Python 3 Conversion

[bheavner]

I've encountered a few typos with setup.py when running with python 3.5. When I tried this:python setup.py install --prefix=/local/tools/HINT-1.1.1 --rgt-data-path=/local/tools/HINT-1.1.1 --rgt-tool=hint

I got the following error:

  File "setup.py", line 132
    except (BadOptionError,AmbiguousOptionError), e:

which I corrected by changing line 132 to:

except (BadOptionError,AmbiguousOptionError) as e:

then I got the following error:

  File "setup.py", line 398
    default_file_permission = 0644
                                 ^
SyntaxError: invalid token

which I corrected by changing line 398 and 299 to:

default_file_permission = 0o644
default_path_permission = 0o755

(apparently python3 doesn't like numbers beginning with 0. Octal numbers start with 0o)

then, the setup works. But then I get some errors when I attempt to run rgt-hint... I'll get to those in another issue.

[bheavner]

It looks like I've hit a block in my python3 efforts - ngslib, which contains BigWigFile and is imported in HINT/signalProcessing.py, appears to be a python 2.7 dependency...

[fabio-t]

Hi @bheavner, sorry for the late reply. We currently only support python 2, and only on Linux. I'm closing #13 and #14 and renaming this issue so that you'll be notified when we get around to make the code python3-friendly.

[fabio-t]

Pull request #46 has provided the first piece of the Python 3 puzzle. Some more work required on HINT, plus extensive testing, and then onto verifying each library's compatibility.

[fabio-t]

This now has higher priority. We'll probably drop Python 2.7 support and completely move to Python 3.

[fabio-t]

Finished with version 0.13.0.