diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000000000000000000000000000000000000..a2cf044e31522de52c481840728da972d9ade173
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,5 @@
+[flake8]
+max-line-length=120
+exclude=lbmpy/plot2d.py
+ lbmpy/session.py
+ignore = W293 W503 W291
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..73c1ace7cf8cf1d79984375aa3f6db811804a3be
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,13 @@
+__pycache__
+.ipynb_checkpoints
+.coverage
+*.pyc
+*.vti
+/build
+/dist
+/*.egg-info
+.cache
+_build
+/.idea
+.cache
+_local_tmp
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9ca03994bb92d1413807a2d0fc95e68204726c9c
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,133 @@
+stages:
+ - test
+ - deploy
+
+
+# -------------------------- Tests ------------------------------------------------------------------------------------
+
+# Normal test - runs on every commit all but "long run" tests
+tests-and-coverage:
+ stage: test
+ except:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ image: i10git.cs.fau.de:5005/software/pystencils/full
+ script:
+ - export NUM_CORES=$(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"
+ tags:
+ - docker
+ - cuda
+ - AVX
+ artifacts:
+ when: always
+ paths:
+ - coverage_report
+
+# Nightly test - runs "long run" jobs only
+test-longrun:
+ stage: test
+ only:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ image: i10git.cs.fau.de:5005/software/pystencils/full
+ script:
+ - export NUM_CORES=$(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=.
+ tags:
+ - docker
+ - cuda
+ - AVX
+ artifacts:
+ paths:
+ - coverage_report
+
+# Minimal tests in windows environment
+minimal-windows:
+ stage: test
+ except:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ tags:
+ - win
+ script:
+ - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
+ - source activate pystencils_dev
+ - env
+ - conda env list
+ - python -c "import numpy"
+ - python setup.py quicktest
+
+minimal-ubuntu:
+ stage: test
+ except:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ image: i10git.cs.fau.de:5005/software/pystencils/minimal_ubuntu
+ script:
+ - python3 setup.py quicktest
+ tags:
+ - docker
+
+minimal-conda:
+ stage: test
+ except:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ image: i10git.cs.fau.de:5005/software/pystencils/minimal_conda
+ script:
+ - python setup.py quicktest
+ tags:
+ - docker
+
+
+# -------------------- Linter & Documentation --------------------------------------------------------------------------
+
+
+flake8-lint:
+ stage: test
+ except:
+ variables:
+ - $ENABLE_NIGHTLY_BUILDS
+ image: i10git.cs.fau.de:5005/software/pystencils/full
+ script:
+ - flake8 lbmpy
+ tags:
+ - docker
+ - cuda
+
+
+build-documentation:
+ stage: test
+ image: i10git.cs.fau.de:5005/software/pystencils/full
+ script:
+ - export PYTHONPATH=`pwd`
+ - mkdir html_doc
+ - sphinx-build -W -b html doc html_doc
+ tags:
+ - docker
+ - cuda
+ artifacts:
+ paths:
+ - html_doc
+
+
+pages:
+ image: i10git.cs.fau.de:5005/software/pystencils/full
+ stage: deploy
+ script:
+ - ls -l
+ - mv coverage_report html_doc
+ - mv html_doc public # folder has to be named "public" for gitlab to publish it
+ artifacts:
+ paths:
+ - public
+ tags:
+ - docker
+ only:
+ - master@pycodegen/lbmpy
diff --git a/conftest.py b/conftest.py
new file mode 100644
index 0000000000000000000000000000000000000000..6c17a79a683ac93fa0afa4f30a1a75d86a66b379
--- /dev/null
+++ b/conftest.py
@@ -0,0 +1,117 @@
+import os
+import pytest
+import tempfile
+import runpy
+import sys
+# 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
+
+# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file
+# at the same time
+try:
+ import pyximport
+ pyximport.install(language_level=3)
+except ImportError:
+ pass
+
+
+SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
+sys.path.insert(0, os.path.abspath('lbmpy'))
+
+
+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, "doc", "conf.py"),
+ os.path.join(SCRIPT_FOLDER, "doc", "img", "mb_discretization", "maxwell_boltzmann_stencil_plot.py")]
+add_path_to_ignore('pystencils_tests/benchmark')
+add_path_to_ignore('_local_tmp')
+
+
+try:
+ import pycuda
+except ImportError:
+ collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_cpu_gpu_equivalence.py")]
+
+try:
+ import waLBerla
+except ImportError:
+ collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_serial_scenarios.py")]
+ collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_datahandling_parallel.py")]
+
+
+collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
+
+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']):
+ collect_ignore.append(f)
+
+
+import nbformat
+from nbconvert import PythonExporter
+
+
+class IPythonMockup:
+ def run_line_magic(self, *args, **kwargs):
+ pass
+
+ def run_cell_magic(self, *args, **kwargs):
+ pass
+
+ def magic(self, *args, **kwargs):
+ pass
+
+ def __bool__(self):
+ return False
+
+
+class IPyNbTest(pytest.Item):
+ def __init__(self, name, parent, code):
+ super(IPyNbTest, self).__init__(name, parent)
+ self.code = code
+ self.add_marker('notebook')
+
+ def runtest(self):
+ 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)
+
+ # 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)
+ 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)
+
+
+class IPyNbFile(pytest.File):
+ def collect(self):
+ exporter = PythonExporter()
+ 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)
+
+ def teardown(self):
+ 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):
+ return IPyNbFile(path, parent)
diff --git a/doc/conf.py b/doc/conf.py
index a56be9f74dcba06275d602dcd3f0349a6e7cbb0c..befdb443869eead8001a173274d827b54a45a641 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,13 +1,59 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
+import datetime
+import sphinx_rtd_theme
import os
import sys
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../../pystencils'))
-sys.path.insert(0, os.path.abspath('../..'))
