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)

cpu/__init__.py

-from pystencils.cpu.kernelcreation import createKernel, addOpenMP
-from pystencils.cpu.cpujit import makePythonFunction
-from pystencils.backends.cbackend import generateC

cpu/cpujit.py

-import os
-import subprocess
-from ctypes import cdll, c_double, c_float, sizeof
-from tempfile import TemporaryDirectory
-from pystencils.backends.cbackend import generateC
-import numpy as np
-import pickle
-import hashlib
-
-from pystencils.transformations import symbolNameToVariableName
-
-CONFIG_GCC = {
-    'compiler': 'g++-4.8',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp',
-}
-CONFIG_INTEL = {
-    'compiler': '/software/intel/2017/bin/icpc',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp -Wl,-rpath=/software/intel/2017/lib/intel64',
-    'env': {
-        'INTEL_LICENSE_FILE': '1713@license4.rrze.uni-erlangen.de',
-        'LM_PROJECT': 'iwia',
-    }
-}
-CONFIG_INTEL_SUPERMUC = {
-    'compiler': '/lrz/sys/intel/studio2017_u1/compilers_and_libraries_2017.1.132/linux/bin/intel64/icpc',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp -Wl,'
-             '-rpath=/lrz/sys/intel/studio2016_u4/compilers_and_libraries_2016.4.258/linux/mkl/lib/intel64',
-    'env': {
-        'INTEL_LICENSE_FILE': '/lrz/sys/intel/licenses',
-    }
-}
-CONFIG_CLANG = {
-    'compiler': 'clang++',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp',
-}
-CONFIG = CONFIG_GCC
-
-
-def ctypeFromString(typename, includePointers=True):
-    import ctypes as ct
-
-    typename = str(typename).replace("*", " * ")
-    typeComponents = typename.split()
-
-    basicTypeMap = {
-        'double': ct.c_double,
-        'float': ct.c_float,
-        'int': ct.c_int,
-        'long': ct.c_long,
-    }
-
-    resultType = None
-    for typeComponent in typeComponents:
-        typeComponent = typeComponent.strip()
-        if typeComponent == "const" or typeComponent == "restrict" or typeComponent == "volatile":
-            continue
-        if typeComponent in basicTypeMap:
-            resultType = basicTypeMap[typeComponent]
-        elif typeComponent == "*" and includePointers:
-            assert resultType is not None
-            resultType = ct.POINTER(resultType)
-
-    return resultType
-
-
-def ctypeFromNumpyType(numpyType):
-    typeMap = {
-        np.dtype('float64'): c_double,
-        np.dtype('float32'): c_float,
-    }
-    return typeMap[numpyType]
-
-
-def compile(code, tmpDir, libFile, createAssemblyCode=False):
-    srcFile = os.path.join(tmpDir, 'source.cpp')
-    with open(srcFile, 'w') as sourceFile:
-        print('#include <iostream>', file=sourceFile)
-        print("#include <cmath>", file=sourceFile)
-        print('extern "C" { ', file=sourceFile)
-        print(code, file=sourceFile)
-        print('}', file=sourceFile)
-
-    compilerCmd = [CONFIG['compiler']] + CONFIG['flags'].split()
-    compilerCmd += [srcFile, '-o', libFile]
-    configEnv = CONFIG['env'] if 'env' in CONFIG else {}
-    env = os.environ.copy()
-    env.update(configEnv)
-    subprocess.call(compilerCmd, env=env)
-
-    assembly = None
-    if createAssemblyCode:
-        assemblyFile = os.path.join(tmpDir, "assembly.s")
-        compilerCmd = [CONFIG['compiler'], '-S', '-o', assemblyFile, srcFile] + CONFIG['flags'].split()
-        subprocess.call(compilerCmd, env=env)
