search

uio-cels / NucDiff

In-depth characterization and annotation of differences between two sets of DNA sequences
Mozilla Public License 2.0
59 stars 10 forks source link

Add to pypi - desire "pip install nucdiff" #2

Open tseemann opened 7 years ago

tseemann commented 7 years ago

Can you please make it pip installable?

It's easier than it looks, although you will need to put your code into subfolder library.

zachcp commented 6 years ago

Hi Team NucDiff,

Similar to @tseemann I though it would be great to have nucdiff installable so I took the liberty of packaging it for pip and for bioconda.

My fork of nuccdiff packages up NucDiff. I used 2to3 to convert to python3 and I believe this should now be compatible with py2/py3. Once installed, the core script is available as nucdiff on the command line.

For bioconda, nucdiff is now installable with conda install nucdiff. The advantage here is that this will take care of the mummer install as well.

Thanks for your open and excellent software,

zach cp

kseniakh commented 6 years ago

Thank you for your initiative, @zachcp !

I have a few questions regarding the installation packages in pip and bioconda.

zachcp commented 6 years ago

Hi @kseniakh,

If you like this idea of distributing your software probably the best thing is to take over the packaging process. As I've already got both pypi and bioconda set up this shouldn't be too much work.

I can look into transferring ownership of the nuccdiff name on pypi. After that you could upload to these repositories whenever you see fit, usually following a release.

The release numbers should match your software version numbers ( I may have gotten it wrong if it wasn't in a standard be location)

Please let me know if I can be of any further hello. In the meantime I'll look at the pypi policy.

Zach cp

tseemann commented 6 years ago

@kseniakh Ideally you would merge in the changes @zachcp has made on his fork, so your repo becomes the primary source.

zachcp commented 6 years ago

@kseniakh it looks like adding you as the owner of the package on pypi is relatively straightforward. You would need to:

  1. Get an account on Pypi
  2. Let me know your username and I'll add you as the Owner of the package.
  3. Thats it. After that you can build/push the package to Pypi when you make a new release.

Once you have ownership of the package on the Pypi, I would recommend accepting my pull request and then, whenever you want to make a release, you can do it yourself ( note: I am happy to walk you through the release process for both Pypi/bioconda)

zach cp

tseemann commented 6 years ago

@zachcp thanks for all this effort and assistance to help @kseniakh , very generous of you.

kseniakh commented 6 years ago

@zachcp thank you very much for your help and assistance! I will do everything that is needed until the end of the week and let you know.

Ksenia

tseemann commented 5 years ago

@kseniakh any update on this?

It seems .a patch was merged to make it python 3 but no new release or tag was made?

Docs still say :" It uses Python 2.7 "