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Scikit-fmm failing in CI on Windows #1073

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wd15 opened this issue Sep 17, 2024 · 3 comments
Closed

Scikit-fmm failing in CI on Windows #1073

wd15 opened this issue Sep 17, 2024 · 3 comments

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@wd15
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wd15 commented Sep 17, 2024

There was a new release of Scikit-fmm. This might be for Numpy 2? The failure can't be reproduced with the environment below (no failures at all on linux).

[tool.poetry.dependencies]
python = "^3.12"
numpy = "^2.1.1"
scipy = "^1.14.1"
future = "^1.0.0"
setuptools = "71.1.0"
matplotlib = "^3.9.2"
packaging = "^24.1"
scikit-fmm = "^2024.9.16"

This might need to be debugged directly on the CI if we don't have access to a Windows machine.

@guyer
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guyer commented Dec 10, 2024

This started working again on December 1st. CI installed scikit_fmm-2024.9.16-cp312-cp312-win_amd64.whl either way and the sha256 changes every run, so not clear what that means.

A few things changed:

% Date: 2024-12-10 17:04:49 - 13 differences
%	/Users/guyer/Desktop/broken
%	/Users/guyer/Desktop/fixed
% Options: ignoreSpaceChanges, ignoreWhiteSpace
% Use up and down arrows to move through differences, ⌃⌥-left and ⌃⌥-right to patch changes from one window to the other.
7a8
>   - _openmp_mutex=4.5=2_gnu

31c32
<   - fltk=1.3.9=h27fc217_1
---
>   - fltk=1.3.10=h5d05227_0

56c57
<   - hdf5=1.14.4=nompi_hd5d9e70_103
---
>   - hdf5=1.14.4=nompi_hd5d9e70_105

80a82
>   - libgcc=14.2.0=h1383e82_1

82c84,85
<   - libhwloc=2.11.1=default_h8125262_1000
---
>   - libgomp=14.2.0=h1383e82_1
>   - libhwloc=2.11.2=default_ha69328c_1001

100c103,104
<   - libxcb=1.16=h013a479_1
---
>   - libwinpthread=12.0.0.r4.gg4f2fc60ca=h57928b3_8
>   - libxcb=1.17.0=h0e4246c_0

106,110d109
<   - m2w64-gcc-libgfortran=5.3.0=6
<   - m2w64-gcc-libs=5.3.0=7
<   - m2w64-gcc-libs-core=5.3.0=7
<   - m2w64-gmp=6.1.0=2
<   - m2w64-libwinpthread-git=5.0.0.4634.697f757=2

115d113
<   - msys2-conda-epoch=20160418=1

128c126
<   - pillow=10.4.0=py312h381445a_1
---
>   - pillow=11.0.0=py312ha41cd45_0

134,135c132
<   - pthread-stubs=0.4=hcd874cb_1001
<   - pthreads-win32=2.9.1=h2466b09_4
---
>   - pthread-stubs=0.4=h0e40799_1002

156,157c153,154
<   - tbb=2021.13.0=hc790b64_0
<   - tbb-devel=2021.13.0=h053bfa6_0
---
>   - tbb=2021.13.0=h62715c5_1
>   - tbb-devel=2021.13.0=h47441b3_1

160c157
<   - tomli=2.1.0=pyhff2d567_0
---
>   - tomli=2.2.1=pyhd8ed1ab_0

177,189c174,182
<   - xorg-fixesproto=5.0=hcd874cb_1002
<   - xorg-kbproto=1.0.7=hcd874cb_1002
<   - xorg-libice=1.1.1=hcd874cb_0
<   - xorg-libsm=1.2.4=hcd874cb_0
<   - xorg-libx11=1.8.9=h0076a8d_1
<   - xorg-libxau=1.0.11=hcd874cb_0
<   - xorg-libxdmcp=1.1.3=hcd874cb_0
<   - xorg-libxext=1.3.4=hcd874cb_2
<   - xorg-libxfixes=5.0.3=hcd874cb_1004
<   - xorg-libxrender=0.9.11=hcd874cb_0
<   - xorg-renderproto=0.11.1=hcd874cb_1002
<   - xorg-xextproto=7.3.0=hcd874cb_1003
<   - xorg-xproto=7.0.31=hcd874cb_1007
---
>   - xorg-libice=1.1.1=h0e40799_1
>   - xorg-libsm=1.2.4=h0e40799_1
>   - xorg-libx11=1.8.10=hf48077a_0
>   - xorg-libxau=1.0.11=h0e40799_1
>   - xorg-libxdmcp=1.1.5=h0e40799_0
>   - xorg-libxext=1.3.6=h0e40799_0
>   - xorg-libxfixes=6.0.1=h0e40799_0
>   - xorg-libxrender=0.9.11=h0e40799_1
>   - xorg-xorgproto=2024.1=h0e40799_1

