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.flake8

+3 −3

Original line number	Diff line number	Diff line
		[flake8]
		max-line-length=120
		exclude=lbmpy/plot.py
		lbmpy/session.py
		ignore = W293 W503 W291 E741
		exclude=src/lbmpy/plot.py
		src/lbmpy/session.py
		ignore = W293 W503 W291 C901 E741

.gitattributes

+1 −1

Original line number	Diff line number	Diff line
		lbmpy/_version.py export-subst
		src/lbmpy/_version.py export-subst

.gitignore

+10 −6

Original line number	Diff line number	Diff line
		__pycache__
		.ipynb_checkpoints
		.coverage
		.coverage*
		*.pyc
		*.vti
		/build
		/html_doc
		/dist
		/*.egg-info
		*.egg-info
		.cache
		_build
		/.idea
		@@ -15,14 +15,18 @@ _local_tmp
		**/pylintrc
		*.bak
		*.tmp
		/lbmpy_tests/db
		/tests/db
		doc/bibtex.json
		/db
		/lbmpy/phasefield/simplex_projection.*.so
		/lbmpy/phasefield/simplex_projection.c
		/src/lbmpy/phasefield/simplex_projection.*.so
		/src/lbmpy/phasefield/simplex_projection.c

		test-report
		report.xml

		# macOS
		**/.DS_Store
		*.uuid

		# benchmark database
		/lbmpy_tests/benchmark/db
		No newline at end of file
		/tests/benchmark/db
		No newline at end of file

.gitlab-ci.yml

+130 −140

Original line number	Diff line number	Diff line
		stages:
		- pretest
		- test
		- "Code Quality"
		- "Tests"
		- "Prerelease-Tests"
		- integration
		- nightly
		- docs
		- deploy

		# -------------------------- Code Quality --------------------------------------------------------------------------------

		# -------------------------- Pre Tests --------------------------------------------------------------------------------

		# Linter for code formatting
		flake8-lint:
		stage: "Code Quality"
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine
		script:
		- nox -s lint
		tags:
		- docker


		# -------------------------- Tests --------------------------------------------------------------------------------

		# Normal test - runs on every commit all but "long run" tests
		tests-and-coverage:
		stage: pretest
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		testsuite-cuda-py3.10:
		stage: "Tests"
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6
		needs: []
		script:
		# - pip install sympy --upgrade
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- mkdir public
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- env
		- pip list
		- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun" --junitxml=report.xml
		- python3 -m coverage xml
		- nox -s "testsuite_gpu-3.10(cupy12)"
		tags:
		- docker
		- cuda11
		- cuda
		- cudaComputeCapability6.1
		- AVX
		coverage: /Total coverage:\s\d+.\d+\%/
		artifacts:
		when: always
		paths:
		- coverage_report
		- test-report
		reports:
		coverage_report:
		coverage_format: cobertura
		path: coverage.xml
		junit: report.xml


		testsuite-cpu-py3.13:
		stage: "Tests"
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine
		needs: []
		script:
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- nox -s "testsuite_cpu-3.13"
		tags:
		- docker
		- AVX
		artifacts:
		when: always
		paths:
		- test-report
		reports:
		junit: report.xml


		# Normal test with longruns
		tests-and-coverage-with-longrun:
		stage: test
		stage: "Tests"
		when: manual
		allow_failure: true
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		@@ -57,161 +86,120 @@ tests-and-coverage-with-longrun:
		- py.test -v -n $NUM_CORES
		tags:
		- docker
		- cuda11
		- cuda
		- cudaComputeCapability6.1
		- AVX

		minimal-conda:
		stage: pretest
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
		script:
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- python setup.py quicktest
		tags:
		- docker
		# -------------------------- Nightly and Pre-Release Tests --------------------------------------------------------------------------------

		# Linter for code formatting
		flake8-lint:
		stage: pretest
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		script:
		- flake8 lbmpy
		tags:
		- docker
		- cuda11

