Bug#937262: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)
On Fri, Dec 13, 2019 at 10:10:03PM +0100, Andreas Tille wrote:
> i$ pdb2pqr
> Traceback (most recent call last):
> File "/usr/bin/pdb2pqr", line 52, in
> from main import mainCommand
> File "/usr/share/pdb2pqr/main.py", line 77, in
> import extensions
> File "/usr/share/pdb2pqr/extensions/__init__.py", line 56, in
> extDict[extName] = __import__(extName,globals(),locals(),[], -1)
> ValueError: level must be >= 0
"""
level specifies whether to use absolute or relative imports. The default
is -1 which indicates both absolute and relative imports will be
attempted. 0 means only perform absolute imports. Positive values for
level indicate the number of parent directories to search relative to the
directory of the module calling __import__().
"""
https://docs.python.org/2.7/library/functions.html#__import__
-1 was removed in 3.3 as implicit relative import are not supported in
3.x. As this code seems to use relative imports you need to change -1 to
1.
> So I tried:
>
> --- a/extensions/__init__.py
> +++ b/extensions/__init__.py
> @@ -53,7 +53,7 @@ _extList = [name for _, name, _ in
> pkgutil.iter_modules(__path__)]
> extDict = {}
>
> for extName in _extList:
> -extDict[extName] = __import__(extName,globals(),locals(),[], -1)
> +extDict[extName] = __import__(extName,globals(),locals(),[], 0)^M
Mindlessly changing the code is almost always a bad idea...
> File "/usr/share/pdb2pqr/extensions/__init__.py", line 57, in
> extDict[extName] = __import__(extName,globals(),locals(),[], 0)
> ModuleNotFoundError: No module named 'chi'
This is expected as it now tries to do "import chi". With 1 it should try
"from . import chi". This fails later, as the source also has implicit
relative imports that needs to be fixed, for example "from aconf import"
in src/utilities.py.
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Bug#937262: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)
On Fri, Dec 13, 2019 at 10:49:45PM +0500, Andrey Rahmatullin wrote:
> > I think at least this is solved now:
> >
> >
> > https://salsa.debian.org/med-team/pdb2pqr/commit/1f4ee901456641140ef18ca8e91e4701e1175410
>
> Nice catch, "env.Append(LIBS=[python_lib])" where "python_lib = 'python' +
> gcv('VERSION')" is definitely the cause.
Yes. I've now a state where the package builds and installs. However,
just calling pdb2pqr fails with
i$ pdb2pqr
Traceback (most recent call last):
File "/usr/bin/pdb2pqr", line 52, in
from main import mainCommand
File "/usr/share/pdb2pqr/main.py", line 77, in
import extensions
File "/usr/share/pdb2pqr/extensions/__init__.py", line 56, in
extDict[extName] = __import__(extName,globals(),locals(),[], -1)
ValueError: level must be >= 0
So I tried:
--- a/extensions/__init__.py
+++ b/extensions/__init__.py
@@ -53,7 +53,7 @@ _extList = [name for _, name, _ in
pkgutil.iter_modules(__path__)]
extDict = {}
for extName in _extList:
-extDict[extName] = __import__(extName,globals(),locals(),[], -1)
+extDict[extName] = __import__(extName,globals(),locals(),[], 0)^M
def setupExtensionsOptions(parser):
"""
which leads to:
$ pdb2pqr
Traceback (most recent call last):
File "/usr/bin/pdb2pqr", line 52, in
from main import mainCommand
File "/usr/share/pdb2pqr/main.py", line 77, in
import extensions
File "/usr/share/pdb2pqr/extensions/__init__.py", line 57, in
extDict[extName] = __import__(extName,globals(),locals(),[], 0)
ModuleNotFoundError: No module named 'chi'
I admit I have no clue whether my change was valid nor what to try next.
Kind regards
Andreas.
--
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Bug#937262: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)
On Thu, 12 Dec 2019, Andreas Tille wrote:
Control: tags -1 help
Hi,
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
'str'
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
Python3.
Any hint would be welcome.
Kind regards
Andreas.
[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.
Scott
Bug#937262: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)
Control: tags -1 help
Hi,
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
'str'
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
Python3.
Any hint would be welcome.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/pdb2pqr
--
http://fam-tille.de
