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.flake8
View file @ 5600b6b6
[flake8]
max-line-length=120
exclude=pystencils/jupyter.py,
pystencils/plot.py
pystencils/session.py
ignore = W293 W503 W291
exclude=src/pystencils/jupyter.py,
src/pystencils/plot.py
src/pystencils/session.py
ignore = W293 W503 W291 C901 E741
.gitattributes 0 → 100644
View file @ 5600b6b6
src/pystencils/_version.py export-subst
.gitignore
View file @ 5600b6b6
__pycache__
.ipynb_checkpoints
.coverage
.coverage*
*.pyc
*.vti
/build
/dist
/*.egg-info
*.egg-info
.cache
_build
/html_doc
/.idea
.vscode
.cache
_local_tmp
RELEASE-VERSION
test-report
src/pystencils/boundaries/createindexlistcython.c
src/pystencils/boundaries/createindexlistcython.*.so
tests/tmp
tests/var
tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
report.xml
coverage_report/
# macOS
**/.DS_Store
*.uuid
.gitlab-ci.yml
View file @ 5600b6b6
stages:
- pretest
- test
- nightly
- docs
- deploy
# -------------------------- Templates ------------------------------------------------------------------------------------
# Base configuration for jobs meant to run at every commit
.every-commit:
rules:
- if: $CI_PIPELINE_SOURCE != "schedule"
# Configuration for jobs meant to run on each commit to pycodegen/pystencils/master
.every-commit-master:
rules:
- if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/pystencils" && $CI_COMMIT_BRANCH == "master"'
# Base configuration for jobs meant to run at a schedule
.scheduled:
rules:
- if: $CI_PIPELINE_SOURCE == "schedule"
# -------------------------- Tests ------------------------------------------------------------------------------------
# Normal test - runs on every commit all but "long run" tests
tests-and-coverage:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
stage: pretest
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
before_script:
- pip install -e .
script:
- env
- pip list
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun"
- 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
- cuda
- 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
# Nightly test - runs "long run" jobs only
test-longrun:
# Normal test with longruns
tests-and-coverage-with-longrun:
stage: test
only:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
when: manual
allow_failure: true
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
before_script:
- pip install sympy --upgrade
- pip install -e .
script:
- env
- pip list
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=.
- mkdir public
- py.test -v -n $NUM_CORES
tags:
- docker
- cuda11
- AVX
# pipeline with latest python version
latest-python:
stage: test
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
before_script:
- pip install -e .
script:
- env
- pip list
- pip install -e .
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- cuda
- AVX
artifacts:
paths:
- coverage_report
when: always
reports:
junit: report.xml
# Minimal tests in windows environment
minimal-windows:
#minimal-windows:
# stage: test
# tags:
# - win
# script:
# - export NUM_CORES=$(nproc --all)
# - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
# - source activate pystencils
# - pip install joblib
# - pip list
# - python -c "import numpy"
# - py.test -v -m "not (notebook or longrun)"
ubuntu:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
tags:
- win
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
before_script:
- ln -s /usr/include/locale.h /usr/include/xlocale.h
- pip3 install -e .
script:
- source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
- source activate pystencils_dev
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- sed -i 's/--doctest-modules //g' pytest.ini
- env
- conda env list
- python -c "import numpy"
- python setup.py quicktest
- pip list
- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- cuda11
- AVX
artifacts:
when: always
reports:
junit: report.xml
minimal-ubuntu:
.multiarch_template:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_ubuntu
extends: .every-commit
allow_failure: true
before_script: &multiarch_before_script
# - pip3 install -v .
- export PYTHONPATH=src
- python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
- sed -i '/^fail_under.*/d' pytest.ini
script:
- python3 setup.py quicktest
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- sed -i 's/--doctest-modules //g' pytest.ini
- env
- pip3 list
- python3 -m pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov=. --junitxml=report.xml tests/test_*vec*.py tests/test_random.py tests/test_half_precision.py
- python3 -m coverage xml
tags:
- docker
- AVX
artifacts:
when: always
paths:
- coverage_report
reports:
coverage_report:
coverage_format: cobertura
path: coverage.xml
junit: report.xml
arm64v8:
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
variables:
QEMU_CPU: "cortex-a76"
before_script:
- *multiarch_before_script
- sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json
ppc64le:
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
before_script:
- *multiarch_before_script
- sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json
arm64v9:
