date:20170918

[med-svn] [coils] branch upstream created (now 09b9759)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch upstream
in repository coils.

at  09b9759   New upstream version 2002

No new revisions were added by this update.

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[med-svn] [coils] branch master created (now f215cab)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository coils.

at  f215cab   Moved packaging from SVN to Git

This branch includes the following new commits:

   new  70d5897   Moved Steffen Möllers work which was stalled to svn to 
keep track of previous work.
   new  3239c78   Uploading coils to the archive (5 year's after initial 
packaging). This shall also prepare for GENtle to share this binary, well, I 
presume we need to craft a coils library for that, eventually. Many thanks go 
to Andreas for having saved my previous work in the Debian Med archive.  So, 
let's celebrate.
   new  c40151e   Put package in Debian Med team maintenance, fixed typo in 
Vcs-Browser, some polishing, upstream-metadata.yaml
   new  9850162   Updated Homepage; upload long pending changes
   new  7029346   2002-3: perl script coils-wrap.pl moved from doc to 
/usr/bin as 'coils-wrap'; improved man pages; updated upstream URL; removed 
requirement to define COILSDIR env var
   new  a5fbc30   ignore generated files in debian/
   new  1d32da8   Removed myself from uploaders ... and uploaded :) 
[sponsoring Laszlo]
   new  6ddf65a   Renamed debian/upstream-metadata.yaml to debian/upstream.
   new  443d94e   debian/upstream: Moved DOI and PMID to the Reference 
namespace.
   new  3b374e6   Added DOI+URL to references
   new  049dfac   Make author field BibTeX compliant
   new  7ec5eee   Fix Vcs fields globally in all remaining packages because 
I'm bored by warnings in logfiles when investigating machine readable files of 
not yet uploaded packages
   new  4d00e90   Mass commit for 2002-4
   new  db057d6   Move debian/upstream to debian/upstream/metadata
   new  fb1f40c   coils: Added references to registries
   new  09b9759   New upstream version 2002
   new  c673829   Updated version 2002 from 'upstream/2002'
   new  f215cab   Moved packaging from SVN to Git

The 18 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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[med-svn] [coils] branch pristine-tar created (now 52da714)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch pristine-tar
in repository coils.

at  52da714   pristine-tar data for coils_2002.orig.tar.gz

This branch includes the following new commits:

   new  52da714   pristine-tar data for coils_2002.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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[med-svn] [coils] 01/01: pristine-tar data for coils_2002.orig.tar.gz

2017-09-18 Thread Andreas Tille

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tille pushed a commit to branch pristine-tar
in repository coils.

commit 52da714fa3997d96872a2a20bb2dd3b89abc8c3d
Author: Andreas Tille 
Date:   Mon Sep 18 09:02:59 2017 +0200

pristine-tar data for coils_2002.orig.tar.gz
---
 coils_2002.orig.tar.gz.delta | Bin 0 -> 1201 bytes
 coils_2002.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/coils_2002.orig.tar.gz.delta b/coils_2002.orig.tar.gz.delta
new file mode 100644
index 000..88a68c7
Binary files /dev/null and b/coils_2002.orig.tar.gz.delta differ
diff --git a/coils_2002.orig.tar.gz.id b/coils_2002.orig.tar.gz.id
new file mode 100644
index 000..54a4895
--- /dev/null
+++ b/coils_2002.orig.tar.gz.id
@@ -0,0 +1 @@
+07d0774c122aa8c2b403f65bcf1431588f2a517f

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[med-svn] r24054 - in trunk/packages/coils: . trunk

2017-09-18 Thread Andreas Tille

Author: tille
Date: 2017-09-18 07:10:12 + (Mon, 18 Sep 2017)
New Revision: 24054

Removed:
   trunk/packages/coils/tags/
   trunk/packages/coils/trunk/debian/
Log:
MOve packaging to Git



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[med-svn] r24055 - trunk/packages/coils/trunk

