test failure with biopython 1.80

[emollier]

Hi,

While introducing biopython 1.80 in Debian experimental, I noticed in Debian Bug#1024835 that pauvre fails when trying to run test suites with:

$ python3 -m unittest discover -v

The error log shows:

Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py", line 636, in <module>
    main()
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py", line 630, in main
    args.func(parser, args)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/pauvre_main.py", line 62, in run_subtool
    import pauvre.synplot as submodule
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_pauvre/build/pauvre/synplot.py", line 46, in <module>
    import Bio.SubsMat.MatrixInfo as MI
ModuleNotFoundError: No module named 'Bio.SubsMat'

This seems to be related to the module Bio.SubsMat being unmaintained in biopython since 1.75; it is quite possible it has been removed in version 1.80. Their NEWS.rst states regarding version 1.75:

A new module substitution_matrices was added to Bio.Align, which includes an Array class that can be used as a substitution matrix. As the Array class is a subclass of a numpy array, mathematical operations can be applied to it directly, and C code that makes use of substitution matrices can directly access the numerical values stored in the substitution matrices. This module is intended as a replacement of Bio.SubsMat, which is currently unmaintained.

In hope this helps, Étienne.

[nileshpatra]

/cc: @conchoecia

[emollier]

Thanks for merging the patch. I guess the issue can be closed now.

Have a nice day, :) Étienne.