-        assembly = open(assemblyFile, 'r').read()
-    return assembly
-
-
-def compileAndLoad(kernelFunctionNode):
-    with TemporaryDirectory() as tmpDir:
-        libFile = os.path.join(tmpDir, "jit.so")
-        compile(generateC(kernelFunctionNode), tmpDir, libFile)
-        loadedJitLib = cdll.LoadLibrary(libFile)
-
-    return loadedJitLib
-
-
-def buildCTypeArgumentList(parameterSpecification, argumentDict):
-    argumentDict = {symbolNameToVariableName(k): v for k, v in argumentDict.items()}
-    ctArguments = []
-    arrayShapes = set()
-    for arg in parameterSpecification:
-        if arg.isFieldArgument:
-            field = argumentDict[arg.fieldName]
-            symbolicField = arg.field
-            if arg.isFieldPtrArgument:
-                ctArguments.append(field.ctypes.data_as(ctypeFromString(arg.dtype)))
-                if symbolicField.hasFixedShape:
-                    if tuple(int(i) for i in symbolicField.shape) != field.shape:
-                        raise ValueError("Passed array '%s' has shape %s which does not match expected shape %s" %
-                                         (arg.fieldName, str(field.shape), str(symbolicField.shape)))
-                if symbolicField.hasFixedShape:
-                    if tuple(int(i) * field.itemsize for i in symbolicField.strides) != field.strides:
-                        raise ValueError("Passed array '%s' has strides %s which does not match expected strides %s" %
-                                         (arg.fieldName, str(field.strides), str(symbolicField.strides)))
-
-                if not symbolicField.isIndexField:
-                    arrayShapes.add(field.shape[:symbolicField.spatialDimensions])
-            elif arg.isFieldShapeArgument:
-                dataType = ctypeFromString(arg.dtype, includePointers=False)
-                ctArguments.append(field.ctypes.shape_as(dataType))
-            elif arg.isFieldStrideArgument:
-                dataType = ctypeFromString(arg.dtype, includePointers=False)
-                baseFieldType = ctypeFromNumpyType(field.dtype)
-                strides = field.ctypes.strides_as(dataType)
-                for i in range(len(field.shape)):
-                    assert strides[i] % sizeof(baseFieldType) == 0
-                    strides[i] //= sizeof(baseFieldType)
-                ctArguments.append(strides)
-            else:
-                assert False
-        else:
-            param = argumentDict[arg.name]
-            expectedType = ctypeFromString(arg.dtype)
-            ctArguments.append(expectedType(param))
-
-    if len(arrayShapes) > 1:
-        raise ValueError("All passed arrays have to have the same size " + str(arrayShapes))
-    return ctArguments
-
-
-def makePythonFunctionIncompleteParams(kernelFunctionNode, argumentDict):
-    func = compileAndLoad(kernelFunctionNode)[kernelFunctionNode.functionName]
-    func.restype = None
-    parameters = kernelFunctionNode.parameters
-
-    def wrapper(**kwargs):
-        from copy import copy
-        fullArguments = copy(argumentDict)
-        fullArguments.update(kwargs)
-        args = buildCTypeArgumentList(parameters, fullArguments)
-        func(*args)
-    return wrapper
-
-
-def makePythonFunction(kernelFunctionNode, argumentDict={}):
-    """
-    Creates C code from the abstract syntax tree, compiles it and makes it accessible as Python function
