1.9: pytest is failing #410

kloczek · 2022-05-22T09:27:42Z

I'm trying to package your module as an rpm package. So I'm using the typical PEP517 based build, install and test cycle used on building packages from non-root account.

python3 -sBm build -w --no-isolation
because I'm calling build with --no-isolation I'm using during all processes only locally installed modules
install .whl file in </install/prefix>
run pytest with PYTHONPATH pointing to sitearch and sitelib inside </install/prefix>

Here is pytest output:

+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9
collected 0 items / 15 errors

================================================================================== ERRORS ==================================================================================
_______________________________________________________ ERROR collecting pygraphviz/tests/test_attribute_defaults.py _______________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_attribute_defaults.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
_____________________________________________________________ ERROR collecting pygraphviz/tests/test_clear.py ______________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_clear.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
_____________________________________________________________ ERROR collecting pygraphviz/tests/test_close.py ______________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_close.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
____________________________________________________________ ERROR collecting pygraphviz/tests/test_drawing.py _____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_drawing.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
________________________________________________________ ERROR collecting pygraphviz/tests/test_edge_attributes.py _________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_edge_attributes.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
_____________________________________________________________ ERROR collecting pygraphviz/tests/test_graph.py ______________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_graph.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
______________________________________________________________ ERROR collecting pygraphviz/tests/test_html.py ______________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_html.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
_____________________________________________________________ ERROR collecting pygraphviz/tests/test_layout.py _____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_layout.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
________________________________________________________ ERROR collecting pygraphviz/tests/test_node_attributes.py _________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_node_attributes.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
___________________________________________________________ ERROR collecting pygraphviz/tests/test_readwrite.py ____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_readwrite.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
________________________________________________________ ERROR collecting pygraphviz/tests/test_repr_mimebundle.py _________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_repr_mimebundle.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
____________________________________________________________ ERROR collecting pygraphviz/tests/test_scraper.py _____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_scraper.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
_____________________________________________________________ ERROR collecting pygraphviz/tests/test_string.py _____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_string.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
____________________________________________________________ ERROR collecting pygraphviz/tests/test_subgraph.py ____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_subgraph.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
____________________________________________________________ ERROR collecting pygraphviz/tests/test_unicode.py _____________________________________________________________
ImportError while importing test module '/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/tests/test_unicode.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib64/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
pygraphviz/__init__.py:24: in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
pygraphviz/agraph.py:15: in <module>
    from . import graphviz as gv
pygraphviz/graphviz.py:13: in <module>
    from . import _graphviz
E   ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)
========================================================================= short test summary info ==========================================================================
ERROR pygraphviz/tests/test_attribute_defaults.py
ERROR pygraphviz/tests/test_clear.py
ERROR pygraphviz/tests/test_close.py
ERROR pygraphviz/tests/test_drawing.py
ERROR pygraphviz/tests/test_edge_attributes.py
ERROR pygraphviz/tests/test_graph.py
ERROR pygraphviz/tests/test_html.py
ERROR pygraphviz/tests/test_layout.py
ERROR pygraphviz/tests/test_node_attributes.py
ERROR pygraphviz/tests/test_readwrite.py
ERROR pygraphviz/tests/test_repr_mimebundle.py
ERROR pygraphviz/tests/test_scraper.py
ERROR pygraphviz/tests/test_string.py
ERROR pygraphviz/tests/test_subgraph.py
ERROR pygraphviz/tests/test_unicode.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 15 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================ 15 errors in 0.76s ============================================================================

The text was updated successfully, but these errors were encountered:

kloczek · 2022-05-22T09:28:16Z

Looks like this issue has the same cause like #409

rossbar · 2022-05-30T17:34:56Z

I'm not especially familiar with this specific packaging workflow and I can't reproduce, probably because I don't have a system-level pytest instance installed. FWIW to build/test wheels I would do something like:

cd <pygraphviz-src-dir>
git clean -xdf
python -m venv ~/venvs/pgv-build
source ~/venvs/pgv-build/bin/activate
python -m pip install --upgrade build wheel
# Build the wheel
python -sBm build -w --no-isolation
# Exit the existing build env here
deactivate
# Create & enter a test env
python -m venv ~/venvs/pgv-test/
source ~/venvs/pgv-test/bin/activate
# Install the wheel you've just built
python -m pip install <pygraphviz-src-dir>/dist/<pgv-wheel>.whl
python -m pip install pytest
pytest --pyargs pygraphviz

