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.flake8

+3 −3

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

.gitattributes

+1 −1

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

.gitignore

+16 −7

Original line number	Diff line number	Diff line
		__pycache__
		.ipynb_checkpoints
		.coverage
		.coverage*
		*.pyc
		*.vti
		/build
		/dist
		/*.egg-info
		*.egg-info
		.cache
		_build
		/html_doc
		/.idea
		.vscode
		.cache
		_local_tmp
		RELEASE-VERSION
		test-report
		pystencils/boundaries/createindexlistcython.c
		pystencils/boundaries/createindexlistcython.*.so
		pystencils_tests/tmp
		pystencils_tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
		pystencils_tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
		No newline at end of file
		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

+141 −99

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

		# Normal test - runs on every commit all but "long run" tests
		tests-and-coverage:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		stage: pretest
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
		before_script:
		- pip install -e .
		script:
		- env
		- pip list
		@@ -19,28 +39,33 @@ tests-and-coverage:
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- mkdir public
		- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
		- python3 -m coverage xml
		- 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:
		- docker
		- cuda11
		- AVX
		coverage: /Total coverage:\s\d+.\d+\%/
		artifacts:
		when: always
		paths:
		- coverage_report
		- test-report
		reports:
		cobertura: coverage.xml
		coverage_report:
		coverage_format: cobertura
		path: coverage.xml
		junit: report.xml

		# pipeline with latest python version
		latest-python:
		# Normal test with longruns
		tests-and-coverage-with-longrun:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
		when: manual
		allow_failure: true
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
		before_script:
		- pip install sympy --upgrade
		- pip install -e .
		script:
		- env
		- pip list
		@@ -48,73 +73,66 @@ latest-python:
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- mkdir public
		- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		- py.test -v -n $NUM_CORES
		tags:
		- docker
		- cuda11
		- AVX
		artifacts:
		when: always
		reports:
		junit: report.xml

		# Nightly test - runs "long run" jobs only
		test-longrun:
		# pipeline with latest python version
		latest-python:
		stage: test
		only:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
		before_script:
		- pip install -e .
		script:
		- env
		- pip list
		- pip install -e .
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. --html test-report/index.html --junitxml=report.xml
		- mkdir public
		- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		tags:
		- docker
		- cuda11
		- AVX
		artifacts:
		when: always
		paths:
		- coverage_report
		- 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)
		- source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
		- source activate pystencils
		- pip list
		- python -c "import numpy"
		- py.test -v -m "not (notebook or longrun)"
		#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
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
		before_script:
		- apt-get -y remove python3-sympy
		- ln -s /usr/include/locale.h /usr/include/xlocale.h
		- pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py \| sed 's/>/=/g'`
		- pip3 install -e .
		script:
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
		- sed -i 's/--doctest-modules //g' pytest.ini
		- env
		- pip3 list
		- pytest-3 -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		- pip list
		- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
		tags:
		- docker
		- cuda11
		@@ -126,10 +144,11 @@ ubuntu:

		.multiarch_template:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		extends: .every-commit
		allow_failure: true
		before_script: &multiarch_before_script
		# - 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:
		@@ -139,75 +158,68 @@ ubuntu:
		- sed -i 's/--doctest-modules //g' pytest.ini
		- env
		- pip3 list
		- pytest-3 -v -n $NUM_CORES --cov-report html --cov-report term --cov=. --junitxml=report.xml pystencils_tests/test_vec.py pystencils_tests/test_random.py
		- 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:
		- docker
		- multiarch
		artifacts:
		when: always
		paths:
		- coverage_report
		reports:
		cobertura: coverage.xml
		coverage_report:
		coverage_format: cobertura
		path: coverage.xml
		junit: report.xml

		arm64v8:
		extends: .multiarch_template
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
		variables:
		PYSTENCILS_SIMD: "neon"
		QEMU_CPU: "cortex-a76"
		before_script:
		- *multiarch_before_script
		- sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json

		ppc64le:
		extends: .multiarch_template
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
		variables:
		PYSTENCILS_SIMD: "vsx"
		before_script:
		- *multiarch_before_script
		- sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json