-
-    The parameters of the kernel are:
-        - numpy arrays for each field used in the kernel. The keyword argument name is the name of the field
-        - all symbols which are not defined in the kernel itself are expected as parameters
-
-    :param kernelFunctionNode: the abstract syntax tree
-    :param argumentDict: parameters passed here are already fixed. Remaining parameters have to be passed to the
-                        returned kernel functor.
-    :return: kernel functor
-    """
-    # build up list of CType arguments
-    try:
-        args = buildCTypeArgumentList(kernelFunctionNode.parameters, argumentDict)
-    except KeyError:
-        # not all parameters specified yet
-        return makePythonFunctionIncompleteParams(kernelFunctionNode, argumentDict)
-    func = compileAndLoad(kernelFunctionNode)[kernelFunctionNode.functionName]
-    func.restype = None
-    return lambda: func(*args)
-
-
-class CachedKernel:
-    def __init__(self, configDict, ast, parameterValues):
-        self.configDict = configDict
-        self.ast = ast
-        self.parameterValues = parameterValues
-        self.funcPtr = None
-
-    def __compile(self):
-        self.funcPtr = makePythonFunction(self.ast, self.parameterValues)
-
-    def __call__(self, *args, **kwargs):
-        if self.funcPtr is None:
-            self.__compile()
-        self.funcPtr(*args, **kwargs)
-
-
-def hashToFunctionName(h):
-    res = "func_%s" % (h,)
-    return res.replace('-', 'm')
-
-
-def createLibrary(cachedKernels, libraryFile):
-    libraryInfoFile = libraryFile + ".info"
-
-    with TemporaryDirectory() as tmpDir:
-        code = ""
-        infoDict = {}
-        for cachedKernel in cachedKernels:
-            s = repr(sorted(cachedKernel.configDict.items()))
-            configHash = hashlib.sha1(s.encode()).hexdigest()
-            cachedKernel.ast.functionName = hashToFunctionName(configHash)
-            kernelCode = generateC(cachedKernel.ast)
-            code += kernelCode + "\n"
-            infoDict[configHash] = {'code': kernelCode,
-                                    'parameterValues': cachedKernel.parameterValues,
-                                    'configDict': cachedKernel.configDict,
-                                    'parameterSpecification': cachedKernel.ast.parameters}
-
-        compile(code, tmpDir, libraryFile)
-        pickle.dump(infoDict, open(libraryInfoFile, "wb"))
-
-
-def loadLibrary(libraryFile):
-    libraryInfoFile = libraryFile + ".info"
-
-    libraryFile = cdll.LoadLibrary(libraryFile)
-    libraryInfo = pickle.load(open(libraryInfoFile, 'rb'))
-
-    def getKernel(**kwargs):
-        s = repr(sorted(kwargs.items()))
-        configHash = hashlib.sha1(s.encode()).hexdigest()
-        if configHash not in libraryInfo:
-            raise ValueError("No such kernel in library")
-        func = libraryFile[hashToFunctionName(configHash)]
-        func.restype = None
-
-        def wrapper(**kwargs):
-            from copy import copy
-            fullArguments = copy(libraryInfo[configHash]['parameterValues'])
-            fullArguments.update(kwargs)
-            args = buildCTypeArgumentList(libraryInfo[configHash]['parameterSpecification'], fullArguments)
-            func(*args)
-        wrapper.configDict = libraryInfo[configHash]['configDict']
-        return wrapper
-
-    return getKernel

