[med-svn] [python-dendropy] 06/06: Adapt patches to new upstream version
Andreas Tille
tille at debian.org
Wed Jul 29 11:20:42 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-dendropy.
commit 16e3163de36731760086dc0d10465ef08dbbb00e
Author: Andreas Tille <tille at debian.org>
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")
--
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