Merge branch 'SrcTree' into 'master'

Refactor source tree layout

See merge request !164

.flake8

 [flake8]
 max-line-length=120
-exclude=lbmpy/plot.py
-        lbmpy/session.py
+exclude=src/lbmpy/plot.py
+        src/lbmpy/session.py
 ignore = W293 W503 W291 C901 E741

.gitignore

 __pycache__
 .ipynb_checkpoints
-.coverage
+.coverage*
 *.pyc
 *.vti
 /build
 /html_doc
 /dist
-/*.egg-info
+*.egg-info
 .cache
 _build
 /.idea
@@ -15,15 +15,15 @@ _local_tmp
 **/pylintrc
 *.bak
 *.tmp
-/lbmpy_tests/db
+/tests/db
 doc/bibtex.json
 /db
-/lbmpy/phasefield/simplex_projection.*.so
-/lbmpy/phasefield/simplex_projection.c
+/src/lbmpy/phasefield/simplex_projection.*.so
+/src/lbmpy/phasefield/simplex_projection.c
 
 # macOS
 **/.DS_Store
 *.uuid
 
 # benchmark database
-/lbmpy_tests/benchmark/db
\ No newline at end of file
+/tests/benchmark/db
\ No newline at end of file

.gitlab-ci.yml

@@ -68,6 +68,7 @@ minimal-conda:
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
   script:
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
+    - pip install -e .
     - python quicktest.py
   tags:
     - docker
@@ -80,7 +81,7 @@ flake8-lint:
       - $ENABLE_NIGHTLY_BUILDS
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
-    - flake8 lbmpy
+    - flake8 src/lbmpy
   tags:
     - docker
     - cuda11
@@ -136,6 +137,8 @@ minimal-sympy-master:
     variables:
       - $ENABLE_NIGHTLY_BUILDS
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
   script:
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
     - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
@@ -212,6 +215,8 @@ pycodegen-integration:
 build-documentation:
   stage: test
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
+  before_script:
+    - pip install -e .
   script:
     - export PYTHONPATH=`pwd`
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

conftest.py

@@ -42,36 +42,35 @@ def add_path_to_ignore(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 cupy
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_cpu_gpu_equivalence.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_cpu_gpu_equivalence.py")]
 
 try:
     import waLBerla
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_datahandling_parallel.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py")]
 
 try:
     import blitzdb
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/benchmark"),
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/benchmark"),
                        os.path.join(SCRIPT_FOLDER,
-                                    "lbmpy_tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py"),
-                       os.path.join(SCRIPT_FOLDER, "lbmpy_tests/full_scenarios/shear_wave/scenario_shear_wave.py"),
-                       os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_json_serializer.py"),
-                       os.path.join(SCRIPT_FOLDER, "lbmpy/db.py")]
+                                    "tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py"),
+                       os.path.join(SCRIPT_FOLDER, "tests/full_scenarios/shear_wave/scenario_shear_wave.py"),
+                       os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py"),
+                       os.path.join(SCRIPT_FOLDER, "src/lbmpy/db.py")]
 
 if platform.system().lower() == 'windows':
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_quicktests.py")]
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_quicktests.py")]
 
 sver = sympy.__version__.split(".")
 if int(sver[0]) == 1 and int(sver[1]) < 2:
-    add_path_to_ignore('lbmpy_tests/phasefield')
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_n_phase_boyer_noncoupled.ipynb")]
+    add_path_to_ignore('tests/phasefield')
+    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_n_phase_boyer_noncoupled.ipynb")]
 
 collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
 

pyproject.toml

@@ -77,7 +77,7 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools.package-data]
 
 [tool.setuptools.packages.find]
-where = ["."]
+where = ["src"]
 include = ["lbmpy", "lbmpy.*"]
 namespaces = false
 

pytest.ini

 [pytest]
+testpaths = src tests doc/notebooks
+pythonpath = src
 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
 markers =
        longrun: tests only run at night since they have large execution time
-       notebook: jupyter notebooks
+       notebook: mark for notebooks
 # these warnings all come from third party libraries.
 filterwarnings =
        ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
@@ -14,15 +16,16 @@ filterwarnings =
 
 [run]
 branch = True
-source = lbmpy
-         lbmpy_tests
+source = src/lbmpy
+         tests
 
 omit = doc/*
-       lbmpy_tests/*
+       tests/*
        setup.py
        conftest.py
        versioneer.py
-       lbmpy/_version.py
+       src/lbmpy/_version.py
+       venv/
 
 [report]
 exclude_lines =
@@ -35,6 +38,7 @@ exclude_lines =
        # Don't complain if tests don't hit defensive assertion code:
        raise AssertionError
        raise NotImplementedError
+       NotImplementedError()
        #raise ValueError
 
        # Don't complain if non-runnable code isn't run:

quicktest.py

@@ -2,7 +2,7 @@
 
 from contextlib import redirect_stdout
 import io
-from lbmpy_tests.test_quicktests import (
+from tests.test_quicktests import (
     test_poiseuille_channel_quicktest,
     test_entropic_methods,
     test_cumulant_ldc

src/lbmpy/analytical_solutions.py

+from typing import Union
+from numpy.typing import NDArray
+
+
+def poiseuille_flow(middle_distance: Union[float, NDArray], height,
+                    ext_force_density: float, dyn_visc: float) -> Union[float, NDArray]:
+    """
+    Analytical solution for plane Poiseuille flow.
+
+    Args:
+        middle_distance: Distance to the middle plane of the channel.
+        height: Distance between the boundaries.
+        ext_force_density: Force density on the fluid normal to the boundaries.
+        dyn_visc: dyn_visc
+
+    Returns:
+        A numpy array of the poiseuille profile if middle_distance is given as array otherwise of velocity of
+        the position given with middle_distance
+    """
+    return ext_force_density * 1. / (2 * dyn_visc) * (height**2.0 / 4.0 - middle_distance**2.0)