cpu/kerncraft.py

-from pystencils.transformations import makeLoopOverDomain, typingFromSympyInspection, \
-    typeAllEquations, moveConstantsBeforeLoop, getOptimalLoopOrdering
-import pystencils.astnodes as ast
-from pystencils.backends.cbackend import CBackend, CustomSympyPrinter
-from pystencils import TypedSymbol
-
-
-def createKerncraftCode(listOfEquations, typeForSymbol=None, ghostLayers=None):
-    """
-    Creates an abstract syntax tree for a kernel function, by taking a list of update rules.
-
-    Loops are created according to the field accesses in the equations.
-
-    :param listOfEquations: list of sympy equations, containing accesses to :class:`pystencils.field.Field`.
-           Defining the update rules of the kernel
-    :param typeForSymbol: a map from symbol name to a C type specifier. If not specified all symbols are assumed to
-           be of type 'double' except symbols which occur on the left hand side of equations where the
-           right hand side is a sympy Boolean which are assumed to be 'bool' .
-    :param ghostLayers: a sequence of pairs for each coordinate with lower and upper nr of ghost layers
-                        if None, the number of ghost layers is determined automatically and assumed to be equal for a
-                        all dimensions
-
-    :return: :class:`pystencils.ast.KernelFunction` node
-    """
-    if not typeForSymbol:
-        typeForSymbol = typingFromSympyInspection(listOfEquations, "double")
-
-    fieldsRead, fieldsWritten, assignments = typeAllEquations(listOfEquations, typeForSymbol)
-    allFields = fieldsRead.union(fieldsWritten)
-
-    optimalLoopOrder = getOptimalLoopOrdering(allFields)
-    cstyleLoopOrder = list(range(len(optimalLoopOrder)))
-
-    body = ast.Block(assignments)
-    code = makeLoopOverDomain(body, "kerncraft", ghostLayers=ghostLayers, loopOrder=cstyleLoopOrder)
-    moveConstantsBeforeLoop(code)
-    loopBody = code.body
-
-    printer = CBackend(sympyPrinter=ArraySympyPrinter())
-
-    FIXED_SIZES = ("XS", "YS", "ZS", "E1S", "E2S")
-
-    result = ""
-    for field in allFields:
-        sizesPermutation = [FIXED_SIZES[i] for i in field.layout]
-        suffix = "".join("[%s]" % (size,) for size in sizesPermutation)
-        result += "%s%s;\n" % (field.name, suffix)
-
-    # add parameter definitions
-    for s in loopBody.undefinedSymbols:
-        if isinstance(s, TypedSymbol):
-            result += "%s %s;\n" % (s.dtype, s.name)
-
-    for element in loopBody.args:
-        result += printer(element)
-        result += "\n"
-    return result
-
-
-class ArraySympyPrinter(CustomSympyPrinter):
-
-    def _print_Access(self, fieldAccess):
-        """"""
-        Loop = ast.LoopOverCoordinate
-        coordinateValues = [Loop.getLoopCounterSymbol(i) + offset for i, offset in enumerate(fieldAccess.offsets)]
-        coordinateValues += list(fieldAccess.index)
-        permutedCoordinates = [coordinateValues[i] for i in fieldAccess.field.layout]
-
-        suffix = "".join("[%s]" % (self._print(a)) for a in permutedCoordinates)
-        return "%s%s" % (self._print(fieldAccess.field.name), suffix)

