Regarding the tempfile.mktemp docstring, this security issue already existed because we're reusing the file name -- but this script doesn't run with special privileges anyway, usually, so I don't think we need to worry about it.
…ile line_graph.py created by previous commit extending test_GenomeDiagram.py)
…graphs at x=0
This also fixes the Jython crash on these tests
… to a warning since some real world files seem to have the wrong length in the LOCUS/ID line
…see also Bug 3069)
…r UnknownSeq objects which caused an out of heap space memory error under Jython 2.5.1
…Seq objects which caused an out of heap space memory error under Jython 2.5.1
Taken from docstrings and reworked -- more to do, though.
Otherwise, clades with no descendents are treated as False in "if not clade" -- wrong behavior!
…ied from the PDF output (and for consistency with other chapters)
e.g. Clade(name='foo', branch_length=0.5)
Simplifies PhyloXML.py a bit. Also added more specific __str__s for Phyloxml, Points and Uri. Plus, this removes a kludge from Phylogeny.
…d -verbose in unit test. These seem to be in debug builds only (?), see Bug 3043
…etter from a string (which used to be a list prior to change last month)