@guyer
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guyer commented Dec 10, 2024

Posting failures here, since Azure discards CI results after about a month:

======================================================================
2024-11-30T00:17:15.0272529Z FAIL: DistanceVariable (fipy.variables.distanceVariable)
2024-11-30T00:17:15.0272866Z Doctest: fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0273196Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0273520Z Traceback (most recent call last):
2024-11-30T00:17:15.0273831Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0274180Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0274542Z AssertionError: Failed doctest test for fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0274905Z   File "D:\a\1\s\fipy\variables\distanceVariable.py", line 68, in DistanceVariable
2024-11-30T00:17:15.0275110Z 
2024-11-30T00:17:15.0275400Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0275760Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 87, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0276072Z Failed example:
2024-11-30T00:17:15.0276346Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0276627Z Exception raised:
2024-11-30T00:17:15.0276899Z     Traceback (most recent call last):
2024-11-30T00:17:15.0277195Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0277507Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0277832Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[5]>", line 1, in <module>
2024-11-30T00:17:15.0278176Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0278445Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0278728Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0279078Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0279383Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0279683Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0280009Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0280284Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0280544Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0280874Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0281496Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 89, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0281814Z Failed example:
2024-11-30T00:17:15.0282133Z     print(var.allclose(answer)) #doctest: +LSM
2024-11-30T00:17:15.0282401Z Expected:
2024-11-30T00:17:15.0282642Z     1
2024-11-30T00:17:15.0282865Z Got:
2024-11-30T00:17:15.0283084Z     False
2024-11-30T00:17:15.0283369Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0283723Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 97, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0284029Z Failed example:
2024-11-30T00:17:15.0284288Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0284544Z Exception raised:
2024-11-30T00:17:15.0284795Z     Traceback (most recent call last):
2024-11-30T00:17:15.0285093Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0285409Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0285727Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[11]>", line 1, in <module>
2024-11-30T00:17:15.0286146Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0286406Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0286697Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0287052Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0287340Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0287638Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0287962Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0288210Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0288468Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0288780Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0289133Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 99, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0289436Z Failed example:
2024-11-30T00:17:15.0289695Z     print(var.allclose(answer)) #doctest: +LSM
2024-11-30T00:17:15.0289956Z Expected:
2024-11-30T00:17:15.0290177Z     1
2024-11-30T00:17:15.0290397Z Got:
2024-11-30T00:17:15.0290619Z     False
2024-11-30T00:17:15.0290909Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0291250Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 110, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0291552Z Failed example:
2024-11-30T00:17:15.0291812Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0292072Z Exception raised:
2024-11-30T00:17:15.0292335Z     Traceback (most recent call last):
2024-11-30T00:17:15.0292629Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0292941Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0293323Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[19]>", line 1, in <module>
2024-11-30T00:17:15.0293641Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0293894Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0294171Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0294513Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0294799Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0295096Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0296353Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0296629Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0296902Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0297216Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0297574Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 121, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0297883Z Failed example:
2024-11-30T00:17:15.0298154Z     print(var.allclose(answer)) #doctest: +LSM
2024-11-30T00:17:15.0298411Z Expected:
2024-11-30T00:17:15.0298635Z     1
2024-11-30T00:17:15.0298872Z Got:
2024-11-30T00:17:15.0299112Z     False
2024-11-30T00:17:15.0299406Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0299759Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 137, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0300071Z Failed example:
2024-11-30T00:17:15.0300331Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0300599Z Exception raised:
