diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca56ea19ead85f478ff90748e19b1365543d0ea9..f8d42093476130b7862c20cc995d647b97989995 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -51,7 +51,14 @@ project(TurTLE)
find_program(PYTHON_EXECUTABLE
python3)
-execute_process(COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/get_version.py OUTPUT_VARIABLE TURTLE_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/get_version.py
+ OUTPUT_VARIABLE TURTLE_VERSION
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/get_version_long.py
+ OUTPUT_VARIABLE TURTLE_VERSION_LONG
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
project(TurTLE
VERSION ${TURTLE_VERSION}
@@ -479,12 +486,25 @@ if(EXISTS "${PROJECT_BINARY_DIR}/bash_setup_for_TurTLE.sh")
DESTINATION "lib/"
)
endif()
+install(FILES "${PROJECT_SOURCE_DIR}/TurTLE/test/B32p1e4_checkpoint_0.h5" DESTINATION share/TurTLE-${TURTLE_VERSION_LONG})
+install(DIRECTORY "${PROJECT_SOURCE_DIR}/TurTLE/test/particle_set" DESTINATION share/TurTLE-${TURTLE_VERSION_LONG}/)
+install(DIRECTORY "${PROJECT_SOURCE_DIR}/TurTLE/test/profiler" DESTINATION share/TurTLE-${TURTLE_VERSION_LONG}/)
#####################################################################################
## Install the python3 wrapper
-# copy command
+# copy python package
install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E copy_directory ${PROJECT_SOURCE_DIR}/TurTLE ${PROJECT_BINARY_DIR}/python/TurTLE/)")
+# install __init__
+configure_file(
+ "${PROJECT_SOURCE_DIR}/TurTLE/__init__.py.in"
+ "${PROJECT_BINARY_DIR}/python/TurTLE/__init__.py"
+ @ONLY)
+# update setup.py
+configure_file(
+ "${PROJECT_SOURCE_DIR}/setup.py.in"
+ "${PROJECT_BINARY_DIR}/python/setup.py"
+ @ONLY)
if(EXISTS "${PROJECT_BINARY_DIR}/host_info.py")
install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_BINARY_DIR}/host_info.py ${PROJECT_BINARY_DIR}/python/TurTLE/)")
else()
@@ -494,7 +514,7 @@ else()
install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/pc_host_info.py ${PROJECT_BINARY_DIR}/python/TurTLE/host_info.py)")
endif()
endif()
-install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/setup.py install --force --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/python/)")
+install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_BINARY_DIR}/python/setup.py install --force --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/python/)")
#####################################################################################
@@ -514,6 +534,11 @@ if (BUILD_TESTING)
COMMAND turtle.test_Parseval
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
### basic particle functionality
+ add_test(
+ NAME test_particles
+ COMMAND turtle.test_particles p2p_sampling on
+ WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
+ set_tests_properties(test_particles PROPERTIES TIMEOUT 2000)
add_test(
NAME test_tracer_set
COMMAND turtle TEST test_tracer_set -n 32 --np 2 --ntpp 2 --simname tracer_set_testsim
@@ -521,7 +546,7 @@ if (BUILD_TESTING)
### compare DNS output to stored results
add_test(
NAME test_NSVEparticles
- COMMAND turtle.test_NSVEparticles --np 2 --ntpp 2 --cpp_random_particles 0
+ COMMAND turtle.test_NSVEparticles --np 2 --ntpp 2
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
set_tests_properties(test_NSVEparticles PROPERTIES TIMEOUT 2000)
### check whether data is messed up by p2p calculations
diff --git a/TurTLE/__init__.py b/TurTLE/__init__.py.in
