GNU bug report logs - #39872
python-anndata fails to build

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From: Roel Janssen <roel <at> gnu.org>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>, 39872 <at> debbugs.gnu.org
Subject: bug#39872: python-anndata fails to build
Date: Wed, 04 Mar 2020 14:27:03 +0100

[Message part 1 (text/plain, inline)]

On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote:
> Build log extract:
> 
> --8<---------------cut here---------------start------------->8---
> starting phase `check'
> running "python setup.py" with command "test" and parameters ()
> running test
> running egg_info
> writing anndata.egg-info/PKG-INFO
> writing dependency_links to anndata.egg-info/dependency_links.txt
> writing requirements to anndata.egg-info/requires.txt
> writing top-level names to anndata.egg-info/top_level.txt
> reading manifest file 'anndata.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> writing manifest file 'anndata.egg-info/SOURCES.txt'
> running build_ext
> anndata (unittest.loader._FailedTest) ... ERROR
> 
> ======================================================================
> ERROR: anndata (unittest.loader._FailedTest)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: anndata
> Traceback (most recent call last):
>   File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
> 3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
>     package = self._get_module_from_name(name)
>   File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
> 3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
>     __import__(name)
>   File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
> 0.6.18/anndata/__init__.py", line 1, in <module>
>     from .base import AnnData
>   File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
> 0.6.18/anndata/base.py", line 21, in <module>
>     from scipy.sparse.sputils import IndexMixin
> ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils'
> (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-
> 1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py)
> 
> 
> ----------------------------------------------------------------------
> Ran 1 test in 0.000s
> 
> FAILED (errors=1)
> Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
> error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
> command "python" "-c" "import setuptools,
> tokenize;__file__='setup.py';f=getattr(tokenize, 'open',
> open)(__file__);code=f.read().replace('\\r\\n',
> '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with
> status 1
> builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-
> 0.6.18.drv' failed with exit code 1
> build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv 
> failed
> View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-
> python-anndata-0.6.18.drv.bz2'.
> guix build: error: build of
> `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv'
> failed
> --8<---------------cut here---------------end--------------->8---
> 
> On master c1febbbf94ee794d7a97dbde12102634f2b13529.

I sent an e-mail from another address that doesn't seem to have made the guix-
patches mailing list.  The attached patches updates the version of python-
anndata, and fixes the build.

Note that for python-zarr I disabled the tests because the majority of the tests
need external packages.  We could add all dependencies to make the test suite
work, but that requires a significant amount of work (for example, the Azure SDK
for Python is one of the external dependencies).

Is it OK to move forward with the disabled test suite for python-zarr?

Kind regards,
Roel Janssen

[0004-gnu-Update-python-anndata-to-0.7.1.patch (text/x-patch, attachment)]

[0003-gnu-Add-python-zarr.patch (text/x-patch, attachment)]

[0002-gnu-Add-python-asciitree.patch (text/x-patch, attachment)]

[0001-gnu-Add-python-numcodecs.patch (text/x-patch, attachment)]

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