# SVE support is still unreliable in GCC 11 (incorrect code for fixed-width vectors, internal compiler errors).
# For half precision Clang is necessary
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
before_script:
- *multiarch_before_script
- sed -i s/march=native/march=armv9-a+sve2+sme/g ~/.config/pystencils/config.json
- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
riscv64:
# RISC-V vector extension are currently not supported by GCC.
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64
variables:
# explicitly set SIMD as detection requires QEMU >= 8.1
PYSTENCILS_SIMD: "rvv"
QEMU_CPU: "rv64,v=true,zicboz=true"
before_script:
- *multiarch_before_script
- sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json
- sed -i s/g\+\+/clang++-15/g ~/.config/pystencils/config.json
minimal-conda:
stage: pretest
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
before_script:
- pip install -e .
script:
- python quicktest.py
tags:
- docker
- cuda
minimal-sympy-master:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
before_script:
- pip install -e .
script:
- python setup.py quicktest
- python -m pip install --upgrade git+https://github.com/sympy/sympy.git
- python quicktest.py
allow_failure: true
tags:
- docker
- cuda
pycodegen-integration:
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
stage: test
when: manual
allow_failure: true
script:
- git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
- cd pycodegen
- git submodule sync --recursive
- git submodule update --init --recursive
- git submodule foreach git fetch origin # compare the latest master version!
- git submodule foreach git reset --hard origin/master
- cd pystencils
- git remote add test $CI_REPOSITORY_URL
- git fetch test
- git reset --hard $CI_COMMIT_SHA
- cd ..
- pip install -e pystencils/
- pip install -e lbmpy/
- cmake --version
- ./install_walberla.sh
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- cd pystencils
- py.test -v -n $NUM_CORES --junitxml=report.xml .
- cd ../lbmpy
- py.test -v -n $NUM_CORES --junitxml=report.xml .
- cd ../walberla/build/
- make -j $NUM_CORES CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample
- make -j $NUM_CORES multiphaseCPU multiphaseGPU FluctuatingMRT FlowAroundSphereCodeGen FieldLayoutAndVectorizationTest GeneratedOutflowBC
- cd apps/benchmarks/UniformGridGPU
- make -j $NUM_CORES
- cd ../UniformGridCPU
- make -j $NUM_CORES
tags:
- docker
- cuda11
- AVX
artifacts:
when: always
reports:
junit: pycodegen/*/report.xml
# -------------------- Scheduled Tasks --------------------------------------------------------------------------
# Nightly test against the latest (pre-release) version of SymPy published on PyPI
nightly-sympy:
stage: nightly
needs: []
extends: .scheduled
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
before_script:
- pip install -e .
- pip install --upgrade --pre sympy
script:
- env
- pip list
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- AVX
- cuda
artifacts:
when: always
reports:
junit: report.xml
# -------------------- Linter & Documentation --------------------------------------------------------------------------
flake8-lint:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
stage: pretest
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
script:
- flake8 pystencils
- flake8 src/pystencils
tags:
- docker
- cuda
build-documentation:
stage: test
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
stage: docs
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
needs: []
before_script:
- pip install -e .
