[Debian-med-packaging] Bug#934254: Bug#934254: Time to provide python3-mne package
Yaroslav Halchenko
debian at onerussian.com
Fri Aug 9 14:42:00 BST 2019
On Fri, 09 Aug 2019, Alexandre Gramfort wrote:
> thanks Yarik for looking into this.
> Unless there is a bug it's perfectly possible to run the mne-python tests
> withing mayavi. All tests that require mayavi are decorated to be skipped
> if mayavi is not installed. See:
> https://github.com/mne-tools/mne-python/blob/master/mne/viz/tests/test_3d.py#L334
ah, great -- then we coudld proceed! I guess I have got too alarmed by
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_coreg_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_fiducials_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_file_traits.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_kit2fiff_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_marker_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_viewer.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/viz/backends/_pyvista.py')
where it looked like imports of mayavi were the culprit.
Next errors which forbid trying to test were attempts to get some absent data files
Here is the full protocol from trying to build/test in that debian-0.18.x
branch (available on salsa), which I guess should have been just skipped due to
MNE_SKIP_SAMPLE_DATASET_TESTS=true, correct? could you please provide a patch?
(git)hopa:~exppsy/mne-python[debian-0.18.x]
$> quilt push -a
Applying patch deb_skip_segfaultingtests
patching file mne/gui/tests/test_kit2fiff_gui.py
Applying patch deb_paths
patching file mne/report.py
Applying patch up_check_numpy
patching file mne/decoding/tests/test_receptive_field.py
Now at patch up_check_numpy
changes on filesystem:
mne/decoding/tests/test_receptive_field.py | 5 ++++-
mne/gui/tests/test_kit2fiff_gui.py | 1 +
mne/report.py | 8 ++++++--
$> fakeroot debian/rules binary
dh binary --with python3 --buildsystem pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:217: python3.7 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/home/yoh/deb/gits/pkg-exppsy/mne-python'
mkdir -p build
dh_auto_build
I: pybuild base:217: /usr/bin/python3 setup.py build
running build
running build_py
copying mne/report.py -> /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne
copying mne/decoding/tests/test_receptive_field.py -> /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/decoding/tests
copying mne/gui/tests/test_kit2fiff_gui.py -> /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/tests
running egg_info
writing mne.egg-info/PKG-INFO
writing dependency_links to mne.egg-info/dependency_links.txt
writing requirements to mne.egg-info/requires.txt
writing top-level names to mne.egg-info/top_level.txt
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.css' under directory 'mne/html'
warning: no files found matching 'mne/datasets' under directory 'mne'
warning: no previously-included files matching '*' found under directory 'examples/MNE-sample-data'
warning: no previously-included files matching '*' found under directory 'examples/MNE-testing-data'
warning: no previously-included files matching '*' found under directory 'examples/MNE-spm-face'
warning: no previously-included files matching '*' found under directory 'examples/MNE-somato-data'
warning: no previously-included files matching '*.pyc' found under directory 'mne'
warning: no previously-included files found matching '.github'
warning: no previously-included files found matching '.github/ISSUE_TEMPLATE'
writing manifest file 'mne.egg-info/SOURCES.txt'
creating /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/html
copying mne/html/bootstrap.min.js -> /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/html
running build_scripts
mkdir -p mne/html
yui-compressor debian/JS/bootstrap/bootstrap.js > /home/yoh/deb/gits/pkg-exppsy/mne-python/mne/html/bootstrap.min.js
printf "\n\n" >> /home/yoh/deb/gits/pkg-exppsy/mne-python/mne/html/bootstrap.min.js
make[1]: Leaving directory '/home/yoh/deb/gits/pkg-exppsy/mne-python'
debian/rules override_dh_auto_test
make[1]: Entering directory '/home/yoh/deb/gits/pkg-exppsy/mne-python'
MNE_DONTWRITE_HOME=true MNE_SKIP_SAMPLE_DATASET_TESTS=true MNE_FORCE_SERIAL=true MNE_SKIP_NETWORK_TESTS=1 \
xvfb-run --auto-servernum --server-num=20 -s "-screen 0 1024x768x24 -ac +extension GLX +render -noreset" \
dh_auto_test
I: pybuild base:217: cd /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build; python3.7 -m pytest
====================================================================================================== test session starts =======================================================================================================
platform linux -- Python 3.7.3rc1, pytest-3.10.1, py-1.7.0, pluggy-0.8.0
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/.hypothesis/examples')
rootdir: /home/yoh/deb/gits/pkg-exppsy/mne-python, inifile: setup.cfg
plugins: localserver-0.5.0, cov-2.6.0, hypothesis-3.71.11
collecting ... Using default location ~/mne_data for testing...
