Merge branch 'master' into hyteg

.flake8

 [flake8]
 max-line-length=120
-exclude=pystencils/jupytersetup.py,
-        pystencils/plot2d.py
+exclude=pystencils/jupyter.py,
+        pystencils/plot.py
         pystencils/session.py
-ignore = W293 W503 W291
+ignore = W293 W503 W291 C901 E741

.gitignore

@@ -10,4 +10,11 @@ __pycache__
 _build
 /.idea
 .cache
-_local_tmp
\ No newline at end of file
+_local_tmp
+RELEASE-VERSION
+test-report
+pystencils/boundaries/createindexlistcython.c
+pystencils/boundaries/createindexlistcython.*.so
+pystencils_tests/tmp
+pystencils_tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
+pystencils_tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
\ No newline at end of file

.gitlab-ci.yml

@@ -11,21 +11,24 @@ tests-and-coverage:
   except:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
+    - env
+    - pip list
     - export NUM_CORES=$(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"
+    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun" --html test-report/index.html
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
   artifacts:
     when: always
     paths:
       - coverage_report
+      - test-report
 
 # Nightly test  - runs "long run" jobs only
 test-longrun:
@@ -33,19 +36,20 @@ test-longrun:
   only:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
     - export NUM_CORES=$(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=.
+    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. --html test-report/index.html
   tags:
     - docker
-    - cuda
+    - cuda11
     - AVX
   artifacts:
     paths:
       - coverage_report
+      - test-report
 
 # Minimal tests in windows environment
 minimal-windows:
@@ -63,29 +67,91 @@ minimal-windows:
     - python -c "import numpy"
     - python setup.py quicktest
 
-minimal-ubuntu:
+ubuntu:
   stage: test
   except:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/minimal_ubuntu
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
   script:
-    - python3 setup.py quicktest
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - sed -i 's/--doctest-modules //g' pytest.ini
+    - pytest-3 -v -m "not longrun"
   tags:
     - docker
+    - cuda11
+    - AVX
 
 minimal-conda:
   stage: test
   except:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/minimal_conda
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
   script:
     - python setup.py quicktest
   tags:
     - docker
+    - cuda
 
 
+minimal-sympy-master:
+  stage: test
+  except:
+    variables:
+      - $ENABLE_NIGHTLY_BUILDS
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  script:
+    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
+    - python setup.py quicktest
+  allow_failure: true
+  tags:
+    - docker
+    - cuda
+
+
+pycodegen-integration:
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: test
+  when: manual
+  allow_failure: true
+  script:
+    - git clone https://gitlab-ci-token:${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 $CI_COMMIT_SHA
+    - cd ..
+    - pip install -e pystencils/
+    - pip install -e lbmpy/
+    - pip install -e pygrandchem/
+    - ./install_walberla.sh
+    - export NUM_CORES=$(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 CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample UniformGridBenchmarkGPU_trt UniformGridBenchmarkGPU_entropic_kbc_n4 FluctuatingMRT
+    - cd apps/benchmarks/UniformGridGPU
+    - make -j $NUM_CORES
+    - cd ../UniformGridGenerated
+    - make -j $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+
 # -------------------- Linter & Documentation --------------------------------------------------------------------------
 
 
@@ -94,31 +160,30 @@ flake8-lint:
   except:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
     - flake8 pystencils
   tags:
     - docker
-    - cuda
 
 
 build-documentation:
   stage: test
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   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
 
 
 pages:
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   stage: deploy
   script:
     - ls -l

.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>
+  - Stephan Seitz <stephan.seitz@fau.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>
+  - Dominik Ernst <dominik.ernst@fau.de>
+  - João Victor Tozatti Risso <joaovictortr@protonmail.com>

MANIFEST.in

 include README.md
 include COPYING.txt
+include RELEASE-VERSION
+global-include *.pyx
+global-exclude boundaries/createindexlistcython.c

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)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
-[coverage report](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 array.
-It runs faster than normal numpy code and even as Cython and numba.
+*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
@@ -17,7 +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)
@@ -35,9 +39,6 @@ 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
 ------------
 
@@ -48,10 +49,12 @@ pip install pystencils[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 an NVIDIA GPU is available and CUDA is installed
+-  `opencl`: basic OpenCL support (experimental)
 - `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.
@@ -63,5 +66,5 @@ pip install pystencils[interactive,gpu,doc]
 Documentation
 -------------
 
-Read the docs [here](http://pycodegen.pages.walberla.net/pystencils) and
+Read the docs [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils) and
 check out the Jupyter notebooks in `doc/notebooks`.

