On Thu, 12 Dec 2019, Andreas Tille wrote:

Control: tags -1 help


it seems pdb2pqr is orphaned upstream.  However, it seems to be worth
keeping inside Debian thus I tried my luck to port it to Python3 in
Git[1].  Unfortunately the build runs into

     scons: Building targets ...
     CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")
     scons: *** [pdb2pqr.py] TypeError : a bytes-like object is required, not 
     Traceback (most recent call last):
       File "/usr/lib/scons/SCons/Action.py", line 1209, in execute
         result = self.execfunction(target=target, source=rsources, env=env)
       File "/usr/lib/scons/SCons/Action.py", line 1371, in __call__
         return self.parent.actfunc(*args, **kw)
       File "./site_scons/site_init.py", line 123, in CopySubAction
         contents = contents.replace(k, v)
     TypeError: a bytes-like object is required, not 'str'
     scons: building terminated because of errors.

I wonder whether it might just be a scons issue.  Please note that I'm
using scons 3.1.1-4 from experimental that is supposed to run with

Any hint would be welcome.

Kind regards


[1] https://salsa.debian.org/med-team/pdb2pqr

I don't see any Python3 changes in that repository. Did you push your changes?

Anyway, the problem is likely in CopySubAction in site_scons/site_init.py.

On line 111, the file 'sourcefile' is opened as binary. Then, when then next line, 'contents = r.read()' is executed, contents ends up as a bytes object. Thus on line 123, when 'contents = contents.replace(k, v)' is executed, contents is a bytes object, whereas k and v are strings. You can't mix strings and bytes objects like that in Python 3.

You could perhaps try opening the file as a text file instead (remove the 'b') from the open function call.


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