I have no idea if this works for your purposes, but it has the advantage of not relying on any system-level installs. For the record the above works as expected. Note also that this works independent of the location of the wheel on the file system. For example, if you cp <src-dir>/dist/<pgv-wheel>.whl <preferred-wheel-dir> then install the wheel from the new location, everything still works as expected.

kloczek · 2022-05-31T13:03:46Z

I'm not especially familiar with this specific packaging workflow and I can't reproduce, probably because I don't have a system-level pytest instance installed. FWIW to build/test wheels I would do something like:

pep517 build procedure it is not packaging specific thing.
Look .. I'm building all my packages in dedicated LXC zones in which is installed all what is listed in build dependencies and those zones are cut off from public network access.
I don't need yet another layer of venv.
As well that exact the same build procedure is already used on package +950 other python modules and ItWorks™️ .. please.

Did you at least try to use procedure which I've described?

rossbar · 2022-05-31T15:21:16Z

pep517 build procedure it is not packaging specific thing.

Yes, I understand, but I have no problems with the build. I can't think of any reason why --no-isolation would have any effect, as there are no Python dependencies that need to be installed. Perhaps the Graphviz version is an issue? If you are building w/ an old (<2.44) graphviz, it's possible that the compilation/linking will "succeed" but the wrapper can be ill-formed and fail at import time.

Did you at least try to use procedure which I've described?

Insofar as I can, but again I don't have a system-level pytest instance installed (i.e. /usr/bin/pytest) so that's the part that I can't test. I'd still use --pyargs to guarantee I was testing the installed wheel though.

kloczek · 2022-05-31T16:18:27Z

Yes, I understand, but I have no problems with the build. I can't think of any reason why --no-isolation would have any effect

Because it hasn't ..
pytest is failing on importing module so whatever it is it is related to what goes to .whl and what is installed in <install/prefix> where that .whl is unpacked.

Yet another clue that something is wrong with import lines.
I've added building documentation after call build module

[tkloczko@devel-g2v pygraphviz-pygraphviz-1.9]$ PYTHONPATH=$PWD/build/$(cd build; ls -d1 lib*) /usr/bin/sphinx-build -n -T -b man doc/source build/sphinx/man
Running Sphinx v4.5.0

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 332, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/doc/source/conf.py", line 63, in <module>
    import pygraphviz
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py", line 24, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/agraph.py", line 15, in <module>
    from . import graphviz as gv
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/graphviz.py", line 13, in <module>
    from . import _graphviz
ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/cmd/build.py", line 272, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/usr/lib/python3.8/site-packages/sphinx/application.py", line 202, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 165, in read
    namespace = eval_config_file(filename, tags)
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 345, in eval_config_file
    raise ConfigError(msg % traceback.format_exc()) from exc
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 332, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/doc/source/conf.py", line 63, in <module>
    import pygraphviz
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py", line 24, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/agraph.py", line 15, in <module>
    from . import graphviz as gv
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/graphviz.py", line 13, in <module>
    from . import _graphviz
ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 332, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/doc/source/conf.py", line 63, in <module>
    import pygraphviz
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py", line 24, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/agraph.py", line 15, in <module>
    from . import graphviz as gv
  File "/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/graphviz.py", line 13, in <module>
    from . import _graphviz
ImportError: cannot import name '_graphviz' from partially initialized module 'pygraphviz' (most likely due to a circular import) (/home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/pygraphviz/__init__.py)

So here as well as you see there are issues related to importing module.

kloczek · 2022-05-31T16:25:25Z

I've added those units to --deselest list to test is it will be possible to build whole package

/home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra --doctest-modules /home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/tkloczko/rpmbuild
collected 134 items