-from sphinx_doc_conf import *
+sys.path.insert(0, os.path.abspath('.'))
+from version_from_git import version_number_from_git
+
+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 = '{}, Martin Bauer'.format(datetime.datetime.now().year)
+author = 'Martin Bauer'
+version = version_number_from_git()
+release = version_number_from_git()
+language = None
+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/3.6', 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'
project = 'lbmpy'
html_logo = "img/logo.png"
diff --git a/doc/img/logo.svg b/doc/img/logo.svg
index ee0a4c64dd0320a8e3bd425bef42de4eb10deffb..54e8e0e4e659eaf4ff47574cc09f86ba420d1543 100644
--- a/doc/img/logo.svg
+++ b/doc/img/logo.svg
@@ -480,6 +480,158 @@
effect="spiro"
id="path-effect4188-7"
is_visible="true" />
+ <marker
+ inkscape:stockid="Arrow1Send"
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+ style="overflow:visible"
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+ id="path1421-6"
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+ transform="matrix(-0.2,0,0,-0.2,-1.2,0)"
+ inkscape:connector-curvature="0" />
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+ <inkscape:path-effect
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inkscape:document-units="mm"
inkscape:current-layer="layer1"
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diff --git a/doc/img/logo_no_text.png b/doc/img/logo_no_text.png
new file mode 100644
index 0000000000000000000000000000000000000000..66896326cbaa7a5784178fc5845666aabfd9bc91
Binary files /dev/null and b/doc/img/logo_no_text.png differ
diff --git a/doc/version_from_git.py b/doc/version_from_git.py
new file mode 100644
index 0000000000000000000000000000000000000000..6392ad7732848485cf1cfd6aa919a208ce0a5b43
--- /dev/null
+++ b/doc/version_from_git.py
@@ -0,0 +1,31 @@
+import subprocess
+
+
+def version_number_from_git(tag_prefix='release/', sha_length=10, version_format="{version}.dev{commits}+{sha}"):
+ def get_released_versions():
+ tags = sorted(subprocess.getoutput('git tag').split('\n'))
+ versions = [t[len(tag_prefix):] for t in tags if t.startswith(tag_prefix)]
+ return versions
+
+ def tag_from_version(v):
+ return tag_prefix + v
+
+ def increment_version(v):
+ parsed_version = [int(i) for i in v.split('.')]
