[BioPython] Some proposed code-cleanup

[Jeffrey Chang]

Great patch!  I've committed it to the source tree.

Thanks,
Jeff


On Wednesday, July 2, 2003, at 05:35  AM, Yves Bastide wrote:

> Jeffrey Chang wrote:
>> On Monday, June 23, 2003, at 01:58  AM, Andreas Kuntzagk wrote:
>>> [...]
>>>
>>> I'm sorry. I tried the regression tests and all seemed fine. What I
>>> didn't notice was, the tests used my already installed biopython and 
>>> not
>>> the code from the build-directory. Grr, why do I keep tripping over 
>>> this
>>> errors? Shouldn't the "python setup.py test" use the directory it is
>>> positioned in? If it is required to set PYTHONPATH before test, it
>>> should be mentioned in the README. I will look into the problems now 
>>> to
>>> see if I could find out.
>> Yes, we should do something about this.  It has caused us problems 
>> many times.  Probably the best thing to do is to modify run_tests.py 
>> to:
>> - identify its directory
>> - insert the build path (../build/lib.XXX/Bio, etc) to the front of 
>> sys.path, if it exists
>> - insert the source path (../Bio) to the front of sys.path, if it 
>> exists
>
> Here's a patch to run_tests.py.  Should do the right thing...
>
>> Jeff
>
> yves
> Index: Tests/run_tests.py
> ===================================================================
> RCS file: /home/repository/biopython/biopython/Tests/run_tests.py,v
> retrieving revision 1.6
> diff -u -p -r1.6 run_tests.py
> --- Tests/run_tests.py	2001/12/17 21:24:51	1.6
> +++ Tests/run_tests.py	2003/07/02 12:31:17
> @@ -25,7 +25,24 @@ import getopt
>  # PyUnit
>  import unittest
>
> +import distutils.util
> +
>  def main(argv):
> +    # insert our pathes in sys.path:
> +    # ../build/lib.*
> +    # ..
> +    # Q. Why this order?
> +    # A. To find the C modules (which are in ../build/lib.*/Bio)
> +    # Q. Then, why ".."?
> +    # A. Because Martel may not be in ../build/lib.*
> +    test_path = sys.path[0] or "."
> +    source_path = os.path.abspath("%s/.." % test_path)
> +    sys.path.insert(1, source_path)
> +    build_path = os.path.abspath("%s/../build/lib.%s-%s" % (
> +        test_path, distutils.util.get_platform(), sys.version[:3]))
> +    if os.access(build_path, os.F_OK):
> +        sys.path.insert(1, build_path)
> +
>      # start off using the GUI
>      use_gui = 1
>
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