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.flake8

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	[flake8]		[flake8]
	max-line-length=120		max-line-length=120
	exclude=pystencils/jupyter.py,		exclude=src/pystencils/jupyter.py,
	pystencils/plot.py		src/pystencils/plot.py
	pystencils/session.py		src/pystencils/session.py
	ignore = W293 W503 W291 C901		ignore = W293 W503 W291 C901 E741

.gitattributes

0 → 100644

+1 −0

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

.gitignore

+17 −2

Original line number	Original line	Diff line number	Diff line
	__pycache__		__pycache__
	.ipynb_checkpoints		.ipynb_checkpoints
	.coverage		.coverage*
	*.pyc		*.pyc
	*.vti		*.vti
	/build		/build
	/dist		/dist
	/*.egg-info		*.egg-info
	.cache		.cache
	_build		_build
			/html_doc
	/.idea		/.idea
			.vscode
	.cache		.cache
	_local_tmp		_local_tmp
	RELEASE-VERSION		RELEASE-VERSION
	test-report		test-report
			src/pystencils/boundaries/createindexlistcython.c
			src/pystencils/boundaries/createindexlistcython.*.so
			tests/tmp
			tests/var
			tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
			tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
			report.xml
			coverage_report/


			# macOS
			**/.DS_Store
			*.uuid

.gitlab-ci.yml

+241 −63

Original line number	Original line	Diff line number	Diff line
	stages:		stages:
			- pretest
	- test		- test
			- nightly
			- docs
	- deploy		- deploy


			# -------------------------- Templates ------------------------------------------------------------------------------------

			# Base configuration for jobs meant to run at every commit
			.every-commit:
			rules:
			- if: $CI_PIPELINE_SOURCE != "schedule"

			# Configuration for jobs meant to run on each commit to pycodegen/pystencils/master
			.every-commit-master:
			rules:
			- if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/pystencils" && $CI_COMMIT_BRANCH == "master"'

			# Base configuration for jobs meant to run at a schedule
			.scheduled:
			rules:
			- if: $CI_PIPELINE_SOURCE == "schedule"

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

	# Normal test - runs on every commit all but "long run" tests		# Normal test - runs on every commit all but "long run" tests
	tests-and-coverage:		tests-and-coverage:
	stage: test		stage: pretest
	except:		extends: .every-commit
	variables:		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
	- $ENABLE_NIGHTLY_BUILDS		before_script:
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		- pip install -e .
	script:		script:
			- env
			- pip list
	- export NUM_CORES=$(nproc --all)		- export NUM_CORES=$(nproc --all)
	- mkdir -p ~/.config/matplotlib		- mkdir -p ~/.config/matplotlib
	- echo "backend:template" > ~/.config/matplotlib/matplotlibrc		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
	- mkdir public		- mkdir public
	- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun" --html test-report/index.html		- pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
			- python -m coverage xml
	tags:		tags:
	- docker		- docker
	- cuda		- cuda11
	- AVX		- AVX
			coverage: /Total coverage:\s\d+.\d+\%/
	artifacts:		artifacts:
	when: always		when: always
	paths:		paths:
	- coverage_report		- coverage_report
	- test-report		- test-report
			reports:
			coverage_report:
			coverage_format: cobertura
			path: coverage.xml
			junit: report.xml

	# Nightly test - runs "long run" jobs only		# Normal test with longruns
	test-longrun:		tests-and-coverage-with-longrun:
	stage: test		stage: test
	only:		when: manual
	variables:		allow_failure: true
	- $ENABLE_NIGHTLY_BUILDS		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		before_script:
			- pip install sympy --upgrade
			- pip install -e .
	script:		script:
			- env
			- pip list
	- export NUM_CORES=$(nproc --all)		- export NUM_CORES=$(nproc --all)
	- mkdir -p ~/.config/matplotlib		- mkdir -p ~/.config/matplotlib
	- echo "backend:template" > ~/.config/matplotlib/matplotlibrc		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
	- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. --html test-report/index.html		- mkdir public
			- py.test -v -n $NUM_CORES
			tags:
			- docker
			- cuda11
			- AVX