Using default location ~/mne_data for testing...
Using default location ~/mne_data for testing...
collected 1200 items / 6 errors / 7 skipped
============================================================================================================= ERRORS =============================================================================================================
__________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/decoding/tests/test_receptive_field.py ___________________________________________________________________
mne/decoding/tests/test_receptive_field.py:29: in <module>
raw = io.read_raw_fif(raw_fname, preload=True)
mne/io/fiff/raw.py:470: in read_raw_fif
preload=preload, verbose=verbose)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-160>:2: in __init__
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/fiff/raw.py:85: in __init__
preload, do_check_fname)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-161>:2: in _read_raw_file
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/fiff/raw.py:153: in _read_raw_file
ff, tree, _ = fiff_open(fname, preload=whole_file)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/io/tests/data/test_raw.fif'
-------------------------------------------------------------------------------------------------------- Captured stdout ---------------------------------------------------------------------------------------------------------
Opening raw data file /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/decoding/tests/../../io/tests/data/test_raw.fif...
__________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/decoding/tests/test_receptive_field.py ___________________________________________________________________
mne/decoding/tests/test_receptive_field.py:29: in <module>
raw = io.read_raw_fif(raw_fname, preload=True)
mne/io/fiff/raw.py:470: in read_raw_fif
preload=preload, verbose=verbose)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-160>:2: in __init__
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/fiff/raw.py:85: in __init__
preload, do_check_fname)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-161>:2: in _read_raw_file
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/fiff/raw.py:153: in _read_raw_file
ff, tree, _ = fiff_open(fname, preload=whole_file)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/io/tests/data/test_raw.fif'
-------------------------------------------------------------------------------------------------------- Captured stdout ---------------------------------------------------------------------------------------------------------
Opening raw data file /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/decoding/tests/../../io/tests/data/test_raw.fif...
__________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/realtime/tests/test_fieldtrip_client.py __________________________________________________________________
mne/realtime/tests/test_fieldtrip_client.py:21: in <module>
from mne.realtime.tests.test_mockclient import _call_base_epochs_public_api
<frozen importlib._bootstrap>:983: in _find_and_load
???
<frozen importlib._bootstrap>:967: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:668: in _load_unlocked
???
<frozen importlib._bootstrap>:638: in _load_backward_compatible
???
/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py:294: in load_module
six.exec_(co, mod.__dict__)
mne/realtime/tests/test_mockclient.py:20: in <module>
events = read_events(event_name)
mne/event.py:246: in read_events
fid, tree, _ = fiff_open(filename)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/realtime/tests/../../io/tests/data/test-eve.fif'
__________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/realtime/tests/test_fieldtrip_client.py __________________________________________________________________
mne/realtime/tests/test_fieldtrip_client.py:21: in <module>
from mne.realtime.tests.test_mockclient import _call_base_epochs_public_api
<frozen importlib._bootstrap>:983: in _find_and_load
???
<frozen importlib._bootstrap>:967: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:668: in _load_unlocked
???
<frozen importlib._bootstrap>:638: in _load_backward_compatible
???
