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