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setup.py
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setup.py
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from setuptools import setup, find_packages
from setuptools.command.install import install
import sysconfig
import os
import laml_libs
from os import walk, listdir
from os.path import join, normpath, isfile
def recursive_list_dir(path):
listing=[]
for x in walk(path):
if isfile(x[0]):
listing.append(x[0].split(path+'/')[1])
for y in listdir(x[0]):
z = normpath(join(x[0],y))
if isfile(z):
listing.append(z.split(path+'/')[1])
return listing
# Note from GC
# 1. If installing from python setup.py install, please `pip install cvxpy` first.
# 2. SCS requires numpy < 1.2 to be installed: https://github.com/bodono/scs-python/issues/32#issuecomment-802977693
# 3. cvxpy fails to install on python 3.12, requires SCS, ECOS and OSQP: https://github.com/cvxpy/cvxpy/issues/1367
# 4. qdldl (dependency of osqp has no wheel for python 3.12): https://github.com/cvxpy/cvxpy/issues/2269
# 5. osqp < 0.6.2 does not depend on qdldl to install cvxpy
param = {
'name': laml_libs.PROGRAM_NAME,
'version': laml_libs.PROGRAM_VERSION,
'description': laml_libs.PROGRAM_DESCRIPTION,
'author': laml_libs.PROGRAM_AUTHOR,
'license': laml_libs.PROGRAM_LICENSE,
'packages': find_packages(),
'package_data': {'':recursive_list_dir('laml_unit_tests')},
'include_package_data': True,
'scripts': ['run_laml.py', 'laml_tests.py', 'extra_laml_tests.py'],
'zip_safe': True,
'install_requires': ['scipy>=1.3.1', 'cvxpy>=1.4', 'treeswift>=1.1.39', 'Mosek>=10.1.16',
'Biopython>=1.71','matplotlib>=2.2.2','setuptools'],
'keywords': 'Phylogenetics Evolution Computational Maximum-likelihood Lineage Tracing',
'long_description': """LAML is a maximum likelihood algorithm under the Probabilistic Mixed-type Missing (PMM) model. Given a lineage tracing experiment character matrix with heterogeneous per-site alphabets and mutation probabilities, LAML will find a maximum likelihood tree topology and estimate branch lengths as well as stochastic dropout and heritable silencing missing data rates.""",
'classifiers': [
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License (GPL)",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],
'entry_points': {
'console_scripts': [
'run_laml= run_laml:main',
],
},
}
setup(**param)