.flake8

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

.gitattributes

+src/lbmpy/_version.py export-subst

.gitignore

 __pycache__
 .ipynb_checkpoints
-.coverage
+.coverage*
 *.pyc
 *.vti
 /build
+/html_doc
 /dist
-/*.egg-info
+*.egg-info
 .cache
 _build
 /.idea
-.cache
-_local_tmp
+_local_tmp
+**/.vscode
\ No newline at end of file
+**/pylintrc
+*.bak
+*.tmp
+/tests/db
+doc/bibtex.json
+/db
+/src/lbmpy/phasefield/simplex_projection.*.so
+/src/lbmpy/phasefield/simplex_projection.c
+
+# macOS
+**/.DS_Store
+*.uuid
+
+# benchmark database
+/tests/benchmark/db
\ No newline at end of file

.gitlab-ci.yml

 stages:
+  - pretest
   - test
+  - nightly
+  - docs
   - deploy
 
+# --------------------------  Templates ------------------------------------------------------------------------------------
 
-# --------------------------  Tests ------------------------------------------------------------------------------------
+# 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/lbmpy" && $CI_COMMIT_BRANCH == "master"'
+
+
+# Base configuration for jobs meant to run at a schedule
+.scheduled:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+
+# --------------------------  Pre Tests --------------------------------------------------------------------------------
 
 # Normal test - runs on every commit all but "long run" tests
 tests-and-coverage:
-  stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
   script:
+    # - pip install sympy --upgrade
     - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
     - mkdir public
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun"
+    - env
+    - pip list
+    - py.test -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --junitxml=report.xml
+    - python3 -m coverage xml
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
+  coverage: /Total coverage:\s\d+.\d+\%/
   artifacts:
     when: always
     paths:
       - coverage_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:
-      - $ENABLE_NIGHTLY_BUILDS
+  when: manual
+  allow_failure: true
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
+    # - pip install sympy --upgrade
     - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=.
+    - env
+    - pip list
+    - py.test -v -n $NUM_CORES
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
-  artifacts:
-    paths:
-      - coverage_report
 
-# Minimal tests in windows environment
-minimal-windows:
-  stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  tags:
-    - win
+minimal-conda:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
   script:
-    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
-    - source activate pystencils_dev
-    - env
-    - conda env list
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - python -c "import numpy"
-    - python setup.py quicktest
+    - pip install -e .
+    - python quicktest.py
+  tags:
+    - docker
 
-ubuntu:
+# Linter for code formatting
+flake8-lint:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  script:
+    - flake8 src/lbmpy
+  tags:
+    - docker
+    - cuda11
+
+# -------------------------- Tests -------------------------------------------------------------------------------------
+
+# pipeline with latest python version
+latest-python:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
   script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
-    - pip3 install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - pytest-3 -v -m "not longrun"
+    - mkdir public
+    - py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
   tags:
     - docker
-    - cuda
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
 
-minimal-conda:
+# Minimal tests in windows environment
+#minimal-windows:
+#  stage: test
+#  except:
+#    variables:
+#      - $ENABLE_NIGHTLY_BUILDS
+#  tags:
+#    - win
+#  script:
+#    - export NUM_CORES=$(nproc --all)
+#    - export MPLBACKEND=Agg
+#    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
+#    - source activate pystencils
+#    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+#    - python -c "import numpy"
+#    - pip install sympy==1.9
+#    - py.test -v -m "not (notebook or longrun)"
+
+minimal-sympy-master:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
+  extends: .every-commit
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
   script:
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - python setup.py quicktest
+    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
+    - pip list
+    - python quicktest.py
+  allow_failure: true
+  tags:
+    - docker
+    - cuda
+
+ubuntu:
+  stage: test
+  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 git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+  script:
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - env
+    - pip3 list
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
   tags:
     - docker
+    - cuda11
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
 
