Fix some compiler warnings and test logic

[dpryan79]

This resolves some compiler warnings that I noticed while making a bioconda recipe for this package. & is used a few places in Wellington where && is quite likely meant instead. Note that & has a higher precedence than >= and other such comparison operators. So there were a few cases in the code where you were testing for things like if(some_value > 0 > 0), which is unlikely to be what you meant.

[coveralls]

Coverage remained the same at 55.956% when pulling aacffec on dpryan79:operator_precedance into 155c58d on jpiper:master.

[dpryan79]

I've added the missing Cython dependency. There's now a bioconda recipe for pyDNase that includes Cython as a requirement.

[dpryan79]

Updated to add shebangs to the scripts. Otherwise you get lovely error messages like:

$ wellington_footprints.py foo.bam
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
/package/anaconda3/envs/pyDNase-0.2.6/bin/wellington_footprints.py: line 3: from: command not found
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
/package/anaconda3/envs/pyDNase-0.2.6/bin/wellington_footprints.py: line 5: from: command not found
/package/anaconda3/envs/pyDNase-0.2.6/bin/wellington_footprints.py: line 7: __version__: command not found
/package/anaconda3/envs/pyDNase-0.2.6/bin/wellington_footprints.py: line 9: syntax error near unexpected token `('
/package/anaconda3/envs/pyDNase-0.2.6/bin/wellington_footprints.py: line 9: `parser = argparse.ArgumentParser(description='Footprint the DHSs in a DNase-seq or ATAC-seq experiment using the Wellington Algorithm.’)'

[jpiper]

Hey thanks so much for this! I am absolutely rammed at work at the moment, but I'll hopefully get around to reviewing this this week and we can cut another release (if I can remember how, PyPi submission has changed a lot in the last few years!)

[jpiper]

Just had a look over - this looks like a no-brainer! That's again for doing this - maybe we should add something to the docs about installing via bioconda?

[dpryan79]

twine upload is your friend when it comes to uploading to pypi :)

Yeah, go ahead and document installing via conda. We've been doing that for most of our stuff and it's cut down on the "I get some cryptic error during the installation" emails.

[dpryan79]

BTW, I've had someone internally report another issue in pyDNase. I'll have a look at it on Monday and see if it's some weird bug or just PEBKAC.