Please port to Python3

[tillea]

Hello,
the Debian Med team is maintaining nanopolish for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If you are interested that we continue to maintain nanopolish in official Debian (and that users of other modern distributions will have no problems to install nanopolish on their systems) I'd recommend you port your code to Python3. The 2to3 tool might be of great help here.
Kind regards, Andreas.

[jts]

Hi @tillea,

If possible could you point me to the problematic python2 scripts?

Jared

[tillea]

On Wed, Aug 07, 2019 at 11:16:14AM -0700, Jared Simpson wrote: If possible could you point me to the problematic python2 scripts?

I have pushed a patch created by 2to3 to the Debian packaging: https://salsa.debian.org/med-team/nanopolish/blob/master/debian/patches/2to3.patch It would be great if you would test these with Python3 and if it works release a new version. Kind regards, Andreas.

[jts]

Thanks, that is helpful. I will incorporate these changes.

Jared

[jts]

Hi @tillea,

@paultsw has just pushed the 2to3 changes. Could you take a look? These changes will be incorporated into the next tagged version.

Jared

[tillea]

Thanks a lot. I'm afraid if I just look I might not spot any issues you might find when doing your usual tests. While I'm running the test suite in the packaging process I guess you will have better insight into the code. Please let me know if you will tag a new release (I'd be happy if this would be in the next 2-3 weeks).
Kind regards, Andreas.

[mr-c]

@jts Maybe update the #! /usr/bin/env python to be python3 ?

nanopolish/scripts/calculate_methylation_frequency.py

Line 1 in b4b4748

#! /usr/bin/env python

nanopolish/scripts/convert_model_to_header.py

Line 1 in b4b4748

#! /usr/bin/env python

nanopolish/scripts/extract_reads_aligned_to_region.py

Line 1 in b4b4748

#!/usr/bin/env python

nanopolish/scripts/nanopolish_makerange.py

Line 1 in b4b4748

#! /usr/bin/env python

and this python invocation to python3:

nanopolish/scripts/convert_all_models.py

Line 16 in b4b4748

ret = os.system("python scripts/convert_model_to_header.py -i %s -f %s > src/%s" % (model_file, function_name, outfile))

Likewise these documentation mentions: https://github.com/jts/nanopolish/blame/master/README.md#L93
https://github.com/jts/nanopolish/blame/b4b4748b9b8616d0de26477140acf1f31a78b706/docs/source/debug.rst#L94
https://github.com/jts/nanopolish/blame/master/docs/source/quickstart_call_methylation.rst#L99

Otherwise, looks good to me, thanks!

[paultsw]

@mr-c Thanks for the suggestions. I've made the above changes.

[jts]

@tillea I've now tagged a version with these changes as 0.11.2 - sorry for the delay. Let me know how it looks.

[mr-c]

Unpacking nanopolish (0.11.2-1) ...
Setting up nanopolish (0.11.2-1) ...
  File "/usr/lib/nanopolish/polya_training/hmmplot.py", line 63
    row_values  = choice(polya[polya['qc_tag'] == 'PASS'][['readname', *state_starts]].values).tolist()
                                                                       ^
SyntaxError: invalid syntax

[jts]

@paultsw can you take a look?

[mr-c]

#684 will help :-)