2024-11-30T00:17:15.0300956Z     Traceback (most recent call last):
2024-11-30T00:17:15.0301259Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0301576Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0301896Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[34]>", line 1, in <module>
2024-11-30T00:17:15.0302217Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0302473Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0302783Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0303127Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0303419Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0303703Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0304014Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0304265Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0304537Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0304861Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0305227Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 140, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0305545Z Failed example:
2024-11-30T00:17:15.0305828Z     print(var.allclose((-tmp / 2, 0.5, 0.5, 0.5 + tmp))) #doctest: +LSM
2024-11-30T00:17:15.0306106Z Expected:
2024-11-30T00:17:15.0306341Z     1
2024-11-30T00:17:15.0306576Z Got:
2024-11-30T00:17:15.0306813Z     False
2024-11-30T00:17:15.0307100Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0307454Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 142, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0307770Z Failed example:
2024-11-30T00:17:15.0308046Z     var.extendVariable(extensionVar, order=1) #doctest: +LSM
2024-11-30T00:17:15.0308330Z Exception raised:
2024-11-30T00:17:15.0308602Z     Traceback (most recent call last):
2024-11-30T00:17:15.0308911Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0309249Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0309578Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[38]>", line 1, in <module>
2024-11-30T00:17:15.0309902Z         var.extendVariable(extensionVar, order=1) #doctest: +LSM
2024-11-30T00:17:15.0310184Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0310542Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 274, in extendVariable
2024-11-30T00:17:15.0310920Z         tmp, extensionValue = extension_velocities(phi, extensionValue, ext_mask=phi < 0., dx=dx, order=order)
2024-11-30T00:17:15.0311229Z                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0311541Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 239, in extension_velocities
2024-11-30T00:17:15.0311878Z         distance, f_ext = cFastMarcher(phi, dx, flag, speed, ext_mask,
2024-11-30T00:17:15.0312159Z                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0312431Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0312766Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0313122Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 143, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0313440Z Failed example:
2024-11-30T00:17:15.0313716Z     print(extensionVar.allclose((1.25, .5, 2, 1.25))) #doctest: +LSM
2024-11-30T00:17:15.0313985Z Expected:
2024-11-30T00:17:15.0314272Z     1
2024-11-30T00:17:15.0314494Z Got:
2024-11-30T00:17:15.0314725Z     False
2024-11-30T00:17:15.0315044Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0315401Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 149, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0315711Z Failed example:
2024-11-30T00:17:15.0315982Z     var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0316258Z Exception raised:
2024-11-30T00:17:15.0316524Z     Traceback (most recent call last):
2024-11-30T00:17:15.0316821Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0317127Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0317459Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[42]>", line 1, in <module>
2024-11-30T00:17:15.0317779Z         var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0318038Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0318320Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0318666Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0318960Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0319277Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0319606Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0319875Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0320135Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0320454Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0320802Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 158, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0321122Z Failed example:
2024-11-30T00:17:15.0321394Z     print(var.allclose((-tmp / 2, 0.5, 1.5, 0.5, 0.5 + tmp,
2024-11-30T00:17:15.0321700Z                          tmp1, 1.5, tmp1, tmp2))) #doctest: +LSM
2024-11-30T00:17:15.0321962Z Expected:
2024-11-30T00:17:15.0322192Z     1
2024-11-30T00:17:15.0322419Z Got:
2024-11-30T00:17:15.0322641Z     False
2024-11-30T00:17:15.0322936Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0323290Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 162, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0323596Z Failed example:
2024-11-30T00:17:15.0323883Z     var.extendVariable(extensionVar, order=1) #doctest: +LSM
2024-11-30T00:17:15.0324240Z Exception raised:
2024-11-30T00:17:15.0324511Z     Traceback (most recent call last):
2024-11-30T00:17:15.0324811Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0325128Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0325446Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[50]>", line 1, in <module>
2024-11-30T00:17:15.0325775Z         var.extendVariable(extensionVar, order=1) #doctest: +LSM
2024-11-30T00:17:15.0326050Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0326355Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 274, in extendVariable
2024-11-30T00:17:15.0326701Z         tmp, extensionValue = extension_velocities(phi, extensionValue, ext_mask=phi < 0., dx=dx, order=order)