			# pipeline with latest python version
			latest-python:
			stage: test
			extends: .every-commit
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
			before_script:
			- pip install -e .
			script:
			- env
			- pip list
			- pip install -e .
			- 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
	tags:		tags:
	- docker		- docker
	- cuda
	- AVX		- AVX
	artifacts:		artifacts:
	paths:		when: always
	- coverage_report		reports:
	- test-report		junit: report.xml


	# Minimal tests in windows environment		# Minimal tests in windows environment
	minimal-windows:		#minimal-windows:
			# stage: test
			# tags:
			# - win
			# script:
			# - export NUM_CORES=$(nproc --all)
			# - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
			# - source activate pystencils
			# - pip install joblib
			# - pip list
			# - python -c "import numpy"
			# - py.test -v -m "not (notebook or longrun)"

			ubuntu:
	stage: test		stage: test
	except:		extends: .every-commit
	variables:		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
	- $ENABLE_NIGHTLY_BUILDS		before_script:
	tags:		- ln -s /usr/include/locale.h /usr/include/xlocale.h
	- win		- pip3 install -e .
	script:		script:
	- source /cygdrive/c/Users/build/Miniconda3/Scripts/activate		- export NUM_CORES=$(nproc --all)
	- source activate pystencils_dev		- mkdir -p ~/.config/matplotlib
			- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
			- sed -i 's/--doctest-modules //g' pytest.ini
	- env		- env
	- conda env list		- pip list
	- python -c "import numpy"		- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
	- python setup.py quicktest		tags:
			- docker
			- cuda11
			- AVX
			artifacts:
			when: always
			reports:
			junit: report.xml

	minimal-ubuntu:		.multiarch_template:
	stage: test		stage: test
	except:		extends: .every-commit
	variables:		allow_failure: true
	- $ENABLE_NIGHTLY_BUILDS		before_script: &multiarch_before_script
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_ubuntu		# - pip3 install -v .
			- export PYTHONPATH=src
			- python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
			- sed -i '/^fail_under.*/d' pytest.ini
	script:		script:
	- python3 setup.py quicktest		- export NUM_CORES=$(nproc --all)
			- mkdir -p ~/.config/matplotlib
			- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
			- sed -i 's/--doctest-modules //g' pytest.ini
			- env
			- pip3 list
			- python3 -m pytest -v -n $NUM_CORES --reruns 2 --cov-report html --cov-report xml --cov=. --junitxml=report.xml tests/test_vec.py tests/test_random.py tests/test_half_precision.py
			- python3 -m coverage xml
	tags:		tags:
	- docker		- docker
			- multiarch
			artifacts:
			when: always
			paths:
			- coverage_report
			reports:
			coverage_report:
			coverage_format: cobertura
			path: coverage.xml
			junit: report.xml

	minimal-conda:		arm64v8:
	stage: test		extends: .multiarch_template
	except:		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
			variables:
			QEMU_CPU: "cortex-a76"
			before_script:
			- *multiarch_before_script

			ppc64le:
			extends: .multiarch_template
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
			before_script:
			- *multiarch_before_script

			arm64v9:
			# SVE support is still unreliable in GCC 13 (incorrect code for fixed-width vectors, internal compiler errors).
			# For half precision Clang is necessary
			extends: .multiarch_template
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
	variables:		variables:
	- $ENABLE_NIGHTLY_BUILDS		# disable pointer authentication to speed up emulation by 3x
			QEMU_CPU: "max,pauth-impdef=on"
			before_script:
			- *multiarch_before_script
			- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json

			riscv64:
			# RISC-V vector extension support is incomplete in GCC 13.
			extends: .multiarch_template
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64
			variables:
			# explicitly set SIMD as detection requires QEMU >= 8.1
			PYSTENCILS_SIMD: "rvv"
			QEMU_CPU: "rv64,v=true,zicboz=true"
			before_script:
			- *multiarch_before_script
			- sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json
			- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json

			minimal-conda:
			stage: pretest
			extends: .every-commit
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
			before_script:
			- pip install -e .
	script:		script:
	- python setup.py quicktest		- python quicktest.py
	tags:		tags:
	- docker		- docker
			- cuda


	minimal-sympy-master:		minimal-sympy-master:
	stage: test		stage: test
	except:		extends: .every-commit
	variables:
	- $ENABLE_NIGHTLY_BUILDS
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
			before_script:
			- pip install -e .
	script:		script:
	- python -m pip install --upgrade git+https://github.com/sympy/sympy.git		- python -m pip install --upgrade git+https://github.com/sympy/sympy.git
	- python setup.py quicktest		- python quicktest.py
	allow_failure: true		allow_failure: true
	tags:		tags:
	- docker		- docker
			- cuda


