Revision b4185c9e4f6ceffca244814de088dbc87d159378 authored by Alex Nitz on 16 March 2017, 20:35:38 UTC, committed by GitHub on 16 March 2017, 20:35:38 UTC
* add mpi support for emcee and kombine rearrange so multiple processes don't try to write the same file in pycbc inference coday cleanup add helper functions to make pools pool fixes fixes * Update pycbc_inference * Update pycbc_inference * Update sampler_emcee.py
1 parent 9aff59f
setup.py
#!/usr/bin/python
# Copyright (C) 2012 Alex Nitz, Andrew Miller, Josh Willis
#
# This program 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 2 of the License, or (at your
# option) any later version.
#
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
setup.py file for PyCBC package
"""
import os, fnmatch, sys, subprocess, shutil
from trace import fullmodname
try:
from setuptools.command.install import install as _install
from setuptools.command.install_egg_info import install_egg_info as egg_info
USE_SETUPTOOLS = True
except:
from distutils.command.install import install as _install
USE_SETUPTOOLS = False
from distutils.errors import DistutilsError
from distutils.core import setup, Command, Extension
from distutils.command.clean import clean as _clean
from distutils.file_util import write_file
from distutils.version import LooseVersion
try:
import numpy.version
if LooseVersion(numpy.version.version) < LooseVersion("1.6.4"):
print (" Numpy >= 1.6.4 is required for pycbc dependencies. \n"
" We found version %s already installed. Please update \n"
" to a more recent version and then retry PyCBC \n"
" installation. \n"
" \n"
" Using pip: [pip install 'numpy>=1.6.4' --upgrade --user] \n"
"" % numpy.version.version)
exit(1)
except ImportError:
pass
requires = ['lal.lal', 'lalsimulation.lalsimulation', 'glue']
setup_requires = []
install_requires = setup_requires + ['Mako>=1.0.1',
'argparse>=1.3.0',
'decorator>=3.4.2',
'scipy>=0.13.0',
'unittest2',
'matplotlib>=1.3.1',
'numpy>=1.6.4',
'pillow',
'h5py>=2.5',
'jinja2',
'mpld3>=0.3',
'pyRXP>=2.1.0',
'pycbc-glue>=1.0.1',
'kombine',
'emcee>=2.2.0',
'corner>=2.0.1',
]
#FIXME Remove me when we bump to h5py > 2.5
try:
import h5py
except ImportError:
setup_requires.append('cython')
else:
import h5py.version
if h5py.version.version < '2.5':
setup_requires.append('cython')
def find_package_data(dirname):
def find_paths(dirname):
items = []
for fname in os.listdir(dirname):
path = os.path.join(dirname, fname)
if os.path.isdir(path):
items += find_paths(path)
elif not path.endswith(".py") and not path.endswith(".pyc"):
items.append(path)
return items
items = find_paths(dirname)
return [os.path.relpath(path, dirname) for path in items]
# Add swig-generated files to the list of things to clean, so they
# get regenerated each time.
class clean(_clean):
def finalize_options (self):
_clean.finalize_options(self)
self.clean_files = []
self.clean_folders = ['docs/_build']
def run(self):
_clean.run(self)
for f in self.clean_files:
try:
os.unlink(f)
print 'removed {0}'.format(f)
except:
pass
for fol in self.clean_folders:
shutil.rmtree(fol, ignore_errors=True)
print 'removed {0}'.format(fol)
class install(_install):
def run(self):
etcdirectory = os.path.join(self.install_data, 'etc')
if not os.path.exists(etcdirectory):
os.makedirs(etcdirectory)
filename = os.path.join(etcdirectory, 'pycbc-user-env.sh')
self.execute(write_file,
(filename, [self.extra_dirs]),
"creating %s" % filename)
env_file = open(filename, 'w')
print >> env_file, "# Source this file to access PyCBC"
print >> env_file, "PATH=" + self.install_scripts + ":$PATH"
print >> env_file, "PYTHONPATH=" + self.install_libbase + ":$PYTHONPATH"
print >> env_file, "export PYTHONPATH"
