fix unicode

tests/test

@@ -0,0 +1 @@
+䔀 blah blah blah

tests/test_amplify.py

@@ -271,4 +271,4 @@ def test_pcr():
         assert tst[0] == seguid(pcr(tst[1:]).seq)
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_assemble_MX4blaster12.py

@@ -137,4 +137,4 @@ def test_MXblaster1():
 
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_assemble_YEp24PGK_XK.py

@@ -38,7 +38,7 @@ def test_empty():
     assert pydna.eq(YEp24PGK_XK, YEp24PGK_XK_correct)
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 
 
 

tests/test_assemble_pGUP1.py

@@ -36,4 +36,4 @@ def test_empty():
     assert pGUP1.seguid() == "42wIByERn2kSe_Exn405RYwhffU"    
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_assembly.py

@@ -136,7 +136,7 @@ def test_assembly():
     print("done!", time.time()-start)
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 
 
 

tests/test_cut_features.py

@@ -27,4 +27,4 @@ def amplicon_to_dseqrecord(a):
     assert len(pcrProdDseqrecord.cut(EcoRI)[1].features) == 17
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_download.py

@@ -37,7 +37,7 @@ def test_pydna_download():
     os.environ["pydna_cache"] = cachevar
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 
 
 

tests/test_dsdna.py

@@ -875,5 +875,5 @@ def test_synced2():
     print()
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 

tests/test_genbankfixer.py

@@ -26,4 +26,4 @@ def test_pydna_gbtext_clean():
         #print('"'+calcseg+'"),')
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_import_ipynb.py

@@ -22,4 +22,4 @@ def test_ipynb_import():
         assert mynotebook.foo() == "bar"
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_map_reads.py

@@ -95,5 +95,5 @@ def test_map2():
 
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 

tests/test_markbudde.py

@@ -33,4 +33,4 @@ def test_empty():
     """
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_parse.py

@@ -115,7 +115,7 @@ def test_parse2():
 
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])
 
 
 

tests/test_pretty.py

@@ -9,27 +9,29 @@
 
 def test_pretty():
 
-    x= u'/label="2micron 2µ"'
+    print(sys.getdefaultencoding())
+    import locale
+    print(locale.getpreferredencoding())
 
     import io
     from Bio import SeqIO
     from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
 
-    raw = open("pydna_read_test.txt", 'r').read()
+    raw = open("pydna_read_test.txt", 'r', encoding="UTF8").read()
 
     handle = io.StringIO(raw)
 
     sr = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
 
     s = sr.format("gb").strip()
 
-    assert s[559:578] == x
+    assert s[559:578] == '/label="2micron 2µ"'
 
     y = pydna._pretty.pretty_string( s[:55]+"circular"+s[63:] )[559:578]
 
-    assert x==y
+    assert '/label="2micron 2µ"'==y
 
-    assert pydna.read("pydna_read_test.txt").format("gb")[559:578] == x
+    assert pydna.read("pydna_read_test.txt").format("gb")[559:578] == '/label="2micron 2µ"'
 
 if __name__ == '__main__':
     pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_primer_design.py

@@ -219,4 +219,4 @@ def test_primer_Design_saving_to_text_file():
     assert r.description == "rv64 t-sequence"
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])

tests/test_utils.py

@@ -153,4 +153,4 @@ def test_cseguid():
 
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[sys.argv[0], '--nocapture'])
+    pytest.cmdline.main([__file__, "-v", "-s"])