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mlemayTTEMartin LEMAY
mlemayTTE
and
Martin LEMAY
authored
ci: Update CI to include new packages, typing and tests (#65)
* Add test and check workflow add pytest, mypy, and linting actions for selected packages * remove duplicated module install * Add test and check workflow add pytest, mypy, and linting actions for selected packages * remove duplicated module install * add dependency for test and set mypy and pytest * Remove py38 and py39 from build * Add sudo to install libgl1 * Update mypy ci and pyprojects and minor corrections * restore doc-test workflow * Exclude build folder from mypy * create separate workflow for typing * remove package build from typing workflow * fix test ci and check typing with single python version * fix tests * linting and test fix * disable coverage * wrap test command to avoid error when no tests * Fix ci trame xml-tools * Fix ci trame xml-tools 2 * Disable failing tests on trame * Disable failing tests on trame linting * Add semantic check * ci: Add semantic check * rerun ci * linting after merge with main * Fix merge issues and ci fix * Remove geomechanics tests from geos-posp * Add ruff to ci and ruff fix --------- Co-authored-by: Martin LEMAY <[email protected]>
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‎.github/workflows/python-package.yml‎

Lines changed: 36 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -8,15 +8,39 @@ concurrency:
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jobs:
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build:
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# Checks if PR title follows conventional semantics
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semantic_pull_request:
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permissions:
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pull-requests: write # for amannn/action-semantic-pull-request to analyze PRs and
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statuses: write # for amannn/action-semantic-pull-request to mark status of analyzed PR
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contents: read
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runs-on: ubuntu-latest
18+
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steps:
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- name: Check if the PR name has conventional semantics
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if: github.event_name == 'pull_request'
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uses: amannn/[email protected]
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id: lint_pr_title
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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wip: true
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# Configure that a scope doesn't need to be provided.
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requireScope: false
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- name: Skip the check on main branch
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if: github.ref_name == 'main'
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run: |
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echo "This is not a Pull-Request, skipping"
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build:
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runs-on: ubuntu-22.04
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strategy:
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fail-fast: false
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max-parallel: 3
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
19-
package-name: ["geos-ats", "geos-mesh", "geos-timehistory", "geos-xml-tools", "hdf5-wrapper", "pygeos-tools"]
42+
python-version: ["3.10", "3.11", "3.12"]
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package-name: ["geos-ats", "geos-mesh", "geos-posp", "geos-timehistory", "geos-trame", "geos-utils", "geos-xml-tools", "geos-xml-viewer", "hdf5-wrapper", "pygeos-tools"]
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steps:
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- uses: actions/checkout@v3
@@ -31,12 +55,15 @@ jobs:
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run: |
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python -m pip install --upgrade pip
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python -m pip install pytest yapf toml
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python -m pip install ${{ matrix.package-name }}/
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python -m pip install ./${{ matrix.package-name }}/[test]
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- name: Lint with yapf
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# working-directory: ./${{ matrix.package-name }}
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run: |
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yapf -r --diff ${{ matrix.package-name }} --style .style.yapf
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# - name: Test with pytest
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# working-directory: ./${{ matrix.package-name }}
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# run: |
42-
# pytest
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yapf -r --diff ./${{ matrix.package-name }} --style .style.yapf
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- name: Test with pytest
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#working-directory: ./${{ matrix.package-name }}
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run:
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# python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
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# wrap pytest to avoid error when no tests in the package
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sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
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‎.github/workflows/typing-check.yml‎

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@@ -0,0 +1,43 @@
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name: "Pull Request Typing Check"
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on:
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- pull_request
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# Cancels in-progress workflows for a PR when updated
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build:
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runs-on: ubuntu-22.04
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strategy:
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fail-fast: false
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max-parallel: 3
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matrix:
18+
# add packages to check typing
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package-name: ["hdf5-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-xml-tools", "hdf5-wrapper"]
20+
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steps:
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- uses: actions/checkout@v3
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- uses: mpi4py/setup-mpi@v1
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
27+
python-version: "3.10"
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cache: 'pip'
29+
- name: Install package
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# working-directory: ./${{ matrix.package-name }}
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run: |
32+
python -m pip install --upgrade pip
33+
python -m pip install mypy ruff
34+
35+
- name: Typing check with mypy
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# working-directory: ./${{ matrix.package-name }}
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run: |
38+
python -m mypy --config-file ./.mypy.ini --check-untyped-defs ./${{ matrix.package-name }}
39+
40+
- name: Format and linting check with ruff
41+
# working-directory: ./${{ matrix.package-name }}
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run: |
43+
python -m ruff check --config .ruff.toml ./geos-utils