2024-11-30T00:17:15.0327009Z                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0327316Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 239, in extension_velocities
2024-11-30T00:17:15.0327656Z         distance, f_ext = cFastMarcher(phi, dx, flag, speed, ext_mask,
2024-11-30T00:17:15.0327979Z                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0328247Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0328557Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0328984Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 163, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0329319Z Failed example:
2024-11-30T00:17:15.0329602Z     print(extensionVar.allclose(answer, rtol = 1e-4)) #doctest: +LSM
2024-11-30T00:17:15.0329875Z Expected:
2024-11-30T00:17:15.0330100Z     1
2024-11-30T00:17:15.0330321Z Got:
2024-11-30T00:17:15.0330552Z     False
2024-11-30T00:17:15.0330827Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0331179Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 173, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0331488Z Failed example:
2024-11-30T00:17:15.0331763Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0332029Z Exception raised:
2024-11-30T00:17:15.0332292Z     Traceback (most recent call last):
2024-11-30T00:17:15.0332596Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0332907Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0333223Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[54]>", line 1, in <module>
2024-11-30T00:17:15.0333570Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0333829Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0334115Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0334460Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0359163Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0359718Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0360058Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0360335Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0360602Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0360927Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0361286Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 174, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0361607Z Failed example:
2024-11-30T00:17:15.0361888Z     print(var.allclose((-0.5, 0.5, -0.5))) #doctest: +LSM
2024-11-30T00:17:15.0362359Z Expected:
2024-11-30T00:17:15.0362590Z     1
2024-11-30T00:17:15.0362873Z Got:
2024-11-30T00:17:15.0363119Z     False
2024-11-30T00:17:15.0363408Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0363771Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 184, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0364090Z Failed example:
2024-11-30T00:17:15.0364372Z     var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0364645Z Exception raised:
2024-11-30T00:17:15.0364907Z     Traceback (most recent call last):
2024-11-30T00:17:15.0365214Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0365522Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0365854Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[58]>", line 1, in <module>
2024-11-30T00:17:15.0366177Z         var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0366447Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0366740Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0367193Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0367499Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0367813Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0368131Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0368398Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0368679Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0369006Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0369368Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 189, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0369690Z Failed example:
2024-11-30T00:17:15.0369993Z     print(numerix.allclose(var, answer, rtol=1e-9)) #doctest: +LSM
2024-11-30T00:17:15.0370284Z Expected:
2024-11-30T00:17:15.0370521Z     True
2024-11-30T00:17:15.0370755Z Got:
2024-11-30T00:17:15.0370978Z     False
2024-11-30T00:17:15.0371261Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0371610Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 210, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0371916Z Failed example:
2024-11-30T00:17:15.0372205Z     var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0372463Z Exception raised:
2024-11-30T00:17:15.0372724Z     Traceback (most recent call last):
2024-11-30T00:17:15.0373027Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0373335Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0373660Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[63]>", line 1, in <module>
2024-11-30T00:17:15.0373981Z         var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0374247Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0374543Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0374913Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0375205Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0375492Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0375815Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0376069Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0376399Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0376705Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0377058Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 211, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0377371Z Failed example:
2024-11-30T00:17:15.0377642Z     var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0377917Z Exception raised:
2024-11-30T00:17:15.0378181Z     Traceback (most recent call last):
2024-11-30T00:17:15.0378485Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0378796Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0379110Z       File "<doctest fipy.variables.distanceVariable.DistanceVariable[64]>", line 1, in <module>
