Bug 1792949 - python-pygraphviz fails to build with Python 3.9: undefined symbol: PyIOBase_Type
Summary: python-pygraphviz fails to build with Python 3.9: undefined symbol: PyIOBase_...
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: python-pygraphviz
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Zbigniew Jędrzejewski-Szmek
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-01-20 12:46 UTC by Miro Hrončok
Modified: 2020-01-22 22:52 UTC (History)
4 users (show)

Fixed In Version: python-pygraphviz-1.5-9.fc32
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2020-01-22 22:52:49 UTC
Type: Bug
Embargoed:


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Description Miro Hrončok 2020-01-20 12:46:54 UTC
python-pygraphviz fails to build with Python 3.9.0a2.

Running Sphinx v2.2.2
Configuration error:
There is a programmable error in your configuration file:
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/sphinx/config.py", line 361, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 81, in execfile_
    exec(code, _globals)
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/doc/source/conf.py", line 50, in <module>
    import pygraphviz
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/__init__.py", line 58, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/agraph.py", line 20, in <module>
    from collections import MutableMapping
ImportError: cannot import name 'MutableMapping' from 'collections' (/usr/lib64/python3.9/collections/__init__.py)

See https://docs.python.org/3.9/whatsnew/3.9.html#removed

"The abstract base classes in collections.abc no longer are exposed in the regular collections module. This will help create a clearer distinction between the concrete classes and the abstract base classes."


For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01161966-python-pygraphviz/

For all our attempts to build python-pygraphviz with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/python-pygraphviz/

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.9:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/

Let us know here if you have any questions.

Python 3.9 will be included in Fedora 33. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.9.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Karthikeyan Singaravelan 2020-01-22 10:23:31 UTC
Upstream PR with fix merged : https://github.com/pygraphviz/pygraphviz/pull/190

Comment 2 Zbigniew Jędrzejewski-Szmek 2020-01-22 13:01:29 UTC
Built in rawhide.

Comment 3 Miro Hrončok 2020-01-22 14:22:20 UTC
Thanks. The journey continues:

Running Sphinx v2.2.2
make: Leaving directory '/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/doc'
Configuration error:
There is a programmable error in your configuration file:
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/sphinx/config.py", line 361, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 81, in execfile_
    exec(code, _globals)
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/doc/source/conf.py", line 50, in <module>
    import pygraphviz
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/__init__.py", line 58, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/agraph.py", line 27, in <module>
    from . import graphviz as gv
  File "/builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/graphviz.py", line 13, in <module>
    from . import _graphviz
ImportError: /builddir/build/BUILD/pygraphviz-pygraphviz-1.5/build/lib.linux-x86_64-3.9/pygraphviz/_graphviz.cpython-39-x86_64-linux-gnu.so: undefined symbol: PyIOBase_Type

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01172691-python-pygraphviz/

Comment 4 Zbigniew Jędrzejewski-Szmek 2020-01-22 22:52:49 UTC
Built in rawhide.


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