		arm64v9:
		# Compiler support for SVE is still pretty rough: GCC 10+11 produce incorrect code for fixed-width vectors,
		# while Clang 12 produces memory-corrupting heisenbugs unless we enable the address sanitizer.
		# In the RNG tests, GCC 10+11 produce an internal compiler error.
		# The memory corruption seems to only happen with qemu-user, not with qemu-system.
		# Once the compilers and QEMU have improved, this job should be cleaned up to match the others.
		# 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:
		PYSTENCILS_SIMD: "sve256,sve512,sve"
		ASAN_OPTIONS: detect_leaks=0
		LD_PRELOAD: /usr/lib/aarch64-linux-gnu/libasan.so.6
		# disable pointer authentication to speed up emulation by 3x
		QEMU_CPU: "max,pauth-impdef=on"
		before_script:
		- *multiarch_before_script
		- sed -i s/march=native/march=armv8-a+sve/g ~/.config/pystencils/config.json
		- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json

		riscv64:
		# The RISC-V vector extension is still experimental and needs special compiler flags.
		# Once they are officially released, this job should be cleaned up to match the others.
		# 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,x-v=true"
		QEMU_CPU: "rv64,v=true,zicboz=true"
		before_script:
		- *multiarch_before_script
		- sed -i 's/march=native/march=rv64imfdv0p10 -menable-experimental-extensions/g' ~/.config/pystencils/config.json
		- sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json
		- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
		- sed -i 's/fopenmp/fopenmp=libgomp -I\/usr\/include\/riscv64-linux-gnu/g' ~/.config/pystencils/config.json

		minimal-conda:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		stage: pretest
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
		before_script:
		- pip install -e .
		script:
		- python setup.py quicktest
		- python quicktest.py
		tags:
		- docker
		- cuda
		@@ -215,13 +227,13 @@ minimal-conda:

		minimal-sympy-master:
		stage: test
		except:
		variables:
		- $ENABLE_NIGHTLY_BUILDS
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
		before_script:
		- pip install -e .
		script:
		- python -m pip install --upgrade git+https://github.com/sympy/sympy.git
		- python setup.py quicktest
		- python quicktest.py
		allow_failure: true
		tags:
		- docker
		@@ -247,7 +259,7 @@ pycodegen-integration:
		- cd ..
		- pip install -e pystencils/
		- pip install -e lbmpy/
		- pip install -e pygrandchem/
		- cmake --version
		- ./install_walberla.sh
		- export NUM_CORES=$(nproc --all)
		- mkdir -p ~/.config/matplotlib
		@@ -256,13 +268,12 @@ pycodegen-integration:
		- py.test -v -n $NUM_CORES --junitxml=report.xml .
		- cd ../lbmpy
		- py.test -v -n $NUM_CORES --junitxml=report.xml .
		- cd ../pygrandchem
		- py.test -v -n $NUM_CORES --junitxml=report.xml .
		- cd ../walberla/build/
		- make CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample UniformGridBenchmarkGPU_trt UniformGridBenchmarkGPU_entropic_kbc_n4 FluctuatingMRT
		- 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 ../UniformGridGenerated
		- cd ../UniformGridCPU
		- make -j $NUM_CORES
		tags:
		- docker
		@@ -273,26 +284,57 @@ pycodegen-integration:
		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 --------------------------------------------------------------------------


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


		build-documentation:
		stage: test
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		stage: docs
		extends: .every-commit
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
		needs: []
		before_script:
		- pip install -e .
		script:
		- export PYTHONPATH=`pwd`
		- mkdir html_doc
		- sphinx-build -b html doc html_doc
		- sphinx-build -W -b html doc html_doc
		@@ -305,7 +347,9 @@ build-documentation:

		pages:
		image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
		extends: .every-commit-master
		stage: deploy
		needs: ["tests-and-coverage", "build-documentation"]
		script:
		- ls -l
		- mv coverage_report html_doc
		@@ -315,5 +359,3 @@ pages:
		- public
		tags:
		- docker
		only:
		- master@pycodegen/pystencils

AUTHORS.txt

+6 −5

Original line number	Diff line number	Diff line
		@@ -3,12 +3,13 @@ Contributors:
		-------------