2024-11-30T00:17:15.0379422Z         var.calcDistanceFunction(order=2) #doctest: +LSM
2024-11-30T00:17:15.0379682Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0379970Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0380445Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0380838Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0381148Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0381469Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0381745Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0382010Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0382324Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0382676Z File "D:\a\1\s\fipy\variables\distanceVariable.py", line 223, in fipy.variables.distanceVariable.DistanceVariable
2024-11-30T00:17:15.0382995Z Failed example:
2024-11-30T00:17:15.0383286Z     print(numerix.allclose(var, answer, rtol=1e-9)) #doctest: +SKFMM
2024-11-30T00:17:15.0383565Z Expected:
2024-11-30T00:17:15.0383801Z     True
2024-11-30T00:17:15.0384029Z Got:
2024-11-30T00:17:15.0384253Z     False
2024-11-30T00:17:15.0384414Z 
2024-11-30T00:17:15.0384553Z 
2024-11-30T00:17:15.0384833Z ======================================================================
2024-11-30T00:17:15.0385153Z FAIL: mesh1D (examples.levelSet.distanceFunction)
2024-11-30T00:17:15.0385461Z Doctest: examples.levelSet.distanceFunction.mesh1D
2024-11-30T00:17:15.0385782Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0386079Z Traceback (most recent call last):
2024-11-30T00:17:15.0386600Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0557896Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0558324Z AssertionError: Failed doctest test for examples.levelSet.distanceFunction.mesh1D
2024-11-30T00:17:15.0560619Z   File "d:\a\1\s\examples\levelSet\distanceFunction\mesh1D.py", line 0, in mesh1D
2024-11-30T00:17:15.0560863Z 
2024-11-30T00:17:15.0561130Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0561465Z File "d:\a\1\s\examples\levelSet\distanceFunction\mesh1D.py", line 44, in examples.levelSet.distanceFunction.mesh1D
2024-11-30T00:17:15.0561745Z Failed example:
2024-11-30T00:17:15.0561990Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0562229Z Exception raised:
2024-11-30T00:17:15.0562451Z     Traceback (most recent call last):
2024-11-30T00:17:15.0562727Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0563002Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0563275Z       File "<doctest examples.levelSet.distanceFunction.mesh1D[8]>", line 1, in <module>
2024-11-30T00:17:15.0563816Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0564035Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0564287Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0564595Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0564850Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0565099Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0565411Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0565678Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0565910Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0566184Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0566518Z File "d:\a\1\s\examples\levelSet\distanceFunction\mesh1D.py", line 55, in examples.levelSet.distanceFunction.mesh1D
2024-11-30T00:17:15.0566800Z Failed example:
2024-11-30T00:17:15.0567039Z     print(numerix.allclose(var, x - dx * nx / 2)) #doctest: +LSM
2024-11-30T00:17:15.0567377Z Expected:
2024-11-30T00:17:15.0567575Z     1
2024-11-30T00:17:15.0567763Z Got:
2024-11-30T00:17:15.0567955Z     False
2024-11-30T00:17:15.0568056Z 
2024-11-30T00:17:15.0568185Z 
2024-11-30T00:17:15.0568420Z ======================================================================
2024-11-30T00:17:15.0568694Z FAIL: circle (examples.levelSet.distanceFunction)
2024-11-30T00:17:15.0568953Z Doctest: examples.levelSet.distanceFunction.circle
2024-11-30T00:17:15.0569238Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0569493Z Traceback (most recent call last):
2024-11-30T00:17:15.0569754Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0570041Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0570345Z AssertionError: Failed doctest test for examples.levelSet.distanceFunction.circle
2024-11-30T00:17:15.0570644Z   File "d:\a\1\s\examples\levelSet\distanceFunction\circle.py", line 0, in circle
2024-11-30T00:17:15.0570818Z 
2024-11-30T00:17:15.0571054Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0571367Z File "d:\a\1\s\examples\levelSet\distanceFunction\circle.py", line 42, in examples.levelSet.distanceFunction.circle
2024-11-30T00:17:15.0571645Z Failed example:
2024-11-30T00:17:15.0571888Z     var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0572127Z Exception raised:
2024-11-30T00:17:15.0572350Z     Traceback (most recent call last):
2024-11-30T00:17:15.0572608Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0572874Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0573160Z       File "<doctest examples.levelSet.distanceFunction.circle[12]>", line 1, in <module>
2024-11-30T00:17:15.0573436Z         var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0573670Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0573995Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0574298Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0574559Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0574824Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0575100Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0575318Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0575541Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0575928Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0576250Z File "d:\a\1\s\examples\levelSet\distanceFunction\circle.py", line 81, in examples.levelSet.distanceFunction.circle
2024-11-30T00:17:15.0576593Z Failed example:
2024-11-30T00:17:15.0576833Z     print(numerix.allclose(var, trialValues)) #doctest: +LSM