cpu/kernelcreation.py

-import sympy as sp
-from pystencils.transformations import resolveFieldAccesses, makeLoopOverDomain, typingFromSympyInspection, \
-    typeAllEquations, getOptimalLoopOrdering, parseBasePointerInfo, moveConstantsBeforeLoop, splitInnerLoop
-from pystencils.types import TypedSymbol, DataType
-from pystencils.field import Field
-import pystencils.astnodes as ast
-
-
-def createKernel(listOfEquations, functionName="kernel", typeForSymbol=None, splitGroups=(),
-                 iterationSlice=None, ghostLayers=None):
-    """
-    Creates an abstract syntax tree for a kernel function, by taking a list of update rules.
-
-    Loops are created according to the field accesses in the equations.
-
-    :param listOfEquations: list of sympy equations, containing accesses to :class:`pystencils.field.Field`.
-           Defining the update rules of the kernel
-    :param functionName: name of the generated function - only important if generated code is written out
-    :param typeForSymbol: a map from symbol name to a C type specifier. If not specified all symbols are assumed to
-           be of type 'double' except symbols which occur on the left hand side of equations where the
-           right hand side is a sympy Boolean which are assumed to be 'bool' .
-    :param splitGroups: Specification on how to split up inner loop into multiple loops. For details see
-           transformation :func:`pystencils.transformation.splitInnerLoop`
-    :param iterationSlice: if not None, iteration is done only over this slice of the field
-    :param ghostLayers: a sequence of pairs for each coordinate with lower and upper nr of ghost layers
-                        if None, the number of ghost layers is determined automatically and assumed to be equal for a
-                        all dimensions
-
-    :return: :class:`pystencils.ast.KernelFunction` node
-    """
-    if not typeForSymbol or typeForSymbol == 'double':
-        typeForSymbol = typingFromSympyInspection(listOfEquations, "double")
-    elif typeForSymbol == 'float':
-        typeForSymbol = typingFromSympyInspection(listOfEquations, "float")
-
-    def typeSymbol(term):
-        if isinstance(term, Field.Access) or isinstance(term, TypedSymbol):
-            return term
-        elif isinstance(term, sp.Symbol):
-            return TypedSymbol(term.name, DataType(typeForSymbol[term.name]))
-        else:
-            raise ValueError("Term has to be field access or symbol")
-
-    fieldsRead, fieldsWritten, assignments = typeAllEquations(listOfEquations, typeForSymbol)
-    allFields = fieldsRead.union(fieldsWritten)
-
-    readOnlyFields = set([f.name for f in fieldsRead - fieldsWritten])
-
-    body = ast.Block(assignments)
-    loopOrder = getOptimalLoopOrdering(allFields)
-    code = makeLoopOverDomain(body, functionName, iterationSlice=iterationSlice,
-                              ghostLayers=ghostLayers, loopOrder=loopOrder)
-
-    if splitGroups:
-        typedSplitGroups = [[typeSymbol(s) for s in splitGroup] for splitGroup in splitGroups]
-        splitInnerLoop(code, typedSplitGroups)
-
-    basePointerInfo = [['spatialInner0'], ['spatialInner1']]
-    basePointerInfos = {field.name: parseBasePointerInfo(basePointerInfo, loopOrder, field) for field in allFields}
-
-    resolveFieldAccesses(code, readOnlyFields, fieldToBasePointerInfo=basePointerInfos)
-    moveConstantsBeforeLoop(code)
-
-    return code
-
-
-def addOpenMP(astNode, schedule="static", numThreads=None):
-    """
-    Parallelizes the outer loop with OpenMP
-
-    :param astNode: abstract syntax tree created e.g. by :func:`createKernel`
-    :param schedule: OpenMP scheduling policy e.g. 'static' or 'dynamic'
-    :param numThreads: explicitly specify number of threads
-    """
-    assert type(astNode) is ast.KernelFunction
-    body = astNode.body
-    threadsClause = "" if numThreads is None else " num_threads(%s)" % (numThreads,)
-    wrapperBlock = ast.PragmaBlock('#pragma omp parallel' + threadsClause, body.takeChildNodes())
-    body.append(wrapperBlock)
-
-    outerLoops = [l for l in body.atoms(ast.LoopOverCoordinate) if l.isOutermostLoop]
-    assert outerLoops, "No outer loop found"
-    assert len(outerLoops) <= 1, "More than one outer loop found. Which one should be parallelized?"
-    outerLoops[0].prefixLines.append("#pragma omp for schedule(%s)" % (schedule,))

