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-rw-r--r--debian/changelog7
-rw-r--r--debian/patches/python3.12.patch85
-rw-r--r--debian/patches/series1
-rw-r--r--ete3/test/test_arraytable.py4
-rw-r--r--ete3/test/test_evol.py28
5 files changed, 109 insertions, 16 deletions
diff --git a/debian/changelog b/debian/changelog
index 2daacd1..c24f719 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+python-ete3 (3.1.3+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * python3.12.patch: new: fix test failures. (Closes: #1058334)
+
+ -- Étienne Mollier <emollier@debian.org> Thu, 14 Dec 2023 18:33:02 +0100
+
python-ete3 (3.1.3+dfsg-1) unstable; urgency=medium
* Team upload.
diff --git a/debian/patches/python3.12.patch b/debian/patches/python3.12.patch
new file mode 100644
index 0000000..29a136c
--- /dev/null
+++ b/debian/patches/python3.12.patch
@@ -0,0 +1,85 @@
+Description: fix deprecated assertions in python 3.12
+Author: Étienne Mollier <emollier@debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058334
+Forwarded: https://github.com/etetoolkit/ete/pull/737
+Last-Update: 2023-12-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-ete3.orig/ete3/test/test_arraytable.py
++++ python-ete3/ete3/test/test_arraytable.py
+@@ -33,7 +33,7 @@
+ 0.23000000000000001, -0.29999999999999999])
+
+ A.remove_column("col4")
+- self.assert_(A.get_column_vector("col4") is None )
++ self.assertIs(A.get_column_vector("col4"), None )
+
+ Abis = A.merge_columns({"merged1": \
+ ["col1", "col2"],\
+@@ -41,7 +41,7 @@
+ ["col5", "col6"]}, \
+ "mean")
+
+- #self.assert_((Abis.get_column_vector("merged1")==numpy.array([-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39, ])).all()==True )
++ #self.assertTrue((Abis.get_column_vector("merged1")==numpy.array([-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39, ])).all())
+
+ # Continue this......
+
+--- python-ete3.orig/ete3/test/test_evol.py
++++ python-ete3/ete3/test/test_evol.py
+@@ -111,10 +111,10 @@
+ sorted(['fb', 'M1', 'M2', 'M7', 'M8']))
+ self.assertEqual(len (tree.get_evol_model('M2').branches), 194)
+ self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569)
+- self.assert_('proportions' in str(tree.get_evol_model('M2')))
+- self.assert_('p2=' in str(tree.get_evol_model('M2')))
+- self.assert_('proportions' not in str(tree.get_evol_model('fb')))
+- self.assert_(' #193' in str(tree.get_evol_model('fb')))
++ self.assertIn('proportions', str(tree.get_evol_model('M2')))
++ self.assertIn('p2=', str(tree.get_evol_model('M2')))
++ self.assertNotIn('proportions', str(tree.get_evol_model('fb')))
++ self.assertIn(' #193', str(tree.get_evol_model('fb')))
+
+ def test_get_most_likely(self):
+ tree = EvolTree (WRKDIR + 'tree.nw')
+@@ -129,7 +129,7 @@
+ tree.workdir = 'protamine/PRM1/paml/'
+ random_swap(tree)
+ tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
+- self.assert_(check_annotation (tree))
++ self.assertTrue(check_annotation (tree))
+
+ def test_deep_copy(self):
+ tree = EvolTree (WRKDIR + 'tree.nw')
+@@ -173,11 +173,11 @@
+ tree = EvolTree('((seq1,seq2),seq3);')
+ tree.link_to_alignment('>seq1\nATGCTG\n>seq2\nATGCTG\n>seq3\nTTGATG\n')
+ tree.run_model('fb')
+- self.assert_('CODONML' in tree.get_evol_model('fb').run)
+- self.assert_('Time used:' in tree.get_evol_model('fb').run)
+- self.assert_('end of tree file' in tree.get_evol_model('fb').run)
+- self.assert_('lnL' in tree.get_evol_model('fb').run)
+- self.assert_(tree.get_descendants()[0].w > 0)
++ self.assertIn('CODONML', tree.get_evol_model('fb').run)
++ self.assertIn('Time used:', tree.get_evol_model('fb').run)
++ self.assertIn('end of tree file', tree.get_evol_model('fb').run)
++ self.assertIn('lnL', tree.get_evol_model('fb').run)
++ self.assertTrue(tree.get_descendants()[0].w > 0)
+
+ def test_run_slr(self):
+ if which('Slr'):
+@@ -185,10 +185,10 @@
+ tree.link_to_alignment('>seq1\nCTGATTCTT\n>seq2\nCTGATTCTT\n>seq3\nATGATTCTT\n')
+ tree.run_model('SLR')
+ print(tree.get_evol_model('SLR').run)
+- self.assert_('Sitewise Likelihood R' in tree.get_evol_model('SLR').run)
+- self.assert_('Positively selected s' in tree.get_evol_model('SLR').run)
+- self.assert_('Conserved sites' in tree.get_evol_model('SLR').run)
+- self.assert_('lnL' in tree.get_evol_model('SLR').run)
++ self.assertIn('Sitewise Likelihood R', tree.get_evol_model('SLR').run)
++ self.assertIn('Positively selected s', tree.get_evol_model('SLR').run)
++ self.assertIn('Conserved sites', tree.get_evol_model('SLR').run)
++ self.assertIn('lnL', tree.get_evol_model('SLR').run)
+
+ def test_marking_trees(self):
+ TREE_PATH = DATAPATH + '/S_example/'
diff --git a/debian/patches/series b/debian/patches/series
index c7f82d2..0b2ba01 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
syntax_fixes.patch
pmodeltest_executable.patch
+python3.12.patch
diff --git a/ete3/test/test_arraytable.py b/ete3/test/test_arraytable.py
index aa270fd..9ef9640 100644
--- a/ete3/test/test_arraytable.py
+++ b/ete3/test/test_arraytable.py
@@ -33,7 +33,7 @@ class Test_Coretype_ArrayTable(unittest.TestCase):
0.23000000000000001, -0.29999999999999999])
A.remove_column("col4")
- self.assert_(A.get_column_vector("col4") is None )
+ self.assertIs(A.get_column_vector("col4"), None )
Abis = A.merge_columns({"merged1": \
["col1", "col2"],\
@@ -41,7 +41,7 @@ class Test_Coretype_ArrayTable(unittest.TestCase):
["col5", "col6"]}, \
"mean")
- #self.assert_((Abis.get_column_vector("merged1")==numpy.array([-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39, ])).all()==True )
+ #self.assertTrue((Abis.get_column_vector("merged1")==numpy.array([-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39, ])).all())