print >> env_file, "export PATH"
env_file.close()
_install.run(self)
def do_setup(*args):
return True
_install._called_from_setup=do_setup
test_results = []
# Run all of the testing scripts
class TestBase(Command):
user_options = []
test_modules = []
def initialize_options(self):
self.scheme = None
self.build_dir = None
def finalize_options(self):
#Populate the needed variables
self.set_undefined_options('build',('build_lib', 'build_dir'))
def find_test_modules(self,pattern):
# Find all the unittests that match a given string pattern
modules= []
for path, dirs, files in os.walk("test"):
for filename in fnmatch.filter(files, pattern):
#add the test directories to the path
sys.path.append(os.path.join(path))
#save the module name for importing
modules.append(fullmodname(filename))
return modules
def run(self):
self.run_command('build')
# Get the list of cpu test modules
self.test_modules = self.find_test_modules("test*.py")
# Run from the build directory
if 'PYTHONPATH' in os.environ:
os.environ['PYTHONPATH'] = self.build_dir + ":" + os.environ['PYTHONPATH']
else:
os.environ['PYTHONPATH'] = self.build_dir
test_results.append("\n" + (self.scheme + " tests ").rjust(30))
for test in self.test_modules:
test_command = 'python ' + 'test/' + test + '.py -s ' + self.scheme
a = subprocess.call(test_command,env=os.environ,shell=True)
if a != 0:
result_str = str(test).ljust(30) + ": Fail : " + str(a)
else:
result_str = str(test).ljust(30) + ": Pass"
test_results.append(result_str)
for test in test_results:
print test
class test(Command):
def has_cuda(self):
import pycbc
return pycbc.HAVE_CUDA
sub_commands = [('test_cpu',None),('test_cuda',has_cuda)]
user_options = []
description = "run the available tests for all compute schemes (cpu, cuda)"
def initialize_options(self):
pass
def finalize_options(self):
pass
def run(self):
for cmd_name in self.get_sub_commands():
self.run_command(cmd_name)
class test_cpu(TestBase):
description = "run all CPU tests"
def initialize_options(self):
TestBase.initialize_options(self)
self.scheme = 'cpu'
class test_cuda(TestBase):
description = "run CUDA tests"
def initialize_options(self):
TestBase.initialize_options(self)
self.scheme = 'cuda'
# write versioning info
def get_version_info():
"""Get VCS info and write version info to version.py
"""
from pycbc import _version_helper
# If this is a pycbc git repo always populate versoin information using GIT
try:
vcs_info = _version_helper.generate_git_version_info()
with open('pycbc/version.py', 'w') as f:
f.write("# coding: utf-8\n")
f.write("# Generated by setup.py for PyCBC on %s.\n\n"
% vcs_info.build_date)
# print general info
f.write('version = \'%s\'\n' % vcs_info.version)
f.write('date = \'%s\'\n' % vcs_info.date)
f.write('release = %s\n' % vcs_info.release)
f.write('last_release = \'%s\'\n' % vcs_info.last_release)
# print git info
f.write('\ngit_hash = \'%s\'\n' % vcs_info.hash)
f.write('git_branch = \'%s\'\n' % vcs_info.branch)
f.write('git_tag = \'%s\'\n' % vcs_info.tag)
f.write('git_author = \'%s\'\n' % vcs_info.author)
f.write('git_committer = \'%s\'\n' % vcs_info.committer)
f.write('git_status = \'%s\'\n' % vcs_info.status)
f.write('git_builder = \'%s\'\n' % vcs_info.builder)
f.write('git_build_date = \'%s\'\n' % vcs_info.build_date)
f.write('git_verbose_msg = """Branch: %s\n'
'Tag: %s\n'
'Id: %s\n'
'Builder: %s\n'
'Build date: %s\n'
'Repository status is %s"""\n' %(vcs_info.branch,
vcs_info.tag,
vcs_info.hash,
vcs_info.builder,
vcs_info.build_date,
vcs_info.status))
f.write('from pycbc._version import *\n')
version = vcs_info.version
# If this is a release or another kind of source distribution of PyCBC
except:
