Clean up and Bug Fixes

pystencils_tests/test_fvm.py

@@ -117,6 +117,7 @@ def test_advection_diffusion_2d(velocity):
     advection_diffusion.runners[2](velocity)
 
 
+@pytest.mark.longrun
 @pytest.mark.parametrize("velocity", list(product([0, -0.047, 0.041], [0, -0.031, 0.023], [0, -0.017, 0.011])))
 def test_advection_diffusion_3d(velocity):
     if 3 not in advection_diffusion.runners:

pystencils_tests/test_kerncraft_coupling.py

@@ -44,7 +44,6 @@ def test_compilation():
     print(mine)
 
 
-@pytest.mark.kerncraft
 def analysis(kernel, machine, model='ecmdata'):
     if model == 'ecmdata':
         model = ECMData(kernel, machine, KerncraftParameters())

pystencils_tests/test_sympy_optimizations.py

-import pytest
-import sympy as sp
-
-import pystencils as ps
-from pystencils.math_optimizations import HAS_REWRITING, optimize_assignments, optims_pystencils_cpu, optimize_ast
-
-
-@pytest.mark.skipif(not HAS_REWRITING, reason="need sympy.codegen.rewriting")
-def test_sympy_optimizations():
-    for target in (ps.Target.CPU, ps.Target.GPU):
-        for op_ast in (True, False):
-            x, y, z = ps.fields('x, y, z:  float32[2d]')
-
-            # Triggers Sympy's expm1 optimization
-            # Sympy's expm1 optimization is tedious to use and the behaviour is highly depended on the sympy version. In
-            # some cases the exp expression has to be encapsulated in brackets or multiplied with 1 or 1.0
-            # for sympy to work properly ...
-            assignments = ps.AssignmentCollection({
-                x[0, 0]: 1.0 * (sp.exp(y[0, 0]) - 1)
-            })
-
-            if not op_ast:
-                assignments = optimize_assignments(assignments, optims_pystencils_cpu)
-            print(assignments)
-
-            ast = ps.create_kernel(assignments, config=ps.CreateKernelConfig(target=target))
-            if op_ast:
-                optimize_ast(ast, optims_pystencils_cpu)
-            code = ps.get_code_str(ast)
-            assert 'expm1(' in code
-
-
-@pytest.mark.skipif(not HAS_REWRITING, reason="need sympy.codegen.rewriting")
-def test_evaluate_constant_terms():
-    for target in (ps.Target.CPU, ps.Target.GPU):
-        x, y, z = ps.fields('x, y, z:  float32[2d]')
-
-        # Triggers Sympy's cos optimization
-        assignments = ps.AssignmentCollection({
-            x[0, 0]: -sp.cos(1) + y[0, 0]
-        })
-
-        assignments = optimize_assignments(assignments, optims_pystencils_cpu)
-
-        ast = ps.create_kernel(assignments, config=ps.CreateKernelConfig(target=target))
-        code = ps.get_code_str(ast)
-        assert 'cos(' not in code
-        print(code)
-
-
-@pytest.mark.skipif(not HAS_REWRITING, reason="need sympy.codegen.rewriting")
-def test_do_not_evaluate_constant_terms():
-    optimizations = ps.math_optimizations.optims_pystencils_cpu
-    optimizations.remove(ps.math_optimizations.evaluate_constant_terms)
-
-    for target in (ps.Target.CPU, ps.Target.GPU):
-        x, y, z = ps.fields('x, y, z:  float32[2d]')
-
-        assignments = ps.AssignmentCollection({
-            x[0, 0]: -sp.cos(1) + y[0, 0]
-        })
-
-        ast = ps.create_kernel(assignments, config=ps.CreateKernelConfig(target=target))
-        code = ps.get_code_str(ast)
-        assert 'cos(' in code
-        print(code)

pystencils_tests/test_types.py

@@ -5,7 +5,7 @@ import ctypes
 
 import pystencils as ps
 from pystencils import data_types
-from pystencils.data_types import TypedSymbol, get_type_of_expression, VectorType, collate_types, create_type,\
+from pystencils.data_types import TypedSymbol, get_type_of_expression, VectorType, collate_types, create_type, \
     typed_symbols, type_all_numbers, matrix_symbols, cast_func, pointer_arithmetic_func, ctypes_from_llvm, PointerType
 
