doc/sphinx/stencil.rst

+*******
+Stencil
+*******
+
+.. automodule:: pystencils.stencil
+   :members:

doc/sphinx/tutorials.rst

@@ -10,11 +10,12 @@ It is a good idea to download them and run them directly to be able to play arou
 
    /notebooks/01_tutorial_getting_started.ipynb
    /notebooks/02_tutorial_basic_kernels.ipynb
-   /notebooks/03_tutorial_advection_diffusion.ipynb
-   /notebooks/04_tutorial_phasefield_spinodal_decomposition.ipynb
-   /notebooks/05_tutorial_phasefield_dentritic_growth.ipynb
-   /notebooks/06_tutorial_datahandling.ipynb
+   /notebooks/03_tutorial_datahandling.ipynb
+   /notebooks/04_tutorial_advection_diffusion.ipynb
+   /notebooks/05_tutorial_phasefield_spinodal_decomposition.ipynb
+   /notebooks/06_tutorial_phasefield_dentritic_growth.ipynb
    /notebooks/demo_assignment_collection.ipynb
+   /notebooks/demo_plotting_and_animation.ipynb
+   /notebooks/demo_derivatives.ipynb
    /notebooks/demo_benchmark.ipynb
    /notebooks/demo_wave_equation.ipynb
-

pyproject.toml

+[project]
+name = "pystencils"
+description = "Speeding up stencil computations on CPUs and GPUs"
+dynamic = ["version"]
+readme = "README.md"
+authors = [
+    { name = "Martin Bauer" },
+    { name = "Jan Hönig " },
+    { name = "Markus Holzer" },
+    { name = "Frederik Hennig" },
+    { email = "cs10-codegen@fau.de" },
+]
+license = { file = "COPYING.txt" }
+requires-python = ">=3.10"
+dependencies = ["sympy>=1.9,<=1.12.1", "numpy>=1.8.0", "appdirs", "joblib", "pyyaml", "fasteners"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Framework :: Jupyter",
+    "Topic :: Software Development :: Code Generators",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
+]
+
+[project.urls]
+"Bug Tracker" = "https://i10git.cs.fau.de/pycodegen/pystencils/-/issues"
+"Documentation" = "https://pycodegen.pages.i10git.cs.fau.de/pystencils/"
+"Source Code" = "https://i10git.cs.fau.de/pycodegen/pystencils"
+
+[project.optional-dependencies]
+gpu = ['cupy']
+alltrafos = ['islpy', 'py-cpuinfo']
+bench_db = ['blitzdb', 'pymongo', 'pandas']
+interactive = [
+    'matplotlib',
+    'ipy_table',
+    'imageio',
+    'jupyter',
+    'pyevtk',
+    'rich',
+    'graphviz',
+]
+use_cython = [
+    'Cython'
+]
+doc = [
+    'sphinx',
+    'sphinx_rtd_theme',
+    'nbsphinx',
+    'sphinxcontrib-bibtex',
+    'sphinx_autodoc_typehints',
+    'pandoc',
+]
+tests = [
+    'pytest',
+    'pytest-cov',
+    'pytest-html',
+    'ansi2html',
+    'pytest-xdist',
+    'flake8',
+    'nbformat',
+    'nbconvert',
+    'ipython',
+    'matplotlib',
+    'py-cpuinfo',
+    'randomgen>=1.18',
+]
+
+[build-system]
+requires = [
+    "setuptools>=61",
+    "versioneer[toml]>=0.29",
+    # 'Cython'
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.package-data]
+pystencils = [
+    "include/*.h",
+    "boundaries/createindexlistcython.pyx"
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["pystencils", "pystencils.*"]
+namespaces = false
+
+[tool.versioneer]
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+VCS = "git"
+style = "pep440"
+versionfile_source = "src/pystencils/_version.py"
+versionfile_build = "pystencils/_version.py"
+tag_prefix = "release/"
+parentdir_prefix = "pystencils-"

pystencils/cache.py

-import os
-
-try:
-    from functools import lru_cache as memorycache
-except ImportError:
-    from backports.functools_lru_cache import lru_cache as memorycache
-
-try:
-    from joblib import Memory
-    from appdirs import user_cache_dir
-    if 'PYSTENCILS_CACHE_DIR' in os.environ:
-        cache_dir = os.environ['PYSTENCILS_CACHE_DIR']
-    else:
-        cache_dir = user_cache_dir('pystencils')
-    disk_cache = Memory(cachedir=cache_dir, verbose=False).cache
-    disk_cache_no_fallback = disk_cache
-except ImportError:
-    # fallback to in-memory caching if joblib is not available
-    disk_cache = memorycache(maxsize=64)
-
-    def disk_cache_no_fallback(o):
-        return o
-
-
-# Disable memory cache:
-# disk_cache = lambda o: o
-# disk_cache_no_fallback = lambda o: o

pystencils/kerncraft_coupling/__init__.py

-from .kerncraft_interface import PyStencilsKerncraftKernel, KerncraftParameters
-
-__all__ = ['PyStencilsKerncraftKernel', 'KerncraftParameters']

pystencils/llvm/__init__.py

-from .kernelcreation import create_kernel
-from .llvmjit import make_python_function
-
-__all__ = ['create_kernel', 'make_python_function']

pystencils/llvm/control_flow.py

-import llvmlite.ir as ir
-
-
-class Loop(object):
-    def __init__(self, builder, start_val, stop_val, step_val=1, loop_name='loop', phi_name="_phi"):
-        self.builder = builder
-        self.start_val = start_val
-        self.stop_val = stop_val
-        self.step_val = step_val
-        self.loop_name = loop_name
-        self.phi_name = phi_name
-
-    def __enter__(self):
-        self.loop_end, self.after, phi = self._for_loop(self.start_val, self.stop_val, self.step_val, self.loop_name,
-                                                        self.phi_name)
-        return phi
-
-    def _for_loop(self, start_val, stop_val, step_val, loop_name, phi_name):
-        # TODO size of int??? unisgned???
-        integer = ir.IntType(64)
-
-        # Loop block
-        pre_loop_bb = self.builder.block
-        loop_bb = self.builder.append_basic_block(name='loop_' + loop_name)
-
-        self.builder.branch(loop_bb)
-
-        # Insert an explicit fall through from the current block to loop_bb
-        self.builder.position_at_start(loop_bb)
-
-        # Add phi
-        phi = self.builder.phi(integer, name=phi_name)
-        phi.add_incoming(start_val, pre_loop_bb)
-
-        loop_end_bb = self.builder.append_basic_block(name=loop_name + "_end_bb")
-        self.builder.position_at_start(loop_end_bb)
-
-        next_var = self.builder.add(phi, step_val, name=loop_name + '_next_it')
-        cond = self.builder.icmp_unsigned('<', next_var, stop_val, name=loop_name + "_cond")
-
-        after_bb = self.builder.append_basic_block(name=loop_name + "_after_bb")
-
-        self.builder.cbranch(cond, loop_bb, after_bb)
-        phi.add_incoming(next_var, loop_end_bb)
-
-        self.builder.position_at_end(loop_bb)
-
-        return loop_end_bb, after_bb, phi
-
-    def __exit__(self, exc_type, exc, exc_tb):
-        self.builder.branch(self.loop_end)
-        self.builder.position_at_end(self.after)

pystencils/session.py

-import pystencils.sympy_gmpy_bug_workaround
-import sympy as sp
-import numpy as np
-import pystencils as ps
-import pystencils.plot2d as plt
-import pystencils.jupytersetup as ps_notebook
-
-
-__all__ = ['sp', 'np', 'ps', 'plt', 'ps_notebook']