doc/sphinx/api.rst

@@ -5,10 +5,12 @@ API Reference
    :maxdepth: 3
 
    kernel_compile_and_call.rst
+   enums.rst
    simplifications.rst
    datahandling.rst
    configuration.rst
    field.rst
+   stencil.rst
    finite_differences.rst
    plot.rst
    ast.rst

doc/sphinx/enums.rst

+************
+Enumerations
+************
+
+.. automodule:: pystencils.enums
+   :members:

doc/sphinx/kernel_compile_and_call.rst

@@ -8,9 +8,14 @@ Creating kernels
 
 .. autofunction:: pystencils.create_kernel
 
-.. autofunction:: pystencils.create_indexed_kernel
+.. autoclass:: pystencils.CreateKernelConfig
+    :members:
 
-.. autofunction:: pystencils.create_staggered_kernel
+.. autofunction:: pystencils.kernelcreation.create_domain_kernel
+
+.. autofunction:: pystencils.kernelcreation.create_indexed_kernel
+
+.. autofunction:: pystencils.kernelcreation.create_staggered_kernel
 
 
 Code printing
@@ -22,11 +27,11 @@ Code printing
 GPU Indexing
 -------------
 
-.. autoclass:: pystencils.gpucuda.AbstractIndexing
+.. autoclass:: pystencils.gpu.AbstractIndexing
    :members:
 
-.. autoclass:: pystencils.gpucuda.BlockIndexing
+.. autoclass:: pystencils.gpu.BlockIndexing
    :members:
 
-.. autoclass:: pystencils.gpucuda.LineIndexing
+.. autoclass:: pystencils.gpu.LineIndexing
    :members:

doc/sphinx/plot.rst

@@ -2,7 +2,7 @@
 Plotting and Animation
 **********************
 
-.. automodule:: pystencils.plot2d
+.. automodule:: pystencils.plot
    :members:
 
 

doc/sphinx/simplifications.rst

@@ -10,13 +10,27 @@ AssignmentCollection
    :members:
 
 
+SimplificationStrategy
+======================
+
+.. autoclass:: pystencils.simp.SimplificationStrategy
+    :members:
+
 Simplifications
 ===============
 
-.. automodule:: pystencils.simp
-   :members:
+.. automodule:: pystencils.simp.simplifications
+    :members:
+
+Subexpression insertion
+=======================
 
+The subexpression insertions have the goal to insert subexpressions which will not reduce the number of FLOPs.
+For example a constant value kept as subexpression will lead to a new variable in the code which will occupy
+a register slot. On the other side a single variable could just be inserted in all assignments.
 
+.. automodule:: pystencils.simp.subexpression_insertion
+    :members:
 
 
 

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-"