.flake8

 [flake8]
 max-line-length=120
-exclude=pystencils/jupyter.py,
-        pystencils/plot.py
-        pystencils/session.py
-ignore = W293 W503 W291 C901
+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
+.coverage*
 *.pyc
 *.vti
 /build
 /dist
-/*.egg-info
+*.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: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install -e .
   script:
+    - env
+    - pip list
     - export NUM_CORES=$(nproc --all)
     - 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
+    - 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
-    - cuda
+    - 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
 
-# Nightly test  - runs "long run" jobs only
-test-longrun:
+# Normal test with longruns
+tests-and-coverage-with-longrun:
   stage: test
-  only:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  when: manual
+  allow_failure: true
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install sympy --upgrade
+    - pip install -e .
   script:
+    - env
+    - pip list
     - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
-    - 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
-    - cuda
+    - cuda11
     - AVX
-  artifacts:
-    paths:
-      - coverage_report
-      - test-report
 
-# Minimal tests in windows environment
-minimal-windows:
+# pipeline with latest python version
+latest-python:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  tags:
-    - win
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
   script:
-    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
-    - source activate pystencils_dev
     - env
-    - conda env list
-    - python -c "import numpy"
-    - python setup.py quicktest
+    - pip list
+    - pip install -e .
+    - export NUM_CORES=$(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
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
+  extends: .every-commit
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
+  before_script:
+    - ln -s /usr/include/locale.h /usr/include/xlocale.h
+    - pip3 install -e .
   script:
+    - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
     - sed -i 's/--doctest-modules //g' pytest.ini
-    - pytest-3 -v -m "not longrun"
+    - env
+    - pip list
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
 
-minimal-conda:
+.multiarch_template:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
+  extends: .every-commit
+  allow_failure: true
+  before_script: &multiarch_before_script
+    # - pip3 install -v .
+    - export PYTHONPATH=src
+    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
+    - sed -i '/^fail_under.*/d' pytest.ini
+  script:
+    - export NUM_CORES=$(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 setup.py quicktest
+    - python quicktest.py
   tags:
     - docker
+    - cuda
 
 
 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
+    - 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
@@ -123,50 +257,89 @@ pycodegen-integration:
     - git fetch test
     - git reset --hard $CI_COMMIT_SHA
     - cd ..
-    - export PYTHONPATH=`pwd`/pystencils:`pwd`/lbmpy:`pwd`/pygrandchem:`pwd`/pystencils_walberla:`pwd`/lbmpy_walberla
+    - pip install -e pystencils/
+    - pip install -e lbmpy/
+    - cmake --version
     - ./install_walberla.sh
     - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
     - cd pystencils
-    - py.test -v -n $NUM_CORES .
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
     - cd ../lbmpy
-    - py.test -v -n $NUM_CORES .
-    - cd ../pygrandchem
-    - py.test -v -n $NUM_CORES .
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
     - 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 $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: pycodegen/*/report.xml
+
+
+# -------------------- Scheduled Tasks --------------------------------------------------------------------------
+
+
+# Nightly test against the latest (pre-release) version of SymPy published on PyPI
+nightly-sympy:
+  stage: nightly
+  needs: []
+  extends: .scheduled
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+    - pip install --upgrade --pre sympy
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(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
-    - cuda
     - 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
-    - cuda
 
 
 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
   tags:
     - docker
-    - cuda
   artifacts:
     paths:
       - html_doc
@@ -174,7 +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
@@ -184,5 +359,3 @@ pages:
       - public
   tags:
     - docker
-  only:
-    - master@pycodegen/pystencils

AUTHORS.txt

@@ -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

+# 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 RELEASE-VERSION
+include AUTHORS.txt
+include CONTRIBUTING.md
+include CHANGELOG.md

README.md

@@ -2,16 +2,16 @@ 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)](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)
 [![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.
 
 *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](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:
@@ -21,7 +21,7 @@ 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)
+                       (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)
@@ -33,15 +33,15 @@ 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)
 discretization = discretize(adv_diff_pde)
 ```
 
-Look at the [documentation](http://pycodegen.pages.walberla.net/pystencils) to learn more.
-
-
 Installation
 ------------
 
@@ -52,22 +52,36 @@ 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.
 ```bash
-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
 -------------
 
-Read the docs [here](http://pycodegen.pages.walberla.net/pystencils) and
-check out the Jupyter notebooks in `doc/notebooks`.
+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/environment.yml

@@ -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

@@ -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
@@ -25,6 +25,12 @@ except ImportError:
 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):
@@ -34,61 +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
-except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/backends/llvm.py')]
-    add_path_to_ignore('pystencils/llvm')
-
 try:
-    import kerncraft
+    import cupy
 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")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/vtk.py")]
 
 collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
 
@@ -150,7 +143,10 @@ class IPyNbFile(pytest.File):
             warnings.filterwarnings("ignore", "IPython.core.inputsplitter is deprecated")
             notebook = nbformat.read(notebook_contents, 4)
             code, _ = exporter.from_notebook_node(notebook)
-        yield IPyNbTest(self.name, self, code)
+        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
@@ -159,4 +155,7 @@ class IPyNbFile(pytest.File):
 def pytest_collect_file(path, parent):
     glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
     if any(path.fnmatch(g) for g in glob_exprs):
-        return IPyNbFile(path, parent)
+        if pytest_version >= 50403:
+            return IPyNbFile.from_parent(fspath=path, parent=parent)
+        else:
+            return IPyNbFile(path, parent)

doc/conf.py

@@ -4,10 +4,11 @@
 import datetime
 import sphinx_rtd_theme
 import os
+import re
 import sys
 
 sys.path.insert(0, os.path.abspath('.'))
-from version_from_git import version_number_from_git
+import pystencils
 
 extensions = [
     'sphinx.ext.autodoc',
@@ -25,11 +26,14 @@ templates_path = ['_templates']
 source_suffix = '.rst'
 master_doc = 'index'
 
-copyright = '{}, Martin Bauer'.format(datetime.datetime.now().year)
-author = 'Martin Bauer'
-version = version_number_from_git()
-release = version_number_from_git()
-language = None
+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'
@@ -47,13 +51,14 @@ 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/1.5.1/', 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/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