Description: make documentation build reproducible
 Some parts of the source involve some nondeterminism or build-time
 variation when converted to the documentation via epydoc, making
 the build unreproducible.
 The first issue is the fact that sets of classes (types) cannot be sorted
 deterministically when converted to lists -- Python 2 uses addresses
 as keys, in Python 3 types are unorderable. This patch uses a list instead
 of a set, which is OK here as the original set contents are expliitly defined,
 constant and small. This is not a bug to be fixed in epydoc as IMHO it's
 already handled as well as possible in epydoc itself, so I had to work
 around the issue here in python-csb; if it can't be sorted that's it. 
 Secondly, function default parameters are included in the documentation,
 which in the case of runmany() contains the number of CPUs in the build host.
 This patch moves this default assignment out of the function header into the
 body, from where it's not included in the documentation.
Author: Sascha Steinbiss <sascha@steinbiss.name>
--- a/csb/bio/sequence/__init__.py
+++ b/csb/bio/sequence/__init__.py
@@ -130,7 +130,7 @@
             SequenceTypes.RNA: NucleicAlphabet,
             SequenceTypes.Unknown: UnknownAlphabet }
     
-    ALL_ALPHABETS = set([ProteinAlphabet, NucleicAlphabet, UnknownAlphabet])
+    ALL_ALPHABETS = [ProteinAlphabet, NucleicAlphabet, UnknownAlphabet]
 
     assert set(MAP) == csb.core.Enum.members(SequenceTypes)
     
@@ -1329,4 +1329,4 @@
         from csb.bio.io.fasta import SequenceAlignmentReader
         return SequenceAlignmentReader(strict=strict).read_a3m(string)
 
-    
\ No newline at end of file
+    
--- a/csb/apps/hhsearch.py
+++ b/csb/apps/hhsearch.py
@@ -252,8 +252,11 @@
                 context.result = self.parser.parse_file(o.name)
                 return context
             
-    def runmany(self, contexts, workers=mp.cpu_count(), cpu=1):
-        
+    def runmany(self, contexts, workers, cpu=1):
+
+        if not workers:
+            workers = mp.cpu_count() 
+
         if workers > len(contexts):
             workers = len(contexts)
 
@@ -278,4 +281,4 @@
     
     
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()