		# -------------------------- Tests -------------------------------------------------------------------------------------

		# pipeline with latest python version
		latest-python:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
		before_script:
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		# Test against latest pystencils 2.0 development version
		pystencils-2.0dev:
		stage: "Prerelease-Tests"
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6
		allow_failure: true
		needs: []
		script:
		- env
		- pip list
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- mkdir public
		- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		- nox -s "testsuite_pystencils2(cupy12)"
		tags:
		- docker
		- AVX
		- cuda
		- cudaComputeCapability6.1
		artifacts:
		when: always
		paths:
		- test-report
		reports:
		junit: report.xml

		# Minimal tests in windows environment
		minimal-windows:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		tags:
		- win
		script:
		- export NUM_CORES=$(nproc --all)
		- export MPLBACKEND=Agg
		- source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
		- source activate pystencils
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- python -c "import numpy"
		- pip install sympy==1.9
		- py.test -v -m "not (notebook or longrun)"

		minimal-sympy-master:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
		stage: "Prerelease-Tests"
		needs: []
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine
		script:
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- python -m pip install --upgrade git+https://github.com/sympy/sympy.git
		- pip list
		- python setup.py quicktest
		- nox -s quicktest -P 3.13 -- --sympy-master
		allow_failure: true
		tags:
		- docker
		- cuda

		ubuntu:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
		# pycodegen-integration:
		# image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		# stage: integration
		# when: manual
		# allow_failure: true
		# script:
		# - env
		# - pip list
		# - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
		# - cd pycodegen
		# - git submodule sync --recursive
		# - git submodule update --init --recursive
		# - git submodule foreach git fetch origin # compare the latest master version!
		# - git submodule foreach git reset --hard origin/master
		# - cd lbmpy
		# - git remote add test $CI_REPOSITORY_URL
		# - git fetch test
		# - git reset --hard $CI_COMMIT_SHA
		# - cd ..
		# - pip install -e pystencils/
		# - pip install -e lbmpy/
		# - ./install_walberla.sh
		# # build all integration tests
		# - cd walberla/build/
		# - make -j $NUM_CORES MicroBenchmarkGpuLbm LbCodeGenerationExample
		# - cd apps/benchmarks/UniformGridGPU
		# - make -j $NUM_CORES
		# - cd ../UniformGridCPU
		# - make -j $NUM_CORES

		# tags:
		# - docker
		# - cuda
		# - cudaComputeCapability6.1
		# - AVX


		# -------------------- Scheduled Tasks --------------------------------------------------------------------------


		nightly-sympy:
		stage: nightly
		rules:
		- if: $CI_PIPELINE_SOURCE == "schedule"
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
		before_script:
		# - apt-get -y remove python3-sympy
		- ln -s /usr/include/locale.h /usr/include/xlocale.h
		# - pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py \| sed 's/>/=/g'`
		- pip3 install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- pip install -e .
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		- pip install --upgrade --pre sympy
		script:
		- env
		- pip list
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- env
		- pip3 list
		- pytest-3 -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		- mkdir public
		- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		tags:
		- docker
		- cuda11
		- AVX
		- cuda
		- cudaComputeCapability6.1
		artifacts:
		when: always
		reports:
		junit: report.xml

		pycodegen-integration:
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		stage: test
		when: manual
		allow_failure: true
		script:
		- env
		- pip list
		- git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
		- cd pycodegen
		- git submodule sync --recursive
		- git submodule update --init --recursive
		- git submodule foreach git fetch origin # compare the latest master version!
		- git submodule foreach git reset --hard origin/master
		- cd lbmpy
		- git remote add test $CI_REPOSITORY_URL
		- git fetch test
		- git reset --hard $CI_COMMIT_SHA
		- cd ..
		- pip install -e pystencils/
		- pip install -e lbmpy/
		- ./install_walberla.sh
		# build all integration tests
		- cd walberla/build/
		- make -j $NUM_CORES MicroBenchmarkGpuLbm LbCodeGenerationExample
		- cd apps/benchmarks/UniformGridGPU
		- make -j $NUM_CORES
		- cd ../UniformGridCPU
		- make -j $NUM_CORES