	pycodegen-integration:		pycodegen-integration:
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
	stage: test		stage: test
	when: manual		when: manual
			allow_failure: true
	script:		script:
	- git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git		- git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
	- cd pycodegen		- cd pycodegen
	@@ -118,50 +257,89 @@ pycodegen-integration:
	- git fetch test		- git fetch test
	- git reset --hard $CI_COMMIT_SHA		- git reset --hard $CI_COMMIT_SHA
	- cd ..		- cd ..
	- export PYTHONPATH=`pwd`/pystencils:`pwd`/lbmpy:`pwd`/pygrandchem:`pwd`/pystencils_walberla:`pwd`/lbmpy_walberla		- pip install -e pystencils/
			- pip install -e lbmpy/
			- cmake --version
	- ./install_walberla.sh		- ./install_walberla.sh
	- export NUM_CORES=$(nproc --all)		- export NUM_CORES=$(nproc --all)
	- mkdir -p ~/.config/matplotlib		- mkdir -p ~/.config/matplotlib
	- echo "backend:template" > ~/.config/matplotlib/matplotlibrc		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
	- cd pystencils		- cd pystencils
	- py.test -v -n $NUM_CORES .		- py.test -v -n $NUM_CORES --junitxml=report.xml .
	- cd ../lbmpy		- cd ../lbmpy
	- py.test -v -n $NUM_CORES .		- py.test -v -n $NUM_CORES --junitxml=report.xml .
	- cd ../pygrandchem
	- py.test -v -n $NUM_CORES .
	- cd ../walberla/build/		- cd ../walberla/build/
	- make CodegenJacobiCPU CodegenJacobiGPU MicroBenchmarkGpuLbm LbCodeGenerationExample		- make -j $NUM_CORES CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample
			- make -j $NUM_CORES multiphaseCPU multiphaseGPU FluctuatingMRT FlowAroundSphereCodeGen FieldLayoutAndVectorizationTest GeneratedOutflowBC
			- cd apps/benchmarks/UniformGridGPU
			- make -j $NUM_CORES
			- cd ../UniformGridCPU
			- make -j $NUM_CORES
	tags:		tags:
	- docker		- docker
	- cuda		- cuda11
	- AVX		- AVX
			artifacts:
			when: always
			reports:
			junit: pycodegen/*/report.xml


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


			# Nightly test against the latest (pre-release) version of SymPy published on PyPI
			nightly-sympy:
			stage: nightly
			needs: []
			extends: .scheduled
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
			before_script:
			- pip install -e .
			- pip install --upgrade --pre sympy
			script:
			- env
			- pip list
			- export NUM_CORES=$(nproc --all)
			- mkdir -p ~/.config/matplotlib
			- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
			- mkdir public
			- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
			tags:
			- docker
			- AVX
			- cuda
			artifacts:
			when: always
			reports:
			junit: report.xml

	# -------------------- Linter & Documentation --------------------------------------------------------------------------		# -------------------- Linter & Documentation --------------------------------------------------------------------------


	flake8-lint:		flake8-lint:
	stage: test		stage: pretest
	except:		extends: .every-commit
	variables:
	- $ENABLE_NIGHTLY_BUILDS
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
	script:		script:
	- flake8 pystencils		- flake8 src/pystencils
	tags:		tags:
	- docker		- docker
	- cuda


	build-documentation:		build-documentation:
	stage: test		stage: docs
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		extends: .every-commit
			image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
			needs: []
			before_script:
			- pip install -e .
	script:		script:
	- export PYTHONPATH=`pwd`
	- mkdir html_doc		- mkdir html_doc
			- sphinx-build -b html doc html_doc
	- sphinx-build -W -b html doc html_doc		- sphinx-build -W -b html doc html_doc
	tags:		tags:
	- docker		- docker
	- cuda
	artifacts:		artifacts:
	paths:		paths:
	- html_doc		- html_doc
	@@ -169,7 +347,9 @@ build-documentation:

	pages:		pages:
	image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
			extends: .every-commit-master
	stage: deploy		stage: deploy
			needs: ["tests-and-coverage", "build-documentation"]
	script:		script:
	- ls -l		- ls -l
	- mv coverage_report html_doc		- mv coverage_report html_doc
	@@ -179,5 +359,3 @@ pages:
	- public		- public
	tags:		tags:
	- docker		- docker
	only:
	- master@pycodegen/pystencils