display_utils.py

-
-
-def toDot(expr, graphStyle={}):
-    """Show a sympy or pystencils AST as dot graph"""
-    from pystencils.astnodes import Node
-    import graphviz
-    if isinstance(expr, Node):
-        from pystencils.backends.dot import dotprint
-        return graphviz.Source(dotprint(expr, short=True, graph_attr=graphStyle))
-    else:
-        from sympy.printing.dot import dotprint
-        return graphviz.Source(dotprint(expr, graph_attr=graphStyle))
-
-
-def highlightCpp(code):
-    """Highlight the given C/C++ source code with Pygments"""
-    from IPython.display import HTML, display
-    from pygments import highlight
-    from pygments.formatters import HtmlFormatter
-    from pygments.lexers import CppLexer
-
-    display(HTML("""
-            <style>
-            {pygments_css}
-            </style>
-            """.format(pygments_css=HtmlFormatter().get_style_defs('.highlight'))))
-    return HTML(highlight(code, CppLexer(), HtmlFormatter()))
-
-
-# ----------------- Embedding of animations as videos in IPython notebooks ---------------------------------------------
-
-
-# -------   Version 1: Animation is embedded as an HTML5 Video tag  ---------------------------------------
-
-VIDEO_TAG = """<video controls width="100%">
- <source src="data:video/x-m4v;base64,{0}" type="video/mp4">
- Your browser does not support the video tag.
-</video>"""
-
-
-def __anim_to_html(anim, fps):
-    from tempfile import NamedTemporaryFile
-    import base64
-
-    if not hasattr(anim, '_encoded_video'):
-        with NamedTemporaryFile(suffix='.mp4') as f:
-            anim.save(f.name, fps=fps, extra_args=['-vcodec', 'libx264', '-pix_fmt',
-                                                   'yuv420p', '-profile:v', 'baseline', '-level', '3.0'])
-            video = open(f.name, "rb").read()
-        anim._encoded_video = base64.b64encode(video).decode('ascii')
-
-    return VIDEO_TAG.format(anim._encoded_video)
-
-
-def disp_as_video(anim, fps=30, show=True, **kwargs):
-    import matplotlib.pyplot as plt
-    from IPython.display import HTML
-
-    try:
-        plt.close(anim._fig)
-        res = __anim_to_html(anim, fps)
-        if show:
-            return HTML(res)
-        else:
-            return HTML("")
-    except KeyboardInterrupt:
-        pass
-# -------   Version 2: Animation is shown in extra matplotlib window ----------------------------------
-
-
-def disp_extra_window(animation, *args,**kwargs):
-    import matplotlib.pyplot as plt
-
-    fig = plt.gcf()
-    try:
-      fig.canvas.manager.window.raise_()
-    except Exception:
-      pass
-    plt.show()
-
-
-# -------   Version 3: Animation is shown in images that are updated directly in website --------------
-
-def disp_image_update(animation, iterations=10000, *args, **kwargs):
-    from IPython import display
-    import matplotlib.pyplot as plt
-
-    try:
-        fig = plt.gcf()
-        animation._init_draw()
-        for i in range(iterations):
-            display.display(fig)
-            animation._step()
-            display.clear_output(wait=True)
-    except KeyboardInterrupt:
-        pass
-
-
-# Dispatcher
-
-animation_display_mode = 'imageupdate'
-display_animation_func = None
-
-
-def disp(*args, **kwargs):
-    if not display_animation_func:
-        raise Exception("Call set_display_mode first")
-    return display_animation_func(*args, **kwargs)
-
-
-def set_display_mode(mode):
-    from IPython import get_ipython
-    ipython = get_ipython()
-    if ipython is None:
-        return
-    global animation_display_mode
-    global display_animation_func
-    animation_display_mode = mode
-    if animation_display_mode == 'video':
-        ipython.magic("matplotlib inline")
-        display_animation_func = disp_as_video
-    elif animation_display_mode == 'window':
-        ipython.magic("matplotlib qt")
-        display_animation_func = disp_extra_window
-    elif animation_display_mode == 'imageupdate':
-        ipython.magic("matplotlib inline")
-        display_animation_func = disp_image_update
-    else:
-        raise Exception("Unknown mode. Available modes 'imageupdate', 'video' and 'window' ")
-
-
-set_display_mode('video')
-
-
-# --------------------- Convenience functions --------------------------------------------------------------------------
-
-
-def makeSurfacePlotAnimation(runFunction, frames=90, interval=30):
-    from mpl_toolkits.mplot3d import Axes3D
-    import matplotlib.animation as animation
-    import matplotlib.pyplot as plt
-    from matplotlib import cm
-
-    fig = plt.figure()
-    ax = fig.add_subplot(111, projection='3d')
-    X, Y, data = runFunction(1)
-    ax.plot_surface(X, Y, data, rstride=2, cstride=2, color='b', cmap=cm.coolwarm,)
-    ax.set_zlim(-1.0, 1.0)
-
-    def updatefig(*args):
-        X, Y, data = runFunction(1)
-        ax.clear()
-        plot = ax.plot_surface(X, Y, data, rstride=2, cstride=2, color='b', cmap=cm.coolwarm,)
-        ax.set_zlim(-1.0, 1.0)
-        return plot,
-
-    return animation.FuncAnimation(fig, updatefig, interval=interval, frames=frames, blit=False)

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('.'))
+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'

doc/img/logo.svg

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doc/index.rst

+pystencils
+==========
+
+Welcome to the documentation of the pystencils code generation tool for stencil codes.
+pystencils can help you to generate blazingly fast code for image processing, numerical simulations or any other task involving numpy arrays.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   sphinx/tutorials.rst
+   sphinx/api.rst
+
+
+.. image:: /img/pystencils_arch_block_diagram.svg
+    :height: 450px
+    :align: center
+
+