../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_attribute_defaults.py ....                               [  2%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_clear.py ...                                             [  5%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_close.py ..                                              [  6%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_drawing.py ...........                                   [ 14%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_edge_attributes.py .....                                 [ 18%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_graph.py ............................................... [ 53%]
.........................                                                                                                                                            [ 72%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_html.py ..                                               [ 73%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_layout.py ..............                                 [ 84%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_node_attributes.py ....                                  [ 87%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_readwrite.py ..                                          [ 88%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_repr_mimebundle.py ...                                   [ 91%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_scraper.py s                                             [ 91%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_string.py ....                                           [ 94%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_subgraph.py ...                                          [ 97%]
../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_unicode.py ....                                          [100%]

============================================================================= warnings summary =============================================================================
BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_layout.py::test_layout_prog_arg[sfdp]
  /home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/agraph.py:1402: RuntimeWarning: Error: remove_overlap: Graphviz not built with triangulation library

    warnings.warn(b"".join(errors).decode(self.encoding), RuntimeWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] ../../BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64/usr/lib64/python3.8/site-packages/pygraphviz/tests/test_scraper.py:9: could not import 'sphinx_gallery': No module named 'sphinx_gallery'
================================================================ 133 passed, 1 skipped, 1 warning in 2.09s =================================================================
/usr/lib/python3.8/site-packages/_pytest/pathlib.py:79: PytestWarning: (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-6e83ff0a-6482-46fc-bbbf-624729838a3a
<class 'OSError'>: [Errno 39] Directory not empty: '/tmp/pytest-of-tkloczko/garbage-6e83ff0a-6482-46fc-bbbf-624729838a3a'
  warnings.warn(
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: python-pygraphviz-1.9-3.fc35.x86_64
Provides: python-pygraphviz = 1.9-3.fc35 python-pygraphviz(x86-64) = 1.9-3.fc35 python3.8dist(pygraphviz) = 1.9 python3dist(pygraphviz) = 1.9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcgraph.so.6()(64bit) libgvc.so.6()(64bit) python(abi) = 3.8 rtld(GNU_HASH)
Obsoletes: python-pygraphviz-doc python3-pygraphviz
Processing files: python-pygraphviz-debugsource-1.9-3.fc35.x86_64
Provides: python-pygraphviz-debugsource = 1.9-3.fc35 python-pygraphviz-debugsource(x86-64) = 1.9-3.fc35
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-pygraphviz-debuginfo-1.9-3.fc35.x86_64
Provides: debuginfo(build-id) = b0269ef6022e5dd35cdefecd627091165c52e3c3 python-pygraphviz-debuginfo = 1.9-3.fc35 python-pygraphviz-debuginfo(x86-64) = 1.9-3.fc35
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-pygraphviz-debugsource(x86-64) = 1.9-3.fc35
Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/tkloczko/rpmbuild/BUILDROOT/python-pygraphviz-1.9-3.fc35.x86_64
error: Installed (but unpackaged) file(s) found:
   /usr/share/doc/pygraphviz-1.9/INSTALL.txt
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_attributes.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_miles.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_simple.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_star.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_subgraph.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/skip_django_simple.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/skip_utf8_encoding.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/plot_attributes.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_miles.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_simple.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_star.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_subgraph.py
   /usr/share/doc/pygraphviz-1.9/examples/skip_django_simple.py
   /usr/share/doc/pygraphviz-1.9/examples/skip_utf8_encoding.py


RPM build errors:
    Installed (but unpackaged) file(s) found:
   /usr/share/doc/pygraphviz-1.9/INSTALL.txt
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_attributes.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_miles.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_simple.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/plot_star.cpython-38.pyc
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   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/skip_django_simple.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/__pycache__/skip_utf8_encoding.cpython-38.pyc
   /usr/share/doc/pygraphviz-1.9/examples/plot_attributes.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_miles.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_simple.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_star.py
   /usr/share/doc/pygraphviz-1.9/examples/plot_subgraph.py
   /usr/share/doc/pygraphviz-1.9/examples/skip_django_simple.py
   /usr/share/doc/pygraphviz-1.9/examples/skip_utf8_encoding.py