2017-09-18 Thread Andreas Tille

Author: tille
Date: 2017-09-18 07:11:21 + (Mon, 18 Sep 2017)
New Revision: 24055

Added:
   trunk/packages/coils/trunk/README.status
Log:
Document move to Git


Added: trunk/packages/coils/trunk/README.status
===
--- trunk/packages/coils/trunk/README.status(rev 0)
+++ trunk/packages/coils/trunk/README.status2017-09-18 07:11:21 UTC (rev 
24055)
@@ -0,0 +1,7 @@
+---
+Format: 1
+Status: git
+SVNDeleteRevision: 24054
+URL: https://git.debian.org/git/debian-med/coils.git
+Comment: >
+  This package is now managed in a Git repository.


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[med-svn] [dicompyler] 01/01: More patches to finally work with wx 3.0

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit 08e0e30cfb5eab52215e6dcd7a49fa7562290a9d
Author: Andreas Tille 
Date:   Mon Sep 18 09:56:51 2017 +0200

More patches to finally work with wx 3.0
---
 debian/changelog   |   7 +
 debian/patches/more_wx30_patches.patch | 374 +
 debian/patches/series  |   1 +
 3 files changed, 382 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 1c3291a..c212ffe 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+dicompyler (0.4.2-5) UNRELEASED; urgency=medium
+
+  * Team upload
+  * More patches to finally work with wx 3.0
+
+ -- Vojtech Kulvait   Mon, 18 Sep 2017 09:54:37 +0200
+
 dicompyler (0.4.2-4) unstable; urgency=medium
 
