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pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
163 stars 92 forks source link

Build tests on Debian GNU/Linux testing #366

Open lopippo opened 3 months ago

lopippo commented 3 months ago

Greetings,

I am packaging version 2.5.10 for Debian.

When I try to build/run the tests, the pymzml module is not found. This is the command line from the top source directory:

$ pybuild --test --test-pytest -i python{version} -p 3.12

from pymzml.file_interface import FileInterface
E   ModuleNotFoundError: No module named 'pymzml'

I guess the path to the pymzml directory is not know here, so I try:

$ PYTHONPATH=$PWD pybuild --test --test-pytest -i python{version} -p 3.12

And then, the build goes on... until the tests for pynumpress that fail because that module is not packaged for Debian (I'll remove the two corresponding test files). And then, the build goes on... until the test for obo because there is a path problem:

E       FileNotFoundError: [Errno 2] No such file or directory: '/home/rusconi/devel/python-pymzml/development/.pybuild/cpython3_3.12_python-pymzml/build/tests/../pymzml/obo'
tests/obo_test.py:34: FileNotFoundError

Would you try to manage to have that pybuild run somehow get to know that pymzml is a subdirectory of the main source directory and that the obo subdirectory of that directory also is correctly referenced during the tests?

I am not sure this is a glitch on your part or on mine :-)

One note: the build.command file in the top source directory is somehow misleading: it does not build, it packages, no ? In fact, nowhere one would know how to run the tests; or is anyone expected to know how to run the tests in a Python development source tree ?

Sincerely, Filippo

MKoesters commented 3 months ago

Hi Filippo,

I never worked with pybuild, but I can have a look? Its a debian specific thing, right?

Best, Manuel