[Cython] Fedora failures with Cython 3.0a5

[Gregory Lee]

Hi Marcel,

For scikit-image, the duplicate nogil issue was fixed as of version 0.17.0.
See: https://github.com/scikit-image/scikit-image/pull/4546

- Greg

On Fri, May 29, 2020 at 8:36 AM Marcel Plch <mplch at redhat.com> wrote:

> In Fedora, we rebuilt 152 packages against Cython 3.0a5 we have found
> some breakages that might be relevant to you. We are not entirely sure
> whether these issues are caused by the individual projects' wrong usage
> of Cython, or if Cython broke them unintentionally. Do any of the
> failures look like Cython bugs to you? We can provide moredetail if one
> looks interesting.  Some expected problems, like python2
> syntax/semantics, were taken into account and noted below as issues of
> the individual projects.
>
> The linked logs will be garbage-collected in about 2 weeks; let us know
> if this happens and we can rebuild the packages.
>
>
> # Missing .pxd files
> Four packages were broken by being unable to locate .pxd files to compile.
> Packages broken by this:
> - mlpack
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01409078-mlpack/builder-live.log.gz
> - MDAnalysis
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01409419-python-MDAnalysis/builder-live.log.gz
> - pplpy
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01411510-python-pplpy/builder-live.log.gz
> - bintrees
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01409724-python-bintrees/builder-live.log.gz
>
> Can this be caused by different import semantics of Python 3?
>
>
> # GIL issues
> In three packages, problems with the GIL occurred. Some operations
> requiring the gil were executed when gil wasn't being held and vice
> versa.
> Packages broken by this:
> - tables
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01408091-python-tables/builder-live.log.gz
> - scikit-image
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01412046-python-scikit-image/builder-live.log.gz
> - ssh2-python
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01412227-python-ssh2-python/builder-live.log.gz
>
>
> # AttributeError in Cython
> One package might have revealed a bug inside of Cython. It triggers a
> scope inside of ExprNodes.py that seems to have a missing attribute that
> should be there. See the log for more info.
> Package broken by this:
> - giacpy
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01410600-python-giacpy/builder-live.log.gz
>
>
> # Some imports fail to be executed
> This might be related to some of the previous problems, or a bug in
> cimport. Two packages failed tests on importing a module from the the
> same package. In fisx, the import was done from  a Cython generated
> file. In cytoolz, a cythonized module was partially initialized,
> possibly due to cyclic import.
> Package broken by this:
> - fisx
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01410439-python-fisx/builder-live.log.gz
> - cytoolz
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01410135-python-cytoolz/builder-live.log.gz
>
>
> # Assignment to a read-only property
> One package broke on error stating attempts to assign to a read only
> properties.
> Package broken by this: Pandas
> https://download.copr.fedorainfracloud.org/results/dormouse/py38cy30a5/fedora-rawhide-x86_64/01408020-python-pandas/builder-live.log.gz
>
>
> Some problems were expected/unrelated:
> - 9 packages use python 2 syntax and don't set the default
> - 2 packages were affected by the -fno-common default in GCC 10
>
> --
> Marcel Plch
>
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