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.flake8

+2 −1
Original line number Original line Diff line number Diff line
@@ -3,4 +3,5 @@ max-line-length=120 
exclude=src/pystencils/jupyter.py,

exclude=src/pystencils/jupyter.py,

        src/pystencils/plot.py

        src/pystencils/plot.py

        src/pystencils/session.py

        src/pystencils/session.py

ignore = W293 W503 W291 C901 E741
 
        src/pystencils/old

ignore = W293 W503 W291 C901 E741 E704

.gitattributes

+1 −1
Original line number Original line Diff line number Diff line 
pystencils/_version.py export-subst
 
src/pystencils/_version.py export-subst

.gitignore

+3 −0
Original line number Original line Diff line number Diff line 
__pycache__

__pycache__

.ipynb_checkpoints

.ipynb_checkpoints



.coverage*

.coverage*

coverage.xml



*.pyc

*.pyc

*.vti

*.vti

/build

/build

.gitlab-ci.yml

+96 −63
Original line number Original line Diff line number Diff line 
stages:

stages:

  - pretest

  - "Code Quality"

  - test

  - "Unit Tests"

  - legacy_test

  - docs

  - deploy

  - deploy









# --------------------------  Tests ------------------------------------------------------------------------------------

# --------------------------  Legacy Tests  ------------------------------------------------------------------------------------



# Normal test - runs on every commit all but "long run" tests

tests-and-coverage:

  stage: pretest

  except:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  before_script:

    - pip install -e .

  script:

    - env

    - pip list

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - mkdir public

    - pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml

    - python -m coverage xml

  tags:

    - docker

    - cuda11

    - AVX

  coverage: /Total coverage:\s\d+.\d+\%/

  artifacts:

    when: always

    paths:

      - coverage_report

      - test-report

    reports:

      coverage_report:

        coverage_format: cobertura

        path: coverage.xml

      junit: report.xml





# Normal test with longruns

# Normal test with longruns

tests-and-coverage-with-longrun:

tests-and-coverage-with-longrun:

  stage: test

  stage: legacy_test

  when: manual

  when: manual

  allow_failure: true

  allow_failure: true

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
@@ -64,7 +32,9 @@ tests-and-coverage-with-longrun: 




# pipeline with latest python version

# pipeline with latest python version

latest-python:

latest-python:

  stage: test

  stage: legacy_test

  allow_failure: true

  when: manual

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS
@@ -107,7 +77,9 @@ latest-python: 
#    - py.test -v -m "not (notebook or longrun)"

#    - py.test -v -m "not (notebook or longrun)"





ubuntu:

ubuntu:

  stage: test

  stage: legacy_test

  allow_failure: true

  when: manual

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS
@@ -133,7 +105,9 @@ ubuntu: 
      junit: report.xml

      junit: report.xml





.multiarch_template:

.multiarch_template:

  stage: test

  stage: legacy_test

  allow_failure: true

  when: manual

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS
@@ -200,7 +174,9 @@ riscv64: 
    - sed -i 's/fopenmp/fopenmp=libgomp -I\/usr\/include\/riscv64-linux-gnu/g' ~/.config/pystencils/config.json

    - sed -i 's/fopenmp/fopenmp=libgomp -I\/usr\/include\/riscv64-linux-gnu/g' ~/.config/pystencils/config.json





minimal-conda:

minimal-conda:

  stage: pretest

  stage: legacy_test

  allow_failure: true

  when: manual

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS
@@ -215,7 +191,9 @@ minimal-conda: 








minimal-sympy-master:

minimal-sympy-master:

  stage: test

  stage: legacy_test

  allow_failure: true

  when: manual

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS
@@ -225,7 +203,6 @@ minimal-sympy-master: 
  script:

  script:

    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git

    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git

    - python quicktest.py

    - python quicktest.py

  allow_failure: true

  tags:

  tags:

    - docker

    - docker

    - cuda

    - cuda
@@ -233,7 +210,7 @@ minimal-sympy-master: 




pycodegen-integration:

pycodegen-integration:

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  stage: test

  stage: legacy_test

  when: manual

  when: manual

  allow_failure: true

  allow_failure: true

  script:

  script:
@@ -275,44 +252,100 @@ pycodegen-integration: 
    reports:

    reports:

      junit: pycodegen/*/report.xml

      junit: pycodegen/*/report.xml





# -------------------- Linter & Documentation --------------------------------------------------------------------------

# -------------------- Code Quality ---------------------------------------------------------------------







flake8-lint:

.qa-base:

  stage: pretest

  stage: "Code Quality"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  needs: []

  except:

  except:

    variables:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  tags:

    - docker



lint:

  extends: .qa-base

  script:

    - nox --session lint



typecheck:

  extends: .qa-base

  script:

