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jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
210 stars 61 forks source link

Test suite vanished from download tarball #122

Open tillea opened 5 years ago

tillea commented 5 years ago

Hi, when I tried to rebuild the Debian package of DendroPy I was pointed to the fact that the test suite code was removed from the archive. So

$ python3 setup.py test

simply fails since there is only data but no code to run the test suite. It would be great if you could provide some test code - most preferably code that does not depend from PAUP which we can not use in Debian since it is non-free. To at least do some testing at all I'm now using

sumtrees.py --summary-target consensus \
         --min-clade-freq=0.95 \
         --edges mean-length \
         --burnin=200 \
         --support-as-labels \
         --output=pythonidae_result.tre \
         pythonidae.mlboots.newick.tre  pythonidae.random.bd0301.midpoint-rooted.tre  pythonidae.random.bd0301.tre

as a continuous integration test. Better ideas are more than welcome, Andreas.

jeetsukumaran commented 5 years ago

I cannot speak for or to the Debian packaging of DendroPy. I have no idea what the state of or changes have been made to DendroPy in the Debian package.

I had previously communicated with Andreas Tille (tille@debian.org) who contacted me regarding the licensing of some of the content of the full DendroPy package. He wanted to make sure that all content was available under an Open Source license. I indicated that while all code was, the test data was not. And could not --- data cannot be copyrighted or licensed as far as I know. I never heard back from him.

The full DendroPy package, as available from its primary source code repos, and as maintained by ourselves, do indeed include the test data:

https://github.com/jeetsukumaran/DendroPy/tree/master/tests/data

jeetsukumaran commented 5 years ago

Ah, looking at the emails, it might be possible that tille@debian.org is, in fact, yourself?

jeetsukumaran commented 5 years ago

And I see now that the issue is with test code itself and not the data?

tillea commented 5 years ago

On Wed, Oct 09, 2019 at 09:14:50AM -0700, Jeet Sukumaran wrote:

And I see now that the issue is with test code itself and not the data? Yes, its me. The test data is fine since as you say it can not be copyrighted. But the code processing the data is missing in the download tarball.