it appears to already exist                    
WARNING  Skipping biopython-1.81-cp311-cp311-win_amd64.whl because it appears to already exist                
Uploading biopython-1.81-cp312-cp312-macosx_10_9_x86_64.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB • 00:01 • 1.9 MB/s
Uploading biopython-1.81-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB • 00:06 • 495.0 kB/s
Uploading biopython-1.81-cp312-cp312-win32.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB • 00:01 • 1.4 MB/s
Uploading biopython-1.81-cp312-cp312-win_amd64.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB • 00:01 • 1.5 MB/s
WARNING  Skipping biopython-1.81-cp37-cp37m-macosx_10_9_x86_64.whl because it appears to already exist        
WARNING  Skipping biopython-1.81-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl because it appears 
         to already exist                                                                                     
WARNING  Skipping                                                                                             
         biopython-1.81-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.w
         hl because it appears to already exist                                                               
WARNING  Skipping biopython-1.81-cp37-cp37m-win32.whl because it appears to already exist                     
WARNING  Skipping biopython-1.81-cp37-cp37m-win_amd64.whl because it appears to already exist                 
WARNING  Skipping biopython-1.81-cp38-cp38-macosx_10_9_x86_64.whl because it appears to already exist         
WARNING  Skipping biopython-1.81-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl because it appears  
         to already exist                                                                                     
WARNING  Skipping                                                                                             
         biopython-1.81-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.wh
         l because it appears to already exist                                                                
WARNING  Skipping biopython-1.81-cp38-cp38-win32.whl because it appears to already exist                      
WARNING  Skipping biopython-1.81-cp38-cp38-win_amd64.whl because it appears to already exist                  
WARNING  Skipping biopython-1.81-cp39-cp39-macosx_10_9_x86_64.whl because it appears to already exist         
WARNING  Skipping biopython-1.81-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl because it appears  
         to already exist                                                                                     
WARNING  Skipping biopython-1.81-cp39-cp39-win32.whl because it appears to already exist                      
WARNING  Skipping biopython-1.81-cp39-cp39-win_amd64.whl because it appears to already exist                  

View at:
https://pypi.org/project/biopython/1.81/

Checksums:

$ md5sum biopython-1.81-cp312-cp312-*
ebb3738e07022733810da3022ddeb563 biopython-1.81-cp312-cp312-macosx_10_9_x86_64.whl
583db4f806c5dc143dcdde1841c586e3 biopython-1.81-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
a906dde5cabe6a02fd1a724ea6ba602c biopython-1.81-cp312-cp312-win32.whl
022b7b367a3c40ee3db191dfdf8b26d3 biopython-1.81-cp312-cp312-win_amd64.whl

$ shasum -a 256 biopython-1.81-cp312-cp312-*
175fcddc9f22a070aa6db54755d60c4b31090cc39f5f5f4b0a9a5d1ae3b45cd7  biopython-1.81-cp312-cp312-macosx_10_9_x86_64.whl
9ec149487f3d1e0cf2b52b6071641c161ed545b0855ff51a71506152e14fc5bb  biopython-1.81-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
daeab15274bbcc0455cbd378636e14f53bc7c5b1f383e77021d7222e72cc3418  biopython-1.81-cp312-cp312-win32.whl
22f5741aca91af0a76c0d5617e58e554fd3374bbd16e0c0ac1facf45b107313b  biopython-1.81-cp312-cp312-win_amd64.whl