Pjotr Prins

Turn Transform methods not handling state into a module

1

The transform methods do not need to keep track of state. I would make this a module, so as to force a more functional style. All you are using is...

You need something to test with

There need to be tests for every method. Please write tests before the methods. I also strongly suggest to look into using cucumber.

Add JOSS to pubmed

111

Pubmed is a resource for biomedical publications. Getting a paper listed is critical for career development in bioinformatics. We have to find out what it takes to get a publication...

dot computation fails when stride contains equal values

6

https://github.com/lebedov/scikits.cuda/blob/master/scikits/cuda/linalg.py#L464 and https://github.com/lebedov/scikits.cuda/blob/master/scikits/cuda/linalg.py#L466 can fail when one matrix has two equal strides (a valid stride of (8,8) leads to either a_f_order=False or b_f_order=False which may not match the partner value)....

Daru does not build on recent gcc

1

The build need this flag ```sh ENV['CPPFLAGS']='-Wno-error=deprecated-declarations' ```

Remove bundler/jeweler dependency

1

Lately I have been writing gems without bundler/jeweler and simply using rake+gem. I don't know who is using biogem right now, but I think we can create a simpler tool...

Create a generator for SciRuby gems

2

We need to adapt biogem to ease gem creation for SciRuby - which may soon be much bigger than BioRuby.

Generate gem without bioruby- and bio- prefixes

1

I see biogem as a souped up jeweler :). Sometimes handy for non-bio gems.

https://github.com/pjotrp/regressiontest very useful tool. Used in bio-table, for example.