2024-11-30T00:17:15.0577072Z Expected:
2024-11-30T00:17:15.0577263Z     True
2024-11-30T00:17:15.0577447Z Got:
2024-11-30T00:17:15.0577642Z     False
2024-11-30T00:17:15.0577743Z 
2024-11-30T00:17:15.0577866Z 
2024-11-30T00:17:15.0578106Z ======================================================================
2024-11-30T00:17:15.0578377Z FAIL: square (examples.levelSet.distanceFunction)
2024-11-30T00:17:15.0578643Z Doctest: examples.levelSet.distanceFunction.square
2024-11-30T00:17:15.0578911Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0579169Z Traceback (most recent call last):
2024-11-30T00:17:15.0579431Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0579713Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0580827Z AssertionError: Failed doctest test for examples.levelSet.distanceFunction.square
2024-11-30T00:17:15.0581133Z   File "d:\a\1\s\examples\levelSet\distanceFunction\square.py", line 0, in square
2024-11-30T00:17:15.0581282Z 
2024-11-30T00:17:15.0581522Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0581868Z File "d:\a\1\s\examples\levelSet\distanceFunction\square.py", line 18, in examples.levelSet.distanceFunction.square
2024-11-30T00:17:15.0582137Z Failed example:
2024-11-30T00:17:15.0582371Z     var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0582599Z Exception raised:
2024-11-30T00:17:15.0582818Z     Traceback (most recent call last):
2024-11-30T00:17:15.0583089Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0583367Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0583647Z       File "<doctest examples.levelSet.distanceFunction.square[0]>", line 1, in <module>
2024-11-30T00:17:15.0583922Z         var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0584147Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0584398Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0584702Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0584955Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0585212Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0585489Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0585708Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0585939Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0586217Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0586548Z File "d:\a\1\s\examples\levelSet\distanceFunction\square.py", line 37, in examples.levelSet.distanceFunction.square
2024-11-30T00:17:15.0586838Z Failed example:
2024-11-30T00:17:15.0587072Z     print(var.allclose(arr)) #doctest: +LSM
2024-11-30T00:17:15.0587285Z Expected:
2024-11-30T00:17:15.0587474Z     1
2024-11-30T00:17:15.0587658Z Got:
2024-11-30T00:17:15.0587854Z     False
2024-11-30T00:17:15.0587955Z 
2024-11-30T00:17:15.0588051Z 
2024-11-30T00:17:15.0588297Z ======================================================================
2024-11-30T00:17:15.0588590Z FAIL: interior (examples.levelSet.distanceFunction)
2024-11-30T00:17:15.0588857Z Doctest: examples.levelSet.distanceFunction.interior
2024-11-30T00:17:15.0589210Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0589478Z Traceback (most recent call last):
2024-11-30T00:17:15.0589737Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0590024Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0590321Z AssertionError: Failed doctest test for examples.levelSet.distanceFunction.interior
2024-11-30T00:17:15.0590619Z   File "d:\a\1\s\examples\levelSet\distanceFunction\interior.py", line 0, in interior
2024-11-30T00:17:15.0590770Z 
2024-11-30T00:17:15.0591014Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0591337Z File "d:\a\1\s\examples\levelSet\distanceFunction\interior.py", line 16, in examples.levelSet.distanceFunction.interior
2024-11-30T00:17:15.0591626Z Failed example:
2024-11-30T00:17:15.0591854Z     var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0592091Z Exception raised:
2024-11-30T00:17:15.0592313Z     Traceback (most recent call last):
2024-11-30T00:17:15.0592566Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0593226Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0593575Z       File "<doctest examples.levelSet.distanceFunction.interior[0]>", line 1, in <module>
2024-11-30T00:17:15.0593855Z         var.calcDistanceFunction(order=1) #doctest: +LSM
2024-11-30T00:17:15.0594080Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0594332Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0594637Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0594889Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0595138Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0595420Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0595642Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0595865Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0596138Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0596457Z File "d:\a\1\s\examples\levelSet\distanceFunction\interior.py", line 34, in examples.levelSet.distanceFunction.interior
2024-11-30T00:17:15.0596727Z Failed example:
2024-11-30T00:17:15.0596961Z     print(var.allclose(values, atol = 1e-10)) #doctest: +LSM
2024-11-30T00:17:15.0597243Z Expected:
2024-11-30T00:17:15.0597445Z     1
2024-11-30T00:17:15.0597641Z Got:
2024-11-30T00:17:15.0597836Z     False
2024-11-30T00:17:15.0597937Z 
2024-11-30T00:17:15.0598041Z 
2024-11-30T00:17:15.0598274Z ======================================================================
2024-11-30T00:17:15.0598547Z FAIL: mesh1D (examples.levelSet.advection)
2024-11-30T00:17:15.0598800Z Doctest: examples.levelSet.advection.mesh1D
2024-11-30T00:17:15.0599074Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0599351Z Traceback (most recent call last):
2024-11-30T00:17:15.0599610Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0599895Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0600178Z AssertionError: Failed doctest test for examples.levelSet.advection.mesh1D
2024-11-30T00:17:15.0600461Z   File "d:\a\1\s\examples\levelSet\advection\mesh1D.py", line 0, in mesh1D
2024-11-30T00:17:15.0600604Z 