similarity index 83%
rename from TurTLE/__init__.py
rename to TurTLE/__init__.py.in
index bef0ac39b35e7abd352732b525f59124d29a8d5f..4c08dcecdbbf90e24cc693e3a2577e8d2b1bfbbd 100644
--- a/TurTLE/__init__.py
+++ b/TurTLE/__init__.py.in
@@ -24,20 +24,11 @@
import os
-import sys
-import pickle
-import pkg_resources
+__version__ = '@TURTLE_VERSION_LONG@'
-__version__ = pkg_resources.require('TurTLE')[0].version
+data_dir = os.path.join('@CMAKE_INSTALL_PREFIX@', 'share/TurTLE-@TURTLE_VERSION_LONG@')
-_dist = pkg_resources.get_distribution('TurTLE')
-dist_loc = os.path.realpath(_dist.location)
-here = os.path.normcase(__file__)
-header_dir = os.path.join(os.path.join(dist_loc, 'TurTLE'), 'cpp')
-lib_dir = os.path.join(dist_loc, 'TurTLE')
-
-homefolder = os.path.expanduser('~')
from .host_info import host_info
from .DNS import DNS
diff --git a/TurTLE/test/profile_scalar.py b/TurTLE/test/profile_scalar.py
index 08ee0f1a5f78434dcf446e2a3b84739a8ea7ba1d..a1ff24090415108d06cf13e460a108ec1518bec3 100644
--- a/TurTLE/test/profile_scalar.py
+++ b/TurTLE/test/profile_scalar.py
@@ -11,8 +11,8 @@ import TurTLE._base
import TurTLE.DNS
from TurTLE._code import _code
-cpp_location = os.path.join(os.path.join(
- TurTLE.lib_dir, 'test'), 'profiler')
+cpp_location = os.path.join(
+ TurTLE.data_dir, 'profiler')
class ADNS(TurTLE.DNS):
diff --git a/TurTLE/test/test_Heun_p2p.py b/TurTLE/test/test_Heun_p2p.py
index a61ab673baefdc2d8096f6846b853f6e6a41c603..ba997c8b687a309d5c95871aa855d122d4f35596 100644
--- a/TurTLE/test/test_Heun_p2p.py
+++ b/TurTLE/test/test_Heun_p2p.py
@@ -11,8 +11,8 @@ import TurTLE._base
import TurTLE.DNS
from TurTLE._code import _code
-cpp_location = os.path.join(os.path.join(
- TurTLE.lib_dir, 'test'), 'particle_set')
+cpp_location = os.path.join(
+ TurTLE.data_dir, 'particle_set')
class ADNS(TurTLE.DNS):
diff --git a/TurTLE/test/test_bfps_resize.py b/TurTLE/test/test_bfps_resize.py
index 4201eff252b97a2d1f2de2d6faabc7d5efe34077..c9d07eb7293e72ac442666fdd76195d8e84793e1 100644
--- a/TurTLE/test/test_bfps_resize.py
+++ b/TurTLE/test/test_bfps_resize.py
@@ -20,7 +20,7 @@ def main():
['NSVE',
'-n', '32',
'--src-simname', 'B32p1e4',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--simname', 'dns_test',
'--np', '4',
diff --git a/TurTLE/test/test_particle_clouds.py b/TurTLE/test/test_particle_clouds.py
index b6c401d18039d2b5b02991bd5a1cf1aae8152a50..17e63175298d79c698cf7afcd0442e35297c72f1 100644
--- a/TurTLE/test/test_particle_clouds.py
+++ b/TurTLE/test/test_particle_clouds.py
@@ -43,7 +43,7 @@ def basic_test():
c.simname = 'basic_cloud_test'
f0 = h5py.File(
os.path.join(
- os.path.join(TurTLE.lib_dir, 'test'),
+ TurTLE.data_dir,
'B32p1e4_checkpoint_0.h5'),
'r')
ic_file = h5py.File(c.get_checkpoint_0_fname(), 'a')
@@ -55,7 +55,7 @@ def basic_test():
'-n', '32',
'--src-simname', 'B32p1e4',
'--forcing_type', 'linear',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--simname', c.simname,
'--np', '4',
@@ -70,7 +70,7 @@ def basic_test():
'--wd', './'])
f0 = h5py.File(
os.path.join(
- os.path.join(TurTLE.lib_dir, 'test'),
+ TurTLE.data_dir,
'B32p1e4_checkpoint_0.h5'),
'r')
f1 = h5py.File(c.get_checkpoint_0_fname(), 'r')
@@ -118,7 +118,7 @@ def nasty_test():
'--src-simname', 'B32p1e4',
'--simname', c.simname,
'--forcing_type', 'linear',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--np', '4',
'--ntpp', '2',