   * Fix Open Patient dialog (Thanks for the patch to Vojtech Kulvait
diff --git a/debian/patches/more_wx30_patches.patch 
b/debian/patches/more_wx30_patches.patch
new file mode 100644
index 000..955cb3b
--- /dev/null
+++ b/debian/patches/more_wx30_patches.patch
@@ -0,0 +1,374 @@
+Author: Vojtech Kulvait 
+Last-Update: Mon, 18 Sep 2017 00:27:42 +0200
+Bug-Debian: https://bugs.debian.org/854837
+Description: More wx3.0 patches to make dicompyler run
+
+--- a/dicompyler/baseplugins/2dview.py
 b/dicompyler/baseplugins/2dview.py
+@@ -10,9 +10,7 @@
+ 
+ import wx
+ from wx.xrc import XmlResource, XRCCTRL, XRCID
+-import wx.lib.pubsub.setuparg1
+-import wx.lib.pubsub.core
+-pub = wx.lib.pubsub.core.Publisher()
++from wx.lib.pubsub import pub
+ from matplotlib import _cntr as cntr
+ from matplotlib import __version__ as mplversion
+ import numpy as np
+@@ -194,18 +192,18 @@ class plugin2DView(wx.Panel):
+ self.Unbind(wx.EVT_RIGHT_DOWN)
+ self.Unbind(wx.EVT_RIGHT_UP)
+ self.Unbind(wx.EVT_MOTION)
+-pub.unsubscribe(self.OnKeyDown)
+-pub.unsubscribe(self.OnMouseWheel)
+-pub.unsubscribe(self.OnRefresh)
++pub.unsubscribe(self.OnKeyDown, 'main.key_down')
++pub.unsubscribe(self.OnMouseWheel, 'main.mousewheel')
++pub.unsubscribe(self.OnRefresh, '2dview.refresh')
+ 
+ def OnDestroy(self, evt):
+ """Unbind to all events before the plugin is destroyed."""
+ 
+-pub.unsubscribe(self.OnUpdatePatient)
+-pub.unsubscribe(self.OnStructureCheck)
+-pub.unsubscribe(self.OnIsodoseCheck)
+-pub.unsubscribe(self.OnDrawingPrefsChange)
+-pub.unsubscribe(self.OnPluginLoaded)
++pub.unsubscribe(self.OnUpdatePatient, 'patient.updated.parsed_data')
++pub.unsubscribe(self.OnStructureCheck, 'structures.checked')
++pub.unsubscribe(self.OnIsodoseCheck, 'isodoses.checked')
++pub.unsubscribe(self.OnDrawingPrefsChange, '2dview.drawingprefs')
++pub.unsubscribe(self.OnPluginLoaded, 'plugin.loaded.2dview')
+ self.OnUnfocus()
+ 
+ def OnStructureCheck(self, msg):
+--- a/dicompyler/baseplugins/anonymize.py
 b/dicompyler/baseplugins/anonymize.py
+@@ -10,9 +10,7 @@
+ 
+ import wx
+ from wx.xrc import XmlResource, XRCCTRL, XRCID
+-import wx.lib.pubsub.setuparg1
+-import wx.lib.pubsub.core
+-pub = wx.lib.pubsub.core.Publisher()
++from wx.lib.pubsub import pub
+ import os, threading
+ from dicompyler import guiutil, util
+ 
+@@ -39,6 +37,7 @@ class plugin:
+ self.parent = parent
+ 
+ # Set up pubsub
++print "Subscibing from anonymize"
+ pub.subscribe(self.OnUpdatePatient, 'patient.updated.raw_data')
+ 
+ # Load the XRC file for our gui resources
+@@ -333,4 +332,10 @@ class AnonymizeDialog(wx.Dialog):
+ else:
+ self.privatetags = False
+ 
+-self.EndModal(wx.ID_OK)
+\ No newline at end of file
++self.EndModal(wx.ID_OK)
++
++def OnDestroy(self, evt):
++"""Unbind to all events before the plugin is destroyed."""
++print "Unsubscribing from anonymize"
++pub.unsubscribe(self.OnUpdatePatient, 'patient.updated.raw_data')
++
+--- a/dicompyler/baseplugins/dvh.py
 b/dicompyler/baseplugins/dvh.py
+@@ -12,9 +12,7 @@
+ 
+ import wx
+ from wx.xrc import XmlResource, XRCCTRL, XRCID
+-import wx.lib.pubsub.setuparg1
+-import wx.lib.pubsub.core
+-pub = wx.lib.pubsub.core.Publisher()
++from wx.lib.pubsub import pub
+ from dicompyler import guiutil, util
+ from dicompyler import dvhdata, guidvh
+ from dicompyler import wxmpl
+@@ -134,9 +132,9 @@ class pluginDVH(wx.Panel):
+ def OnDestroy(self, evt):
+ """Unbind to all events before the plugin is destroyed."""
+ 
+-pub.unsubscribe(self.OnUpdatePatient)
+-pub.unsubscribe(self.OnStructureCheck)
+-pub.unsubscribe(self.OnStructureSelect)
++pub.unsubscribe(self.OnUpdatePatient, 'patient.updated.parsed_data')
++pub.unsubscribe(self.OnStructureCheck, 'structures.checked')
++pub.unsubscribe(self.OnStructureSelect, 'structure.selected')
+

[med-svn] [dicompyler] branch master updated (06e12fa -> 08e0e30)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository dicompyler.

  from  06e12fa   Upload to unstable, fix closes statement (hoping that 
"may be" is correct)
   new  08e0e30   More patches to finally work with wx 3.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog   |   7 +
 debian/patches/more_wx30_patches.patch | 374 +
 debian/patches/series  |   1 +
 3 files changed, 382 insertions(+)
 create mode 100644 debian/patches/more_wx30_patches.patch

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[med-svn] [coils] tag debian/2002-5 created (now 4ea2814)

2017-09-18 Thread Andreas Tille

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tille pushed a change to tag debian/2002-5
in repository coils.

at  4ea2814   (commit)
No new revisions were added by this update.

