performance tweaks for merge()
indices were not being checked correctly
Andreas Tille pointed out that the build_sphinx command doesn't actually work, and I confirmed that locally. replace with more canonical sphinx build command
Merge branch 'master' of github.com:biom-format/biom-format
transform methods now circumvent expensive typecast
Merge branch 'master' of github.com:biom-format/biom-format
Added Daniel's benchmarking code and sparse database backend code.
Added biom-format config file support, basically the same as QIIME.
Can now load different sparse matrix backends through either biom config file or programmatically (very similar to matplotlib's use() function for backend renderers). all_tests.py still needs to be updated to use this new functionality, and so does print_biom_python_config.py.
Added new invalid backend exception type, updated print_biom_python_config.py to handle invalid backends.
Added a method from pycogent's unit_test module and fixed Daniel's database code so that the unit tests run now. test_dbdata.py fails some of its tests, and prints debugging info out.
adding biom logos
Merge branch 'master' of github.com:biom-format/biom-format
added rebuildIndices to SparseMat
initial csmat implementation
sorting returned items() calls and removed some comments
allow to pass in CSMat
Can "data_pump" data into parsers, added a light CSMat parser
forcing CSMat
added test for the light biom parser for csmat