# Continue this......
diff --git a/ete3/test/test_evol.py b/ete3/test/test_evol.py
index d9008f1..6c2aff7 100644
--- a/ete3/test/test_evol.py
+++ b/ete3/test/test_evol.py
@@ -111,10 +111,10 @@ class TestEvolEvolTree(unittest.TestCase):
sorted(['fb', 'M1', 'M2', 'M7', 'M8']))
self.assertEqual(len (tree.get_evol_model('M2').branches), 194)
self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569)
- self.assert_('proportions' in str(tree.get_evol_model('M2')))
- self.assert_('p2=' in str(tree.get_evol_model('M2')))
- self.assert_('proportions' not in str(tree.get_evol_model('fb')))
- self.assert_(' #193' in str(tree.get_evol_model('fb')))
+ self.assertIn('proportions', str(tree.get_evol_model('M2')))
+ self.assertIn('p2=', str(tree.get_evol_model('M2')))
+ self.assertNotIn('proportions', str(tree.get_evol_model('fb')))
+ self.assertIn(' #193', str(tree.get_evol_model('fb')))
def test_get_most_likely(self):
tree = EvolTree (WRKDIR + 'tree.nw')
@@ -129,7 +129,7 @@ class TestEvolEvolTree(unittest.TestCase):
tree.workdir = 'protamine/PRM1/paml/'
random_swap(tree)
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
- self.assert_(check_annotation (tree))
+ self.assertTrue(check_annotation (tree))
def test_deep_copy(self):
tree = EvolTree (WRKDIR + 'tree.nw')
@@ -173,11 +173,11 @@ class TestEvolEvolTree(unittest.TestCase):
tree = EvolTree('((seq1,seq2),seq3);')
tree.link_to_alignment('>seq1\nATGCTG\n>seq2\nATGCTG\n>seq3\nTTGATG\n')
tree.run_model('fb')
- self.assert_('CODONML' in tree.get_evol_model('fb').run)
- self.assert_('Time used:' in tree.get_evol_model('fb').run)
- self.assert_('end of tree file' in tree.get_evol_model('fb').run)
- self.assert_('lnL' in tree.get_evol_model('fb').run)
- self.assert_(tree.get_descendants()[0].w > 0)
+ self.assertIn('CODONML', tree.get_evol_model('fb').run)
+ self.assertIn('Time used:', tree.get_evol_model('fb').run)
+ self.assertIn('end of tree file', tree.get_evol_model('fb').run)
+ self.assertIn('lnL', tree.get_evol_model('fb').run)
+ self.assertTrue(tree.get_descendants()[0].w > 0)
def test_run_slr(self):
if which('Slr'):
@@ -185,10 +185,10 @@ class TestEvolEvolTree(unittest.TestCase):
tree.link_to_alignment('>seq1\nCTGATTCTT\n>seq2\nCTGATTCTT\n>seq3\nATGATTCTT\n')
tree.run_model('SLR')
print(tree.get_evol_model('SLR').run)
- self.assert_('Sitewise Likelihood R' in tree.get_evol_model('SLR').run)
- self.assert_('Positively selected s' in tree.get_evol_model('SLR').run)
- self.assert_('Conserved sites' in tree.get_evol_model('SLR').run)
- self.assert_('lnL' in tree.get_evol_model('SLR').run)
+ self.assertIn('Sitewise Likelihood R', tree.get_evol_model('SLR').run)
+ self.assertIn('Positively selected s', tree.get_evol_model('SLR').run)
+ self.assertIn('Conserved sites', tree.get_evol_model('SLR').run)
+ self.assertIn('lnL', tree.get_evol_model('SLR').run)
def test_marking_trees(self):
TREE_PATH = DATAPATH + '/S_example/'
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-02 14:53:51 +0000