Upgrading obsolete code to deprecated code
SearchIO hmmer3-text: Don't overload the hit_list variable with different datatypes

No functional change, just a rename of a variable to make the code less confusing

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
SearchIO: Add optionalcascade getter/setter to allow Hit objects without HSPs

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
SearchIO hmmer3-text: HSP entries can be empty for valid hits

This should fix bug #3400 and still needs a test

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Fix stray comma
ElementTree deprecated getchildren in Python 2.7
Fix test_bgzf.py under Python 3 (use text mode handle)
Phylo: in to_networkx, use float edge weights (Bug #3405)

Bug reported by Aleksey Kladov: https://redmine.open-bio.org/issues/3405
Allow Jython 2.5 failures on TravisCI

TODO - Work out if and how to fix Jython installation under TravisCI once again
Remove deprecated private function in SFF code
Mention Ion Torrent in SffIO docstring
Fix typo in error message
Fix typo in blastall wrapper
Add new Blast 2.2.27+ arguments to wrappers
Ignore new blastx arguments if testing with old BLAST+
BLAST 2.2.27+ dropped -frame_shift_penalty argument
Remove deprecated Bio.File.StringHandle and SGMLStripper

Also removes Bio.ParserSupport.SGMLStrippingConsumer
Remove centre setters, add explicit deprecation warning to getters.

i.e. This change makes the deprecated aliases read only, and adds an
explicit warning when reading the values. Previously only got a warning
on setting the value via the deprecated alias.
Clarify docstrings of deprecated BLAST functions.

No code changes, don't need TravisCI to test this: [ci skip]
Avoid ResourceWarning: unclosed file in these doctests