		tags:
		- docker
		- cuda11
		- AVX

		# -------------------- Documentation and deploy ------------------------------------------------------------------------

		build-documentation:
		stage: test
		stage: docs
		needs: []
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
		before_script:
		- pip install -e .
		script:
		- export PYTHONPATH=`pwd`
		- pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
		@@ -219,7 +207,8 @@ build-documentation:
		- sphinx-build -W -b html doc html_doc
		tags:
		- docker
		- cuda11
		- cuda
		- cudaComputeCapability6.1
		artifacts:
		paths:
		- html_doc
		@@ -227,7 +216,10 @@ build-documentation:

		pages:
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		rules:
		- if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/lbmpy" && $CI_COMMIT_BRANCH == "master"'
		stage: deploy
		needs: ["testsuite-cuda-py3.10", "build-documentation"]
		script:
		- ls -l
		- mv coverage_report html_doc
		@@ -237,5 +229,3 @@ pages:
		- public
		tags:
		- docker
		only:
		- master@pycodegen/lbmpy

AUTHORS.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -11,3 +11,4 @@ Contributors:
		- Rudolf Weeber <weeber@icp.uni-stuttgart.de>
		- Christian Godenschwager <christian.godenschwager@fau.de>
		- Jan Hönig <jan.hoenig@fau.de>
		- Philipp Suffa <philipp.suffa@fau.de>

COPYING.txt

+0 −12

Original line number	Diff line number	Diff line
		------------------------ Important ---------------------------------

		lbmpy is under the following GNU AGPLv3 license.
		This license holds for the sources of lbmpy itself as well
		as for all kernels generated with lbmpy i.e.
		the output of lbmpy is also protected by the GNU AGPLv3 license.

		----------------------------------------------------------------------




		GNU AFFERO GENERAL PUBLIC LICENSE
		Version 3, 19 November 2007

MANIFEST.in

+1 −5

Original line number	Diff line number	Diff line
		include README.md
		include COPYING.txt
		include AUTHORS.txt
		include CONTRIBUTING.md
		global-include *.pyx
		include versioneer.py
		include lbmpy/_version.py
		include CHANGELOG.md

README.md

+1 −0

Original line number	Diff line number	Diff line
		@@ -71,6 +71,7 @@ Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/lbmpy/-/
		If you use lbmpy in a publication, please cite the following articles:

		Overview:
		- F. Hennig et al, Advanced Automatic Code Generation for Multiple Relaxation-Time Lattice Boltzmann Methods. SIAM Journal on Scientific Computing, 2023. https://doi.org/10.1137/22M1531348 ([Preprint](https://arxiv.org/abs/2211.02435))
		- M. Bauer et al, lbmpy: Automatic code generation for efficient parallel lattice Boltzmann methods. Journal of Computational Science, 2021. https://doi.org/10.1016/j.jocs.2020.101269 ([Preprint](https://arxiv.org/abs/2001.11806))

		Multiphase:

binder/environment.yml

+2 −2

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@
		# conda env create -f conda_environment_user.yml
		# . activate pystencils
		#
		# If you have CUDA installed and want to use your GPU, uncomment the last line to install pycuda
		# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy
		#
		# ----------------------------------------------------------------------------------------------------------------------

		@@ -33,4 +33,4 @@ dependencies:
		- pyevtk # VTK output for serial simulations
		- blitzdb # file-based No-SQL database to store simulation results
		- pystencils
		#- pycuda # add this if you have CUDA installed
		#- cupy # add this if you have CUDA or ROCm installed

conftest.py

+51 −21

Original line number	Diff line number	Diff line
		@@ -5,12 +5,17 @@ import runpy
		import sys
		import warnings
		import platform
		import pathlib

		import nbformat
		from nbconvert import PythonExporter
		import nbconvert
		import sympy

		from lbmpy._compat import IS_PYSTENCILS_2

		# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it
		# at the same time
		if not IS_PYSTENCILS_2:
		from pystencils.cpu import cpujit

		# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file
		@@ -19,9 +24,9 @@ try:
		import pyximport

		pyximport.install(language_level=3)
		from lbmpy.phasefield.simplex_projection import simplex_projection_2d # NOQA
		except ImportError:
		pass
		from lbmpy.phasefield.simplex_projection import simplex_projection_2d # NOQA

		SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
		sys.path.insert(0, os.path.abspath('lbmpy'))
		@@ -42,33 +47,42 @@ def add_path_to_ignore(path):

		collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
		os.path.join(SCRIPT_FOLDER, "doc", "img", "mb_discretization", "maxwell_boltzmann_stencil_plot.py")]
		add_path_to_ignore('pystencils_tests/benchmark')
		add_path_to_ignore('_local_tmp')

		if IS_PYSTENCILS_2:
		# TODO: Fix these step-by-step
		collect_ignore += [
		os.path.join(SCRIPT_FOLDER, "doc", "notebooks", "10_tutorial_conservative_allen_cahn_two_phase.ipynb"),
		os.path.join(SCRIPT_FOLDER, "tests", "test_compiled_in_boundaries.ipynb")
		]

		try:
		import pycuda
		import cupy
		except ImportError:
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_cpu_gpu_equivalence.py")]
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_cpu_gpu_equivalence.py")]

		try:
		import waLBerla
		except ImportError:
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_datahandling_parallel.py")]
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py")]

		try:
		import blitzdb
		except ImportError:
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/benchmark"),
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/benchmark"),
		os.path.join(SCRIPT_FOLDER,
		"lbmpy_tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py")]
		"tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py"),
		os.path.join(SCRIPT_FOLDER, "tests/full_scenarios/shear_wave/scenario_shear_wave.py"),
		os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py"),
		os.path.join(SCRIPT_FOLDER, "src/lbmpy/db.py")]

		if platform.system().lower() == 'windows':
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_quicktests.py")]
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_quicktests.py")]

		sver = sympy.__version__.split(".")
		if int(sver[0]) == 1 and int(sver[1]) < 2:
		add_path_to_ignore('lbmpy_tests/phasefield')
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_n_phase_boyer_noncoupled.ipynb")]
		add_path_to_ignore('tests/phasefield')
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_n_phase_boyer_noncoupled.ipynb")]

		collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]

		@@ -104,22 +118,29 @@ class IPyNbTest(pytest.Item):

		# disable matplotlib output
		exec("import matplotlib.pyplot as p; "
		"p.close('all'); "
		"p.switch_backend('Template')", global_dict)

		# in notebooks there is an implicit plt.show() - if this is not called a warning is shown when the next
		# plot is created. This warning is suppressed here
		# Also animations cannot be shown, which also leads to a warning.
		exec("import warnings;"
		"warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*');",
		"warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*');"
		"warnings.filterwarnings('ignore', 'Animation was deleted without rendering anything.*');",
		global_dict)
		with tempfile.NamedTemporaryFile() as f:
		f.write(self.code.encode())
		f.flush()
		runpy.run_path(f.name, init_globals=global_dict, run_name=self.name)

		# Close any open figures
		exec("import matplotlib.pyplot as p; "
		"p.close('all')", global_dict)


		class IPyNbFile(pytest.File):
		def collect(self):
		exporter = PythonExporter()
		exporter = nbconvert.PythonExporter()
		exporter.exclude_markdown = True
		exporter.exclude_input_prompt = True

		@@ -138,6 +159,15 @@ class IPyNbFile(pytest.File):
		pass


		if pytest_version >= 70000:
		# Since pytest 7.0, usage of `py.path.local` is deprecated and `pathlib.Path` should be used instead
		import pathlib

		def pytest_collect_file(file_path: pathlib.Path, parent):
		glob_exprs = ["demo.ipynb", "tutorial.ipynb", "test_*.ipynb"]
		if any(file_path.match(g) for g in glob_exprs):
		return IPyNbFile.from_parent(path=file_path, parent=parent)
		else:
		def pytest_collect_file(path, parent):
		glob_exprs = ["demo.ipynb", "tutorial.ipynb", "test_*.ipynb"]
		if any(path.fnmatch(g) for g in glob_exprs):

doc/conf.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -33,7 +33,7 @@ version = re.sub(r'(\d+\.\d+)\.\d+(.*)', r'\1\2', lbmpy.__version__)
		version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
		# The full version, including alpha/beta/rc tags.
		release = lbmpy.__version__
		language = None
		language = 'en'
		exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
		default_role = 'any'
		pygments_style = 'sphinx'

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doc/notebooks/00_tutorial_lbmpy_walberla_overview.ipynb