Fix conftest. Fix deprecated usage of scipy.ndimage.gaussian_filter. Fix array...

Fix conftest. Fix deprecated usage of scipy.ndimage.gaussian_filter. Fix array data types in BoundaryOffsetInfo.

conftest.py

@@ -3,7 +3,6 @@ import runpy
 import sys
 import tempfile
 import warnings
-import pathlib
 
 import nbformat
 import pytest
@@ -17,32 +16,38 @@ import pytest
 # at the same time
 try:
     import pyximport
+
     pyximport.install(language_level=3)
     from pystencils.boundaries.createindexlistcython import *  # NOQA
 except ImportError:
     pass
 
 SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
-sys.path.insert(0, os.path.abspath('pystencils'))
+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 = [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))
+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, 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')
+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:
@@ -50,46 +55,60 @@ try:
 except ImportError:
     collect_ignore += [
         os.path.join(SCRIPT_FOLDER, "tests/kernelcreation/test_gpu.py"),
-        os.path.join(SCRIPT_FOLDER, "src/pystencils/backend/jit/gpu_cupy.py")
+        os.path.join(SCRIPT_FOLDER, "src/pystencils/backend/jit/gpu_cupy.py"),
     ]
-    add_path_to_ignore('src/pystencils/gpu')
+    add_path_to_ignore("src/pystencils/gpu")
 
 try:
     import waLBerla
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "docs/source/tutorials/03_tutorial_datahandling.ipynb"),
-                       os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/parallel_datahandling.py"),
-                       os.path.join(SCRIPT_FOLDER, "tests/runtime/test_datahandling_parallel.py"),
-                       os.path.join(SCRIPT_FOLDER, "tests/runtime/test_small_block_benchmark.ipynb")]
+    collect_ignore += [
+        os.path.join(
+            SCRIPT_FOLDER, "docs/source/tutorials/03_tutorial_datahandling.ipynb"
+        ),
+        os.path.join(
+            SCRIPT_FOLDER, "src/pystencils/datahandling/parallel_datahandling.py"
+        ),
+        os.path.join(SCRIPT_FOLDER, "tests/runtime/test_datahandling_parallel.py"),
+        os.path.join(SCRIPT_FOLDER, "tests/runtime/test_small_block_benchmark.ipynb"),
+    ]
 
 try:
     import blitzdb
 except ImportError:
-    add_path_to_ignore('src/pystencils/runhelper')
+    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")]
+    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")]
+    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, "src/pystencils/datahandling/vtk.py")
+    ]
 
-collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
+collect_ignore += [os.path.join(SCRIPT_FOLDER, "setup.py")]
 
-for root, sub_dirs, files in os.walk('.'):
+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']):
+        if f.endswith(".ipynb") and not any(
+            f.startswith(k) for k in ["demo", "tutorial", "test", "doc"]
+        ):
             collect_ignore.append(f)
 
 
@@ -111,39 +130,50 @@ class IPyNbTest(pytest.Item):
     def __init__(self, name, parent, code):
         super(IPyNbTest, self).__init__(name, parent)
         self.code = code
-        self.add_marker('notebook')
+        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}
+        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)
+        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
-        exec("import warnings;"
-             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*')",
-             global_dict)
+        exec(
+            "import warnings;"
+            "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):
         from nbconvert import PythonExporter
+
         exporter = PythonExporter()
         exporter.exclude_markdown = True
         exporter.exclude_input_prompt = True
 
-        notebook_contents = self.path.open(encoding='utf-8')
+        notebook_contents = self.path.open(encoding="utf-8")
 
         with warnings.catch_warnings():
-            warnings.filterwarnings("ignore", "IPython.core.inputsplitter is deprecated")
+            warnings.filterwarnings(
+                "ignore", "IPython.core.inputsplitter is deprecated"
+            )
             notebook = nbformat.read(notebook_contents, 4)
             code, _ = exporter.from_notebook_node(notebook)
         if pytest_version >= 50403:
@@ -155,10 +185,21 @@ class IPyNbFile(pytest.File):
         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(path=pathlib.Path(path), parent=parent)
-        else:
-            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)

src/pystencils/boundaries/boundaryhandling.py

@@ -410,11 +410,11 @@ class BoundaryOffsetInfo:
     @staticmethod
     def offset_from_dir(dir_idx, dim):
         return tuple([sp.IndexedBase(symbol, shape=(1,))[dir_idx]
-                      for symbol in BoundaryOffsetInfo._offset_symbols(dim)])
+                      for symbol in BoundaryOffsetInfo._untyped_offset_symbols(dim)])
 
     @staticmethod
     def inv_dir(dir_idx):
-        return sp.IndexedBase(BoundaryOffsetInfo._inv_dir_symbol(), shape=(1,))[dir_idx]
+        return sp.IndexedBase(BoundaryOffsetInfo._untyped_inv_dir_symbol(), shape=(1,))[dir_idx]
 
     # ---------------------------------- Internal ---------------------------------------------
 
@@ -425,7 +425,7 @@ class BoundaryOffsetInfo:
 
     def get_array_declarations(self) -> list[Assignment]:
         asms = []
-        for i, offset_symb in enumerate(BoundaryOffsetInfo._offset_symbols(self._dim)):
+        for i, offset_symb in enumerate(self._offset_symbols(self._dim)):
             offsets = tuple(d[i] for d in self._stencil)
             asms.append(Assignment(offset_symb, offsets))
 
@@ -434,16 +434,22 @@ class BoundaryOffsetInfo:
             inverse_dir = tuple([-i for i in direction])
             inv_dirs.append(str(self._stencil.index(inverse_dir)))
 
-        asms.append(Assignment(BoundaryOffsetInfo._inv_dir_symbol(), tuple(inv_dirs)))
+        asms.append(Assignment(self._inv_dir_symbol(), tuple(inv_dirs)))
         return asms
 
+    def _offset_symbols(self, dim, dtype: PsIntegerType = SInt(32)):
+        return [TypedSymbol(f"c{d}", Arr(dtype, len(self._stencil))) for d in ['x', 'y', 'z'][:dim]]
+    
     @staticmethod
-    def _offset_symbols(dim, dtype: PsIntegerType = SInt(32)):
-        return [TypedSymbol(f"c{d}", Arr(dtype)) for d in ['x', 'y', 'z'][:dim]]
+    def _untyped_offset_symbols(dim):
+        return [sp.Symbol(f"c{d}") for d in ['x', 'y', 'z'][:dim]]
+
+    def _inv_dir_symbol(self, dtype: PsIntegerType = SInt(32)):
+        return TypedSymbol("invdir", Arr(dtype, len(self._stencil)))
 
     @staticmethod
-    def _inv_dir_symbol(dtype: PsIntegerType = SInt(32)):
-        return TypedSymbol("invdir", Arr(dtype))
+    def _untyped_inv_dir_symbol(dtype: PsIntegerType = SInt(32)):
+        return sp.Symbol("invdir")
 
 
 def create_boundary_kernel(field, index_field, stencil, boundary_functor, target=Target.CPU, **kernel_creation_args):