    - nox --session typecheck



# -------------------- Unit Tests ---------------------------------------------------------------------



.testsuite-base:

  stage: "Unit Tests"

  needs: []

  coverage: /Total coverage:\s\d+.\d+\%/

  artifacts:

    when: always

    paths:

      - coverage_report

      - test-report

    reports:

      coverage_report:

        coverage_format: cobertura

        path: coverage.xml

      junit: report.xml



"testsuite-gpu-py3.10":

  extends: .testsuite-base

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6

  script:

  script:

    - flake8 src/pystencils

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - mkdir public

    - nox --session "testsuite-3.10(cupy12)"

  tags:

    - docker

    - cuda11

    - AVX



"testsuite-cpu-py3.13":

  extends: .testsuite-base

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  script:

    - nox --session "testsuite-3.13(cpu)"

  tags:

    - docker

    - AVX



"testsuite-experimental-jit-py3.10":

  extends: .testsuite-base

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  script:

    - nox -s "testsuite-3.10(cpu)" -- --experimental-cpu-jit

  tags:

  tags:

    - docker

    - docker

    - AVX



# -------------------- Documentation ---------------------------------------------------------------------









build-documentation:

build-documentation:

  stage: test

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation

  stage: docs

  before_script:

  needs: []

    - pip install -e .

  script:

  script:

    - mkdir html_doc

    - nox --session docs -- --fail-on-warnings

    - sphinx-build -b html doc  html_doc

    - sphinx-build -W -b html doc  html_doc

  tags:

  tags:

    - docker

    - docker

    - cuda11

  artifacts:

  artifacts:

    paths:

    paths:

      - html_doc

      - docs/build/html









pages:

pages:

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  image: alpine:latest

  stage: deploy

  stage: deploy

  needs: ["testsuite-gpu-py3.10", "build-documentation"]

  script:

  script:

    - ls -l

    - mv docs/build/html public

    - mv coverage_report html_doc

    - mv coverage_report public/coverage_report

    - mv html_doc public  # folder has to be named "public" for gitlab to publish it

  artifacts:

  artifacts:

    paths:

    paths:

      - public

      - public

README.md

+32 −0
Original line number Original line Diff line number Diff line 
# pystencils 2.0 Development Branch



You are currently viewing the development branch `v2.0-dev` for *pystencils 2.0*.

This version marks a complete redesign of pystencil's internal structure.

The type system, code generators, and just-in-time-compilers are being completely rebuilt here.



## Early Adoption



The development version of pystencils is now ready for early adoption by users.

Install the current pre-release version either directly through pip:



```

pip install "git+https://i10git.cs.fau.de/pycodegen/pystencils.git@v2.0-dev"

```



Or clone the repository locally and do an editable install:

```

git clone -b v2.0-dev https://i10git.cs.fau.de/pycodegen/pystencils.git

pip install -e pystencils

```



## Documentation



 - Documentation for the current development version can be found [here](https://pycodegen.pages.i10git.cs.fau.de/docs/pystencils/2.0dev/)

 - Progress toward the 2.0 release is being tracked [here](https://i10git.cs.fau.de/pycodegen/pystencils/-/milestones/3#tab-issues)



## Contributing



Please refer to [the contribution guide](https://pycodegen.pages.i10git.cs.fau.de/docs/pystencils/2.0dev/contributing/index.html).



---



pystencils

pystencils

==========

==========

conftest.py

+79 −43
Original line number Original line Diff line number Diff line
@@ -3,31 +3,32 @@ import runpy 
import sys

import sys

import tempfile

import tempfile

import warnings

import warnings

import pathlib





import nbformat

import nbformat

import pytest

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

# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it

# at the same time

# at the same time

from pystencils.cpu import cpujit

# TODO: replace with new backend

# from pystencils.cpu import cpujit





# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file

# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file

# at the same time

# at the same time

try:

try:

    import pyximport

    import pyximport



    pyximport.install(language_level=3)

    pyximport.install(language_level=3)

    from pystencils.boundaries.createindexlistcython import *  # NOQA

except ImportError:

except ImportError:

    pass

    pass







SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))

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.