 
@@ -114,11 +114,11 @@ def test_Basic_data_type():
     assert s.dtype.is_uint()
     assert s.dtype.is_complex() == 0
 
-    assert typed_symbols(("s"), str).dtype.is_other()
-    assert typed_symbols(("s"), bool).dtype.is_other()
-    assert typed_symbols(("s"), np.void).dtype.is_other()
+    assert typed_symbols("s", str).dtype.is_other()
+    assert typed_symbols("s", bool).dtype.is_other()
+    assert typed_symbols("s", np.void).dtype.is_other()
 
-    assert typed_symbols(("s"), np.float64).dtype.base_name == 'double'
+    assert typed_symbols("s", np.float64).dtype.base_name == 'double'
     # removed for old sympy version
     # assert typed_symbols(("s"), np.float64).dtype.sympy_dtype == typed_symbols(("s"), float).dtype.sympy_dtype
 

pytest.ini

@@ -5,6 +5,14 @@ addopts = --doctest-modules --durations=20  --cov-config pytest.ini
 markers =
        kerncraft: tests depending on kerncraft
        notebook: mark for notebooks
+# these warnings all come from third party libraries.
+filterwarnings =
+       ignore:an integer is required:DeprecationWarning
+       ignore:\s*load will be removed, use:PendingDeprecationWarning
+       ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
+       ignore:.*is a deprecated alias for the builtin `bool`:DeprecationWarning
+       ignore:'contextfilter' is renamed to 'pass_context':DeprecationWarning
+       ignore:Using or importing the ABCs from 'collections' instead of from 'collections.abc':DeprecationWarning
 
 [run]
 branch = True

setup.py

 import distutils
 import io
 import os
-import sys
 from contextlib import redirect_stdout
 from importlib import import_module
 
@@ -11,6 +10,7 @@ import versioneer
 
 try:
     import cython  # noqa
+
     USE_CYTHON = True
 except ImportError:
     USE_CYTHON = False
@@ -32,13 +32,13 @@ class SimpleTestRunner(distutils.cmd.Command):
     @staticmethod
     def _run_tests_in_module(test):
         """Short test runner function - to work also if py.test is not installed."""
-        test = 'pystencils_tests.' + test
+        test = f'pystencils_tests.{test}'
         mod, function_name = test.rsplit('.', 1)
         if isinstance(mod, str):
             mod = import_module(mod)
 
         func = getattr(mod, function_name)
-        print(f"   -> {function_name} in {mod.__name__}" )
+        print(f"   -> {function_name} in {mod.__name__}")
         with redirect_stdout(io.StringIO()):
             func()
 
@@ -76,7 +76,7 @@ def cython_extensions(*extensions):
 
 
 def get_cmdclass():
-    cmdclass={"quicktest": SimpleTestRunner}
+    cmdclass = {"quicktest": SimpleTestRunner}
     cmdclass.update(versioneer.get_cmdclass())
     return cmdclass
 
@@ -91,7 +91,7 @@ setuptools.setup(name='pystencils',
                  author_email='cs10-codegen@fau.de',
                  url='https://i10git.cs.fau.de/pycodegen/pystencils/',
                  packages=['pystencils'] + ['pystencils.' + s for s in setuptools.find_packages('pystencils')],
-                 install_requires=['sympy>=1.2', 'numpy>=1.8.0', 'appdirs', 'joblib'],
+                 install_requires=['sympy>=1.5.1,<=1.9', 'numpy>=1.8.0', 'appdirs', 'joblib'],
                  package_data={'pystencils': ['include/*.h',
                                               'kerncraft_coupling/templates/*',
                                               'backends/cuda_known_functions.txt',
@@ -122,7 +122,9 @@ setuptools.setup(name='pystencils',
                      'autodiff': ['pystencils-autodiff'],
                      'doc': ['sphinx', 'sphinx_rtd_theme', 'nbsphinx',
                              'sphinxcontrib-bibtex', 'sphinx_autodoc_typehints', 'pandoc'],
-                     'use_cython': ['Cython']
+                     'use_cython': ['Cython'],
+                     'kerncraft': ['osaca', 'kerncraft'],
+                     'llvm_jit': ['llvmlite']
                  },
                  tests_require=['pytest',
                                 'pytest-cov',