+ parsed_version[-1] += 1
+ return '.'.join(str(i) for i in parsed_version)
+
+ latest_release = get_released_versions()[-1]
+ commits_since_tag = subprocess.getoutput('git rev-list {}..HEAD --count'.format(tag_from_version(latest_release)))
+ sha = subprocess.getoutput('git rev-parse HEAD')[:sha_length]
+ is_dirty = len(subprocess.getoutput("git status --untracked-files=no -s")) > 0
+
+ if int(commits_since_tag) == 0:
+ version_string = latest_release
+ else:
+ next_version = increment_version(latest_release)
+ version_string = version_format.format(version=next_version, commits=commits_since_tag, sha=sha)
+
+ if is_dirty:
+ version_string += ".dirty"
+ return version_string
diff --git a/lbmpy_tests/test_chapman_enskog.py b/lbmpy_tests/test_chapman_enskog.py
index 47b2cb37e6fbd297f5888f276bee83a2a16c5937..8cabf4f2ba5488cb49103a10133fef52f74e0c1c 100644
--- a/lbmpy_tests/test_chapman_enskog.py
+++ b/lbmpy_tests/test_chapman_enskog.py
@@ -1,9 +1,7 @@
import pytest
import sympy as sp
import functools
-from sympy.abc import a, b, x, y, z
-from pystencils.fd import expand_diff_products, combine_diff_products, Diff, \
- expand_diff_linear, normalize_diff_order
+from pystencils.fd import Diff, normalize_diff_order
from pystencils.sympyextensions import multidimensional_sum
from lbmpy.chapman_enskog.chapman_enskog_higher_order import determine_higher_order_moments, get_solvability_conditions
from lbmpy.chapman_enskog.chapman_enskog_steady_state import SteadyStateChapmanEnskogAnalysisSRT, \
@@ -15,29 +13,6 @@ from lbmpy.creationfunctions import create_lb_method
from lbmpy.forcemodels import Guo
-def test_derivative_expand_collect():
- original = Diff(x*y*z)
- result = combine_diff_products(combine_diff_products(expand_diff_products(original))).expand()
- assert original == result
-
- original = -3 * y * z * Diff(x) + 2 * x * z * Diff(y)
- result = expand_diff_products(combine_diff_products(original)).expand()
- assert original == result
-
- original = a + b * Diff(x ** 2 * y * z)
- expanded = expand_diff_products(original)
- collect_res = combine_diff_products(combine_diff_products(combine_diff_products(expanded)))
- assert collect_res == original
-
-
-def test_diff_expand_using_linearity():
- eps = sp.symbols("epsilon")
- funcs = [a, b]
- test = Diff(eps * Diff(a+b))
- result = expand_diff_linear(test, functions=funcs)
- assert result == eps * Diff(Diff(a)) + eps * Diff(Diff(b))
-
-
def test_srt():
for stencil in ['D2Q9', 'D3Q19', 'D3Q27']:
for continuous_eq in (False, True):
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000000000000000000000000000000000000..2d69c7f60c6319ca21d470f78676aa8b17a7e44b
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,37 @@
+[pytest]
+python_files = test_*.py *_test.py scenario_*.py
+norecursedirs = *.egg-info .git .cache .ipynb_checkpoints htmlcov
+addopts = --doctest-modules --durations=20 --cov-config pytest.ini
+
+[run]
+branch = True
+source = lbmpy
+ lbmpy_tests
+
+omit = doc/*
+ lbmpy_tests/*
+ setup.py
+ conftest.py
+
+[report]
+exclude_lines =
+ # Have to re-enable the standard pragma
+ pragma: no cover
+
+ def __repr__
+
+ # Don't complain if tests don't hit defensive assertion code:
+ raise AssertionError
+ raise NotImplementedError
+ #raise ValueError
+
+ # Don't complain if non-runnable code isn't run:
+ if 0:
+ if False:
+ if __name__ == .__main__.:
+
+skip_covered = True
+fail_under = 90
+
+[html]
+directory = coverage_report
diff --git a/setup.py b/setup.py
index 8e4c3b010788f22efa6ab27842a80618d973accc..71278613b8c6123ec3055744e63e4b3ae50cd92a 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,53 @@
import os
import sys
+import io
from setuptools import setup, find_packages
-sys.path.insert(0, os.path.abspath('..'))
-from custom_pypi_index.pypi_index import get_current_dev_version_from_git
+import distutils
+from contextlib import redirect_stdout
+from importlib import import_module
+sys.path.insert(0, os.path.abspath('doc'))
+from version_from_git import version_number_from_git
+
+
+quick_tests = [
+ 'test_serial_scenarios.test_ldc_mrt',
+ 'test_force_on_boundary.test_force_on_boundary',
+]
+
+
+class SimpleTestRunner(distutils.cmd.Command):
+ """A custom command to run selected tests"""
+
+ description = 'run some quick tests'
+ user_options = []
+
+ @staticmethod
+ def _run_tests_in_module(test):
+ """Short test runner function - to work also if py.test is not installed."""
+ test = 'lbmpy_tests.' + test
+ mod, function_name = test.rsplit('.', 1)
+ if isinstance(mod, str):
+ mod = import_module(mod)
+
+ func = getattr(mod, function_name)
+ print(" -> %s in %s" % (function_name, mod.__name__))
+ with redirect_stdout(io.StringIO()):
+ func()
+
+ def initialize_options(self):
+ pass
+
+ def finalize_options(self):
+ pass
+
+ def run(self):
+ """Run command."""
+ for test in quick_tests:
+ self._run_tests_in_module(test)
setup(name='lbmpy',
- version=get_current_dev_version_from_git(),
+ version=version_number_from_git(),
description='Code Generation for Lattice Boltzmann Methods',
author='Martin Bauer',
license='AGPLv3',
@@ -30,4 +71,7 @@ setup(name='lbmpy',
'interactive': ['pystencils[interactive]', 'scipy', 'scikit-image', 'cython'],
'doc': ['pystencils[doc]'],
},
+ cmdclass={
+ 'quicktest': SimpleTestRunner
+ }
)