 pycodegen-integration:
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   stage: test
   when: manual
+  allow_failure: true
   script:
+    - env
+    - pip list
     - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
     - cd pycodegen
     - git submodule sync --recursive
     - git submodule update --init --recursive
     - git submodule foreach git fetch origin   # compare the latest master version!
     - git submodule foreach git reset --hard origin/master
-    - cd pystencils
+    - cd lbmpy
     - git remote add test $CI_REPOSITORY_URL
     - git fetch test
     - git reset --hard $CI_COMMIT_SHA
     - cd ..
     - pip install -e pystencils/
     - pip install -e lbmpy/
-    - pip install -e pygrandchem/
     - ./install_walberla.sh
-    - export NUM_CORES=$(nproc --all)
-    - mkdir -p ~/.config/matplotlib
-    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
-    - cd pystencils
-    - py.test -v -n $NUM_CORES .
-    - cd ../lbmpy
-    - py.test -v -n $NUM_CORES .
-    - cd ../pygrandchem
-    - py.test -v -n $NUM_CORES .
-    - cd ../walberla/build/
-    - make CodegenJacobiCPU CodegenJacobiGPU CodegenPoisson MicroBenchmarkGpuLbm LbCodeGenerationExample UniformGridBenchmarkGPU_trt UniformGridBenchmarkGPU_entropic_kbc_n4
+    # build all integration tests
+    - cd walberla/build/
+    - make -j $NUM_CORES MicroBenchmarkGpuLbm LbCodeGenerationExample
     - cd apps/benchmarks/UniformGridGPU
     - make -j $NUM_CORES
-    - cd ../UniformGridGenerated
+    - cd ../UniformGridCPU
     - make -j $NUM_CORES
+
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
 
-# -------------------- Linter & Documentation --------------------------------------------------------------------------
+# -------------------- Scheduled Tasks --------------------------------------------------------------------------
 
 
-flake8-lint:
-  stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+nightly-sympy:
+  stage: nightly
+  extends: .scheduled
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+    - pip install --upgrade --pre sympy
   script:
-    - flake8 lbmpy
+    - 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
+
 
+# -------------------- Documentation and deploy ------------------------------------------------------------------------
 
 build-documentation:
-  stage: test
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: docs
+  needs: []
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
+  before_script:
+    - pip install -e .
   script:
     - export PYTHONPATH=`pwd`
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
     - mkdir html_doc
-    - sphinx-build -W -b html doc  html_doc
+    - sphinx-build -W -b html doc html_doc
   tags:
     - docker
-    - cuda
+    - cuda11
   artifacts:
     paths:
       - html_doc
@@ -167,7 +270,9 @@ 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
@@ -177,5 +282,3 @@ pages:
       - public
   tags:
     - docker
-  only:
-    - master@pycodegen/lbmpy

AUTHORS.txt

+
+Contributors:
+-------------
+
+  - Martin Bauer <martin.bauer@fau.de>
+  - Markus Holzer <markus.holzer@fau.de>
+  - Michael Kuron <mkuron@icp.uni-stuttgart.de>
+  - Stephan Seitz <stephan.seitz@fau.de>
+  - Frederik Hennig <frederik.hennig@fau.de>
+  - Helen Schottenhamml <helen.schottenhamml@fau.de>
+  - Rudolf Weeber <weeber@icp.uni-stuttgart.de>
+  - Christian Godenschwager <christian.godenschwager@fau.de>
+  - Jan Hönig <jan.hoenig@fau.de>

CHANGELOG.md

+# Change Log
+
+## Unreleased
+
+### Removed
+* Removing OpenCL support because it is not supported by pystencils anymore

CONTRIBUTING.md

+# Contributing
+
+lbmpy is built on the open-source python framework [pystencils](https://pypi.org/project/pystencils/). Please consider the [contribution guideline](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CONTRIBUTING.md) of pystencils for contributing to lbmpy.
\ No newline at end of file

COPYING.txt

-------------------------   Important ---------------------------------
-
-lbmpy is under the following GNU AGPLv3 license. 
-This license holds for the sources of lbmpy itself as well 
-as for all kernels generated with lbmpy i.e. 
-the output of lbmpy is also protected by the GNU AGPLv3 license. 
-
-----------------------------------------------------------------------
-
-
-
-                    
                     GNU AFFERO GENERAL PUBLIC LICENSE
                        Version 3, 19 November 2007
 

MANIFEST.in

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

README.md

@@ -2,9 +2,9 @@ lbmpy
 =====
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/lbmpy/master?filepath=doc%2Fnotebooks)
-[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.walberla.net/lbmpy)
+[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.i10git.cs.fau.de/lbmpy)
 [![pipeline status](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/lbmpy/commits/master)
-[![coverage report](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/coverage.svg)](http://pycodegen.pages.walberla.net/lbmpy/coverage_report)
+[![coverage report](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/lbmpy/coverage_report)
 
 
 Run fast fluid simulations based on the lattice Boltzmann method in Python on CPUs and GPUs.
@@ -16,11 +16,12 @@ It even comes with an integrated Chapman Enskog analysis based on sympy!
 