.isort.cfg

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	@@ -2,3 +2,4 @@
	line_length=100		line_length=100
	balanced_wrapping=True		balanced_wrapping=True
	multi_line_output=4		multi_line_output=4
			known_third_party=sympy

AUTHORS.txt

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	@@ -3,12 +3,13 @@ Contributors:
	-------------		-------------

	- Martin Bauer <martin.bauer@fau.de>		- Martin Bauer <martin.bauer@fau.de>
			- Markus Holzer <markus.holzer@fau.de>
	- Stephan Seitz <stephan.seitz@fau.de>		- Stephan Seitz <stephan.seitz@fau.de>
			- Michael Kuron <mkuron@icp.uni-stuttgart.de>
	- Jan Hönig <jan.hoenig@fau.de>		- Jan Hönig <jan.hoenig@fau.de>
	- Nils Kohl <nils.kohl@fau.de>
	- Julian Hammer <julian.hammer@fau.de>		- Julian Hammer <julian.hammer@fau.de>
	- Christian Godenschwager <christian.godenschwager@fau.de>		- Nils Kohl <nils.kohl@fau.de>
	- Markus Holzer <markus.holzer@fau.de>		- Frederik Hennig <frederik.hennig@fau.de>
	- Michael Kuron <mkuron@icp.uni-stuttgart.de>
	- Dominik Ernst <dominik.ernst@fau.de>		- Dominik Ernst <dominik.ernst@fau.de>
	- João Victor Tozatti Risso <joaovictortr@protonmail.com>		- Christian Godenschwager <christian.godenschwager@fau.de>
			- Dominik Thoennes <dominik.thoennes@fau.de>

CHANGELOG.md

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			# Change Log

			## Unreleased

			### Removed
			* LLVM backend because it was not used much and not good integrated in pystencils.
			* OpenCL backend because it was not used much and not good integrated in pystencils.

CONTRIBUTING.md

0 → 100644

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			# Contributing

			Contributions to pystencils are always welcome, and they are greatly appreciated!
			A list of open problems can be found [here]( https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
			Of course, it is also always appreciated to bring own ideas and problems to the community!


			Please submit all contributions to the official [GitLab repository](https://i10git.cs.fau.de/pycodegen/pystencils) in the form of a Merge Request. Please do not submit git diffs or files containing the changes.
			There also exists a GitHub repository, which is only a mirror to the GitLab repository. Contributions to the GitHub repository are not considered.

			`pystencils` is an open-source python package under the license of AGPL3. Thus we consider the act of contributing to the code by submitting a Merge Request as the "Sign off" or agreement to the AGPL3 license.

			You can contribute in many different ways:

			## Types of Contributions

			### Report Bugs

			Report bugs at [https://i10git.cs.fau.de/pycodegen/pystencils/-/issues](https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).

			For pystencils, it is often necessary to provide the python and [SymPy](https://www.sympy.org/en/index.html) versions used and hardware information like the
			processor architecture and the compiler version used to compile the generated kernels.

			### Fix Issues

			Look through the GitLab issues. Different tags are indicating the status of the issues.
			The "bug" tag indicates problems with pystencils, while the "feature" tag shows ideas that should be added in the future.

			### Write Documentation

			The documentation of pystencils can be found [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils/). Jupyter notebooks are used to provide an
			interactive start to pystencils. It is always appreciated if new document notebooks are provided
			since this helps others a lot.

			## Get Started!

			Ready to contribute? Here is how to set up `pystencils` for local development.

			1. Fork the `pystencils` repo on GitLab.
			2. Clone your fork locally:
			```bash
			$ git clone https://i10git.cs.fau.de/your-name/pystencils
			```
			3. Install your local copy into a virtualenv. It is also recommended to use anaconda or miniconda to manage the python environments.
			```bash
			$ mkvirtualenv pystencils
			$ cd pystencils/
			$ pip install -e .
			```
			4. Create a branch for local development:
			```bash
			$ git checkout -b name-of-your-bugfix-or-feature
			```
			Now you can make your changes locally.