script:
- export PYTHONPATH=`pwd`
- mkdir html_doc
- sphinx-build -b html doc html_doc
- sphinx-build -W -b html doc html_doc
tags:
- docker
- cuda
artifacts:
paths:
- html_doc
......@@ -119,7 +347,9 @@ build-documentation:
pages:
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
extends: .every-commit-master
stage: deploy
needs: ["tests-and-coverage", "build-documentation"]
script:
- ls -l
- mv coverage_report html_doc
......@@ -129,5 +359,3 @@ pages:
- public
tags:
- docker
only:
- master@pycodegen/pystencils
.isort.cfg
View file @ 5600b6b6
......@@ -2,3 +2,4 @@
line_length=100
balanced_wrapping=True
multi_line_output=4
known_third_party=sympy
AUTHORS.txt
View file @ 5600b6b6
......@@ -3,12 +3,13 @@ Contributors:
-------------
- Martin Bauer <martin.bauer@fau.de>
- Markus Holzer <markus.holzer@fau.de>
- Stephan Seitz <stephan.seitz@fau.de>
- Michael Kuron <mkuron@icp.uni-stuttgart.de>
- Jan Hönig <jan.hoenig@fau.de>
- Nils Kohl <nils.kohl@fau.de>
- Julian Hammer <julian.hammer@fau.de>
- Christian Godenschwager <christian.godenschwager@fau.de>
- Markus Holzer <markus.holzer@fau.de>
- Michael Kuron <mkuron@icp.uni-stuttgart.de>
- Nils Kohl <nils.kohl@fau.de>
- Frederik Hennig <frederik.hennig@fau.de>
- Dominik Ernst <dominik.ernst@fau.de>
- João Victor Tozatti Risso <joaovictortr@protonmail.com>
- Christian Godenschwager <christian.godenschwager@fau.de>
- Dominik Thoennes <dominik.thoennes@fau.de>
CHANGELOG.md 0 → 100644
View file @ 5600b6b6
# Change Log
## Unreleased
### Removed
* LLVM backend because it was not used much and not good integrated in pystencils.
* OpenCL backend because it was not used much and not good integrated in pystencils.
CONTRIBUTING.md 0 → 100644
View file @ 5600b6b6
# Contributing
Contributions to pystencils are always welcome, and they are greatly appreciated!
A list of open problems can be found [here]( https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
Of course, it is also always appreciated to bring own ideas and problems to the community!
Please submit all contributions to the official [GitLab repository](https://i10git.cs.fau.de/pycodegen/pystencils) in the form of a Merge Request. Please do not submit git diffs or files containing the changes.
There also exists a GitHub repository, which is only a mirror to the GitLab repository. Contributions to the GitHub repository are not considered.
`pystencils` is an open-source python package under the license of AGPL3. Thus we consider the act of contributing to the code by submitting a Merge Request as the "Sign off" or agreement to the AGPL3 license.
You can contribute in many different ways:
## Types of Contributions
### Report Bugs
Report bugs at [https://i10git.cs.fau.de/pycodegen/pystencils/-/issues](https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
For pystencils, it is often necessary to provide the python and [SymPy](https://www.sympy.org/en/index.html) versions used and hardware information like the
processor architecture and the compiler version used to compile the generated kernels.
### Fix Issues
Look through the GitLab issues. Different tags are indicating the status of the issues.
The "bug" tag indicates problems with pystencils, while the "feature" tag shows ideas that should be added in the future.
### Write Documentation
The documentation of pystencils can be found [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils/). Jupyter notebooks are used to provide an
interactive start to pystencils. It is always appreciated if new document notebooks are provided
since this helps others a lot.
## Get Started!
Ready to contribute? Here is how to set up `pystencils` for local development.
1. Fork the `pystencils` repo on GitLab.
2. Clone your fork locally:
```bash
$ git clone https://i10git.cs.fau.de/your-name/pystencils
```
3. Install your local copy into a virtualenv. It is also recommended to use anaconda or miniconda to manage the python environments.
```bash
$ mkvirtualenv pystencils
$ cd pystencils/
$ pip install -e .
```
4. Create a branch for local development:
```bash
$ git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
5. When you're done making changes, check that your changes pass flake8 and the
tests
```bash
$ flake8 pystencils
$ py.test -v -n $NUM_CORES -m "not longrun" .
```
To get all packages needed for development, a requirements list can be found [here](https://i10git.cs.fau.de/pycodegen/pycodegen/-/blob/master/conda_environment_dev.yml). This includes flake8 and pytest.
6. Commit your changes and push your branch to GitHub::
```bash
$ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature
```
7. Submit a Merge Request on GitLab.
## Merge Request Guidelines
Before you submit a Merge Request, check that it meets these guidelines:
1. All functionality that is implemented through this Merge Request should be covered by unit tests. These are implemented in `pystencil_tests`
2. If the Merge Request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
3. If you have a maintainer status for `pystencils`, you can merge Merge Requests to the master branch. However, every Merge Request needs to be reviewed by another developer. Thus it is not allowed to merge a Merge Request, which is submitted by oneself.