Really examples and INSTALL.txt should not go to .whl

Archive:  /home/tkloczko/rpmbuild/BUILD/pygraphviz-pygraphviz-1.9/dist/pygraphviz-1.9-cp38-cp38-linux_x86_64.whl
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
     855  Defl:N      484  43% 02-09-2022 18:07 3d3612c6  pygraphviz/__init__.py
  390744  Defl:N   107576  73% 05-31-2022 16:14 56c8d265  pygraphviz/_graphviz.cpython-38-x86_64-linux-gnu.so
   69768  Defl:N    13810  80% 02-09-2022 18:07 d3d1d8b3  pygraphviz/agraph.py
    8977  Defl:N     2622  71% 02-09-2022 18:07 743ce116  pygraphviz/graphviz.i
    6930  Defl:N     1693  76% 02-09-2022 18:07 6adde015  pygraphviz/graphviz.py
  188417  Defl:N    32856  83% 02-09-2022 18:07 4b4307e9  pygraphviz/graphviz_wrap.c
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--------          -------  ---                            -------
  728870           179208  75%                            37 files

kloczek · 2022-05-31T16:27:15Z

Really examples and INSTALL.txt should not go to .whl

pygraphviz/setup.py

Lines 62 to 70 in 3053c66

    
           data = [ 
        
               (docdirbase, glob("*.txt")), 
        
               (os.path.join(docdirbase, "examples"), glob("examples/*.py")), 
        
               (os.path.join(docdirbase, "examples"), glob("examples/*.dat")), 
        
               (os.path.join(docdirbase, "examples"), glob("examples/*.dat.gz")), 
        
           ] 
        
           package_data = { 
        
               "": ["*.txt"], 
        
           }

rossbar · 2022-05-31T16:34:52Z

So here as well as you see there are issues related to importing module.

Yes, the error crops up at import time, but I still suspect this is a build error. As noted with the workflow I posted originally, I have no problem building/installing/testing the wheel. What graphviz version are you building against?

kloczek · 2022-05-31T16:55:50Z

Full list of symbols in linked DSO

[tkloczko@devel-g2v pygraphviz]$ objdump -t _graphviz.cpython-38-x86_64-linux-gnu.so

_graphviz.cpython-38-x86_64-linux-gnu.so:     file format elf64-x86-64

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rossbar · 2022-05-31T17:14:47Z

I don't know how to interpret the above. The easiest way to check the graphviz version is to check one of the cmd line tools, e.g. neato -V. This will only work if the full graphviz suite is installed, if you only have the dev pkgs installed, then perhaps checking with the pkg manager, something like rpm -qa | grep graphviz

nieder · 2024-03-26T12:07:17Z

@kloczek I was able to succeed doing something very similar by adding PYTEST_ADDOPTS="--import-mode=importlib" to my test command (cf https://build.opensuse.org/projects/devel:languages:python/packages/python-pygraphviz/files/python-pygraphviz.spec). With that extra option, then my tests run and all pass (vs getting the partially initialized module error).

kloczek · 2024-03-26T12:11:23Z

With that extra option, then my tests run and all pass (vs getting the partially initialized module error).

Did you compile module with LTO?

nieder · 2024-03-27T11:40:32Z

(re LTO) Not knowingly.

/sw/bin/python3.10 setup.py build_ext --include-dirs=/sw/include --library-dirs=/sw/lib/graphviz-2.38
/sw/bin/python3.10 setup.py install --root=`pwd`/tempdist
PYTEST_ADDOPTS="--import-mode=importlib" PYTHONPATH=`pwd`/tempdist/sw/lib/python3.10/site-packages /sw/bin/pytest-3.10 -vv || exit 2

rossbar mentioned this issue May 30, 2022

1.9: issue with circular import on generate documentation #409

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1.9: pytest is failing #410

1.9: pytest is failing #410

kloczek commented May 22, 2022

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kloczek commented May 31, 2022 •

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nieder commented Mar 26, 2024

kloczek commented Mar 26, 2024

nieder commented Mar 27, 2024

1.9: pytest is failing #410

1.9: pytest is failing #410

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kloczek commented May 22, 2022

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kloczek commented May 31, 2022 • edited

rossbar commented May 31, 2022

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nieder commented Mar 26, 2024

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kloczek commented May 31, 2022 •

edited