diff --git a/TurTLE/test/test_particles.py b/TurTLE/test/test_particles.py
index 4568ea3c35050c47e947dc65b568c809dcff9073..f3afb7f7cbd659311845a6d0c32f00fa9653b022 100644
--- a/TurTLE/test/test_particles.py
+++ b/TurTLE/test/test_particles.py
@@ -27,7 +27,7 @@ def main():
['NSVEcomplex_particles',
'-n', '32',
'--src-simname', 'B32p1e4',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--np', '4',
'--ntpp', '1',
@@ -37,6 +37,7 @@ def main():
'--checkpoints_per_file', '{0}'.format(3),
'--nparticles', '{0}'.format(nparticles),
'--particle-rand-seed', '2',
+ '--cpp_random_particles', '0',
'--njobs', '{0}'.format(njobs),
'--wd', './'] +
sys.argv[3:])
diff --git a/TurTLE/test/test_turtle_NSE.py b/TurTLE/test/test_turtle_NSE.py
index 4c39a2cd676aeaa5e16548d6969bb5784abf9b27..6fe5633dfa35e2a5ed1acf4ebc5b4000bb8792d2 100644
--- a/TurTLE/test/test_turtle_NSE.py
+++ b/TurTLE/test/test_turtle_NSE.py
@@ -49,7 +49,7 @@ def main_basic():
['NSVE',
'-n', '32',
'--src-simname', 'B32p1e4',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--simname', 'nsve_for_comparison',
'--np', '4',
@@ -130,7 +130,7 @@ def main_long():
['NSVE',
'-n', '64',
'--src-simname', 'B32p1e4',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--simname', 'nsve_for_long_comparison',
'--np', '4',
diff --git a/TurTLE/test/test_turtle_NSVEparticles.py b/TurTLE/test/test_turtle_NSVEparticles.py
index 8c22f512de8bf8a1fdefd5c6a8221c32b2ca1259..8d5d614da4d5ebe529f61953bc87d0651221600a 100644
--- a/TurTLE/test/test_turtle_NSVEparticles.py
+++ b/TurTLE/test/test_turtle_NSVEparticles.py
@@ -57,7 +57,7 @@ def main():
['NSVEparticles',
'-n', '32',
'--src-simname', 'B32p1e4',
- '--src-wd', TurTLE.lib_dir + '/test',
+ '--src-wd', TurTLE.data_dir,
'--src-iteration', '0',
'--simname', 'dns_nsveparticles',
'--np', '4',
@@ -69,12 +69,13 @@ def main():
'--checkpoints_per_file', '{0}'.format(3),
'--nparticles', '{0}'.format(nparticles),
'--particle-rand-seed', '2',
+ '--cpp_random_particles', '0',
'--njobs', '{0}'.format(njobs),
'--wd', './'] +
sys.argv[1:])
f0 = h5py.File(
os.path.join(
- os.path.join(TurTLE.lib_dir, 'test'),
+ TurTLE.data_dir,
'B32p1e4_checkpoint_0.h5'),
'r')
f1 = h5py.File(c.get_checkpoint_0_fname(), 'r')
diff --git a/cpp/kspace.hpp b/cpp/kspace.hpp
index da1b4669c4e2b7e2282df9c025d934921df321d6..f082f11ed9f73e9dd5b5ba9f11ed0d17a060f777 100644
--- a/cpp/kspace.hpp
+++ b/cpp/kspace.hpp
@@ -48,8 +48,10 @@ enum kspace_dealias_type {ONE_HALF, TWO_THIRDS, SMOOTH};
* - has methods for filtering.
* - has CLOOP methods, useful for computing arbitrary formulas over the
* Fourier space grid (i.e. use lambda expressions).
+ *
+ * \tparam be field backend, currently only FFTW is possible.
+ * \tparam dt dealiasing mode, either ONE_HALF, TWO_THIRDS or SMOOTH.
*/
-
template <field_backend be,
kspace_dealias_type dt>
class kspace
@@ -85,6 +87,10 @@ class kspace
typename fftw_interface<rnumber>::complex *__restrict__ a,
const double kmax);
+ /**
+ * \tparam rnumber type of real number, float or double.
+ * \tparam fc field components, ONE, THREE or THREExTHREE.
+ */
template <typename rnumber,
field_components fc>
void Gauss_filter(
@@ -103,6 +109,11 @@ class kspace
typename fftw_interface<rnumber>::complex *__restrict__ a,
const double sigma);
+ /**
+ * \tparam rnumber type of real number, float or double.
+ * \tparam fc field components, ONE, THREE or THREExTHREE.
+ * \return exit mode (integer), EXIT_SUCCESS or arbitrary value for failure.