## Tips
To run a subset of tests:
```bash
$ py.test my_test.py
```
\ No newline at end of file
MANIFEST.in
View file @ 5600b6b6
include README.md
include COPYING.txt
include RELEASE-VERSION
include AUTHORS.txt
include CONTRIBUTING.md
include CHANGELOG.md
README.md
View file @ 5600b6b6
......@@ -2,15 +2,16 @@ pystencils
==========
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/pystencils/master?filepath=doc%2Fnotebooks)
[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.walberla.net/pystencils)
[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](https://pycodegen.pages.i10git.cs.fau.de/pystencils)
[![pypi-package](https://badge.fury.io/py/pystencils.svg)](https://badge.fury.io/py/pystencils)
[![pipeline status](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.walberla.net/pystencils/coverage_report)
[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/pystencils/coverage_report)
Run blazingly fast stencil codes on numpy arrays.
*pystencils* uses sympy to define stencil operations, that can be executed on numpy arrays.
Exploiting the stencil structure makes *pystencils* run faster than normal numpy code and even as Cython and numba,
[as demonstrated in this notebook](http://pycodegen.pages.walberla.net/pystencils/notebooks/demo_benchmark.html).
[as demonstrated in this notebook](https://pycodegen.pages.i10git.cs.fau.de/pystencils/notebooks/demo_benchmark.html).
Here is a code snippet that computes the average of neighboring cells:
......@@ -20,7 +21,7 @@ import numpy as np
f, g = ps.fields("f, g : [2D]")
stencil = ps.Assignment(g[0, 0],
(f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
(f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
kernel = ps.create_kernel(stencil).compile()
f_arr = np.random.rand(1000, 1000)
......@@ -32,15 +33,15 @@ kernel(f=f_arr, g=g_arr)
It comes with automatic finite difference discretization for PDEs:
```python
import pystencils as ps
import sympy as sp
c, v = ps.fields("c, v(2): [2D]")
adv_diff_pde = ps.fd.transient(c) - ps.fd.diffusion(c, sp.symbols("D")) + ps.fd.advection(c, v)
discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)
discretization = discretize(adv_diff_pde)
```
Look at the [documentation](http://pycodegen.pages.walberla.net/pystencils) to learn more.
Installation
------------
......@@ -51,7 +52,7 @@ pip install pystencils[interactive]
Without `[interactive]` you get a minimal version with very little dependencies.
All options:
- `gpu`: use this if an Nvidia GPU is available and CUDA is installed
- `gpu`: use this if an NVIDIA or AMD GPU is available and CUDA or ROCm is installed
- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
- `bench_db`: functionality to store benchmark result in object databases
- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.
......@@ -59,12 +60,28 @@ All options:
Options can be combined e.g.
```bash
pip install pystencils[interactive,gpu,doc]
```
pip install pystencils[interactive, gpu, doc]
```
pystencils is also fully compatible with Windows machines. If working with visual studio and cupy makes sure to run example files first to ensure that cupy can find the compiler's executable.
Documentation
-------------
Read the docs [here](http://pycodegen.pages.walberla.net/pystencils) and
check out the Jupyter notebooks in `doc/notebooks`.
Read the docs [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils) and
check out the Jupyter notebooks in `doc/notebooks`. The **Changelog** of pystencils can be found [here](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CHANGELOG.md).
Authors
-------
Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/AUTHORS.txt) of pystencils.
