[med-svn] [lambda-align] 01/02: exclude 1.9 pre-releases, revert patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository lambda-align.

commit 63a86a5e4c9809179b6d8610df16bf484f3393ca
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 18 11:27:31 2016 +0100

    exclude 1.9 pre-releases, revert patches
---
 debian/changelog                          | 10 ++++++----
 debian/patches/cast-min-initializer.patch |  2 +-
 debian/patches/fix-documentation.patch    | 30 +++++++++++++++---------------
 debian/watch                              |  2 +-
 4 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 47bf09d..586a27f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,14 @@
-lambda-align (1.9.1-1) UNRELEASED; urgency=medium
+lambda-align (1.0.0-4) unstable; urgency=medium
 
   * Team upload.
-  * New upstream version
-  * d/watch: no recompression since no change in upstream tarball is needed
+  * d/watch: 
+     - no recompression since no change in upstream tarball is needed
+     - exclude 1.9 pre-releases
+       Closes: #848543
   * debhelper 10
   * Remove extra license files in d/rules rather than in a patch
 
- -- Andreas Tille <tille at debian.org>  Sun, 18 Dec 2016 09:05:46 +0100
+ -- Andreas Tille <tille at debian.org>  Sun, 18 Dec 2016 09:21:15 +0100
 
 lambda-align (1.0.0-3) unstable; urgency=medium
 
diff --git a/debian/patches/cast-min-initializer.patch b/debian/patches/cast-min-initializer.patch
index 7e0ec0b..e61163a 100644
--- a/debian/patches/cast-min-initializer.patch
+++ b/debian/patches/cast-min-initializer.patch
@@ -7,7 +7,7 @@ Forwarded: https://github.com/seqan/lambda/issues/68
 Applied-Upstream: https://github.com/seqan/lambda/commit/cdb7e755af9829e26bf6e5f9ddbb07b5102038ef
 --- a/src/lambda.hpp
 +++ b/src/lambda.hpp
-@@ -784,8 +784,8 @@ seedLooksPromising(LocalDataHolder<TGlob
+@@ -701,8 +701,8 @@
          }
  
          effectiveLength = std::min({
diff --git a/debian/patches/fix-documentation.patch b/debian/patches/fix-documentation.patch
index a62d8e7..3fa5502 100644
--- a/debian/patches/fix-documentation.patch
+++ b/debian/patches/fix-documentation.patch
@@ -2,9 +2,20 @@ Description: fix documentation strings
 Author: Sascha Steinbiss <satta at debian.org>
 Forwarded: https://github.com/seqan/lambda/pull/65
 Applied-Upstream: https://github.com/seqan/lambda/pull/65
+--- a/src/holders.hpp
++++ b/src/holders.hpp
+@@ -174,7 +174,7 @@
+                   << "\033[0m\n\n";
+ 
+         if (rem != stats.hitsFinal)
+-            std::cout << "WARNING: hits dont add up\n";
++            std::cout << "WARNING: hits don't add up\n";
+     }
+ 
+     if (options.verbosity >= 1)
 --- a/src/options.hpp
 +++ b/src/options.hpp
-@@ -615,14 +615,14 @@ parseCommandLine(LambdaOptions & options
+@@ -587,14 +587,14 @@
  //         "STR"));
  //     setValidValues(parser, "query-alphabet", "dna5 aminoacid");
  //     setDefaultValue(parser, "query-alphabet", "dna5");
@@ -21,7 +32,7 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
  //     addOption(parser, ArgParseOption("sa", "seeding-alphabet",
  //         "alphabet to use during seeding (reduction possible)",
  //         ArgParseArgument::STRING,
-@@ -754,7 +754,7 @@ parseCommandLine(LambdaOptions & options
+@@ -710,7 +710,7 @@
      addSection(parser, "Scoring");
  
      addOption(parser, ArgParseOption("sc", "scoring-scheme",
@@ -30,14 +41,14 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
          "[ignored for BlastN]",
          ArgParseArgument::INTEGER));
      setDefaultValue(parser, "scoring-scheme", "62");
-@@ -1128,12 +1128,14 @@ parseCommandLine(LambdaIndexerOptions &
+@@ -1033,12 +1033,14 @@
      // Setup ArgumentParser.
      ArgumentParser parser("lambda_indexer");
  
 +    setShortDescription(parser, "indexer for creating lambda-compatible databases");
 +
      // Define usage line and long description.
-     addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta [-i INDEX.lambda]\\fP");
+     addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP");
  
      sharedSetup(parser);
  
@@ -46,14 +57,3 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
  
      addSection(parser, "Input Options");
      addOption(parser, ArgParseOption("d", "database",
---- a/src/holders.hpp
-+++ b/src/holders.hpp
-@@ -199,7 +199,7 @@ void printStats(StatsHolder const & stat
-                   << "\033[0m\n\n";
- 
-         if (rem != stats.hitsFinal)
--            std::cout << "WARNING: hits dont add up\n";
-+            std::cout << "WARNING: hits don't add up\n";
- 
-         std::cout << "Detailed Non-Wall-Clock times:\n"
-                   << " genSeeds: " << stats.timeGenSeeds << "\n"
diff --git a/debian/watch b/debian/watch
index 54433c9..245105e 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,2 @@
 version=4
-https://github.com/seqan/lambda/tags .*/lambda-v?(\d.*)\.tar.gz
+https://github.com/seqan/lambda/tags .*/lambda-v?(\d+\.[0-8][.\d]*)\.tar.gz

-- 
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