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commit 16e3163de36731760086dc0d10465ef08dbbb00e Author: Andreas Tille <[email protected]> Date: Wed Jul 29 12:55:27 2015 +0200 Adapt patches to new upstream version --- debian/changelog | 2 +- ...where-encoding-for-default-locale-is-None.patch | 11 +- ...PAUP-based-tests-unless-path-to-PAUP-is-p.patch | 252 +-------------------- 3 files changed, 7 insertions(+), 258 deletions(-) diff --git a/debian/changelog b/debian/changelog index bb23207..77909f6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -python-dendropy (4.0.2-1) unstable; urgency=low +python-dendropy (4.0.3-1) UNRELEASED; urgency=low * Initial release (Closes: #790408) diff --git a/debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch b/debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch index 309b3ec..ab4ee2c 100644 --- a/debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch +++ b/debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch @@ -7,13 +7,11 @@ Subject: [PATCH] Fix bug where encoding for default locale is None. dendropy/utility/textprocessing.py | 3 +++ 1 file changed, 3 insertions(+) -diff --git a/dendropy/utility/textprocessing.py b/dendropy/utility/textprocessing.py -index 1227e52..872a4e2 100644 --- a/dendropy/utility/textprocessing.py +++ b/dendropy/utility/textprocessing.py -@@ -32,6 +32,9 @@ import codecs - - ENCODING = locale.getdefaultlocale()[1] +@@ -35,6 +35,9 @@ ENCODING = locale.getdefaultlocale()[1] + if ENCODING == None: + ENCODING = 'UTF-8' +if ENCODING == None: + ENCODING = 'UTF-8' @@ -21,6 +19,3 @@ index 1227e52..872a4e2 100644 def bytes_to_text(s): """ Converts a byte string (as read from, e.g., standard input) --- -2.1.4 - diff --git a/debian/patches/0002-Do-not-run-PAUP-based-tests-unless-path-to-PAUP-is-p.patch b/debian/patches/0002-Do-not-run-PAUP-based-tests-unless-path-to-PAUP-is-p.patch index ab1f878..be86680 100644 --- a/debian/patches/0002-Do-not-run-PAUP-based-tests-unless-path-to-PAUP-is-p.patch +++ b/debian/patches/0002-Do-not-run-PAUP-based-tests-unless-path-to-PAUP-is-p.patch @@ -11,9 +11,9 @@ Subject: [PATCH] Do not run PAUP-based tests unless path to PAUP is provided --- a/README.rst +++ b/README.rst -@@ -52,6 +52,21 @@ and more. - Testing - ======= +@@ -67,6 +67,21 @@ Testing + If this variable is not set or set to "NONE", then any tests that rely on + PAUP* will NOT be run. +.. note:: + @@ -33,249 +33,3 @@ Subject: [PATCH] Do not run PAUP-based tests unless path to PAUP is provided Tests can be run by typing:: $ python -m dendropy.test ---- a/dendropy/interop/paup.py -+++ b/dendropy/interop/paup.py -@@ -43,7 +43,7 @@ _LOG = messaging.get_logger(__name__) - - import dendropy - --PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "paup") -+PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "NONE") - if PAUP_PATH == "NONE": - DENDROPY_PAUP_INTEROPERABILITY = False - else: ---- a/dendropy/test/test_datamodel_split_bitmasks.py -+++ b/dendropy/test/test_datamodel_split_bitmasks.py -@@ -141,111 +141,115 @@ class SplitDistributionTestCases(Extende - use_tree_weights=use_weights, - expected_num_trees=num_trees) - --class SplitCountTest(ExtendedTestCase): -- -- @classmethod -- def setUpClass(cls): -- if sys.version_info.major < 3: -- cls.assertRaisesRegex = cls.assertRaisesRegexp -- -- def check_split_counting(self, -- tree_filename, -- test_as_rooted, -- parser_rooting_interpretation, -- test_ignore_tree_weights=False, -- dp_ignore_tree_weights=False, -- ): -- tree_filepath = pathmap.tree_source_path(tree_filename) -- ps = paup.PaupService() -- paup_sd = ps.get_split_distribution_from_files( -- tree_filepaths=[tree_filepath], -- is_rooted=test_as_rooted, -- use_tree_weights=not test_ignore_tree_weights, -- burnin=0, -- taxa_definition_filepath=tree_filepath -+if not paup.DENDROPY_PAUP_INTEROPERABILITY: -+ _LOG.warn("PAUP interoperability not available: skipping split counting tests") -+else: -+ -+ class SplitCountTest(ExtendedTestCase): -+ -+ @classmethod -+ def setUpClass(cls): -+ if sys.version_info.major < 3: -+ cls.assertRaisesRegex = cls.assertRaisesRegexp -+ -+ def check_split_counting(self, -+ tree_filename, -+ test_as_rooted, -+ parser_rooting_interpretation, -+ test_ignore_tree_weights=False, -+ dp_ignore_tree_weights=False, -+ ): -+ tree_filepath = pathmap.tree_source_path(tree_filename) -+ ps = paup.PaupService() -+ paup_sd = ps.get_split_distribution_from_files( -+ tree_filepaths=[tree_filepath], -+ is_rooted=test_as_rooted, -+ use_tree_weights=not test_ignore_tree_weights, -+ burnin=0, -+ taxa_definition_filepath=tree_filepath -+ ) -+ taxon_namespace = paup_sd.taxon_namespace -+ dp_sd = dendropy.SplitDistribution(taxon_namespace=taxon_namespace) -+ dp_sd.ignore_edge_lengths = True -+ dp_sd.ignore_node_ages = True -+ dp_sd.ignore_tree_weights = dp_ignore_tree_weights -+ taxa_mask = taxon_namespace.all_taxa_bitmask() -+ taxon_namespace.is_mutable = False -+ trees = dendropy.TreeList.get_from_path(tree_filepath, -+ "nexus", -+ rooting=parser_rooting_interpretation, -+ taxon_namespace=taxon_namespace) -+ for tree in trees: -+ self.assertIs(tree.taxon_namespace, taxon_namespace) -+ self.assertIs(tree.taxon_namespace, dp_sd.taxon_namespace) -+ dp_sd.count_splits_on_tree( -+ tree, -+ is_bipartitions_updated=False) -+ self.assertEqual(dp_sd.total_trees_counted, paup_sd.total_trees_counted) -+ taxa_mask = taxon_namespace.all_taxa_bitmask() -+ for split in dp_sd.split_counts: -+ if not dendropy.Bipartition.is_trivial_bitmask(split, taxa_mask): -+ # if split not in paup_sd.split_counts: -+ # print("{}: {}".format(split, split in paup_sd.split_counts)) -+ # s2 = taxon_namespace.normalize_bitmask(split) -+ # print("{}: {}".format(s2, s2 in paup_sd.split_counts)) -+ # s3 = ~split & taxon_namespace.all_taxa_bitmask() -+ # print("{}: {}".format(s3, s3 in paup_sd.split_counts)) -+ self.assertIn(split, paup_sd.split_counts, "split not found") -+ self.assertEqual(dp_sd.split_counts[split], paup_sd.split_counts[split], "incorrect split frequency") -+ del paup_sd.split_counts[split] -+ remaining_splits = list(paup_sd.split_counts.keys()) -+ for split in remaining_splits: -+ if dendropy.Bipartition.is_trivial_bitmask(split, taxa_mask): -+ del paup_sd.split_counts[split] -+ self.assertEqual(len(paup_sd.split_counts), 0) -+ -+ def test_basic_split_count_with_incorrect_rootings_raises_error(self): -+ assertion_error_regexp1 = re.compile("(incorrect split frequency|split not found)") -+ test_cases = ( -+ ('pythonidae.reference-trees.nexus', True, "force-unrooted", assertion_error_regexp1), -+ ('feb032009.trees.nexus', False, "force-rooted", assertion_error_regexp1), - ) -- taxon_namespace = paup_sd.taxon_namespace -- dp_sd = dendropy.SplitDistribution(taxon_namespace=taxon_namespace) -- dp_sd.ignore_edge_lengths = True -- dp_sd.ignore_node_ages = True -- dp_sd.ignore_tree_weights = dp_ignore_tree_weights -- taxa_mask = taxon_namespace.all_taxa_bitmask() -- taxon_namespace.is_mutable = False -- trees = dendropy.TreeList.get_from_path(tree_filepath, -- "nexus", -- rooting=parser_rooting_interpretation, -- taxon_namespace=taxon_namespace) -- for tree in trees: -- self.assertIs(tree.taxon_namespace, taxon_namespace) -- self.assertIs(tree.taxon_namespace, dp_sd.taxon_namespace) -- dp_sd.count_splits_on_tree( -- tree, -- is_bipartitions_updated=False) -- self.assertEqual(dp_sd.total_trees_counted, paup_sd.total_trees_counted) -- taxa_mask = taxon_namespace.all_taxa_bitmask() -- for split in dp_sd.split_counts: -- if not dendropy.Bipartition.is_trivial_bitmask(split, taxa_mask): -- # if split not in paup_sd.split_counts: -- # print("{}: {}".format(split, split in paup_sd.split_counts)) -- # s2 = taxon_namespace.normalize_bitmask(split) -- # print("{}: {}".format(s2, s2 in paup_sd.split_counts)) -- # s3 = ~split & taxon_namespace.all_taxa_bitmask() -- # print("{}: {}".format(s3, s3 in paup_sd.split_counts)) -- self.assertIn(split, paup_sd.split_counts, "split not found") -- self.assertEqual(dp_sd.split_counts[split], paup_sd.split_counts[split], "incorrect split frequency") -- del paup_sd.split_counts[split] -- remaining_splits = list(paup_sd.split_counts.keys()) -- for split in remaining_splits: -- if dendropy.Bipartition.is_trivial_bitmask(split, taxa_mask): -- del paup_sd.split_counts[split] -- self.assertEqual(len(paup_sd.split_counts), 0) -- -- def test_basic_split_count_with_incorrect_rootings_raises_error(self): -- assertion_error_regexp1 = re.compile("(incorrect split frequency|split not found)") -- test_cases = ( -- ('pythonidae.reference-trees.nexus', True, "force-unrooted", assertion_error_regexp1), -- ('feb032009.trees.nexus', False, "force-rooted", assertion_error_regexp1), -- ) -- for test_case, test_as_rooted, parser_rooting_interpretation, assertion_error_regexp in test_cases: -- with self.assertRaisesRegex(AssertionError, assertion_error_regexp): -- self.check_split_counting( -- test_case, -- test_as_rooted=test_as_rooted, -- parser_rooting_interpretation=parser_rooting_interpretation) -- -- def test_basic_split_count_with_incorrect_weight_treatment_raises_error(self): -- assertion_error_regexp1 = re.compile("incorrect split frequency") -- test_cases = ( -- ("cetaceans.mb.no-clock.mcmc.weighted-01.trees", False), -- ("cetaceans.mb.strict-clock.mcmc.weighted-01.trees", True), -- ) -- for test_case, test_as_rooted in test_cases: -- with self.assertRaisesRegex(AssertionError, assertion_error_regexp1): -- self.check_split_counting( -- test_case, -- test_as_rooted=test_as_rooted, -- parser_rooting_interpretation="default-rooted", -- test_ignore_tree_weights=False, -- dp_ignore_tree_weights=False, -- ) -- -- def test_basic_split_counting_under_different_rootings(self): -- test_cases = ( -- 'pythonidae.reference-trees.nexus', -- 'feb032009.trees.nexus', -- 'maj-rule-bug1.trees.nexus', -- 'maj-rule-bug2.trees.nexus', -- ) -- for is_rooted in (True, False): -- if is_rooted: -- rooting = "force-rooted" -- else: -- rooting = "force-unrooted" -- for test_case in test_cases: -- self.check_split_counting( -- test_case, -- test_as_rooted=is_rooted, -- parser_rooting_interpretation=rooting) -+ for test_case, test_as_rooted, parser_rooting_interpretation, assertion_error_regexp in test_cases: -+ with self.assertRaisesRegex(AssertionError, assertion_error_regexp): -+ self.check_split_counting( -+ test_case, -+ test_as_rooted=test_as_rooted, -+ parser_rooting_interpretation=parser_rooting_interpretation) -+ -+ def test_basic_split_count_with_incorrect_weight_treatment_raises_error(self): -+ assertion_error_regexp1 = re.compile("incorrect split frequency") -+ test_cases = ( -+ ("cetaceans.mb.no-clock.mcmc.weighted-01.trees", False), -+ ("cetaceans.mb.strict-clock.mcmc.weighted-01.trees", True), -+ ) -+ for test_case, test_as_rooted in test_cases: -+ with self.assertRaisesRegex(AssertionError, assertion_error_regexp1): -+ self.check_split_counting( -+ test_case, -+ test_as_rooted=test_as_rooted, -+ parser_rooting_interpretation="default-rooted", -+ test_ignore_tree_weights=False, -+ dp_ignore_tree_weights=False, -+ ) -+ -+ def test_basic_split_counting_under_different_rootings(self): -+ test_cases = ( -+ 'pythonidae.reference-trees.nexus', -+ 'feb032009.trees.nexus', -+ 'maj-rule-bug1.trees.nexus', -+ 'maj-rule-bug2.trees.nexus', -+ ) -+ for is_rooted in (True, False): -+ if is_rooted: -+ rooting = "force-rooted" -+ else: -+ rooting = "force-unrooted" -+ for test_case in test_cases: -+ self.check_split_counting( -+ test_case, -+ test_as_rooted=is_rooted, -+ parser_rooting_interpretation=rooting) - - class CladeMaskTest(unittest.TestCase): - -@@ -374,7 +378,8 @@ class TestTreeSplitSupportCredibilitySco - 30.89000000000001 + len(self.trees.taxon_namespace)) - - if __name__ == "__main__": -- if paup.DENDROPY_PAUP_INTEROPERABILITY: -- unittest.main() -- else: -- _LOG.warn("PAUP interoperability not available: skipping split counting tests") -+ unittest.main() -+ # if paup.DENDROPY_PAUP_INTEROPERABILITY: -+ # unittest.main() -+ # else: -+ # _LOG.warn("PAUP interoperability not available: skipping split counting tests") -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-dendropy.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
