Move os.environ['LANG'] = 'C' into just those unit tests which call e…

…xternal tools. Having it in run_tests.py was changing the default encoding causing problems on Python 3 with special characters in plain text files

Tests/run_tests.py

@@ -89,10 +89,12 @@ def main(argv):
     if os.access(build_path, os.F_OK):
         sys.path.insert(1, build_path)
 
-    # Use "export LANG=C" (which should work on Linux and similar) to
-    # try to avoid problems detecting optional command line tools on
-    # non-English OS (we may want 'command not found' in English)
-    os.environ['LANG']='C'
+    # Using "export LANG=C" (which should work on Linux and similar) can
+    # avoid problems detecting optional command line tools on
+    # non-English OS (we may want 'command not found' in English).
+    # HOWEVER, we do not want to change the default encoding which is
+    # rather important on Python 3 with unicode.
+    #lang = os.environ['LANG']
 
     # get the command line options
     try:

Tests/test_Clustalw_tool.py

@@ -18,6 +18,9 @@
 
 #################################################################
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 clustalw_exe = None
 if sys.platform=="win32":
     #TODO - Check the path?

Tests/test_Dialign_tool.py

@@ -12,6 +12,9 @@
 from Bio import MissingExternalDependencyError
 from Bio.Align.Applications import DialignCommandline
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 dialign_exe = None
 if sys.platform=="win32":
     raise MissingExternalDependencyError("DIALIGN2-2 not available on Windows")

Tests/test_Emboss.py

@@ -21,6 +21,9 @@
 
 #################################################################
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 exes_wanted = ["water", "needle", "seqret", "transeq", "seqmatchall",
                "embossversion"]
 exes = dict() #Dictionary mapping from names to exe locations

Tests/test_EmbossPhylipNew.py

@@ -17,6 +17,9 @@
 from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
 from Bio.Emboss.Applications import FTreeDistCommandline, FDNAParsCommandline
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 exes_wanted = ['fdnadist', 'fneighbor', 'fprotdist','fprotpars','fconsense',
                'fseqboot', 'ftreedist', 'fdnapars']
 exes = dict() #Dictionary mapping from names to exe locations

Tests/test_Mafft_tool.py

@@ -16,6 +16,9 @@
 from Bio import MissingExternalDependencyError
 from Bio.Align.Applications import MafftCommandline
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 mafft_exe = None
 if sys.platform=="win32":
     raise MissingExternalDependencyError("Testing with MAFFT not implemented on Windows yet")

Tests/test_Muscle_tool.py

@@ -15,6 +15,9 @@
 
 #################################################################
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 muscle_exe = None
 if sys.platform=="win32":
     try:

Tests/test_Prank_tool.py

@@ -16,6 +16,9 @@
 from Bio.Align.Applications import PrankCommandline
 from Bio.Nexus.Nexus import NexusError
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 prank_exe = None
 if sys.platform=="win32":
     try:

Tests/test_Probcons_tool.py

@@ -12,6 +12,9 @@
 from Bio import AlignIO, SeqIO, MissingExternalDependencyError
 from Bio.Align.Applications import ProbconsCommandline
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 probcons_exe = None
 if sys.platform=="win32":
     raise MissingExternalDependencyError("PROBCONS not available on Windows")

Tests/test_TCoffee_tool.py

@@ -12,6 +12,9 @@
 from Bio import AlignIO, SeqIO, MissingExternalDependencyError
 from Bio.Align.Applications import TCoffeeCommandline
 
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
 t_coffee_exe = None
 if sys.platform=="win32":
     raise MissingExternalDependencyError(\