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Re: Packaging DendroPy for Debian - test suite failures



(1) I've tagged the releases. Sorry about that.

(2) With regards to SumTrees, things are a little more complicated.
SumTrees is indeed an end-user application, distributed with DendroPy.

    http://dendropy.org/programs/sumtrees.html

In fact, not only are there many people who install DendroPy only to use SumTrees (i.e., without programming with the library), arguably, there are *more* people who do this than actually use the library independently. In hindsight, separating the two might have made more sense. Unfortunately, I am not certain this can easily be changed now without being too disruptive.

One option might be to tweak the ``setup.py`` logic to allow for specification of the script install location for the scripts (perhaps by reading an environmental variable or some custom text file), or even disallows their installation altogether. I do not know if this is already supported, but if not, it can easily be implemented. However it will then be introducing a idiosyncratic mechanism to the already-fragile Python deployment system.

-- jeet


On 6/24/15 8:28 AM, Andreas Tille wrote:
Hi Jeet,

On Tue, Jun 23, 2015 at 10:49:47AM -0400, Jeet Sukumaran wrote:
Just pushed a revision to master that incorporates the below fix, i.e.,
PAUP-based tests skipped unless an environmental variable explicitly set to
the path of the PAUP binary.

Thanks a lot - this works nicely.  I have two further remarks:

1. Please make sure you tag each release on Github.  Github currently
knows only 4.0.0 while pypi.python.org has 4.0.2

2. The install procedure installs a script
        /usr/bin/sumtrees.py
Could you please explain the role of this script?

The problem why I'm asking is the following:  According to the Debian
Python policy we provide two packages: python-dendropy and
python3-dendropy containing the modules for Python and Python3.  If
each package would contain /usr/bin/sumtrees.py the packages would
not be co-installable which would make no sense.  My primitive hack
to work around this was to rename the file in the Python3 package to
sumtrees3.py which is a rather poor solution but worked just for the
development process here.

My favorite solution would be to put the script just to

    /usr/share/doc/python-dendropy/examples/sumtrees.py and
    /usr/share/doc/python3-dendropy/examples/sumtrees.py

respectively.  Would you confirm that this script is rather an example
or is it really a tool that a user should call?  In the latter case I
need to think about what to do as a proper solution.  One way would be
to create an additional package named dendropy (without the python- in
front) that is a user oriented application depending from
python3-dendropy (since Debian is in favour of Python3) and provide
/usr/bin/sumtrees (without the .py extension since this is also Debian
policy to not force the language a script was written to the users).

Just let me know what role sumtrees would play according to your
opinion.

Kind regards

        Andreas.


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