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Description
For some reason, xarray v2024.10.0 and above breaks CI on Ubuntu, with Python 3.12. At the end of this issue is a snippet of the CI failure, saved because the logs will delete later on. I placed an exclusive upper bound on this version in #303, even though I cannot reproduce the error on an available WSL instance.
This is the commit in xarray that made the breaking change.
@elevans @ctrueden thoughts on how to proceed here? Does this failure affect PyImageJ in any way?
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| Testing ImageJ2 + original ImageJ |
-------------------------------------
============================= test session starts ==============================
platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
PyQt5 5.15.11 -- Qt runtime 5.15.15 -- Qt compiled 5.15.14
rootdir: /home/runner/work/napari-imagej/napari-imagej
configfile: pyproject.toml
plugins: napari-plugin-engine-0.2.0, qt-4.4.0, cov-6.0.0, npe2-0.7.7, napari-0.5.4, env-1.1.5
collected 167 items
tests/test_java.py Oct 29, 2024 9:56:42 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
======= BEGIN JAVA VERSIONS =======
io.scif:scifio 0.45.0
net.imagej:ij 1.54f (no minimum)
net.imagej:imagej 2.15.0 (no minimum)
net.imagej:imagej-common 2.0.4
net.imagej:imagej-legacy 1.2.1
net.imagej:imagej-ops 2.0.0
net.imglib2:imglib2-imglyb 1.1.0
net.imglib2:imglib2-unsafe 1.0.0
org.scijava:scijava-common 2.97.0
org.scijava:scijava-search 2.0.4
sc.fiji:fiji NOT PRESENT
======== END JAVA VERSIONS ========
...
tests/test_scripting.py .
tests/test_settings.py ......
tests/types/test_converters.py .....................................
tests/types/test_enums.py .
tests/types/test_trackmate.py s
tests/types/test_type_conversions.py ......
tests/types/test_widget_mappings.py ................
tests/utilities/test_module_utils.py ..................................
tests/utilities/test_progress.py
Frangi Vesselness: 100%|██████████| 3/3 [00:00<00:00, 23921.89it/s]
....
tests/widgets/test_info_bar.py .
tests/widgets/test_menu.py ..s.ss...F...
tests/widgets/test_napari_imagej.py .............
tests/widgets/test_parameter_widgets.py ...................
tests/widgets/test_result_runner.py ...
tests/widgets/test_result_tree.py .......
tests/widgets/test_searchbar.py ..
=================================== FAILURES ===================================
_________________________ test_modification_in_imagej __________________________
asserter = <function asserter.<locals>.assertFunc at 0x7f9d28dcdf80>
qtbot = <pytestqt.qtbot.QtBot object at 0x7f9d40f0c920>
ij = <java object 'net.imagej.ImageJ'>
gui_widget = <napari_imagej.widgets.menu.NapariImageJMenu object at 0x7f9dc8927140>
def test_modification_in_imagej(asserter, qtbot, ij, gui_widget: NapariImageJMenu):
if settings.headless():
pytest.skip("Only applies when not running headlessly")
if not settings.include_imagej_legacy:
pytest.skip("Tests legacy behavior")
to_button: ToIJButton = gui_widget.to_ij
from_button: FromIJButton = gui_widget.from_ij
# Show the button
qtbot.mouseClick(gui_widget.gui_button, Qt.LeftButton, delay=1)
# Add some data to the viewer
sample_data = numpy.ones((100, 100, 3), dtype=numpy.uint8)
image: Image = Image(data=sample_data, name="test_to")
current_viewer().add_layer(image)
# Press the button, handle the Dialog
qtbot.mouseClick(to_button, Qt.LeftButton, delay=1)
# Assert that the data is in the legacy UI
asserter(lambda: ij.WindowManager.getCurrentImage() is not None)
imp = ij.WindowManager.getCurrentImage()
assert imp.getTitle() == "test_to"
# Edit the data
imp.getProcessor().invert()
imp.updateAndDraw()
# Press the button, handle the Dialog
qtbot.mouseClick(from_button, Qt.LeftButton, delay=1)
# Assert the returned data is inverted
asserter(lambda: "test_to [1]" in current_viewer().layers)
modified_layer = current_viewer().layers["test_to [1]"].data
> assert numpy.all(modified_layer[0, :, :] == 254)
tests/widgets/test_menu.py:470:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/xarray/core/_typed_ops.py:457: in __eq__
return self._binary_op(other, nputils.array_eq)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/xarray/core/dataarray.py:4786: in _binary_op
name = result_name([self, other])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
objects = [<xarray.DataArray array([[[254, 254, 254],
[254, 254, 254],
[254, 254, 254],
...,
[25... (row) float64 800B 0.0 1.0 2.0 3.0 4.0 ... 95.0 96.0 97.0 98.0 99.0
* col (col) float64 24B 0.0 1.0 2.0, 254]
def result_name(objects: Iterable[Any]) -> Any:
# use the same naming heuristics as pandas:
# https://github.com/blaze/blaze/issues/458#issuecomment-51936356
> names = {getattr(obj, "name", _DEFAULT_NAME) for obj in objects}
E TypeError: unhashable type: 'numpy.ndarray'
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/xarray/core/utils.py:1206: TypeError
=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/copy.py:151
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/copy.py:151: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.
rv = reductor(4)
../../../../../opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/copy.py:261
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/copy.py:261: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.
y.__setstate__(state)
src/napari_imagej/types/converters/trackmate.py:26
/home/runner/work/napari-imagej/napari-imagej/src/napari_imagej/types/converters/trackmate.py:26: SyntaxWarning: invalid escape sequence '\d'
if match("TrackMate-\d.*\.jar", fname): # noqa
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/widgets/test_menu.py::test_modification_in_imagej - TypeError: unhashable type: 'numpy.ndarray'
======= 1 failed, 162 passed, 4 skipped, 3 warnings in 64.71s (0:01:04) ========
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