### Please cite us
If you use pystencils in a publication, please cite the following articles:
Overview:
- M. Bauer et al, Code Generation for Massively Parallel Phase-Field Simulations. Association for Computing Machinery, 2019. https://doi.org/10.1145/3295500.3356186
Performance Modelling:
- D. Ernst et al, Analytical performance estimation during code generation on modern GPUs. Journal of Parallel and Distributed Computing, 2023. https://doi.org/10.1016/j.jpdc.2022.11.003
binder/environment.yml
View file @ 5600b6b6
......@@ -7,14 +7,14 @@
# conda env create -f conda_environment_user.yml
# . activate pystencils
#
# If you have CUDA installed and want to use your GPU, uncomment the last line to install pycuda
# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy
#
# ----------------------------------------------------------------------------------------------------------------------
name: pystencils
dependencies:
# Basic dependencies:
- python >= 3.6
- python >= 3.8
- numpy
- sympy >= 1.1
- appdirs # to find default cache directory on each platform
......@@ -32,4 +32,4 @@ dependencies:
- ipy_table # HTML tables for jupyter notebooks
- pyevtk # VTK output for serial simulations
- blitzdb # file-based No-SQL database to store simulation results
#- pycuda # add this if you have CUDA installed
#- cupy # add this if you have CUDA or ROCm installed
conftest.py
View file @ 5600b6b6
import os
import pytest
import tempfile
import runpy
import sys
import tempfile
import warnings
import nbformat
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
# at the same time
from pystencils.cpu import cpujit
......@@ -14,12 +20,17 @@ try:
pyximport.install(language_level=3)
except ImportError:
pass
from pystencils.boundaries.createindexlistcython import * # NOQA
SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
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.reverse()
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):
......@@ -28,34 +39,49 @@ def add_path_to_ignore(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")]
add_path_to_ignore('pystencils_tests/benchmark')
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:
import pycuda
import cupy
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/pystencils_tests/test_cudagpu.py")]
add_path_to_ignore('pystencils/gpucuda')
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_gpu.py")]
add_path_to_ignore('src/pystencils/gpu')
try:
import llvmlite
import waLBerla
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/backends/llvm.py')]
add_path_to_ignore('pystencils/llvm')
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_aligned_array.py"),
os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py"),
os.path.join(SCRIPT_FOLDER, "doc/notebooks/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")]
try:
import kerncraft
import blitzdb
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_kerncraft_coupling.py")]
add_path_to_ignore('pystencils/kerncraft_coupling')
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 blitzdb
import islpy
except ImportError:
add_path_to_ignore('pystencils/runhelper')
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")]
try:
import pyevtk
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/vtk.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
......@@ -65,10 +91,6 @@ for root, sub_dirs, files in os.walk('.'):
collect_ignore.append(f)
import nbformat
from nbconvert import PythonExporter
class IPythonMockup:
def run_line_magic(self, *args, **kwargs):
pass
......@@ -115,10 +137,16 @@ class IPyNbFile(pytest.File):
exporter.exclude_markdown = True
exporter.exclude_input_prompt = True
notebook_contents = self.fspath.open()
notebook = nbformat.read(notebook_contents, 4)
code, _ = exporter.from_notebook_node(notebook)
yield IPyNbTest(self.name, self, code)
notebook_contents = self.fspath.open(encoding='utf-8')
with warnings.catch_warnings():
warnings.filterwarnings("ignore", "IPython.core.inputsplitter is deprecated")
notebook = nbformat.read(notebook_contents, 4)
code, _ = exporter.from_notebook_node(notebook)
if pytest_version >= 50403:
yield IPyNbTest.from_parent(name=self.name, parent=self, code=code)
else:
yield IPyNbTest(self.name, self, code)
def teardown(self):
pass
......@@ -127,4 +155,7 @@ class IPyNbFile(pytest.File):
def pytest_collect_file(path, parent):
glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
if any(path.fnmatch(g) for g in glob_exprs):
return IPyNbFile(path, parent)
if pytest_version >= 50403:
return IPyNbFile.from_parent(fspath=path, parent=parent)
else:
return IPyNbFile(path, parent)
doc/conf.py 100644 → 100755
View file @ 5600b6b6
......@@ -4,10 +4,11 @@
import datetime
import sphinx_rtd_theme
import os
import re
import sys
sys.path.insert(0, os.path.abspath('.'))
from version_from_git import version_number_from_git
import pystencils
extensions = [
'sphinx.ext.autodoc',
......@@ -25,11 +26,14 @@ templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
copyright = '{}, Martin Bauer'.format(datetime.datetime.now().year)
author = 'Martin Bauer'
version = version_number_from_git()
release = version_number_from_git()
language = None
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'
......@@ -47,13 +51,14 @@ nbsphinx_execute = 'never'
nbsphinx_codecell_lexer = 'python3'
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),
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"
html_logo = 'img/logo.png'
doc/index.rst
View file @ 5600b6b6
......@@ -14,5 +14,6 @@ pystencils can help you to generate blazingly fast code for image processing, nu
.. image:: /img/pystencils_arch_block_diagram.svg
:height: 450px
:align: center
doc/notebooks/01_tutorial_getting_started.ipynb
View file @ 5600b6b6
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