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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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Numpy and Cython as build dependencies, PEP518 #840

Closed fbeghini closed 4 years ago

fbeghini commented 4 years ago

biom-format now requires that numpy and cython should be present in the build environment prior the builing. By implementing the PEP518, https://github.com/biocore/biom-format/blob/fd84172794d14a741a5764234d7a28416b9dba08/setup.py#L18-L21 and https://github.com/biocore/biom-format/blob/fd84172794d14a741a5764234d7a28416b9dba08/setup.py#L24-L27 are not longer required.

Also, this PR resolves the issue of having biom-format in install_requires installed before cython, which leads to a failure

    Complete output (12 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-hani473s/biom-format/setup.py", line 25, in <module>
        from Cython.Build import cythonize
    ModuleNotFoundError: No module named 'Cython'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-hani473s/biom-format/setup.py", line 27, in <module>
        raise ImportError("cython must be installed prior to installing biom")
    ImportError: cython must be installed prior to installing biom
wasade commented 4 years ago

Thanks, @fbeghini, this is great! Would you mind adding a brief note into the ChangeLog?

The build is failing at the moment -- unsure why Travis is not automatically highlighting that in the PR and am attempting to diagnose that. The failure appears to be unrelated to changes in this PR.

fbeghini commented 4 years ago

Yes, the changelog is now updated!

williamjevne commented 4 years ago

Is there any way to help close this? It would be great to have this functionality.

wasade commented 4 years ago

Ya, sorry, this fell off my radar -- thanks for the ping