			5. When you're done making changes, check that your changes pass flake8 and the
			tests
			```bash
			$ flake8 pystencils
			$ py.test -v -n $NUM_CORES -m "not longrun" .

			```

			To get all packages needed for development, a requirements list can be found [here](https://i10git.cs.fau.de/pycodegen/pycodegen/-/blob/master/conda_environment_dev.yml). This includes flake8 and pytest.

			6. Commit your changes and push your branch to GitHub::
			```bash
			$ git add .
			$ git commit -m "Your detailed description of your changes."
			$ git push origin name-of-your-bugfix-or-feature
			```
			7. Submit a Merge Request on GitLab.

			## Merge Request Guidelines

			Before you submit a Merge Request, check that it meets these guidelines:

			1. All functionality that is implemented through this Merge Request should be covered by unit tests. These are implemented in `pystencil_tests`
			2. If the Merge Request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
			3. If you have a maintainer status for `pystencils`, you can merge Merge Requests to the master branch. However, every Merge Request needs to be reviewed by another developer. Thus it is not allowed to merge a Merge Request, which is submitted by oneself.

			## Tips

			To run a subset of tests:
			```bash
			$ py.test my_test.py
			```
			No newline at end of file

MANIFEST.in

+3 −3

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	include README.md		include AUTHORS.txt
	include COPYING.txt		include CONTRIBUTING.md
	include RELEASE-VERSION		include CHANGELOG.md

README.md

+28 −14

Original line number	Original line	Diff line number	Diff line
	@@ -2,16 +2,16 @@ pystencils
	==========		==========

	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/pystencils/master?filepath=doc%2Fnotebooks)		[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/pystencils/master?filepath=doc%2Fnotebooks)
	[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.walberla.net/pystencils)		[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](https://pycodegen.pages.i10git.cs.fau.de/pystencils)
	[![pypi-package](https://badge.fury.io/py/pystencils.svg)](https://badge.fury.io/py/pystencils)		[![pypi-package](https://badge.fury.io/py/pystencils.svg)](https://badge.fury.io/py/pystencils)
	[![pipeline status](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)		[![pipeline status](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
	[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.walberla.net/pystencils/coverage_report)		[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/pystencils/coverage_report)

	Run blazingly fast stencil codes on numpy arrays.		Run blazingly fast stencil codes on numpy arrays.

	pystencils uses sympy to define stencil operations, that can be executed on numpy arrays.		pystencils uses sympy to define stencil operations, that can be executed on numpy arrays.
	Exploiting the stencil structure makes pystencils run faster than normal numpy code and even as Cython and numba,		Exploiting the stencil structure makes pystencils run faster than normal numpy code and even as Cython and numba,
	[as demonstrated in this notebook](http://pycodegen.pages.walberla.net/pystencils/notebooks/demo_benchmark.html).		[as demonstrated in this notebook](https://pycodegen.pages.i10git.cs.fau.de/pystencils/notebooks/demo_benchmark.html).


	Here is a code snippet that computes the average of neighboring cells:		Here is a code snippet that computes the average of neighboring cells:
	@@ -33,15 +33,15 @@ kernel(f=f_arr, g=g_arr)
	It comes with automatic finite difference discretization for PDEs:		It comes with automatic finite difference discretization for PDEs:

	```python		```python
			import pystencils as ps
			import sympy as sp

	c, v = ps.fields("c, v(2): [2D]")		c, v = ps.fields("c, v(2): [2D]")
	adv_diff_pde = ps.fd.transient(c) - ps.fd.diffusion(c, sp.symbols("D")) + ps.fd.advection(c, v)		adv_diff_pde = ps.fd.transient(c) - ps.fd.diffusion(c, sp.symbols("D")) + ps.fd.advection(c, v)
	discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)		discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)
	discretization = discretize(adv_diff_pde)		discretization = discretize(adv_diff_pde)
	```		```

	Look at the [documentation](http://pycodegen.pages.walberla.net/pystencils) to learn more.


	Installation		Installation
	------------		------------

	@@ -52,12 +52,10 @@ pip install pystencils[interactive]
	Without `[interactive]` you get a minimal version with very little dependencies.		Without `[interactive]` you get a minimal version with very little dependencies.

