csb-toolbox/csb

A Python framework for structural bioinformatics.

csb's Issues

Syntax error in entry points definitions

There's a comma missing in the entry point definition section of setup.py. This popped up as the command line test failed when building a conda package based on the pypi package.

Using a non-tuple sequence for multidimensional indexing

Multidimensional indexing must use tuple after using the slice command when indexing, arr[tuple(seq)] instead of arr[seq].

In the package for example under csb.numeric.pad:
slices = [slice(s[i], -s[i]) for i in range(len(s))]
y[slices] = x

Instead of y[slices], it should be y[tuple(slices)]

Currently it throws a future warning as:
FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.

Please migrate away from Epydoc if possible

Hi,
I'm forwarding a bug report against the Debian package. It would be nice if you could migrate away from Epydoc in your next release.
Kind regards, Andreas.

Add to bioconda repository

Hey guys.

Back in the day I got the package into Debian, but honestly I'm now almost exclusively using conda for my environments. I saw that there's a package by @ivan-kalev in his private anaconda repo, and some others by other people/projects, but it's not yet in bioconda I think? I'd be happy to get it there if there's interest.

Setup.py faces encoding issues

Hi,
I reported an issue on the Debian Med developers list. After I implemented the suggesed patch this issue vanished.
Hope this helps, Andreas.