# the Ubuntu pipeline uses an older version of pytest which uses deprecated functionality.

# This leads to many warinings in the test and coverage pipeline.

# 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_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))
@@ -36,58 +37,79 @@ def add_path_to_ignore(path): 
    if not os.path.exists(path):

    if not os.path.exists(path):

        return

        return

    global collect_ignore

    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"),

collect_ignore = [

                  os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit")]

    os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),

add_path_to_ignore('tests/benchmark')

    os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit"),

add_path_to_ignore('_local_tmp')

]

add_path_to_ignore("tests/benchmark")

add_path_to_ignore("_local_tmp")









try:

try:

    import cupy

    import cupy

except ImportError:

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_gpu.py")]

    collect_ignore += [

    add_path_to_ignore('src/pystencils/gpu')

        os.path.join(SCRIPT_FOLDER, "tests/kernelcreation/test_gpu.py"),

        os.path.join(SCRIPT_FOLDER, "src/pystencils/backend/jit/gpu_cupy.py"),

    ]

    add_path_to_ignore("src/pystencils/gpu")





try:

try:

    import waLBerla

    import waLBerla

except ImportError:

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_aligned_array.py"),

    collect_ignore += [

                       os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py"),

        os.path.join(

                       os.path.join(SCRIPT_FOLDER, "doc/notebooks/03_tutorial_datahandling.ipynb"),

            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/test_small_block_benchmark.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:

try:

    import blitzdb

    import blitzdb

except ImportError:

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_parameterstudy.py")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py")]





try:

try:

    import islpy

    import islpy

except ImportError:

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:

try:

    import graphviz

    import graphviz

except ImportError:

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/backends/dot.py")]

    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:

try:

    import pyevtk

    import pyevtk

except ImportError:

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:

    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)

            collect_ignore.append(f)
@@ -109,38 +131,50 @@ class IPyNbTest(pytest.Item): 
    def __init__(self, name, parent, code):

    def __init__(self, name, parent, code):

        super(IPyNbTest, self).__init__(name, parent)

        super(IPyNbTest, self).__init__(name, parent)

        self.code = code

        self.code = code

        self.add_marker('notebook')

        self.add_marker("notebook")





    @pytest.mark.filterwarnings("ignore:IPython.core.inputsplitter is deprecated")

    def runtest(self):

    def runtest(self):

        global_dict = {'get_ipython': lambda: IPythonMockup(),

        global_dict = {"get_ipython": lambda: IPythonMockup(), "is_test_run": True}

                       'is_test_run': True}





        # disable matplotlib output

        # disable matplotlib output

        exec("import matplotlib.pyplot as p; "

        exec(

             "p.switch_backend('Template')", global_dict)

            "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

        # 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

        # plot is created. This warning is suppressed here

        exec("import warnings;"

        exec(

             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*')",

            "import warnings;"

             global_dict)

            "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:

        with tempfile.NamedTemporaryFile() as f:

            f.write(self.code.encode())

            f.write(self.code.encode())

            f.flush()

            f.flush()

            runpy.run_path(f.name, init_globals=global_dict, run_name=self.name)

            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):

class IPyNbFile(pytest.File):

    def collect(self):

    def collect(self):

        from nbconvert import PythonExporter



        exporter = PythonExporter()

        exporter = PythonExporter()

        exporter.exclude_markdown = True

        exporter.exclude_markdown = True

        exporter.exclude_input_prompt = True

        exporter.exclude_input_prompt = True





        notebook_contents = self.fspath.open(encoding='utf-8')

        notebook_contents = self.path.open(encoding="utf-8")





        with warnings.catch_warnings():

        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)

            notebook = nbformat.read(notebook_contents, 4)

            code, _ = exporter.from_notebook_node(notebook)

            code, _ = exporter.from_notebook_node(notebook)

        if pytest_version >= 50403:

        if pytest_version >= 50403:
@@ -152,10 +186,12 @@ class IPyNbFile(pytest.File): 
        pass

        pass









def pytest_collect_file(path, parent):

def pytest_collect_file(file_path: pathlib.Path, parent):

    glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]

    glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]

    if any(path.fnmatch(g) for g in glob_exprs):

    if any(file_path.match(g) for g in glob_exprs):

        if pytest_version >= 50403:

        return IPyNbFile.from_parent(path=file_path, parent=parent)

            return IPyNbFile.from_parent(fspath=path, parent=parent)



        else:



            return IPyNbFile(path, parent)
 
#   Fixtures



from tests.fixtures import *

doc/conf.py

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#!/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/index.rst

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Original line number Original line Diff line number Diff line 
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

doc/sphinx/api.rst

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API Reference

=============



.. toctree::

   :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/ast.rst

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Original line number Original line Diff line number Diff line 
*********************************************

For developers: AST Nodes and Transformations

*********************************************





AST Nodes

=========



.. automodule:: pystencils.astnodes

   :members:







Transformations

===============





.. automodule:: pystencils.transformations

   :members:

doc/sphinx/configuration.rst

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*************

Configuration

*************



.. automodule:: pystencils.cpu.cpujit
 
 No newline at end of file

doc/sphinx/datahandling.rst

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************

DataHandling

************



.. autoclass:: pystencils.datahandling.DataHandling

   :members:
 
 No newline at end of file

doc/sphinx/enums.rst

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************

Enumerations

************



.. automodule:: pystencils.enums

   :members:

doc/sphinx/field.rst

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*****

Field

*****



.. automodule:: pystencils.field

   :members:
 