 Common test scenarios can be set up quickly:
 ```python
-from lbmpy.scenarios import create_channel
+from pystencils import Target
+from lbmpy.session import *
 
-ch = create_channel(domain_size=(300,100, 100), force=1e-7, method="trt",
+ch = create_channel(domain_size=(300, 100, 100), force=1e-7, method=Method.TRT,
                     equilibrium_order=2, compressible=True,
-                    relaxation_rates=[1.97, 1.6], optimization={'target': 'gpu'})
+                    relaxation_rates=[1.97, 1.6], optimization={'target': Target.GPU})
 ```
 
 To find out more, check out the interactive [tutorial notebooks online with binder](https://mybinder.org/v2/gh/mabau/lbmpy/master?filepath=doc%2Fnotebooks).
@@ -39,7 +40,7 @@ pip install lbmpy[interactive]
 Without `[interactive]` you get a minimal version with very little dependencies.
 
 All options:
-- `gpu`: use this if nVidia GPU is available and CUDA is installed
+- `gpu`: use this if a NVIDIA GPU is available and CUDA is installed
 - `opencl`: use this to enable the target `opencl` (execution using OpenCL)
 - `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
 - `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.
@@ -53,5 +54,30 @@ pip install lbmpy[interactive,gpu,doc]
 Documentation
 -------------
 
-Read the docs [here](http://pycodegen.pages.walberla.net/lbmpy) and
+Read the docs [here](http://pycodegen.pages.i10git.cs.fau.de/lbmpy) and
 check out the Jupyter notebooks in `doc/notebooks`. 
+
+Contributing
+-------
+To see how to open issues, submit bug reports, create feature requests or submit your additions to lbmpy please refer to
+[contribution documentation](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CONTRIBUTING.md) of pystencils since lbmpy is heavily build on pystencils.
+
+
+Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/lbmpy/-/blob/master/AUTHORS.txt) of lbmpy.
+
+
+### Please cite us
+
+If you use lbmpy in a publication, please cite the following articles:
+
+Overview:
+  - F. Hennig et al, Advanced Automatic Code Generation for Multiple Relaxation-Time Lattice Boltzmann Methods. SIAM Journal on Scientific Computing, 2023. https://doi.org/10.1137/22M1531348 ([Preprint](https://arxiv.org/abs/2211.02435))
+  - M. Bauer et al, lbmpy: Automatic code generation for efficient parallel lattice Boltzmann methods. Journal of Computational Science, 2021. https://doi.org/10.1016/j.jocs.2020.101269 ([Preprint](https://arxiv.org/abs/2001.11806))
+
+Multiphase:
+   - M. Holzer et al, Highly efficient lattice Boltzmann multiphase simulations of immiscible fluids at high-density ratios on CPUs and GPUs through code generation. The International Journal of High Performance Computing Applications, 2021. https://doi.org/10.1177/10943420211016525
+
+
+### Further Reading
+
+- F. Hennig et al, Automatic Code Generation for the Cumulant Lattice Boltzmann Method. ICMMES, 2021. [Poster Link](https://www.researchgate.net/publication/353224406_Automatic_Code_Generation_for_the_Cumulant_Lattice_Boltzmann_Method)

binder/environment.yml

@@ -7,7 +7,7 @@
 #     conda env create -f conda_environment_user.yml
 #     . activate pystencils
 #
-# If you have CUDA installed and want to use your GPU, uncomment the last line to install pycuda
+# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy
 #
 # ----------------------------------------------------------------------------------------------------------------------
 
@@ -33,4 +33,4 @@ dependencies:
       - pyevtk # VTK output for serial simulations
       - blitzdb # file-based No-SQL database to store simulation results
       - pystencils
-      #- pycuda # add this if you have CUDA installed
+      #- cupy # add this if you have CUDA or ROCm installed

conftest.py

@@ -4,6 +4,11 @@ import tempfile
 import runpy
 import sys
 import warnings
+import platform
+
+import nbformat
+from nbconvert import PythonExporter
+import sympy
 # 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
@@ -12,15 +17,22 @@ from pystencils.cpu import cpujit
 # at the same time
 try:
     import pyximport
+
     pyximport.install(language_level=3)
+
+    from lbmpy.phasefield.simplex_projection import simplex_projection_2d  # NOQA
 except ImportError:
     pass
-from lbmpy.phasefield.simplex_projection import simplex_projection_2d  # NOQA
-
 
 SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
 sys.path.insert(0, os.path.abspath('lbmpy'))
 
