diff options
author | Étienne Mollier <emollier@debian.org> | 2023-12-14 18:33:02 +0100 |
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committer | Étienne Mollier <emollier@debian.org> | 2023-12-14 18:33:02 +0100 |
commit | 1e55c160e4c5cdc8df9ab87f5422eb9309e3bc51 (patch) | |
tree | a7cb09c97242a985a54eabf825d6fdca5c5875be | |
parent | 2706f5b7cf83d2a8faea02e397f755a351a272bb (diff) |
fix deprecated assertions in python 3.12
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
Last-Update: 2023-12-14
Gbp-Pq: Name python3.12.patch
-rw-r--r-- | ete3/test/test_arraytable.py | 4 | ||||
-rw-r--r-- | ete3/test/test_evol.py | 28 |
2 files changed, 16 insertions, 16 deletions
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/' |