[med-svn] [theseus] annotated tag upstream/3.3.0 created (now 1bc627b)

[Andreas Tille]

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tille pushed a change to annotated tag upstream/3.3.0
in repository theseus.

        at  1bc627b   (tag)
   tagging  34df5dbf3284c51000d1ab23443e1f683539916f (commit)
 tagged by  Andreas Tille
        on  Thu Aug 24 15:18:48 2017 +0200

- Log -----------------------------------------------------------------
Upstream version 3.3.0

Andreas Tille (54):
      Typos and restructuring some paragraphs
      Trying to prepare new upstream version (closes #534630) but upstream is unclear about latest version (Website says 1.4.3 is latest, tgz is named 1.4.0 as well as error.h contains this version string)
      Latest upstream, fixed e-mail of upstream
      Added libtool Build-Depends, bumped Standards-Version, but the package does NOT compile because of gcc options -arch (and others) as well as libtool option -o.  Needs further investigation!
      Large chunk of changes concerning: Switch to quilt, use short debhelper 7 debian/rules file, use debian/{docs,manpages,examples}, do not tweak upstream tarball, added missing suggests
      Fix library building and compilation options; add README.source to mention quilt; some lintian issues
      Make sure thesaus_align script will be installed properly; Remove outdated parapgraph from README.Debian
      Mention the fix which closes  #542879  in changelog
      Fixed broken patch
      Start working on new upstream version of theseus
      Adapt patch to new upstream version
      Adapt patches to new upstream version; Make sure muscle instead of non-free clustalw will be used as aligner and adjust dependency of muscle accordingly; source format 3
      Packaging for new upstream version; UNRELEASED because one of the examples segfaults
      New upstream version, removed several patches which are either applied upstream or non-functional (break the build - the latter might harm performance, thus further optimisation should be considered)
      New upstream version
      Fixed Vcs fields, Standards-Version 3.9.3
      Do not mention quilt explicitely which is not needed with source version 3.0 (quilt)
      Remove explicite quilt call in debian/rules
      Create debian/upstream files from citation.bib; attention: here we now have another example for multiple references - just testing hereby how this works out
      Debhelper 9 to enable hardening; Hardening requires code patches which is NOT YET FINISHED (so it does not build as is)
      Some more patches removing assigned but not used variables; does not yet build!
      Does compile with hardening flags but linker problem remains
      Prevent trying to link with Apple specific linker option
      Enable linking pthread
      DEP5 copyright
      Upload to unstable
      Fix debian/upstream syntax
      Fixed cut-n-pasto
      unique punctuation in authors field
      Apply patch by Simon Ruderich to really build with hardening flags and upload to unstable
      Fix typo - thanks to Robert Campbell <robert.campbell at queensu.ca> for pointing this up
      Remove duplicated citation information
      Close the according bug number
      New upstream version (most patches applied)
      Drop debian/docs which had the only purpose to install the removed citation.bib file
      Upload to experimental
      New upstream version including needed patches
      cme fix dpkg-control
      xz compression; upload to unstable
      New upstream version; cme fix dpkg-control
      Adapt patches to new upstream version
      debian/README.source: removed since redundant
      Upload to unstable
      New upstream version
      Fix PATHes in theseus_align
      Split examples into separate binary package; update debian/copyright
      New upstream version, add missing license statement
      New upstream version
      fix package split issue
      Fix package split issue finally
      Enable building arch independent packages separately
      Add autopkgtest and upload to unstable
      * Depends: muscle instead of Suggests since its usage in test suite
      New upstream version 3.3.0

Charles Plessy (1):
      Correction of a minor formatting bug.

James McCoy (1):
      Move debian/upstream to debian/upstream/metadata

Morten Kjeldgaard (10):
      Creating trunk directory
      [svn-inject] Applying Debian modifications to trunk
      Clean target now works. Hyphen issues in manpages resolved.
      makefile patched before clean target
      Upstream has carried out various changes at my request, so
      abstracts removed from citation.bib, due to copyright issues
      README.Debian file added, explaining the peculiarity of the
      Fixed spelling mistakes in README.Debian
      Theseus FTBFS on archs armel and lpia because libatlas-base-dev
      Fix FTBFS on certain platforms that lack the Atlas libraries

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