+ */
template <typename rnumber,
field_components fc>
int filter(
diff --git a/get_version_long.py b/get_version_long.py
new file mode 100644
index 0000000000000000000000000000000000000000..20accf0bf5a560fe621c64b56f20e210f54ec4e8
--- /dev/null
+++ b/get_version_long.py
@@ -0,0 +1,64 @@
+################################################################################
+# #
+# Copyright 2019 Max Planck Institute for Dynamics and Self-Organization #
+# #
+# This file is part of TurTLE. #
+# #
+# TurTLE is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published #
+# by the Free Software Foundation, either version 3 of the License, #
+# or (at your option) any later version. #
+# #
+# TurTLE is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details. #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with TurTLE. If not, see <http://www.gnu.org/licenses/> #
+# #
+# Contact: Cristian.Lalescu@ds.mpg.de #
+# #
+################################################################################
+
+
+
+import datetime
+import subprocess
+
+def main():
+ # get current time
+ now = datetime.datetime.now()
+ # obtain version
+ try:
+ git_branch = subprocess.check_output(['git',
+ 'rev-parse',
+ '--abbrev-ref',
+ 'HEAD']).strip().split()[-1].decode()
+ git_revision = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip()
+ git_date = datetime.datetime.fromtimestamp(int(subprocess.check_output(['git', 'log', '-1', '--format=%ct']).strip()))
+ except:
+ git_revision = ''
+ git_branch = ''
+ git_date = now
+ if git_branch == '':
+ # there's no git available or something
+ VERSION = '{0:0>4}{1:0>2}{2:0>2}.{3:0>2}{4:0>2}{5:0>2}'.format(
+ git_date.year, git_date.month, git_date.day,
+ git_date.hour, git_date.minute, git_date.second)
+ VERSION_py = VERSION
+ else:
+ VERSION = subprocess.check_output(['git', 'describe', '--tags']).strip().decode().split('-')[0]
+ if (('develop' in git_branch) or
+ ('feature' in git_branch) or
+ ('bugfix' in git_branch)):
+ VERSION_py = subprocess.check_output(
+ ['git', 'describe', '--tags', '--dirty']).strip().decode().replace('-g', '+g').replace('-dirty', '.dirty').replace('-', '.post')
+ else:
+ VERSION_py = VERSION
+ print(VERSION_py)
+ return VERSION_py
+
+if __name__ == '__main__':
+ main()
+
diff --git a/setup.py b/setup.py.in
similarity index 62%
rename from setup.py
rename to setup.py.in
index a4f43074563d4f1a29226347a72bec13ca53bb6a..369f51430a095ae3132e27842d42197b7cac7d48 100644
--- a/setup.py
+++ b/setup.py.in
@@ -26,65 +26,20 @@
AUTHOR = 'Cristian C Lalescu'
AUTHOR_EMAIL = 'Cristian.Lalescu@ds.mpg.de'
-import os
-import shutil
-import datetime
-import sys
-import subprocess
import pickle
### package versioning
-import get_version
-VERSION = get_version.main()
+VERSION = '@TURTLE_VERSION_LONG@'
print('This is TurTLE version ' + VERSION)
-
-import distutils.cmd
-
-class CompileLibCommand(distutils.cmd.Command):
- description = 'Compile TurTLE library.'
- user_options = [
- ('timing-output=', None, 'Toggle timing output.'),
- ('fftw-estimate=', None, 'Use FFTW ESTIMATE.'),
- ('split-fftw-many=', None, 'Turn on SPLIT_FFTW_MANY.'),
- ('disable-fftw-omp=', None, 'Turn Off FFTW OpenMP.'),
- ]
- def initialize_options(self):
- self.timing_output = 0
- self.fftw_estimate = 0
- self.disable_fftw_omp = 0
- self.split_fftw_many = 0
- return None
- def finalize_options(self):
- self.timing_output = (int(self.timing_output) == 1)
- self.split_fftw_many = (int(self.split_fftw_many) == 1)
- self.fftw_estimate = (int(self.fftw_estimate) == 1)
- self.disable_fftw_omp = (int(self.disable_fftw_omp) == 1)
- return None
- def run(self):
- ### save compiling information
- pickle.dump(
- {'install_date' : now,
- 'VERSION' : VERSION,
- 'git_revision' : git_revision},
- open('turtle/install_info.pickle', 'wb'),
- protocol = 2)
- return None
-
from setuptools import setup
setup(
name = 'TurTLE',
packages = ['TurTLE', 'TurTLE/test'],
install_requires = ['numpy>=1.8', 'h5py>=2.2.1'],
- package_data = {'TurTLE': ['test/B32p1e4_checkpoint_0.h5',
- 'test/particle_set/NSVEparticle_set.hpp',
- 'test/particle_set/NSVEparticle_set.cpp',
- 'test/profiler/scalar_evolution.hpp',
- 'test/profiler/scalar_evolution.cpp',
- 'test/profiler/Kraichnan_scalar_v1.hpp',
- 'test/profiler/Kraichnan_scalar_v1.cpp',
- ]},
+ # package data is installed by CMake
+ #package_data = {'TurTLE': []},
entry_points = {
'console_scripts': [
'turtle = TurTLE.__main__:main',