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/'