## 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, see <http:##www.gnu.org#licenses#>.
##
###############################################################################
import unittest
import subprocess
from ginkgo_tests import get_logger
from ginkgo_tests import get_ginkgo_program_path
from ginkgo_tests import run_program
_LOG = get_logger("test_cmdopts")
class CmdOptsTest(unittest.TestCase):
def setUp(self):
self.prog_path = get_ginkgo_program_path("test_cmdopt")
def check_opts_parsing(self, cmd, expected_strings):
_LOG.info('Testing arguments parsing: "%s"' % cmd)
stdout, stderr, returncode = run_program(cmd)
assert returncode == 0, "Program exited with error code %d:\n%s" % (p1.returncode, stderr)
stdout = stdout.split("\n")
for idx, expected in enumerate(expected_strings):
_LOG.info('Line %d: %s (correct = "%s")' % (idx+1, stdout[idx], expected))
assert stdout[idx] == expected, \
'Expecting "%s", but found "%s" in line %d of stdout' \
% (expected, stdout[idx], idx+1)
## (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, see <http:##www.gnu.org#licenses#>.
##
###############################################################################
import unittest
from ginkgo_tests import get_logger
from ginkgo_tests import get_ginkgo_program_path
from ginkgo_tests import run_program
from ginkgo_tests import run_external_tests
_LOG = get_logger("test_asciigrid")
class TextUtilsTest(unittest.TestCase):
def setUp(self):
self.prog_path = get_ginkgo_program_path("test_asciigrid")
def testTextUtils(self):
run_external_tests(self.prog_path, _LOG, "ASCII Grid parsing tests")
if __name__ == "__main__":
unittest.main()
##
###############################################################################
import unittest
import subprocess
from ginkgo_tests import get_logger
from ginkgo_tests import get_ginkgo_program_path
from ginkgo_tests import run_program
from ginkgo_tests import run_external_tests
import sys
from dendropy import datasets
from dendropy import splits
from dendropy import treedists
_LOG = get_logger("test_tree")
def to_parent_array(tree, include_labels=False, include_edge_lens=False):
pa = []
edge_lens = []
node_pa = {}
for node in tree.preorder_node_iter():
node_pa[node] = len(pa)
if node.parent_node is not None:
if node.taxon is not None:
pa.append("%s:'%s'" % (node_pa[node.parent_node], node.taxon.label))
else:
pa.append(str(node_pa[node.parent_node]))
else:
pa.append(str(-1))
if include_edge_lens:
## (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, see <http:##www.gnu.org#licenses#>.
##
###############################################################################
import unittest
from ginkgo_tests import get_logger
from ginkgo_tests import get_ginkgo_program_path
from ginkgo_tests import run_program
from ginkgo_tests import run_external_tests
_LOG = get_logger("test_filesys")
class TextUtilsTest(unittest.TestCase):
def setUp(self):
self.prog_path = get_ginkgo_program_path("test_filesys")
def testTextUtils(self):
run_external_tests(self.prog_path, _LOG, "filesys tests")
if __name__ == "__main__":
unittest.main()
## (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, see <http:##www.gnu.org#licenses#>.
##
###############################################################################
import unittest
from ginkgo_tests import get_logger
from ginkgo_tests import get_ginkgo_program_path
from ginkgo_tests import run_program
from ginkgo_tests import run_external_tests
_LOG = get_logger("test_textutils")
class TextUtilsTest(unittest.TestCase):
def setUp(self):
self.prog_path = get_ginkgo_program_path("test_textutil")
def testTextUtils(self):
run_external_tests(self.prog_path, _LOG, "textutils tests")
if __name__ == "__main__":
unittest.main()