‎.mypy.ini‎

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@@ -0,0 +1,19 @@
1+
[mypy]
2+
python_version = 3.10
3+
4+
# strict = true
5+
warn_unreachable = true
6+
implicit_reexport = true
7+
show_error_codes = true
8+
show_column_numbers = true
9+
ignore_missing_imports = true
10+
warn_unused_configs = true
11+
allow_redefinition = false
12+
13+
# ignore files in the tests directory
14+
[mypy-tests.*]
15+
ignore_errors = True
16+
17+
# ignore files in the build directory
18+
[mypy-build.*]
19+
ignore_errors = True

‎.ruff.toml‎

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1+
# Exclude a variety of commonly ignored directories.
2+
extend-exclude = ["tests/data"]
3+
4+
line-length = 120
5+
indent-width = 4
6+
7+
# Assume Python 3.9
8+
target-version = "py39"
9+
10+
[lint]
11+
12+
# Allow fix for all enabled rules (when `--fix`) is provided.
13+
fixable = ["ALL"]
14+
unfixable = []
15+
16+
# Allow unused variables when underscore-prefixed.
17+
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
18+
19+
select = [
20+
"E", # pycodestyle errors
21+
"W", # pycodestyle warnings
22+
"F", # pyflakes
23+
# "UP", # pyupgrade deactivate since python39
24+
"B", # flake8-bugbear
25+
"SIM", # flake8-simplify
26+
"ANN", # flake8-annotations
27+
"C4", # flake8-comprehensions
28+
# "I", # isort - manage by yapf
29+
"D", # pydocstyle
30+
]
31+
32+
ignore = [
33+
"E501", # line too long, handled by yapf
34+
"B008", # do not perform function calls in argument defaults
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"C901", # too complex
36+
"W191", # indentation contains tabs
37+
"D100",
38+
"D101",
39+
"D104", # Missing docstring in public package in __init__.py files
40+
"UP007",
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"ANN401", # allows Any return
42+
]
43+
44+
[lint.pydocstyle]
45+
convention = "google"
46+
47+
[format]
48+
# Like Black, use double quotes for strings.
49+
quote-style = "double"
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51+
# Like Black, indent with spaces, rather than tabs.
52+
indent-style = "space"
53+
54+
# Like Black, respect magic trailing commas.
55+
skip-magic-trailing-comma = false
56+
57+
# Like Black, automatically detect the appropriate line ending.
58+
line-ending = "auto"
59+
60+
# Enable auto-formatting of code examples in docstrings. Markdown,
61+
# reStructuredText code/literal blocks and doctests are all supported.
62+
docstring-code-format = true
63+
64+
# Set the line length limit used when formatting code snippets in
65+
# docstrings.
66+
docstring-code-line-length = "dynamic"

‎docs/conf.py‎

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Original file line numberDiff line numberDiff line change
@@ -17,8 +17,8 @@
1717

1818
# Add python modules to be documented
1919
python_root = '..'
20-
python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper',
21-
'pygeos-tools', 'geos-geomechanics' )
20+
python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'pygeos-tools', 'geos-geomechanics' )
21+
2222
for m in python_modules:
2323
sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
2424

@@ -42,15 +42,16 @@
4242
# Add any Sphinx extension module names here, as strings. They can be
4343
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
4444
# ones.
45-
extensions = [ 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput',
46-
'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon',
47-
'sphinx.ext.todo', 'sphinx.ext.viewcode' ]
45+
extensions = [
46+
'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 'sphinx.ext.autodoc',
47+
'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
48+
]
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4950
autoclass_content = 'both'
5051
autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy" ]
5152
autodoc_typehints = 'none'
5253
autodoc_typehints_format = 'short'
53-
suppress_warnings = [""]
54+
suppress_warnings = [ "" ]
5455
typehints_defaults = 'braces'
5556

5657
# The suffix(es) of source filenames.

‎geos-ats/pyproject.toml‎

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2626
"pyyaml",
2727
"tqdm",
2828
"requests",
29+
"scipy",
2930
"GitPython",
3031
"google-cloud-storage",
3132
"pip-system-certs",
@@ -51,3 +52,22 @@ include-package-data = true
5152

5253
[tool.setuptools.package-data]
5354
"*" = ["*.js", "*.css", "*.zip"]
55+
56+
[tool.pytest.ini_options]
57+
addopts = [
58+
"--import-mode=importlib",
59+
]
60+
console_output_style = "count"
61+
python_classes = "Test"
62+
python_files = "tests_*.py"
63+
python_functions = "tests*"
64+
testpaths = ["tests"]
65+
pythonpath = [
66+
"src",
67+
]
68+
norecursedirs = "bin"
69+
filterwarnings = []
70+
71+
[tool.coverage.run]
72+
branch = true
73+
source = ["src/geos/"]

‎geos-geomechanics/src/geos/geomechanics/model/MohrCircle.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
import numpy.typing as npt
66
from typing_extensions import Self
77

