[Bug 217269] /science/py-pyteomics: Update to 3.4.1

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=217269

            Bug ID: 217269
           Summary: /science/py-pyteomics: Update to 3.4.1
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: Individual Port(s)
          Assignee: freebsd-ports-bugs at FreeBSD.org
          Reporter: joneum at bsdproject.de

Created attachment 180183
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=180183&action=edit
Patch

http://pythonhosted.org/pyteomics/changelog.html#id1

        Add selenocysteine (“U”) and pyrrolysine (“O”) to
pyteomics.mass.std_aa_mass and pyteomics.mass.std_aa_comp.
        An optional parameter encoding is now accepted by text file readers
(pyteomics.mgf.read() and pyteomics.fasta.read()). This can be useful for MGF
files with non-ASCII spectrum titles or comments.
        New function pyteomics.mass.mass.isotopologues().
        Performance improvements in pyteomics.electrochem.pI().
        Fix the issue in pyteomics.xml which resulted in very long processing
times for indexed XML files with a byte ordering mark (BOM).
        Support all standard and non-standard data array names in
pyteomics.mzml.
        Change default value of retrieve_refs in pyteomics.mzid.read() to True.
        Preserve unit information extracted from cvParam tags in PSI XML files.
        Fix in pyteomics.mzxml, other minor fixes.


poudriere build fine for:
10.3 amd + i386
11.0 amd + i386
12-current amd + i386 (r313761)

portlint is also fine.


Cheers
jochen

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