 No newline at end of file

doc/sphinx/finite_differences.rst

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******************

Finite Differences

******************



.. automodule:: pystencils.fd

   :members:

doc/sphinx/kernel_compile_and_call.rst

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*****************************************

Creating and calling kernels from Python

*****************************************





Creating kernels

----------------



.. autofunction:: pystencils.create_kernel



.. autoclass:: pystencils.CreateKernelConfig

    :members:



.. autofunction:: pystencils.kernelcreation.create_domain_kernel



.. autofunction:: pystencils.kernelcreation.create_indexed_kernel



.. autofunction:: pystencils.kernelcreation.create_staggered_kernel





Code printing

-------------



.. autofunction:: pystencils.show_code





GPU Indexing

-------------



.. autoclass:: pystencils.gpu.AbstractIndexing

   :members:



.. autoclass:: pystencils.gpu.BlockIndexing

   :members:



.. autoclass:: pystencils.gpu.LineIndexing

   :members:

doc/sphinx/plot.rst

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**********************

Plotting and Animation

**********************



.. automodule:: pystencils.plot

   :members:

doc/sphinx/simplifications.rst

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***************************************

Assignment Collection & Simplifications

***************************************





AssignmentCollection

====================



.. autoclass:: pystencils.AssignmentCollection

   :members:





SimplificationStrategy

======================



.. autoclass:: pystencils.simp.SimplificationStrategy

    :members:



Simplifications

===============



.. 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

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*******

Stencil

*******



.. automodule:: pystencils.stencil

   :members:

docs/.gitignore

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build



#   sphinx.ext.autosummary generated files

**/generated

docs/Makefile

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# Minimal makefile for Sphinx documentation

#



# You can set these variables from the command line, and also

# from the environment for the first two.

SPHINXOPTS    ?=

SPHINXBUILD   ?= sphinx-build

SOURCEDIR     = source

BUILDDIR      = build



# Put it first so that "make" without argument is like "make help".

help:

	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)



.PHONY: help html clean



# Catch-all target: route all unknown targets to Sphinx using the new

# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

# %: Makefile



html:

	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)



clean:

	rm -rf source/api/generated

	rm -rf source/api/symbolic/generated

	rm -rf source/backend/generated

	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 No newline at end of file

docs/make.bat

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@ECHO OFF



pushd %~dp0



REM Command file for Sphinx documentation



if "%SPHINXBUILD%" == "" (

	set SPHINXBUILD=sphinx-build

)

set SOURCEDIR=source

set BUILDDIR=build



%SPHINXBUILD% >NUL 2>NUL

if errorlevel 9009 (

	echo.

	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx

	echo.installed, then set the SPHINXBUILD environment variable to point

	echo.to the full path of the 'sphinx-build' executable. Alternatively you

	echo.may add the Sphinx directory to PATH.

	echo.

	echo.If you don't have Sphinx installed, grab it from

	echo.https://www.sphinx-doc.org/

	exit /b 1

)



if "%1" == "" goto help



%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%

goto end



:help

%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%



:end

popd

docs/source/_templates/autosummary/recursive_class.rst

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{% extends "!autosummary/class.rst" %}



   {% block methods %}



   {% if methods %}

   .. rubric:: {{ _('Methods') }}



   .. autosummary::

      :toctree:

   {% for item in methods %}

      ~{{ name }}.{{ item }}

   {%- endfor %}

   {% endif %}

   {% endblock %}



   {% block attributes %}

   {% if attributes %}

   .. rubric:: {{ _('Attributes') }}



   .. autosummary::

      :toctree:

   {% for item in attributes %}

      ~{{ name }}.{{ item }}

   {%- endfor %}

   {% endif %}

   {% endblock %}

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docs/source/api/symbolic/assignments.md

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# Assignments and AssignmentCollection



```{eval-rst}



.. py:class:: pystencils.Assignment



    Monkeypatched variant of `sympy.codegen.ast.Assignment`.

    Represents an assignment of an expression to a symbol.



.. autosummary::

    :toctree: generated

    :nosignatures:

    :template: autosummary/recursive_class.rst



    pystencils.AssignmentCollection

```

docs/source/api/symbolic/index.md

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# Symbolic Toolbox



:::{toctree}

:maxdepth: 1



field

assignments

sympyextensions

:::

docs/source/backend/errors.rst

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*********************

Errors and Exceptions

*********************



.. automodule:: pystencils.backend.exceptions

    :members:

docs/source/backend/extensions.rst

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************************************

Extensions and Experimental Features

************************************



.. automodule:: pystencils.backend.extensions

docs/source/backend/iteration_space.rst

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****************

Iteration Spaces

****************



.. automodule:: pystencils.backend.kernelcreation.iteration_space

    :members:
 
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