added failing test

to help debug issue #7
added test of passing an alternative finder function

this shows how to handle the issue #7 use case with no changes to the MinimalFastaParser code. I don't think issue warrants an code change, but since I wrote this test it doesn't hurt to add it to PyCogent.
have gamma return a float when x=2
Merge pull request #41 from wasade/gamma_return_type

have gamma return a float when x=2
Subtracted 18 (hydrate) from all ProteinWeights as this is already added in WeightCalculator when necessary.
can now use PyCogent within the IPython notebook

[FIXED] trap stream IOErrors that arise in IPython notebook

--HG--
extra : rebase_source : 66b156b11ab8678306047dced17b06245baee7cf
Closes #43
Merge pull request #49 from gregcaporaso/issue-43

removed dead link
Merge pull request #8 from gregcaporaso/issue-7

added a test while investigating issue #7
Merge pull request #42 from jonatanfan/master

Subtracted 18 (hydrate) from all ProteinWeights as this is already added...
fixes #51
updated parser for safer handling of output generated with --allhits
Merge pull request #52 from gregcaporaso/issue-51

fixes #51 by making uclust's --allhits parameter accessible via the app controller
Merge pull request #47 from mikerobeson/master

Paired-end assembly app controllers.
Merge pull request #56 from mikerobeson/master

fixed path issue in 'join_paired_end_reads_seqprep' function
Merge pull request #57 from mikerobeson/master

paired-end joining app controllers updated for better QIIME compatibility.
updated to default to tempdir.gettempdir() - fixes #60
updated unit tests
Merge pull request #61 from gregcaporaso/issue-60

fix to make default temp dir in get_tmp_filename work across platforms
tmp dir is now always accessible to user; fixes #62