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Remove deprecated Bio.HMM#5009

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peterjc wants to merge 1 commit intobiopython:masterfrom
peterjc:drop_hmm
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Remove deprecated Bio.HMM#5009
peterjc wants to merge 1 commit intobiopython:masterfrom
peterjc:drop_hmm

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@peterjc peterjc commented Jun 17, 2025

See #4544 for why there wasn't a top level deprecation warning.

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peterjc commented Jun 17, 2025

Looks like something is amiss on Windows-2019 Python 3.13 (unrelated to this change), LINK : fatal error LNK1104: cannot open file 'python313t.lib'

Looks like https://docs.python.org/3.13/whatsnew/3.13.html#whatsnew313-free-threaded-cpython is somehow being enabled...

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Let's keep an empty Bio/HMM/init.py for now.

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peterjc commented Jun 17, 2025

OK then...

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mdehoon commented Jun 19, 2025

Looks like https://docs.python.org/3.13/whatsnew/3.13.html#whatsnew313-free-threaded-cpython is somehow being enabled...

This seems.to be related:
actions/setup-python#1123

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peterjc commented Jun 21, 2025

That does look like the Windows issue - thanks.

Shall we merge this now?

We still have an empty `Bio.HMM`, see biopython#4544
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peterjc commented Jul 11, 2025

Rebased to check the CI issues are resolved.

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codecov bot commented Jul 11, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.32%. Comparing base (1b5e9cc) to head (b1819b2).
⚠️ Report is 80 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #5009      +/-   ##
==========================================
+ Coverage   85.47%   86.32%   +0.84%     
==========================================
  Files         286      282       -4     
  Lines       59907    59442     -465     
==========================================
+ Hits        51207    51311     +104     
+ Misses       8700     8131     -569     

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