/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py:294: in load_module
six.exec_(co, mod.__dict__)
mne/realtime/tests/test_mockclient.py:20: in <module>
events = read_events(event_name)
mne/event.py:246: in read_events
fid, tree, _ = fiff_open(filename)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/realtime/tests/../../io/tests/data/test-eve.fif'
_____________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/realtime/tests/test_mockclient.py _____________________________________________________________________
mne/realtime/tests/test_mockclient.py:20: in <module>
events = read_events(event_name)
mne/event.py:246: in read_events
fid, tree, _ = fiff_open(filename)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/realtime/tests/../../io/tests/data/test-eve.fif'
_____________________________________________________________________ ERROR collecting .pybuild/cpython3_3.7_mne/build/mne/realtime/tests/test_mockclient.py _____________________________________________________________________
mne/realtime/tests/test_mockclient.py:20: in <module>
events = read_events(event_name)
mne/event.py:246: in read_events
fid, tree, _ = fiff_open(filename)
</home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/externals/decorator.py:decorator-gen-6>:2: in fiff_open
???
mne/utils/_logging.py:89: in wrapper
return function(*args, **kwargs)
mne/io/open.py:119: in fiff_open
fid = _fiff_get_fid(fname)
mne/io/open.py:47: in _fiff_get_fid
fid = open(fname, "rb") # Open in binary mode
E FileNotFoundError: [Errno 2] No such file or directory: '/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/realtime/tests/../../io/tests/data/test-eve.fif'
--------------------------------------------------------- generated xml file: /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/junit-results.xml ---------------------------------------------------------
==================================================================================================== short test summary info =====================================================================================================
ERROR mne/decoding/tests/test_receptive_field.py
ERROR mne/decoding/tests/test_receptive_field.py
ERROR mne/realtime/tests/test_fieldtrip_client.py
ERROR mne/realtime/tests/test_fieldtrip_client.py
ERROR mne/realtime/tests/test_mockclient.py
ERROR mne/realtime/tests/test_mockclient.py
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_coreg_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_fiducials_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_file_traits.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_kit2fiff_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_marker_gui.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/gui/_viewer.py')
SKIP [1] /usr/lib/python3/dist-packages/_pytest/doctest.py:361: unable to import module local('/home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build/mne/viz/backends/_pyvista.py')
======================================================================================================== warnings summary ========================================================================================================
/usr/lib/python3/dist-packages/pyparsing.py:3245
/usr/lib/python3/dist-packages/pyparsing.py:3245: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
elif isinstance( exprs, collections.Iterable ):
/usr/lib/python3/dist-packages/jinja2/runtime.py:318
/usr/lib/python3/dist-packages/jinja2/runtime.py:318: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping
/usr/lib/python3/dist-packages/jinja2/sandbox.py:82
/usr/lib/python3/dist-packages/jinja2/sandbox.py:82: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import MutableSet, MutableMapping, MutableSequence
/usr/lib/python3/dist-packages/jinja2/sandbox.py:82: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import MutableSet, MutableMapping, MutableSequence
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:303
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:303: DeprecationWarning: invalid escape sequence \w
if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:372
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:372: DeprecationWarning: invalid escape sequence \*
return [self['Signature'].replace('*', '\*')] + ['']
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:503
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:503: DeprecationWarning: invalid escape sequence \*
signature = '%s%s' % (func_name, signature.replace('*', '\*'))
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:520
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:520: DeprecationWarning: invalid escape sequence \*
signature = self['Signature'].replace('*', '\*')
-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================================= 7 skipped, 8 warnings, 6 error in 6.92 seconds =========================================================================================
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=2: cd /home/yoh/deb/gits/pkg-exppsy/mne-python/.pybuild/cpython3_3.7_mne/build; python3.7 -m pytest
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 3.7 returned exit code 13
make[1]: *** [debian/rules:33: override_dh_auto_test] Error 25
make[1]: Leaving directory '/home/yoh/deb/gits/pkg-exppsy/mne-python'
make: *** [debian/rules:18: binary] Error 2
fakeroot debian/rules binary 10.02s user 2.21s system 89% cpu 13.590 total
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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