	All options:		All options:
	- `gpu`: use this if an Nvidia GPU is available and CUDA is installed		- `gpu`: use this if an NVIDIA or AMD GPU is available and CUDA or ROCm is installed
	- `pyopencl`: basic OpenCL support (experimental)
	- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl		- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
	- `bench_db`: functionality to store benchmark result in object databases		- `bench_db`: functionality to store benchmark result in object databases
	- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.		- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.
	- `autodiff`: enable derivation of adjoint kernels and generation of Torch/Tensorflow operations
	- `doc`: packages to build documentation		- `doc`: packages to build documentation

	Options can be combined e.g.		Options can be combined e.g.
	@@ -65,9 +63,25 @@ Options can be combined e.g.
	pip install pystencils[interactive, gpu, doc]		pip install pystencils[interactive, gpu, doc]
	```		```

			pystencils is also fully compatible with Windows machines. If working with visual studio and cupy makes sure to run example files first to ensure that cupy can find the compiler's executable.

	Documentation		Documentation
	-------------		-------------

	Read the docs [here](http://pycodegen.pages.walberla.net/pystencils) and		Read the docs [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils) and
	check out the Jupyter notebooks in `doc/notebooks`.		check out the Jupyter notebooks in `doc/notebooks`. The Changelog of pystencils can be found [here](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CHANGELOG.md).

			Authors
			-------

			Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/AUTHORS.txt) of pystencils.

			### Please cite us

			If you use pystencils in a publication, please cite the following articles:

			Overview:
			- M. Bauer et al, Code Generation for Massively Parallel Phase-Field Simulations. Association for Computing Machinery, 2019. https://doi.org/10.1145/3295500.3356186

			Performance Modelling:
			- D. Ernst et al, Analytical performance estimation during code generation on modern GPUs. Journal of Parallel and Distributed Computing, 2023. https://doi.org/10.1016/j.jpdc.2022.11.003

binder/environment.yml

+3 −3

Original line number	Original line	Diff line number	Diff line
	@@ -7,14 +7,14 @@
	# conda env create -f conda_environment_user.yml		# conda env create -f conda_environment_user.yml
	# . activate pystencils		# . 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
	#		#
	# ----------------------------------------------------------------------------------------------------------------------		# ----------------------------------------------------------------------------------------------------------------------

	name: pystencils		name: pystencils
	dependencies:		dependencies:
	# Basic dependencies:		# Basic dependencies:
	- python >= 3.6		- python >= 3.8
	- numpy		- numpy
	- sympy >= 1.1		- sympy >= 1.1
	- appdirs # to find default cache directory on each platform		- appdirs # to find default cache directory on each platform
	@@ -32,4 +32,4 @@ dependencies:
	- ipy_table # HTML tables for jupyter notebooks		- ipy_table # HTML tables for jupyter notebooks
	- pyevtk # VTK output for serial simulations		- pyevtk # VTK output for serial simulations
	- blitzdb # file-based No-SQL database to store simulation results		- blitzdb # file-based No-SQL database to store simulation results
	#- pycuda # add this if you have CUDA installed		#- cupy # add this if you have CUDA or ROCm installed

conftest.py

+53 −34

Original line number	Original line	Diff line number	Diff line
	import os		import os
	import pytest
	import tempfile
	import runpy		import runpy
	import sys		import sys
			import tempfile
			import warnings

			import nbformat
			import pytest
			from nbconvert import PythonExporter

			from pystencils.boundaries.createindexlist import * # NOQA
	# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it		# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it
	# at the same time		# at the same time
	from pystencils.cpu import cpujit		from pystencils.cpu import cpujit
	@@ -14,12 +20,17 @@ try:
	pyximport.install(language_level=3)		pyximport.install(language_level=3)
	except ImportError:		except ImportError:
	pass		pass