2024-11-30T00:17:15.0600849Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0601202Z File "d:\a\1\s\examples\levelSet\advection\mesh1D.py", line 47, in examples.levelSet.advection.mesh1D
2024-11-30T00:17:15.0601575Z Failed example:
2024-11-30T00:17:15.0601810Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0602048Z Exception raised:
2024-11-30T00:17:15.0602283Z     Traceback (most recent call last):
2024-11-30T00:17:15.0602546Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0602852Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0603131Z       File "<doctest examples.levelSet.advection.mesh1D[12]>", line 1, in <module>
2024-11-30T00:17:15.0603395Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0603610Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0603867Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0604167Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0604417Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0604675Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0604966Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0605663Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0605895Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0606182Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0606496Z File "d:\a\1\s\examples\levelSet\advection\mesh1D.py", line 75, in examples.levelSet.advection.mesh1D
2024-11-30T00:17:15.0606756Z Failed example:
2024-11-30T00:17:15.0606991Z     print(var.allclose(answer)) #doctest: +LSM
2024-11-30T00:17:15.0607208Z Expected:
2024-11-30T00:17:15.0607394Z     1
2024-11-30T00:17:15.0607578Z Got:
2024-11-30T00:17:15.0607762Z     False
2024-11-30T00:17:15.0607879Z 
2024-11-30T00:17:15.0607975Z 
2024-11-30T00:17:15.0608239Z ======================================================================
2024-11-30T00:17:15.0608510Z FAIL: trench (examples.levelSet.advection)
2024-11-30T00:17:15.0608757Z Doctest: examples.levelSet.advection.trench
2024-11-30T00:17:15.0609019Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0609277Z Traceback (most recent call last):
2024-11-30T00:17:15.0609534Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0609812Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0610113Z AssertionError: Failed doctest test for examples.levelSet.advection.trench
2024-11-30T00:17:15.0610397Z   File "d:\a\1\s\examples\levelSet\advection\trench.py", line 0, in trench
2024-11-30T00:17:15.0610540Z 
2024-11-30T00:17:15.0610784Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0611086Z File "d:\a\1\s\examples\levelSet\advection\trench.py", line 37, in examples.levelSet.advection.trench
2024-11-30T00:17:15.0611351Z Failed example:
2024-11-30T00:17:15.0611574Z     var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0611796Z Exception raised:
2024-11-30T00:17:15.0612013Z     Traceback (most recent call last):
2024-11-30T00:17:15.0612273Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0612546Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0645421Z       File "<doctest examples.levelSet.advection.trench[16]>", line 1, in <module>
2024-11-30T00:17:15.0645938Z         var.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0646174Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0646447Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0646752Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0647014Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0647493Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0647775Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0648003Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0648222Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0648499Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0648797Z File "d:\a\1\s\examples\levelSet\advection\trench.py", line 52, in examples.levelSet.advection.trench
2024-11-30T00:17:15.0649065Z Failed example:
2024-11-30T00:17:15.0649306Z     print(var.allclose(answer, atol = 1e-1)) #doctest: +LSM
2024-11-30T00:17:15.0649527Z Expected:
2024-11-30T00:17:15.0649728Z     1
2024-11-30T00:17:15.0649909Z Got:
2024-11-30T00:17:15.0650096Z     False
2024-11-30T00:17:15.0650332Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0650638Z File "d:\a\1\s\examples\levelSet\advection\trench.py", line 73, in examples.levelSet.advection.trench
2024-11-30T00:17:15.0650901Z Failed example:
2024-11-30T00:17:15.0651258Z     print(var.allclose(answer, atol = 1e-1)) #doctest: +LSM
2024-11-30T00:17:15.0651483Z Expected:
2024-11-30T00:17:15.0651675Z     1
2024-11-30T00:17:15.0651869Z Got:
2024-11-30T00:17:15.0652054Z     False
2024-11-30T00:17:15.0652169Z 
2024-11-30T00:17:15.0652268Z 
2024-11-30T00:17:15.0652506Z ======================================================================
2024-11-30T00:17:15.0652773Z FAIL: square (examples.levelSet.surfactant)
2024-11-30T00:17:15.0653019Z Doctest: examples.levelSet.surfactant.square
2024-11-30T00:17:15.0653289Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0653546Z Traceback (most recent call last):
2024-11-30T00:17:15.0653802Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0654116Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0654399Z AssertionError: Failed doctest test for examples.levelSet.surfactant.square
2024-11-30T00:17:15.0654694Z   File "d:\a\1\s\examples\levelSet\surfactant\square.py", line 0, in square
2024-11-30T00:17:15.0654838Z 
2024-11-30T00:17:15.0655078Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0655390Z File "d:\a\1\s\examples\levelSet\surfactant\square.py", line 8, in examples.levelSet.surfactant.square
2024-11-30T00:17:15.0655652Z Failed example:
2024-11-30T00:17:15.0655898Z     distanceVariable.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0656129Z Exception raised:
2024-11-30T00:17:15.0656355Z     Traceback (most recent call last):
2024-11-30T00:17:15.0656620Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0656892Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0657173Z       File "<doctest examples.levelSet.surfactant.square[0]>", line 1, in <module>
