.flake8

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

.gitattributes

+src/pystencils/_version.py export-subst

.gitignore

+__pycache__
+.ipynb_checkpoints
+.coverage*
+*.pyc
+*.vti
+/build
+/dist
+*.egg-info
+.cache
+_build
+/html_doc
+/.idea
+.vscode
+.cache
+_local_tmp
+RELEASE-VERSION
+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

+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: $CI_PIPELINE_SOURCE == "schedule"
+
+# --------------------------  Tests ------------------------------------------------------------------------------------
+
+# Normal test - runs on every commit all but "long run" tests
+tests-and-coverage:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
+    - python -m coverage xml
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  coverage: /Total coverage:\s\d+.\d+\%/
+  artifacts:
+    when: always
+    paths:
+      - coverage_report
+      - test-report
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+      junit: report.xml
+
+# Normal test with longruns
+tests-and-coverage-with-longrun:
+  stage: test
+  when: manual
+  allow_failure: true
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install sympy --upgrade
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - 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 $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+
+
+# Minimal tests in windows environment
+#minimal-windows:
+#  stage: test
+#  tags:
+#    - win
+#  script:
+#    - export NUM_CORES=$(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
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
+  before_script:
+    - ln -s /usr/include/locale.h /usr/include/xlocale.h
+    - 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
+    - pip list
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+
+.multiarch_template:
+  stage: test
+  extends: .every-commit
+  allow_failure: true
+  before_script: &multiarch_before_script
+    # - pip3 install -v .
+    - export PYTHONPATH=src
+    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
+    - sed -i '/^fail_under.*/d' pytest.ini
+  script:
+    - export NUM_CORES=$(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 --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
+    - AVX
+  artifacts:
+    when: always
+    paths:
+      - coverage_report
+    reports:
+      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:
+    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
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json
+
+arm64v9:
+  # SVE support is still unreliable in GCC 11 (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
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/march=native/march=armv9-a+sve2+sme/g ~/.config/pystencils/config.json
+    - sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
+
+riscv64:
+  # RISC-V vector extension are currently not supported by GCC.
+  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++-15/g ~/.config/pystencils/config.json
+
+minimal-conda:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
+  script:
+    - python quicktest.py
+  tags:
+    - docker
+    - cuda
+
+
+minimal-sympy-master:
+  stage: test
+  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 quicktest.py
+  allow_failure: true
+  tags:
+    - docker
+    - cuda
+
+
+pycodegen-integration:
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: test
+  when: manual
+  allow_failure: true
+  script:
+    - 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 pystencils
+    - git remote add test $CI_REPOSITORY_URL
+    - git fetch test
+    - git reset --hard $CI_COMMIT_SHA
+    - cd ..
+    - pip install -e pystencils/
+    - pip install -e lbmpy/
+    - cmake --version
+    - ./install_walberla.sh
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - cd pystencils
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
+    - cd ../lbmpy
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
+    - cd ../walberla/build/
+    - 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 $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: pycodegen/*/report.xml
+
+
+# -------------------- Scheduled Tasks --------------------------------------------------------------------------
+
+
+# Nightly test against the latest (pre-release) version of SymPy published on PyPI
+nightly-sympy:
+  stage: nightly
+  needs: []
+  extends: .scheduled
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+    - pip install --upgrade --pre sympy
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(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 --------------------------------------------------------------------------
+
+
+flake8-lint:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  script:
+    - flake8 src/pystencils
+  tags:
+    - docker
+
+
+build-documentation:
+  stage: docs
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
+  needs: []
+  before_script:
+    - pip install -e .
+  script:
+    - mkdir html_doc
+    - sphinx-build -b html doc  html_doc
+    - sphinx-build -W -b html doc  html_doc
+  tags:
+    - docker
+  artifacts:
+    paths:
+      - html_doc
+
+
+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
+    - mv html_doc public  # folder has to be named "public" for gitlab to publish it
+  artifacts:
+    paths:
+      - public
+  tags:
+    - docker

.isort.cfg

+[settings]
+line_length=100
+balanced_wrapping=True
+multi_line_output=4
+known_third_party=sympy

AUTHORS.txt

+
+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>
+  - Julian Hammer <julian.hammer@fau.de>
+  - Nils Kohl <nils.kohl@fau.de>
+  - Frederik Hennig <frederik.hennig@fau.de>
+  - Dominik Ernst <dominik.ernst@fau.de>
+  - Christian Godenschwager <christian.godenschwager@fau.de>
+  - Dominik Thoennes <dominik.thoennes@fau.de>

CHANGELOG.md

+# 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

+# 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

-include README.md
-include COPYING.txt
+include AUTHORS.txt
+include CONTRIBUTING.md
+include CHANGELOG.md

README.md

 pystencils
 ==========
 
+[![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)](https://pycodegen.pages.i10git.cs.fau.de/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)
+[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/pystencils/coverage_report)
 
