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tests/test_evol.py: port assertions to python3.12. #737

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tests/test_evol.py: port assertions to python3.12. #737

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28 changes: 14 additions & 14 deletions tests/test_evol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,10 +73,10 @@ def test_load_model(self):
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(open(WRKDIR + 'tree.nw'))
Expand All @@ -91,7 +91,7 @@ def test_labelling_tree(self):
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(open(WRKDIR + 'tree.nw'))
Expand Down Expand Up @@ -135,22 +135,22 @@ def test_run_codeml(self):
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'):
tree = EvolTree('((seq1,seq2),seq3);')
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/'
Expand Down