2024-11-30T00:17:15.0657463Z         distanceVariable.calcDistanceFunction() #doctest: +LSM
2024-11-30T00:17:15.0657705Z         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0657952Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 312, in calcDistanceFunction
2024-11-30T00:17:15.0658262Z         self._value = distance(numerix.reshape(self._value, shape), dx=dx, order=order).flatten()
2024-11-30T00:17:15.0658516Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0658772Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 110, in distance
2024-11-30T00:17:15.0659060Z         d = cFastMarcher(phi, dx, flag, None, ext_mask,
2024-11-30T00:17:15.0659276Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0659497Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0659680Z 
2024-11-30T00:17:15.0659800Z 
2024-11-30T00:17:15.0660033Z ======================================================================
2024-11-30T00:17:15.0660315Z FAIL: expandingCircle (examples.levelSet.surfactant)
2024-11-30T00:17:15.0660587Z Doctest: examples.levelSet.surfactant.expandingCircle
2024-11-30T00:17:15.0660859Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0661119Z Traceback (most recent call last):
2024-11-30T00:17:15.0661417Z   File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 2256, in runTest
2024-11-30T00:17:15.0661701Z     raise self.failureException(self.format_failure(new.getvalue()))
2024-11-30T00:17:15.0661992Z AssertionError: Failed doctest test for examples.levelSet.surfactant.expandingCircle
2024-11-30T00:17:15.0662300Z   File "d:\a\1\s\examples\levelSet\surfactant\expandingCircle.py", line 0, in expandingCircle
2024-11-30T00:17:15.0662482Z 
2024-11-30T00:17:15.0662730Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0663042Z File "d:\a\1\s\examples\levelSet\surfactant\expandingCircle.py", line 26, in examples.levelSet.surfactant.expandingCircle
2024-11-30T00:17:15.0663382Z Failed example:
2024-11-30T00:17:15.0663603Z     for step in range(steps):
2024-11-30T00:17:15.0663840Z         velocity.setValue(surfactantVariable.interfaceVar * k)
2024-11-30T00:17:15.0664100Z         distanceVariable.extendVariable(velocity)
2024-11-30T00:17:15.0664346Z         timeStepDuration = cfl * dx / velocity.max()
2024-11-30T00:17:15.0664746Z         distanceVariable.updateOld()
2024-11-30T00:17:15.0665005Z         advectionEquation.solve(distanceVariable, dt = timeStepDuration)
2024-11-30T00:17:15.0665282Z         surfactantEquation.solve(surfactantVariable, dt=1)
2024-11-30T00:17:15.0665543Z         totalTime += timeStepDuration #doctest: +LSM
2024-11-30T00:17:15.0665774Z Exception raised:
2024-11-30T00:17:15.0666002Z     Traceback (most recent call last):
2024-11-30T00:17:15.0666255Z       File "C:\Miniconda\envs\myEnvironment\Lib\doctest.py", line 1368, in __run
2024-11-30T00:17:15.0666525Z         exec(compile(example.source, filename, "single",
2024-11-30T00:17:15.0666803Z       File "<doctest examples.levelSet.surfactant.expandingCircle[4]>", line 3, in <module>
2024-11-30T00:17:15.0667089Z         distanceVariable.extendVariable(velocity)
2024-11-30T00:17:15.0667403Z       File "D:\a\1\s\fipy\variables\distanceVariable.py", line 274, in extendVariable
2024-11-30T00:17:15.0667708Z         tmp, extensionValue = extension_velocities(phi, extensionValue, ext_mask=phi < 0., dx=dx, order=order)
2024-11-30T00:17:15.0667984Z                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0668265Z       File "C:\Miniconda\envs\myEnvironment\Lib\site-packages\skfmm\pfmm.py", line 239, in extension_velocities
2024-11-30T00:17:15.0668563Z         distance, f_ext = cFastMarcher(phi, dx, flag, speed, ext_mask,
2024-11-30T00:17:15.0668797Z                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-11-30T00:17:15.0669017Z     ValueError: flag must be a 1D to 12-D array of integers
2024-11-30T00:17:15.0669292Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0669614Z File "d:\a\1\s\examples\levelSet\surfactant\expandingCircle.py", line 54, in examples.levelSet.surfactant.expandingCircle
2024-11-30T00:17:15.0669885Z Failed example:
2024-11-30T00:17:15.0670141Z     print(numerix.sqrt(numerix.sum(error) / numerix.sum(error > 0)) < 0.02) #doctest: +LSM
2024-11-30T00:17:15.0670382Z Expected:
2024-11-30T00:17:15.0670577Z     1
2024-11-30T00:17:15.0670757Z Got:
2024-11-30T00:17:15.0670956Z     False
2024-11-30T00:17:15.0671075Z 
2024-11-30T00:17:15.0671171Z 
2024-11-30T00:17:15.0671412Z ----------------------------------------------------------------------
2024-11-30T00:17:15.0671761Z Ran 541 tests in 128.015s
2024-11-30T00:17:15.0671900Z 
2024-11-30T00:17:15.0672107Z FAILED (failures=9)
2024-11-30T00:17:15.0672371Z !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
2024-11-30T00:17:15.0672661Z Skipped 83 doctest examples because the `tvtk` package cannot be imported
2024-11-30T00:17:15.0672952Z !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
2024-11-30T00:17:15.0673106Z 
2024-11-30T00:17:15.0673399Z python      3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 15:47:54) [MSC v.1941 64 bit (AMD64)]
2024-11-30T00:17:15.0673691Z fipy        3.4.5+11.ge7afd1a58
2024-11-30T00:17:15.0673909Z numpy       2.1.3
2024-11-30T00:17:15.0674114Z pysparse    not installed
2024-11-30T00:17:15.0674320Z scipy       1.14.1
2024-11-30T00:17:15.0674519Z matplotlib  3.9.2
2024-11-30T00:17:15.0674732Z mpi4py      not installed
2024-11-30T00:17:15.0674949Z petsc4py    not installed
2024-11-30T00:17:15.0675159Z pyamgx      not installed
2024-11-30T00:17:15.0675375Z PyTrilinos  not installed
2024-11-30T00:17:15.0675580Z mayavi      4.8.2
2024-11-30T00:17:15.0675778Z gmsh        4.13.1
2024-11-30T00:17:15.0675981Z solver      scipy

@guyer
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guyer commented Dec 10, 2024

Seems to work now

@guyer guyer closed this as not planned Won't fix, can't repro, duplicate, stale Dec 10, 2024
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