Merge master

.gitignore

@@ -16,4 +16,10 @@ _local_tmp
 doc/bibtex.json
 /db
 /lbmpy/phasefield/simplex_projection.*.so
-/lbmpy/phasefield/simplex_projection.c
\ No newline at end of file
+/lbmpy/phasefield/simplex_projection.c
+
+# macOS
+**/.DS_Store
+
+# benchmark database
+/lbmpy_tests/benchmark/db
\ No newline at end of file

.gitlab-ci.yml

 stages:
+  - pretest
   - test
   - deploy
 
 
-# --------------------------  Tests ------------------------------------------------------------------------------------
+# --------------------------  Pre Tests --------------------------------------------------------------------------------
 
 # Normal test - runs on every commit all but "long run" tests
 tests-and-coverage:
-  stage: test
+  stage: pretest
   except:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
-    - env
-    - pip list
+    # - pip install sympy --upgrade
     - export NUM_CORES=$(nproc --all)
     - mkdir -p ~/.config/matplotlib
     - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
@@ -36,6 +36,33 @@ tests-and-coverage:
       cobertura: coverage.xml
       junit: report.xml
 
+minimal-conda:
+  stage: pretest
+  except:
+    variables:
+      - $ENABLE_NIGHTLY_BUILDS
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  script:
+    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+    - python setup.py quicktest
+  tags:
+    - docker
+
+# Linter for code formatting
+flake8-lint:
+  stage: pretest
+  except:
+    variables:
+      - $ENABLE_NIGHTLY_BUILDS
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  script:
+    - flake8 lbmpy
+  tags:
+    - docker
+    - cuda11
+
+# -------------------------- Tests -------------------------------------------------------------------------------------
+
 # pipeline with latest python version
 latest-python:
   stage: test
@@ -106,6 +133,22 @@ minimal-windows:
     - python -c "import numpy"
     - py.test -v -n $NUM_CORES -m "not (notebook or longrun)"
 
+minimal-sympy-master:
+  stage: test
+  except:
+    variables:
+      - $ENABLE_NIGHTLY_BUILDS
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  script:
+    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
+    - pip list
+    - python setup.py quicktest
+  allow_failure: true
+  tags:
+    - docker
+    - cuda
+
 ubuntu:
   stage: test
   except:
@@ -113,9 +156,9 @@ ubuntu:
       - $ENABLE_NIGHTLY_BUILDS
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
   before_script:
-    - apt-get -y remove python3-sympy
+    # - apt-get -y remove python3-sympy
     - ln -s /usr/include/locale.h /usr/include/xlocale.h
-    - pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py | sed 's/>/=/g'`
+    # - pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py | sed 's/>/=/g'`
     - pip3 install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
   script:
     - export NUM_CORES=$(nproc --all)
@@ -132,18 +175,6 @@ ubuntu:
     reports:
       junit: report.xml
 
-minimal-conda:
-  stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
-  script:
-    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
-    - python setup.py quicktest
-  tags:
-    - docker
-
 pycodegen-integration:
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   stage: test
@@ -179,25 +210,11 @@ pycodegen-integration:
     - cuda11
     - AVX
 
-# -------------------- Linter & Documentation --------------------------------------------------------------------------
-
-
-flake8-lint:
-  stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
-  script:
-    - flake8 lbmpy
-  tags:
-    - docker
-    - cuda11
-
+# -------------------- Documentation and deploy ------------------------------------------------------------------------
 
 build-documentation:
   stage: test
-  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
   script:
     - export PYTHONPATH=`pwd`
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

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

MANIFEST.in

 include README.md
 include COPYING.txt
-include RELEASE-VERSION
+include AUTHORS.txt
+include CONTRIBUTING.md
 global-include *.pyx
 include versioneer.py
 include lbmpy/_version.py

README.md

@@ -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).
@@ -55,3 +56,27 @@ Documentation
 
 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:
+  - 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)

conftest.py

@@ -4,6 +4,9 @@ import tempfile
 import runpy
 import sys
 import warnings
+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
@@ -12,12 +15,12 @@ from pystencils.cpu import cpujit
 # at the same time
 try:
     import pyximport
+
     pyximport.install(language_level=3)
 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'))
 
@@ -40,7 +43,6 @@ collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
 add_path_to_ignore('pystencils_tests/benchmark')
 add_path_to_ignore('_local_tmp')
 
-
 try:
     import pycuda
 except ImportError:
@@ -49,18 +51,17 @@ except ImportError:
 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")]
 
 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")]
+                       os.path.join(SCRIPT_FOLDER,
+                                    "lbmpy_tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py")]
 
-import sympy
 sver = sympy.__version__.split(".")
-if (int(sver[0]) == 1 and int(sver[1]) < 2):
+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")]
 
@@ -72,10 +73,6 @@ 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

doc/conf.py

@@ -26,8 +26,8 @@ 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'
+author = 'Martin Bauer, Markus Holzer'
 # 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)