version = '1.7.0dev'
release = 'False'
date = hash = branch = tag = author = committer = status = builder = build_date = ''
with open('pycbc/version.py', 'w') as f:
f.write("# Generated by setup.py for PyCBC.\n\n")
# print general infov
f.write('version = \'%s\'\n' % version)
f.write('date = \'%s\'\n' % date)
f.write('release = %s\n' % release)
# print git info
f.write('\ngit_hash = \'%s\'\n' % hash)
f.write('git_branch = \'%s\'\n' % branch)
f.write('git_tag = \'%s\'\n' % tag)
f.write('git_author = \'%s\'\n' % author)
f.write('git_committer = \'%s\'\n' % committer)
f.write('git_status = \'%s\'\n' % status)
f.write('git_builder = \'%s\'\n' % builder)
f.write('git_build_date = \'%s\'\n' % build_date)
f.write('git_verbose_msg = """Version: %s Release: %s \n'
' """\n' % (version, release))
f.write('from pycbc._version import *\n')
from pycbc import version
version = version.version
return version
class build_docs(Command):
user_options = []
description = "Build the documentation pages"
def initialize_options(self):
pass
def finalize_options(self):
pass
def run(self):
subprocess.check_call("cd docs; cp Makefile.std Makefile; cp conf_std.py conf.py; sphinx-apidoc "
" -o ./ -f -A 'PyCBC dev team' -V '0.1' ../pycbc && make html",
stderr=subprocess.STDOUT, shell=True)
class build_gh_pages(Command):
user_options = []
description = "Build the documentation pages for GitHub"
def initialize_options(self):
pass
def finalize_options(self):
pass
def run(self):
subprocess.check_call("mkdir -p _gh-pages/latest && touch _gh-pages/.nojekyll && "
"cd docs; cp Makefile.gh_pages Makefile; cp conf_std.py conf.py; sphinx-apidoc "
" -o ./ -f -A 'PyCBC dev team' -V '0.1' ../pycbc && make html",
stderr=subprocess.STDOUT, shell=True)
cmdclass = { 'test' : test,
'build_docs' : build_docs,
'build_gh_pages' : build_gh_pages,
'install' : install,
'test_cpu':test_cpu,
'test_cuda':test_cuda,
'clean' : clean,
}
extras_require = {'cuda': ['pycuda>=2015.1', 'scikit-cuda']}
# do the actual work of building the package
VERSION = get_version_info()
setup (
name = 'PyCBC',
version = VERSION,
description = 'Gravitational wave CBC analysis toolkit',
author = 'Ligo Virgo Collaboration - PyCBC team',
author_email = 'alex.nitz@ligo.org',
url = 'https://github.com/ligo-cbc/pycbc',
download_url = 'https://github.com/ligo-cbc/pycbc/tarball/v%s' % VERSION,
keywords = ['ligo', 'physics', 'gravity', 'signal processing'],
cmdclass = cmdclass,
setup_requires = setup_requires,
extras_require = extras_require,
install_requires = install_requires,
scripts = [
'bin/minifollowups/pycbc_injection_minifollowup',
'bin/minifollowups/pycbc_foreground_minifollowup',
'bin/minifollowups/pycbc_sngl_minifollowup',
'bin/minifollowups/pycbc_single_template_plot',
'bin/minifollowups/pycbc_plot_chigram',
'bin/minifollowups/pycbc_page_coincinfo',
'bin/minifollowups/pycbc_page_injinfo',
'bin/minifollowups/pycbc_page_snglinfo',
'bin/minifollowups/pycbc_plot_trigger_timeseries',
'bin/pycbc_banksim',
'bin/pycbc_banksim_combine_banks',
'bin/pycbc_banksim_match_combine',
'bin/pycbc_faithsim',
'bin/pycbc_inspiral',
'bin/pycbc_inspiral_skymax',
'bin/pycbc_live',
'bin/pycbc_live_nagios_monitor',
'bin/pycbc_single_template',
'bin/pycbc_multi_inspiral',
'bin/pycbc_make_banksim',
'bin/pycbc_splitbank',
'bin/pycbc_hdf5_splitbank',
'bin/pycbc_split_inspinj',
'bin/pycbc_geom_aligned_2dstack',
'bin/pycbc_geom_aligned_bank',
'bin/pycbc_geom_nonspinbank',
'bin/pycbc_aligned_bank_cat',
'bin/pycbc_aligned_stoch_bank',
'bin/pycbc_make_faithsim',
'bin/pycbc_get_ffinal',
'bin/pycbc_tmpltbank_to_chi_params',
'bin/pycbc_bank_verification',
'bin/pycbc_run_sqlite',
'bin/pycbc_inj_cut',
'bin/pycbc_upload_xml_to_gracedb',