	from pystencils.boundaries.createindexlistcython import * # NOQA


	SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))		SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
	sys.path.insert(0, os.path.abspath('pystencils'))		sys.path.insert(0, os.path.abspath('pystencils'))

			# the Ubuntu pipeline uses an older version of pytest which uses deprecated functionality.
			# This leads to many warinings in the test and coverage pipeline.
			pytest_numeric_version = [int(x, 10) for x in pytest.__version__.split('.')]
			pytest_numeric_version.reverse()
			pytest_version = sum(x * (100 ** i) for i, x in enumerate(pytest_numeric_version))


	def add_path_to_ignore(path):		def add_path_to_ignore(path):
	if not os.path.exists(path):		if not os.path.exists(path):
	@@ -28,46 +39,49 @@ def add_path_to_ignore(path):
	collect_ignore += [os.path.join(SCRIPT_FOLDER, path, f) for f in os.listdir(os.path.join(SCRIPT_FOLDER, path))]		collect_ignore += [os.path.join(SCRIPT_FOLDER, path, f) for f in os.listdir(os.path.join(SCRIPT_FOLDER, path))]


	collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py")]		collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
	add_path_to_ignore('pystencils_tests/benchmark')		os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit")]
			add_path_to_ignore('tests/benchmark')
	add_path_to_ignore('_local_tmp')		add_path_to_ignore('_local_tmp')


	collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/autodiff.py")]

	try:		try:
	import pycuda		import cupy
	except ImportError:		except ImportError:
	collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/pystencils_tests/test_cudagpu.py")]		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_gpu.py")]
	add_path_to_ignore('pystencils/gpucuda')		add_path_to_ignore('src/pystencils/gpu')

	try:		try:
	import llvmlite		import waLBerla
	except ImportError:		except ImportError:
	collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/backends/llvm.py')]		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_aligned_array.py"),
	add_path_to_ignore('pystencils/llvm')		os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py"),
			os.path.join(SCRIPT_FOLDER, "doc/notebooks/03_tutorial_datahandling.ipynb"),
			os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/parallel_datahandling.py"),
			os.path.join(SCRIPT_FOLDER, "tests/test_small_block_benchmark.ipynb")]

	try:		try:
	import kerncraft		import blitzdb
	except ImportError:		except ImportError:
	collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_kerncraft_coupling.py"),		add_path_to_ignore('src/pystencils/runhelper')
	os.path.join(SCRIPT_FOLDER, "pystencils_tests/benchmark/benchmark.py")]		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_parameterstudy.py")]
	add_path_to_ignore('pystencils/kerncraft_coupling')		collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py")]

	try:		try:
	import waLBerla		import islpy
	except ImportError:		except ImportError:
	collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_aligned_array.py"),		collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/integer_set_analysis.py")]
	os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_datahandling_parallel.py"),
	os.path.join(SCRIPT_FOLDER, "doc/notebooks/03_tutorial_datahandling.ipynb"),
	os.path.join(SCRIPT_FOLDER, "pystencils/datahandling/parallel_datahandling.py"),
	os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_small_block_benchmark.ipynb")]

	try:		try:
	import blitzdb		import graphviz
	except ImportError:		except ImportError:
	add_path_to_ignore('pystencils/runhelper')		collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/backends/dot.py")]
			collect_ignore += [os.path.join(SCRIPT_FOLDER, "doc/notebooks/01_tutorial_getting_started.ipynb")]

			try:
			import pyevtk
			except ImportError:
			collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/vtk.py")]

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

	@@ -77,10 +91,6 @@ for root, sub_dirs, files in os.walk('.'):
	collect_ignore.append(f)		collect_ignore.append(f)


	import nbformat
	from nbconvert import PythonExporter


	class IPythonMockup:		class IPythonMockup:
	def run_line_magic(self, args, *kwargs):		def run_line_magic(self, args, *kwargs):
	pass		pass
	@@ -127,9 +137,15 @@ class IPyNbFile(pytest.File):
	exporter.exclude_markdown = True		exporter.exclude_markdown = True
