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Bug#936802: kmer: Python2 removal in sid/bullseye

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  Bug#936802: kmer: Python2 removal in sid/bullseye Andreas Tille <andreas@an3as.eu> - 2019-12-19 18:20 +0100
    Bug#936802: kmer: Python2 removal in sid/bullseye Scott Talbert <swt@techie.net> - 2019-12-19 19:40 +0100
      Bug#936802: kmer: Python2 removal in sid/bullseye Andreas Tille <andreas@an3as.eu> - 2019-12-19 20:40 +0100

#12160 — Bug#936802: kmer: Python2 removal in sid/bullseye

Control: tags -1 help

Hi,

I tried to convert kmer to Python3 in Git[1].  Unfortunately I'm stumbling
upon an issue in the test suite:

...
python3 /usr/bin/../lib/atac/bin/AtacDriver.py /tmp/atac-test.doxZJ4/results/work/LeprvsTuber.matches.extended

Traceback (most recent call last):
  File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 18, in <module>
    import MyFile
  File "/usr/lib/atac/lib/MyFile.py", line 6, in <module>
    class myfile(file):
NameError: name 'file' is not defined
PYTHONPATH=/usr/bin/../lib/atac/lib
Chainer failed.


Any idea what's wrong here?

Kind regards

        Andreas.


[1] https://salsa.debian.org/med-team/kmer

-- 
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#12161

On Thu, 19 Dec 2019, Andreas Tille wrote:

> Traceback (most recent call last):
>  File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 18, in <module>
>    import MyFile
>  File "/usr/lib/atac/lib/MyFile.py", line 6, in <module>
>    class myfile(file):
> NameError: name 'file' is not defined
> PYTHONPATH=/usr/bin/../lib/atac/lib
> Chainer failed.

The 'file' class doesn't exist anymore in Python 3.  You'll have to 
rewrite myfile to not use it.

Scott

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#12162

Hi Scott,

thanks a lot for your hint.

On Thu, Dec 19, 2019 at 01:34:08PM -0500, Scott Talbert wrote:
> 
> The 'file' class doesn't exist anymore in Python 3.  You'll have to rewrite
> myfile to not use it.

OK, I simply went with

...
@@ -608,6 +608,11 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
  
  # from __future__ import generators  # Necessary before Python 2.3
  
+-class myfile(file):
++class myfile():
+     "A temporary anonymous file"
+     def __init__(self):
+         filename = tempfile.mktemp()
 @@ -27,8 +27,8 @@ class ListLikeFileIter:
          self._fileIter = iter(self._fileptr.readline,"")
      def __del__(self):
...


This brings me to the next error where a Module written in C is not
found:



python3 /usr/bin/../lib/atac/bin/AtacDriver.py /tmp/atac-test.XqdEPl/results/work/LeprvsTuber.matches.extended

Traceback (most recent call last):
  File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 26, in <module>
    import localAlignerInterface
ModuleNotFoundError: No module named 'localAlignerInterface'
PYTHONPATH=/usr/bin/../lib/atac/lib
Chainer failed.



The file /usr/lib/atac/lib/localAlignerInterfacemodule.so exists
but it seems the Python3 script can't load it.


Kind regards

        Andreas.

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