[med-svn] [python-csb] 01/04: make build reproducible

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository python-csb.

commit 74f0581523845d3f310f30040c4d23fe5a949247
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sun Jun 5 00:50:10 2016 +0000

    make build reproducible
---
 debian/changelog                  |  8 ++++++
 debian/patches/reproducible.patch | 57 +++++++++++++++++++++++++++++++++++++++
 debian/patches/series             |  1 +
 3 files changed, 66 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 3541aef..87d6cd1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+python-csb (1.2.3+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * Make build reproducible.
+    - Address build time variation and sorting issues.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Sun, 05 Jun 2016 00:49:19 +0000
+
 python-csb (1.2.3+dfsg-2) unstable; urgency=medium
 
   * Fix d/watch
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
new file mode 100644
index 0000000..21371e1
--- /dev/null
+++ b/debian/patches/reproducible.patch
@@ -0,0 +1,57 @@
+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 at 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()
diff --git a/debian/patches/series b/debian/patches/series
index 3f27449..e5ac533 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 exclude_online_tests.patch
+reproducible.patch

-- 
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