## 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()