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 installed and want to use your GPU, uncomment the last line to install pycuda
+#
+# ----------------------------------------------------------------------------------------------------------------------
+
+name: pystencils
+dependencies:
+  # Basic dependencies:
+  - python >= 3.6
+  - 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
+      #- pycuda # add this if you have CUDA installed

binder/start

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

conftest.py

 import os
-import pytest
-import tempfile
 import runpy
 import sys
+import tempfile
+import warnings
+
+import nbformat
+import pytest
+from nbconvert import PythonExporter
+
+from pystencils.boundaries.createindexlistcython 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
@@ -14,12 +20,17 @@ try:
     pyximport.install(language_level=3)
 except ImportError:
     pass
-from pystencils.boundaries.createindexlistcython import *  # NOQA
 
 
 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):
@@ -28,34 +39,68 @@ def add_path_to_ignore(path):
     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")]
+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')
 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/pystencils_tests/test_cudagpu.py")]
+    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')]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/test_basic_usage_llvm.ipynb')]
     add_path_to_ignore('pystencils/llvm')
 
 try:
     import kerncraft
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_kerncraft_coupling.py")]
+    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')
 
+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"),
+                       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")]
+
 try:
     import blitzdb
 except ImportError:
     add_path_to_ignore('pystencils/runhelper')
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_parameterstudy.py")]
 
+try:
+    import islpy
+except ImportError:
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "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, "doc/notebooks/01_tutorial_getting_started.ipynb")]
+
+try:
+    import pyevtk
+except ImportError:
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/datahandling/vtk.py")]
+
+# TODO: Remove if Ubuntu 18.04 is no longer supported
+if pytest_version < 50403:
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_jupyter_extensions.ipynb")]
 
 collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
 
@@ -65,10 +110,6 @@ 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
@@ -89,6 +130,7 @@ class IPyNbTest(pytest.Item):
         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}
@@ -114,10 +156,16 @@ class IPyNbFile(pytest.File):
         exporter.exclude_markdown = True
         exporter.exclude_input_prompt = True
 
-        notebook_contents = self.fspath.open()
-        notebook = nbformat.read(notebook_contents, 4)
-        code, _ = exporter.from_notebook_node(notebook)
-        yield IPyNbTest(self.name, self, code)
+        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
@@ -126,4 +174,7 @@ 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

@@ -54,6 +54,7 @@ intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),
                        }
 
 autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/pystencils.bib']
 
 project = 'pystencils'
 html_logo = "img/logo.png"

doc/img/logo_large.svg

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="379.82614mm"
+   height="189.91307mm"
+   viewBox="0 0 1345.8407 672.92033"
+   id="svg2"
+   version="1.1"
+   inkscape:version="0.92.3 (2405546, 2018-03-11)"
+   sodipodi:docname="logo_large.svg"
+   inkscape:export-filename="/home/martin/code/pycodegen/pystencils/doc/img/github_repo_card.png"
+   inkscape:export-xdpi="85.599998"
+   inkscape:export-ydpi="85.599998">
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+     id="defs4">
+    <inkscape:path-effect
+       effect="spiro"
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+       is_visible="true" />
+    <inkscape:path-effect
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+       is_visible="true" />
+    <filter
+       y="-0.25"
+       height="1.5"
+       inkscape:menu-tooltip="Darkens the edge with an inner blur and adds a flexible glow"
+       inkscape:menu="Shadows and Glows"
+       inkscape:label="Dark And Glow"
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+       id="filter4596">
+      <feGaussianBlur
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+         result="result6"
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+      <feBlend
+         in="result10"
+         mode="normal"
+         in2="result6"
+         id="feBlend4618" />
+    </filter>
+    <filter
+       y="-0.25"
+       height="1.5"
+       inkscape:menu-tooltip="Darkens the edge with an inner blur and adds a flexible glow"
+       inkscape:menu="Shadows and Glows"
+       inkscape:label="Dark And Glow"
+       style="color-interpolation-filters:sRGB"
+       id="filter4620">
+      <feGaussianBlur
+         stdDeviation="5"
+         result="result6"
+         id="feGaussianBlur4622" />
+      <feComposite
+         result="result8"
+         in="SourceGraphic"
+         operator="atop"
+         in2="result6"
+         id="feComposite4624" />
+      <feComposite
+         result="result9"
+         operator="over"
+         in2="SourceAlpha"
+         in="result8"
+         id="feComposite4626" />
+      <feColorMatrix
+         values="1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 "
+         result="result10"
+         id="feColorMatrix4628" />
+      <feBlend