-![alt text](doc/img/logo.png)
+Run blazingly fast stencil codes 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,
+[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:
+```python
+import pystencils as ps
+import numpy as np
+
+f, g = ps.fields("f, g : [2D]")
+stencil = ps.Assignment(g[0, 0],
+                       (f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
+kernel = ps.create_kernel(stencil).compile()
+
+f_arr = np.random.rand(1000, 1000)
+g_arr = np.empty_like(f_arr)
+kernel(f=f_arr, g=g_arr)
+```
+
+*pystencils* is mostly used for numerical simulations using finite difference or finite volume methods.
+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)
+discretization = discretize(adv_diff_pde)
+```
+
+Installation
+------------
+
+```bash
+pip install pystencils[interactive]
+```
+
+Without `[interactive]` you get a minimal version with very little dependencies.
+
+All options:
+- `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.
+- `doc`: packages to build documentation
+
+Options can be combined e.g.
+```bash
+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`. 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/apt.txt

+build-essential
+graphviz
+ffmpeg

binder/environment.yml

+
+# ----------------------------------------------------------------------------------------------------------------------
+# Environment with all dependencies to use pystencils
+#
+#
+# Download conda at https://conda.io/miniconda.html and create this environment by running:
+#     conda env create -f conda_environment_user.yml
+#     . activate pystencils
+#
+# 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 >= 3.8
+  - numpy
+  - sympy >= 1.1
+  - appdirs # to find default cache directory on each platform
+  - joblib # caching on hard-disk, this is optional, but if not installed lbmpy is really slow
+  - cython # speed up boundary list computation (optional)
+  - matplotlib
+  - imageio
+  - pandas
+  - scipy
+  - pip
+  - pip:
+      - islpy # used to optimize staggered kernels
+      - py-cpuinfo # get cpu info like cache sizes, supported vector instruction sets, ...
+      - graphviz  # can show abstract syntax trees as formatted graphs
+      - ipy_table  # HTML tables for jupyter notebooks
+      - pyevtk # VTK output for serial simulations
+      - blitzdb # file-based No-SQL database to store simulation results
+      #- cupy # add this if you have CUDA or ROCm installed

binder/start

+#!/bin/bash
+
+python3 setup.py develop
+
+exec "$@"
\ No newline at end of file

conftest.py

+import os
+import runpy
+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
+# at the same time
+from pystencils.cpu import cpujit
+
+# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file
+# at the same time
+try:
+    import pyximport
+    pyximport.install(language_level=3)
+except ImportError:
+    pass
+
+
+SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
+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):
+    if not os.path.exists(path):
+        return
+    global collect_ignore
+    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"),
+                  os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit")]
+add_path_to_ignore('tests/benchmark')
+add_path_to_ignore('_local_tmp')
+
+
+try:
+    import cupy
+except ImportError:
+    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, "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, "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('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, "src/pystencils/integer_set_analysis.py")]
+
+try:
+    import graphviz
+except ImportError:
+    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')]
+
+for root, sub_dirs, files in os.walk('.'):
+    for f in files:
+        if f.endswith(".ipynb") and not any(f.startswith(k) for k in ['demo', 'tutorial', 'test', 'doc']):
+            collect_ignore.append(f)
+
+
+class IPythonMockup:
+    def run_line_magic(self, *args, **kwargs):
+        pass
+
+    def run_cell_magic(self, *args, **kwargs):
+        pass
+
+    def magic(self, *args, **kwargs):
+        pass
+
+    def __bool__(self):
+        return False
+
+
+class IPyNbTest(pytest.Item):
+    def __init__(self, name, parent, code):
+        super(IPyNbTest, self).__init__(name, parent)
+        self.code = code
+        self.add_marker('notebook')
+
+    @pytest.mark.filterwarnings("ignore:IPython.core.inputsplitter is deprecated")
+    def runtest(self):
+        global_dict = {'get_ipython': lambda: IPythonMockup(),
+                       'is_test_run': True}
+
+        # disable matplotlib output
+        exec("import matplotlib.pyplot as p; "
+             "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
+        exec("import warnings;"
+             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*')",
+             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)
+
+
+class IPyNbFile(pytest.File):
+    def collect(self):
+        exporter = PythonExporter()
+        exporter.exclude_markdown = True
+        exporter.exclude_input_prompt = True
+
+        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)
+            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)
+
+    def teardown(self):
+        pass
+
+
+def pytest_collect_file(path, parent):
+    glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
+    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)

doc/conf.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
+import datetime
+import sphinx_rtd_theme
 import os
+import re
 import sys
 
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../..'))
-from sphinx_doc_conf import *
+sys.path.insert(0, os.path.abspath('.'))
+import pystencils
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'nbsphinx',
+    'sphinxcontrib.bibtex',
+    'sphinx_autodoc_typehints',
+]
+
+add_module_names = False
+templates_path = ['_templates']
+source_suffix = '.rst'
+master_doc = 'index'
+
+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 = 'en'
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
+default_role = 'any'
+pygments_style = 'sphinx'
+todo_include_todos = False
+
+# Options for HTML output
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme = 'sphinx_rtd_theme'
+htmlhelp_basename = 'pystencilsdoc'
+html_sidebars = {'**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html']}
+
+# NbSphinx configuration
+nbsphinx_execute = 'never'
+nbsphinx_codecell_lexer = 'python3'
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None),
+                       'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+                       'matplotlib': ('https://matplotlib.org/', None),
+                       'sympy': ('https://docs.sympy.org/latest/', None),
+                       }
+
+autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/pystencils.bib']
 
 project = 'pystencils'
-html_logo = "img/logo.png"
+html_logo = 'img/logo.png'

doc/img/logo_large.svg

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doc/index.rst

@@ -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