		- Martin Bauer <martin.bauer@fau.de>
		- Markus Holzer <markus.holzer@fau.de>
		- Stephan Seitz <stephan.seitz@fau.de>
		- Michael Kuron <mkuron@icp.uni-stuttgart.de>
		- Jan Hönig <jan.hoenig@fau.de>
		- Nils Kohl <nils.kohl@fau.de>
		- Julian Hammer <julian.hammer@fau.de>
		- Christian Godenschwager <christian.godenschwager@fau.de>
		- Markus Holzer <markus.holzer@fau.de>
		- Michael Kuron <mkuron@icp.uni-stuttgart.de>
		- Nils Kohl <nils.kohl@fau.de>
		- Frederik Hennig <frederik.hennig@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

0 → 100644

+7 −0

Original line number	Diff line number	Diff line
		# 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

+87 −0

Original line number	Diff line number	Diff line
		# 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 −6

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

README.md

+23 −6

Original line number	Diff line number	Diff line
		@@ -33,6 +33,9 @@ kernel(f=f_arr, g=g_arr)
		It comes with automatic finite difference discretization for PDEs:

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

		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)
		discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)
		@@ -49,12 +52,10 @@ pip install pystencils[interactive]
		Without `[interactive]` you get a minimal version with very little dependencies.

		All options:
		- `gpu`: use this if an NVIDIA GPU is available and CUDA is installed
		- `opencl`: basic OpenCL support (experimental)
		- `gpu`: use this if an NVIDIA or AMD GPU is available and CUDA or ROCm is installed
		- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
		- `bench_db`: functionality to store benchmark result in object databases
		- `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

		Options can be combined e.g.
		@@ -62,9 +63,25 @@ Options can be combined e.g.
		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
		-------------

		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	Diff line number	Diff line
		@@ -7,14 +7,14 @@
		# 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
		#
		# ----------------------------------------------------------------------------------------------------------------------

		name: pystencils
		dependencies:
		# Basic dependencies:
		- python >= 3.6
		- python >= 3.8
		- numpy
		- sympy >= 1.1
		- appdirs # to find default cache directory on each platform
		@@ -32,4 +32,4 @@ dependencies:
		- ipy_table # HTML tables for jupyter notebooks
		- pyevtk # VTK output for serial simulations
		- 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

+16 −35

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ import nbformat
		import pytest
		from nbconvert import PythonExporter

		from pystencils.boundaries.createindexlistcython import * # NOQA
		from pystencils.boundaries.createindexlist import * # NOQA
		# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it
		# at the same time
		from pystencils.cpu import cpujit
		@@ -40,67 +40,48 @@ def add_path_to_ignore(path):


		collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
		os.path.join(SCRIPT_FOLDER, "pystencils", "opencl", "opencl.autoinit")]
		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')


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

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

		try:
		import llvmlite
		import cupy
		except ImportError:
		collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/backends/llvm.py')]
		collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/test_basic_usage_llvm.ipynb')]
		add_path_to_ignore('pystencils/llvm')

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

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

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

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

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

		# TODO: Remove if Ubuntu 18.04 is no longer supported
		if pytest_version < 50403:
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_jupyter_extensions.ipynb")]
		collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/vtk.py")]

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

doc/conf.py

100644 → 100755

+4 −4

Original line number	Diff line number	Diff line
		@@ -26,14 +26,14 @@ templates_path = ['_templates']
		source_suffix = '.rst'
		master_doc = 'index'

		copyright = f'{datetime.datetime.now().year}, Martin Bauer'
		author = 'Martin Bauer'
		copyright = f'{datetime.datetime.now().year}, Martin Bauer, Markus Holzer, Frederik Hennig'
		author = 'Martin Bauer, Markus Holzer, Frederik Hennig'
		# The short X.Y version (including .devXXXX, rcX, b1 suffixes if present)
		version = re.sub(r'(\d+\.\d+)\.\d+(.*)', r'\1\2', pystencils.__version__)
		version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
		# The full version, including alpha/beta/rc tags.
		release = pystencils.__version__
		language = None
		language = 'en'
		exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
		default_role = 'any'
		pygments_style = 'sphinx'
		@@ -51,7 +51,7 @@ nbsphinx_execute = 'never'
		nbsphinx_codecell_lexer = 'python3'

		# 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),
		'matplotlib': ('https://matplotlib.org/', None),
		'sympy': ('https://docs.sympy.org/latest/', None),

doc/index.rst

+1 −0

Original line number	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
		:height: 450px
		:align: center

doc/notebooks/01_tutorial_getting_started.ipynb

+370 −387

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