Added warning message when os.rmdir cannot remove temporary training directory.
Fix pairwise.py version check in absence of compiled modules

This addresses Issue #9 "QIIME dev does not play nice with PyCogent dev"
Issue warning via warnings module instead of sys.stdout
Merge pull request #4 from kylebittinger/prevent-rdp-oserror

Added warning message when os.rmdir cannot remove temporary training dir
[bug fixed]: name.py might parse wrong when the species name has more than 2 words (e.g. Mustela putorius furo)
Merge pull request #10 from pm67nz/master

A fix for Issue #9 "QIIME dev does not play nice with PyCogent dev"
added a test into test_ensembl/test_host.py to check if it correctly parses a db name that contains a three words species name.
Merge pull request #12 from Skylersun/master

[FIXED]: name.py might parse wrong when the species name has more than 2 words
allow migrating alignement gaps when seqs of same length

[NEW] replaceSeqs has aa_to_codon argument, defaulting to True. This state
    allows inserting gaps from an alignment of aa's into DNA sequence alignment.
    When aa_to_codon is False, ungapped sequences must be the same length.
    Useful for getting annotations from genomes onto sliced syntenic alignments.
modify cookbook example to show aln.replaceSeqs(seqs, aa_to_codons=True) usage
gitignore tests/test_draw.py output files
Tidy up some of the drawing code a bit
Cope with zero-height sequence drawings

With a long, ungapped, featureless sequence, there is actually nothing to draw, but surrounding code still wants to know the size and scale of it.
Merge pull request #14 from pm67nz/master

Drawing code tidy and fixes for when there are no tracks to draw.
enable custom feature creation for genbank parsing

[NEW] RichGenbankParser gets a add_annotation argument. This is a user specified
    callback function fort constructing annotations. This is useful for handling
    incomplete feature specifications for less well characterised genomes.
    Usage is documented in the cookbook.
RichGenbankParser correctly adds rc features

[FIXED] spans for reverse complemented features were being incorrectly reversed.
    This has been fixed and a test file and associetaed test added.
cannot inherit from annotation _Feature

[CHANGED] adding a test to expose problems with inheriting from
    cogent.core.annotation._Feature. Many methods are hard-wired to return
    a _Feature class instance. This patch just introduces a test demonstrating
    this issue. A fix is in the next patch.
support subclassing of _Feature

[FIXED] patch that improves support for inheriting from _Feature. This patch
    allows the test introduced in the previous patch to pass.
Bug fixes for t_two_sample and mc_t_two_sample.

Fixed bug in cogent.maths.stats.test.t_two_sample that returned a t-statistic with the wrong sign if the first distribution contained multiple values and the second distribution contained only a single value (this was validated against R's t.test). Unit test has been updated accordingly.

cogent.maths.stats.test.mc_t_two_sample now handles distributions (as well as permuted distributions) without variance (in the past it would crash with an uninformative error message in these cases). For example, if comparing [1,1,2] to [2,2,1], a possible permutation is [1,1,1] vs [2,2,2], which would return a t-statistic of None. This caused mc_t_two_sample to crash. This was validated against R's Deducer::perm.t.test.

To fix these bugs, added new optional argument none_on_zero_variance to cogent.maths.stats.test.t_two_sample and cogent.maths.stats.test.t_one_observation that is True by default to not modify the previous behavior or change the interface of the two functions.

Updated and added unit tests for these special cases.
Added check for t == 0 when negating t.

Added corresponding unit test.