+# 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):
@@ -31,32 +43,35 @@ def add_path_to_ignore(path):
 
 collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
                   os.path.join(SCRIPT_FOLDER, "doc", "img", "mb_discretization", "maxwell_boltzmann_stencil_plot.py")]
-add_path_to_ignore('pystencils_tests/benchmark')
 add_path_to_ignore('_local_tmp')
 
-
 try:
-    import pycuda
+    import cupy
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_cpu_gpu_equivalence.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_cpu_gpu_equivalence.py")]
 
 try:
     import waLBerla
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_serial_scenarios.py")]
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_datahandling_parallel.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py")]
 
 try:
     import blitzdb
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/benchmark"),
-                       os.path.join(SCRIPT_FOLDER, "lbmpy_tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/benchmark"),
+                       os.path.join(SCRIPT_FOLDER,
+                                    "tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py"),
+                       os.path.join(SCRIPT_FOLDER, "tests/full_scenarios/shear_wave/scenario_shear_wave.py"),
+                       os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py"),
+                       os.path.join(SCRIPT_FOLDER, "src/lbmpy/db.py")]
+
+if platform.system().lower() == 'windows':
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_quicktests.py")]
 
-import sympy
 sver = sympy.__version__.split(".")
-if (int(sver[0]) == 1 and int(sver[1]) < 2):
-    add_path_to_ignore('lbmpy_tests/phasefield')
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_n_phase_boyer_noncoupled.ipynb")]
+if int(sver[0]) == 1 and int(sver[1]) < 2:
+    add_path_to_ignore('tests/phasefield')
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_n_phase_boyer_noncoupled.ipynb")]
 
 collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
 
@@ -66,10 +81,6 @@ for root, sub_dirs, files in os.walk('.'):
             collect_ignore.append(f)
 
 
-import nbformat
-from nbconvert import PythonExporter
-
-
 class IPythonMockup:
     def run_line_magic(self, *args, **kwargs):
         pass
@@ -96,18 +107,25 @@ class IPyNbTest(pytest.Item):
 
         # disable matplotlib output
         exec("import matplotlib.pyplot as p; "
+             "p.close('all'); "
              "p.switch_backend('Template')", global_dict)
 
         # in notebooks there is an implicit plt.show() - if this is not called a warning is shown when the next
         # plot is created. This warning is suppressed here
+        # Also animations cannot be shown, which also leads to a warning.
         exec("import warnings;"
-             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*');",
+             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*');"
+             "warnings.filterwarnings('ignore', 'Animation was deleted without rendering anything.*');",
              global_dict)
         with tempfile.NamedTemporaryFile() as f:
             f.write(self.code.encode())
             f.flush()
             runpy.run_path(f.name, init_globals=global_dict, run_name=self.name)
 
+        #   Close any open figures
+        exec("import matplotlib.pyplot as p; "
+             "p.close('all')", global_dict)
+
 
 class IPyNbFile(pytest.File):
     def collect(self):
@@ -121,13 +139,28 @@ 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
 
 
-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 >= 70000:
+    #   Since pytest 7.0, usage of `py.path.local` is deprecated and `pathlib.Path` should be used instead
+    import pathlib
+
+    def pytest_collect_file(file_path: pathlib.Path, parent):
+        glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
+        if any(file_path.match(g) for g in glob_exprs):
+            return IPyNbFile.from_parent(path=file_path, parent=parent)
+else:
+    def pytest_collect_file(path, parent):
+        glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
+        if any(path.fnmatch(g) for g in glob_exprs):
+            if pytest_version >= 50403:
+                return IPyNbFile.from_parent(fspath=path, parent=parent)
+            else:
+                return IPyNbFile(path, parent)

doc/conf.py

@@ -5,9 +5,10 @@ import datetime
 import sphinx_rtd_theme
 import os
 import sys
+import re
+import lbmpy
 
 sys.path.insert(0, os.path.abspath('.'))
-from version_from_git import version_number_from_git
 
 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', lbmpy.__version__)
+version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
+# The full version, including alpha/beta/rc tags.
+release = lbmpy.__version__
+language = 'en'
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 default_role = 'any'
 pygments_style = 'sphinx'
@@ -54,6 +58,7 @@ intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),
                        }
 
 autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/lbmpy.bib']
 
 project = 'lbmpy'
-html_logo = "img/logo.png"
+html_logo = 'img/logo.png'

doc/index.rst

@@ -6,6 +6,9 @@ lbmpy
     :maxdepth: 2
 
     sphinx/tutorials.rst
+    sphinx/methods.rst
+    sphinx/boundary_conditions.rst
+    sphinx/forcemodels.rst
     sphinx/api.rst