## This file is part of PASTA and is forked from SATe2.
## See "LICENSE.txt" for terms and conditions of usage.
#############################################################################
"""
File and path management.
"""
import os
import sys
import re
import tempfile
import shutil
from threading import Lock
from pasta import get_logger
_LOG = get_logger(__name__)
_ILLEGAL_FILENAME_PATTERN = re.compile(r'[^-_a-zA-Z0-9.]')
def get_safe_filename(filename):
return "".join(_ILLEGAL_FILENAME_PATTERN.split(filename))
def quoted_file_path(path):
if '"' not in path:
return '"'+ path + '"'
elif "'" not in path:
return "'" + path + "'"
else:
path = path.replace('"', r'\"')
return '"' + path + '"'
def open_with_intermediates(filepath, mode):
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Jiaye Yu, Mark Holder, and Jeet Sukumaran, University of Kansas
"""
SATe testing suite.
"""
import unittest
import re
import os
from pasta import get_logger
from pasta.configure import get_configuration
_LOG = get_logger("pasta.tests")
try:
import pkg_resources
TESTS_DIR = pkg_resources.resource_filename("pasta", "test")
#SCRIPTS_DIR = pkg_resources.resource_filename("pasta", os.path.join(os.pardir, "scripts"))
_LOG.info("using pkg_resources path mapping")
except:
LOCAL_DIR = os.path.dirname(__file__)
TESTS_DIR = os.path.join(LOCAL_DIR, os.path.pardir)
PACKAGE_DIR = os.path.join(TESTS_DIR, os.path.pardir)
#SCRIPTS_DIR = os.path.join(PACKAGE_DIR, os.path.pardir, "scripts")
_LOG.info("using local filesystem path mapping")
TESTS_DATA_DIR = os.path.join(TESTS_DIR, "data")
TESTS_OUTPUT_DIR = os.path.join(TESTS_DIR, "output")
# uym2 added
# June 2017
# utils for tree decomposition
from dendropy import Tree, Node
try:
from queue import Queue # python 3
except:
from Queue import Queue # python 2
from sys import argv
from pasta import get_logger
_LOG = get_logger(__name__)
def min_cluster_size_bisect(a_tree,max_size):
for node in a_tree.postorder_node_iter():
if node.is_leaf():
node.nleaf = 1
else:
node.nleaf = 0
max_child = None
max_nleaf = 0
for ch in node.child_node_iter():
node.nleaf += ch.nleaf
if ch.nleaf > max_nleaf:
max_nleaf = ch.nleaf
max_child = ch
if node.nleaf > max_size:
node.remove_child(max_child)
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Jiaye Yu, Mark Holder, and Jeet Sukumaran, University of Kansas
"""
SATe testing suite.
"""
import unittest
import re
import os
from pasta import get_logger
from pasta.configure import get_configuration
_LOG = get_logger("pasta.tests")
try:
import pkg_resources
TESTS_DIR = pkg_resources.resource_filename("pasta", "test")
#SCRIPTS_DIR = pkg_resources.resource_filename("pasta", os.path.join(os.pardir, "scripts"))
_LOG.info("using pkg_resources path mapping")
except:
LOCAL_DIR = os.path.dirname(__file__)
TESTS_DIR = os.path.join(LOCAL_DIR, os.path.pardir)
PACKAGE_DIR = os.path.join(TESTS_DIR, os.path.pardir)
#SCRIPTS_DIR = os.path.join(PACKAGE_DIR, os.path.pardir, "scripts")
_LOG.info("using local filesystem path mapping")
TESTS_DATA_DIR = os.path.join(TESTS_DIR, "data")
TESTS_OUTPUT_DIR = os.path.join(TESTS_DIR, "output")
