OS X PyFR origin/develop branch: documention make failure

General
1

Peter, Freddie, et. al.,

I’m getting an error when attempting to make the documentation or run the pyfr/main.py scripts. I believe it may be due to the new python 3.3 dependency, but I wasn’t certain. If I have both python and python3 executables installed on my system pointing to 2.7.9 and 3.4.2; respectively, how do I ensure that PyFR uses python3 instead of python? The stack trace for the error I’m seeing is as follows:

Traceback (most recent call last):
File "/Users/zdavis/Applications/PyFR/pyfr/scripts/pyfr", line 6, in <module>
import pyfr.scripts.mesh
File "/Users/zdavis/Applications/PyFR/pyfr/scripts/mesh.py", line 10, in <module>
from pyfr.readers import BaseReader, get_reader_by_name, get_reader_by_extn
File "/Users/zdavis/Applications/PyFR/pyfr/readers/__init__.py", line 3, in <module>
from pyfr.readers.base import BaseReader
File "/Users/zdavis/Applications/PyFR/pyfr/readers/base.py", line 10
class BaseReader(object, metaclass=ABCMeta):
^
SyntaxError: invalid syntax

Best Regards,

Zach Davis

2

Hi Zach,

To avoid conflicts between different version of python and other dependencies I would suggest using virtualenv:

http://docs.python-guide.org/en/latest/dev/virtualenvs/

I am planning to add something to the User Guide in the near future suggesting the use of virtualenvs.

Cheers

Peter

3

Hi Peter,

That seems to have resolved my earlier issue—thanks! I’ve got another one with regards to generating the documentation:

(venv)[zdavis@Minerva doc]$ make latexpdf

sphinx-build -b latex -d build/doctrees src build/latex
Making output directory...
Running Sphinx v1.2.3
Exception occurred:
File "/Users/zdavis/Applications/PyFR/venv/lib/python3.4/site-packages/sphinx/application.py", line 333, in setup_extension
mod = __import__(extension, None, None, ['setup'])
File "/Users/zdavis/Applications/PyFR/doc/ext/tikz.py", line 166
except OSError, err:
^
SyntaxError: invalid syntax
The full traceback has been saved in /var/folders/x1/5xnw6dh50s78d6hcc234g8vh0000gn/T/sphinx-err-w21_0s8_.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <[https://bitbucket.org/birkenfeld/sphinx/issues/](https://bitbucket.org/birkenfeld/sphinx/issues/)>. Thanks!
make: *** [latexpdf] Error 1

Best Regards,

Zach Davis

4

Hi Zach,

Can you try with Sphinx 1.3b3 and see if that fixes things?

Cheers

Peter

5

Hi Zach,

Looks as if 2to3 never found its way into the doc/ext directory. Can
you try running:

2to3 doc/ext > changes.patch && patch -p0 < changes.patch

and try again?

Regards, Freddie.

6

Hi Freddie,

Here’s the output I get from your instructions:

(venv)[zdavis@Minerva doc]$ 2to3 doc/ext > changes.patch && patch -p0 < changes.patch

RefactoringTool: Skipping implicit fixer: buffer
RefactoringTool: Skipping implicit fixer: idioms
RefactoringTool: Skipping implicit fixer: set_literal
RefactoringTool: Skipping implicit fixer: ws_comma
RefactoringTool: Can't open doc/ext: [Errno 2] No such file or directory: 'doc/ext'
RefactoringTool: No files need to be modified.
RefactoringTool: There was 1 error:
RefactoringTool: Can't open doc/ext: [Errno 2] No such file or directory: 'doc/ext’

Peter,

I’m looking for that specific version in the pip repository. I’ll let you know what happens once I locate it.

Best Regards,

Zach Davis

7

Hi Zach,

Can you try running it from the root PyFR directory?

Regards, Freddie.

8

Hi Freddie,

My bad…that worked. Thanks!

Best Regards,

Zach Davis