	exporter.exclude_input_prompt = True		exporter.exclude_input_prompt = True

	notebook_contents = self.fspath.open()		notebook_contents = self.fspath.open(encoding='utf-8')

			with warnings.catch_warnings():
			warnings.filterwarnings("ignore", "IPython.core.inputsplitter is deprecated")
	notebook = nbformat.read(notebook_contents, 4)		notebook = nbformat.read(notebook_contents, 4)
	code, _ = exporter.from_notebook_node(notebook)		code, _ = exporter.from_notebook_node(notebook)
			if pytest_version >= 50403:
			yield IPyNbTest.from_parent(name=self.name, parent=self, code=code)
			else:
	yield IPyNbTest(self.name, self, code)		yield IPyNbTest(self.name, self, code)

	def teardown(self):		def teardown(self):
	@@ -139,4 +155,7 @@ class IPyNbFile(pytest.File):
	def pytest_collect_file(path, parent):		def pytest_collect_file(path, parent):
	glob_exprs = ["demo.ipynb", "tutorial.ipynb", "test_*.ipynb"]		glob_exprs = ["demo.ipynb", "tutorial.ipynb", "test_*.ipynb"]
	if any(path.fnmatch(g) for g in glob_exprs):		if any(path.fnmatch(g) for g in glob_exprs):
			if pytest_version >= 50403:
			return IPyNbFile.from_parent(fspath=path, parent=parent)
			else:
	return IPyNbFile(path, parent)		return IPyNbFile(path, parent)

doc/conf.py

100644 → 100755

+13 −8

Original line number	Original line	Diff line number	Diff line
	@@ -4,10 +4,11 @@
	import datetime		import datetime
	import sphinx_rtd_theme		import sphinx_rtd_theme
	import os		import os
			import re
	import sys		import sys

	sys.path.insert(0, os.path.abspath('.'))		sys.path.insert(0, os.path.abspath('.'))
	from version_from_git import version_number_from_git		import pystencils

	extensions = [		extensions = [
	'sphinx.ext.autodoc',		'sphinx.ext.autodoc',
	@@ -25,11 +26,14 @@ templates_path = ['_templates']
	source_suffix = '.rst'		source_suffix = '.rst'
	master_doc = 'index'		master_doc = 'index'

	copyright = '{}, Martin Bauer'.format(datetime.datetime.now().year)		copyright = f'{datetime.datetime.now().year}, Martin Bauer, Markus Holzer, Frederik Hennig'
	author = 'Martin Bauer'		author = 'Martin Bauer, Markus Holzer, Frederik Hennig'
	version = version_number_from_git()		# The short X.Y version (including .devXXXX, rcX, b1 suffixes if present)
	release = version_number_from_git()		version = re.sub(r'(\d+\.\d+)\.\d+(.*)', r'\1\2', pystencils.__version__)
	language = None		version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
			# The full version, including alpha/beta/rc tags.
			release = pystencils.__version__
			language = 'en'
	exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']		exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
	default_role = 'any'		default_role = 'any'
	pygments_style = 'sphinx'		pygments_style = 'sphinx'
	@@ -47,13 +51,14 @@ nbsphinx_execute = 'never'
	nbsphinx_codecell_lexer = 'python3'		nbsphinx_codecell_lexer = 'python3'

	# Example configuration for intersphinx: refer to the Python standard library.		# Example configuration for intersphinx: refer to the Python standard library.
	intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),		intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None),
	'numpy': ('https://docs.scipy.org/doc/numpy/', None),		'numpy': ('https://docs.scipy.org/doc/numpy/', None),
	'matplotlib': ('https://matplotlib.org/', None),		'matplotlib': ('https://matplotlib.org/', None),
	'sympy': ('https://docs.sympy.org/latest/', None),		'sympy': ('https://docs.sympy.org/latest/', None),
	}		}

	autodoc_member_order = 'bysource'		autodoc_member_order = 'bysource'
			bibtex_bibfiles = ['sphinx/pystencils.bib']

	project = 'pystencils'		project = 'pystencils'
	html_logo = "img/logo.png"		html_logo = 'img/logo.png'

doc/index.rst

+1 −0

Original line number	Original line	Diff line number	Diff line
	@@ -14,5 +14,6 @@ pystencils can help you to generate blazingly fast code for image processing, nu

	.. image:: /img/pystencils_arch_block_diagram.svg		.. image:: /img/pystencils_arch_block_diagram.svg
	:height: 450px		:height: 450px
			:align: center

doc/notebooks/01_tutorial_getting_started.ipynb

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.flake8

.gitattributes

.gitignore

.gitlab-ci.yml

.isort.cfg

AUTHORS.txt

CHANGELOG.md

CONTRIBUTING.md

MANIFEST.in

README.md

binder/environment.yml

conftest.py

doc/conf.py

doc/index.rst

doc/notebooks/01_tutorial_getting_started.ipynb