Copy MOTHUR input files to temp dir instead of working dir.


git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1115 4565cf14-4326-0410-8d81-eccf4396eebe
Added new mc_t_two_sample function to compute Monte Carlo permutations for a two-sample t-test.

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1116 4565cf14-4326-0410-8d81-eccf4396eebe
Added name_unnamed to multifurcating()


git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1117 4565cf14-4326-0410-8d81-eccf4396eebe
added tests for name_unnamed in multifurcating()


git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1118 4565cf14-4326-0410-8d81-eccf4396eebe
updated doc to reflect change in error message

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1119 4565cf14-4326-0410-8d81-eccf4396eebe
fixed doctest, displayed values not matching due to numerical precision

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1120 4565cf14-4326-0410-8d81-eccf4396eebe
updated doctests, tolerance for precision and changes to asciiArt display

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1121 4565cf14-4326-0410-8d81-eccf4396eebe
fix doctest, numerical precision issue

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1122 4565cf14-4326-0410-8d81-eccf4396eebe
fix doctests, numerical precision differences

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1123 4565cf14-4326-0410-8d81-eccf4396eebe
fix doctest, update to accomodate numpy change of displaying NaN as nan

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1124 4565cf14-4326-0410-8d81-eccf4396eebe
doctest fix, numerical precision issue

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1125 4565cf14-4326-0410-8d81-eccf4396eebe
fix doctest, display order of seqs changed

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1126 4565cf14-4326-0410-8d81-eccf4396eebe
fix regression in progressive align

[NEW] Tree.bifurcating now has the name_unnamed argument, matching the API of
	multifurcating
[FIXED] TreeAlign now uses the name_unnamed argument to as the likelihood code
	all assumes tree nodes to be named.
[FIXED] Added a test of TreeAlign that also estimates the tree.

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1127 4565cf14-4326-0410-8d81-eccf4396eebe
fix doctest, order of seqs changed in printed repr

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1128 4565cf14-4326-0410-8d81-eccf4396eebe
mod the TreeAlign test so more stable

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1129 4565cf14-4326-0410-8d81-eccf4396eebe
fix some typos in the documentation

Thanks to Ben Kaehler for pointing these out!

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1130 4565cf14-4326-0410-8d81-eccf4396eebe
updated ckd3 to accomodate changes in numpy

[FIXED] Numpy changes the behaviour of a C macro based on the
	detected Python version. That macro is included in Cython
	and, in some circumstances, breaks the PyCogent build.
	The (backward compatible) fix is to tell the macro what
	behaviour to have.
[CHANGED] Updated all C files generated from Cython using Cython 0.16

Thanks to Ben Kaehler for finding this and providing the patch!

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1131 4565cf14-4326-0410-8d81-eccf4396eebe
cogent.draw.distribution_plots now uses matplotlib proxy Artists for legend creation (this simplifies the code a bit). Added ability to set the size of plot figures through two new optional parameters to generate_box_plots and generate_comparative_plots. matplotlib's new tight_layout() functionality is now used instead of our homegrown version of tight_layout(), and more robust checks have been put in place in case it fails (which does happen sometimes).

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1132 4565cf14-4326-0410-8d81-eccf4396eebe
Updated my name to be consistent with other occurrences.

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1133 4565cf14-4326-0410-8d81-eccf4396eebe
removed code tagged for being discontinued prior to release

[CHANGED] the last remnant of using reportlab now gone

git-svn-id: https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk@1134 4565cf14-4326-0410-8d81-eccf4396eebe