'bin/pycbc_dark_vs_bright_injections',
'bin/pycbc_make_html_page',
'bin/pycbc_optimal_snr',
'bin/pycbc_fit_sngl_trigs',
'bin/pycbc_randomize_inj_dist_by_optsnr',
'bin/hdfcoinc/pycbc_calculate_psd',
'bin/hdfcoinc/pycbc_average_psd',
'bin/hdfcoinc/pycbc_coinc_mergetrigs',
'bin/hdfcoinc/pycbc_coinc_findtrigs',
'bin/hdfcoinc/pycbc_coinc_bank2hdf',
'bin/hdfcoinc/pycbc_coinc_statmap',
'bin/hdfcoinc/pycbc_coinc_statmap_inj',
'bin/hdfcoinc/pycbc_page_foreground',
'bin/hdfcoinc/pycbc_page_foundmissed',
'bin/hdfcoinc/pycbc_page_ifar',
'bin/hdfcoinc/pycbc_page_snrifar',
'bin/hdfcoinc/pycbc_page_snrratehist',
'bin/hdfcoinc/pycbc_page_sensitivity',
'bin/hdfcoinc/pycbc_page_banktriggerrate',
'bin/hdfcoinc/pycbc_coinc_hdfinjfind',
'bin/hdfcoinc/pycbc_page_snrchi',
'bin/hdfcoinc/pycbc_page_segments',
'bin/hdfcoinc/pycbc_page_segtable',
'bin/hdfcoinc/pycbc_page_segplot',
'bin/hdfcoinc/pycbc_page_vetotable',
'bin/hdfcoinc/pycbc_plot_psd_file',
'bin/hdfcoinc/pycbc_plot_psd_timefreq',
'bin/hdfcoinc/pycbc_plot_range',
'bin/hdfcoinc/pycbc_foreground_censor',
'bin/hdfcoinc/pycbc_plot_hist',
'bin/hdfcoinc/pycbc_page_recovery',
'bin/hdfcoinc/pycbc_page_injtable',
'bin/hdfcoinc/pycbc_strip_injections',
'bin/hdfcoinc/pycbc_page_coinc_snrchi',
'bin/hdfcoinc/pycbc_distribute_background_bins',
'bin/hdfcoinc/pycbc_combine_statmap',
'bin/hdfcoinc/pycbc_stat_dtphase',
'bin/hdfcoinc/pycbc_plot_singles_vs_params',
'bin/hdfcoinc/pycbc_plot_singles_timefreq',
'bin/hdfcoinc/pycbc_plot_throughput',
'bin/hdfcoinc/pycbc_plot_background_coincs',
'bin/hdfcoinc/pycbc_plot_bank_bins',
'bin/hdfcoinc/pycbc_merge_psds',
'bin/hdfcoinc/pycbc_plot_gating',
'bin/hdfcoinc/pycbc_fit_sngls_by_template',
'bin/hdfcoinc/pycbc_fit_sngls_over_param',
'bin/hdfcoinc/pycbc_fit_sngls_binned',
'bin/hwinj/pycbc_generate_hwinj',
'bin/hwinj/pycbc_generate_hwinj_from_xml',
'bin/hwinj/pycbc_plot_hwinj',
'bin/hwinj/pycbc_insert_frame_hwinj',
'bin/pycbc_submit_dax',
'bin/mvsc/pycbc_mvsc_get_features',
'bin/pycbc_coinc_time',
'bin/pygrb/pycbc_make_offline_grb_workflow',
'bin/pygrb/pycbc_make_grb_summary_page',
'bin/pycbc_condition_strain',
'bin/inference/pycbc_make_inference_workflow',
'bin/inference/pycbc_inference',
'bin/inference/pycbc_inference_plot_acceptance_rate',
'bin/inference/pycbc_inference_plot_acf',
'bin/inference/pycbc_inference_plot_acl',
'bin/inference/pycbc_inference_plot_corner',
'bin/inference/pycbc_inference_plot_geweke',
'bin/inference/pycbc_inference_plot_movie',
'bin/inference/pycbc_inference_plot_posterior',
'bin/inference/pycbc_inference_plot_prior',
'bin/inference/pycbc_inference_plot_samples',
'bin/inference/pycbc_inference_table_summary',
'bin/plotting/pycbc_plot_waveform',
'bin/plotting/pycbc_banksim_plot_eff_fitting_factor',
'bin/plotting/pycbc_banksim_table_point_injs',
'bin/plotting/pycbc_banksim_plot_fitting_factors',
'bin/workflows/pycbc_create_sbank_workflow',
'bin/workflows/pycbc_create_uberbank_workflow',
'bin/workflows/pycbc_make_coinc_search_workflow',
'bin/workflows/pycbc_make_psd_estimation_workflow',
'bin/workflows/pycbc_create_bank_verifier_workflow',
'bin/pycbc_compress_bank',
'bin/pycbc_ringinj',
'tools/einsteinathome/pycbc_build_eah.sh'
],
packages = [
'pycbc',
'pycbc.fft',
'pycbc.types',
'pycbc.filter',
'pycbc.psd',
'pycbc.waveform',
'pycbc.events',
'pycbc.noise',
'pycbc.vetoes',
'pycbc.tmpltbank',
'pycbc.workflow',
'pycbc.results',
'pycbc.io',
'pycbc.inference',
'pycbc.inject',
],
package_data = {'pycbc.workflow': find_package_data('pycbc/workflow'),
'pycbc.results': find_package_data('pycbc/results'),
'pycbc.tmpltbank': find_package_data('pycbc/tmpltbank')},
)
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