8-
from geos.geomechanics.processing.geomechanicsCalculatorFunctions import (
8+
from geos_posp.processing.geomechanicsCalculatorFunctions import (
99
computeStressPrincipalComponentsFromStressVector, )
1010

1111
__doc__ = """

‎geos-geomechanics/src/geos/geomechanics/model/MohrCoulomb.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -92,5 +92,5 @@ def computeFailureEnvelop(
9292
element is the ordinates.
9393
"""
9494
sigmaMin: float = ( self.m_sigmaMin if stressNormalMin is None else stressNormalMin )
95-
stressNormal: npt.NDArray[ np.float64 ] = np.linspace( sigmaMin, stressNormalMax, n )
95+
stressNormal: npt.NDArray[ np.float64 ] = np.linspace( sigmaMin, stressNormalMax, n ).astype( np.float64 )
9696
return ( stressNormal, np.array( self.computeShearStress( stressNormal ) ) )

‎geos-geomechanics/src/geos/geomechanics/processing/geomechanicsCalculatorFunctions.py‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,11 @@
11
# SPDX-License-Identifier: Apache-2.0
22
# # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
33
# SPDX-FileContributor: Alexandre Benedicto, Martin Lemay
4+
from typing import Any
45
import numpy as np
56
import numpy.typing as npt
67

7-
from geos.geomechanics.model.MohrCoulomb import MohrCoulomb
8+
from geos_posp.processing.MohrCoulomb import MohrCoulomb
89
from geos.utils.algebraFunctions import getAttributeMatrixFromVector
910
from geos.utils.PhysicalConstants import (
1011
EPSILON, )
@@ -30,7 +31,7 @@ def specificGravity( density: npt.NDArray[ np.float64 ], specificDensity: float
3031

3132
if abs( specificDensity ) < EPSILON:
3233
return np.full_like( density, np.nan )
33-
return density / specificDensity
34+
return ( density / specificDensity ).astype( np.float64 )
3435

3536

3637
# https://en.wikipedia.org/wiki/Elastic_modulus
@@ -666,7 +667,7 @@ def criticalPorePressure(
666667
# assertion frictionAngle < np.pi/2., so sin(frictionAngle) != 1
667668
cohesiveTerm: npt.NDArray[ np.float64 ] = ( rockCohesion * np.cos( frictionAngle ) /
668669
( 1 - np.sin( frictionAngle ) ) )
669-
residualTerm: npt.NDArray[ np.float64 ] = ( 3 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
670+
residualTerm: npt.NDArray[ np.floating[ Any ] ] = ( 3 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
670671
return cohesiveTerm + residualTerm
671672

672673

@@ -848,7 +849,8 @@ def shearCapacityUtilization( traction: npt.NDArray[ np.float64 ], rockCohesion:
848849
assert traction.shape[ 1 ] == 3, "Traction vector must have 3 components."
849850

850851
scu: npt.NDArray[ np.float64 ] = np.full( traction.shape[ 0 ], np.nan )
851-
for i, tractionVec in enumerate( traction ):
852+
for i in range( traction.shape[ 0 ] ):
853+
tractionVec: npt.NDArray[ np.float64 ] = traction[ i ]
852854
# use -1 to agree with Geos convention (i.e., compression with negative stress)
853855
stressNormal: npt.NDArray[ np.float64 ] = -1.0 * tractionVec[ 0 ]
854856

‎geos-geomechanics/tests/testsFunctionsGeomechanicsCalculator.py‎

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Original file line numberDiff line numberDiff line change
@@ -9,7 +9,6 @@
99

1010
import numpy as np
1111
import numpy.typing as npt
12-
import pandas as pd # type: ignore[import-untyped]
1312
from typing_extensions import Self
1413

1514
dir_path = os.path.dirname( os.path.realpath( __file__ ) )
@@ -247,9 +246,9 @@ def test_shearCapacityUtilization( self: Self ) -> None:
247246

248247
# calculation
249248
obtained: npt.NDArray[ np.float64 ] = fcts.shearCapacityUtilization( traction, rockCohesion, frictionAngle )
250-
expected: npt.NDArray[ np.float64 ] = np.array( [ 0.899, 0.923, 0.982, 1.004, 1.048 ] )
249+
expected: list[ float ] = [ 0.899, 0.923, 0.982, 1.004, 1.048 ]
251250

252-
self.assertSequenceEqual( np.round( obtained, 3 ).flatten().tolist(), expected.tolist() )
251+
self.assertSequenceEqual( np.round( obtained, 3 ).flatten().tolist(), expected )
253252

254253
def test_computeStressPrincipalComponents( self: Self ) -> None:
255254
"""Test calculation of stress principal components from stress tensor."""

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