Mvisani patch 1

[mvisani]

• I hereby agree to dual licence this and any previous contributions under both
  the Biopython License Agreement AND the BSD 3-Clause License.

• I have read the CONTRIBUTING.rst file, have run pre-commit
  locally, and understand that continuous integration checks will be used to
  confirm the Biopython unit tests and style checks pass with these changes.

• I have added my name to the alphabetical contributors listings in the files
  NEWS.rst and CONTRIB.rst as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

Reduces the time complexity of the UPGMA implementation.

[peterjc]

Test failures:

======================================================================
FAIL: test_upgma (test_TreeConstruction.DistanceTreeConstructorTest)
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Traceback (most recent call last):
  File "/home/circleci/project/biopython-1.82.dev0/Tests/test_TreeConstruction.py", line 235, in test_upgma
    self.assertTrue(Consensus._equal_topology(tree, ref_tree))
AssertionError: False is not true

======================================================================
FAIL: test_upgma_msa (test_TreeConstruction.DistanceTreeConstructorTest)
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Traceback (most recent call last):
  File "/home/circleci/project/biopython-1.82.dev0/Tests/test_TreeConstruction.py", line 226, in test_upgma_msa
    self.assertTrue(Consensus._equal_topology(tree, ref_tree))
AssertionError: False is not true

======================================================================
FAIL: DistanceTreeConstructor (Bio.Phylo.TreeConstruction)
Doctest: Bio.Phylo.TreeConstruction.DistanceTreeConstructor
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Traceback (most recent call last):
  File "/home/circleci/.pyenv/versions/3.9.18/lib/python3.9/doctest.py", line 2205, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.Phylo.TreeConstruction.DistanceTreeConstructor
  File "/home/circleci/.pyenv/versions/3.9.18/lib/python3.9/site-packages/Bio/Phylo/TreeConstruction.py", line 590, in DistanceTreeConstructor

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File "/home/circleci/.pyenv/versions/3.9.18/lib/python3.9/site-packages/Bio/Phylo/TreeConstruction.py", line 613, in Bio.Phylo.TreeConstruction.DistanceTreeConstructor
Failed example:
    print(upgmatree)
Expected:
    Tree(rooted=True)
        Clade(branch_length=0, name='Inner4')
            Clade(branch_length=0.18749999999999994, name='Inner1')
                Clade(branch_length=0.07692307692307693, name='Epsilon')
                Clade(branch_length=0.07692307692307693, name='Delta')
            Clade(branch_length=0.11057692307692304, name='Inner3')
                Clade(branch_length=0.038461538461538464, name='Inner2')
                    Clade(branch_length=0.11538461538461536, name='Gamma')
                    Clade(branch_length=0.11538461538461536, name='Beta')
                Clade(branch_length=0.15384615384615383, name='Alpha')
Got:
    Tree(rooted=True)
        Clade(branch_length=0, name='Inner4')
            Clade(name='Inner1')
                Clade(name='Epsilon')
                Clade(name='Delta')
            Clade(name='Inner3')
                Clade(name='Inner2')
                    Clade(name='Beta')
                    Clade(name='Alpha')
                Clade(name='Gamma')
----------------------------------------------------------------------
File "/home/circleci/.pyenv/versions/3.9.18/lib/python3.9/site-packages/Bio/Phylo/TreeConstruction.py", line 649, in Bio.Phylo.TreeConstruction.DistanceTreeConstructor
Failed example:
    print(upgmatree)
Expected:
    Tree(rooted=True)
        Clade(branch_length=0, name='Inner4')
            Clade(branch_length=0.18749999999999994, name='Inner1')
                Clade(branch_length=0.07692307692307693, name='Epsilon')
                Clade(branch_length=0.07692307692307693, name='Delta')
            Clade(branch_length=0.11057692307692304, name='Inner3')
                Clade(branch_length=0.038461538461538464, name='Inner2')
                    Clade(branch_length=0.11538461538461536, name='Gamma')
                    Clade(branch_length=0.11538461538461536, name='Beta')
                Clade(branch_length=0.15384615384615383, name='Alpha')
Got:
    Tree(rooted=True)
        Clade(branch_length=0, name='Inner4')
            Clade(name='Inner1')
                Clade(name='Epsilon')
                Clade(name='Delta')
            Clade(name='Inner3')
                Clade(name='Inner2')
                    Clade(name='Beta')
                    Clade(name='Alpha')
                Clade(name='Gamma')


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Do the tests still work for you locally?