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[med-svn] [coils] 02/06: Standards-Version: 4.1.0 (no changes needed)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository coils.

commit 00b2d1e0a1f3faa2a1e735c8662966865113fa72
Author: Andreas Tille 
Date:   Mon Sep 18 09:06:29 2017 +0200

Standards-Version: 4.1.0 (no changes needed)
---
 debian/changelog | 1 +
 debian/control   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 2d0ac06..fbfca97 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ coils (2002-6) UNRELEASED; urgency=low
   [ Andreas Tille ]
   * Moved packaging from SVN to Git
   * debhelper 10
+  * Standards-Version: 4.1.0 (no changes needed)
 
  -- Andreas Tille   Mon, 18 Sep 2017 09:03:04 +0200
 
diff --git a/debian/control b/debian/control
index fa93679..ef40bef 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
perl
-Standards-Version: 3.9.4
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/coils.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/coils.git
 Homepage: http://www.russelllab.org/coils/

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[med-svn] [coils] branch master updated (f215cab -> 4ea2814)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch master
in repository coils.

  from  f215cab   Moved packaging from SVN to Git
   new  b754289   debhelper 10
   new  00b2d1e   Standards-Version: 4.1.0 (no changes needed)
   new  7f0945d   hardening=+all
   new  cea5a47   Fix DEP5 issues
   new  7e13fe3   Add fake watch file
   new  4ea2814   Upload to unstable

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog |  9 +++--
 debian/compat|  2 +-
 debian/control   |  4 ++--
 debian/copyright | 10 +-
 debian/rules |  2 ++
 debian/watch |  4 
 6 files changed, 21 insertions(+), 10 deletions(-)
 mode change 100644 => 100755 debian/rules
 create mode 100644 debian/watch

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[med-svn] [coils] 05/06: Add fake watch file

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository coils.

commit 7e13fe3b45202894c8d3e93cd845903a81932a73
Author: Andreas Tille 
Date:   Mon Sep 18 09:14:36 2017 +0200

Add fake watch file
---
 debian/changelog | 1 +
 debian/watch | 4 
 2 files changed, 5 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 7339b7a..ba8621c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -11,6 +11,7 @@ coils (2002-5) UNRELEASED; urgency=low
   * Standards-Version: 4.1.0 (no changes needed)
   * hardening=+all
   * Fix DEP5 issues
+  * Add fake watch file
 
  -- Andreas Tille   Mon, 18 Sep 2017 09:07:04 +0200
 
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 000..a45d4a4
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+ https://people.debian.org/~eriberto/ 
FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz

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[med-svn] [coils] 04/06: Fix DEP5 issues

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository coils.

commit cea5a479abea58a914fe01d919d314182c6ae9a0
Author: Andreas Tille 
Date:   Mon Sep 18 09:13:45 2017 +0200

Fix DEP5 issues
---
 debian/changelog |  1 +
 debian/copyright | 10 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index b487e3c..7339b7a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -10,6 +10,7 @@ coils (2002-5) UNRELEASED; urgency=low
   * debhelper 10
   * Standards-Version: 4.1.0 (no changes needed)
   * hardening=+all
+  * Fix DEP5 issues
 
  -- Andreas Tille   Mon, 18 Sep 2017 09:07:04 +0200
 
diff --git a/debian/copyright b/debian/copyright
index a547d02..36d771c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Contact: Rob Russel 
 Source: http://www.russelllab.org/coils/coils.tar.gz
 
@@ -7,9 +7,9 @@ Copyright: (C) 2002 Robert B. Russel and its employing 
institute, the
   EMBL - European Molecular Biology Lab
   Meyerhofstrasse 1, 69917 Heidelberg, Germany
   
-License: GPLv2
+License: GPL-2
 
-License: GPLv2
+License: GPL-2
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; version 2 dated June, 1991.
@@ -28,6 +28,6 @@ License: GPLv2
 Files: debian/*
 Copyright: © 2005-2010 Steffen Moeller 
© 2011 Laszlo Kajan 
-   © 2011-2013 Andreas Tille 
-License: GPLv2
+   © 2011-2017 Andreas Tille 
+License: GPL-2
 

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[med-svn] [coils] 06/06: Upload to unstable

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository coils.

commit 4ea28141d0b1ccac98488102982c3290c9cd2e8c
Author: Andreas Tille 
Date:   Mon Sep 18 10:03:05 2017 +0200

Upload to unstable
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ba8621c..fcd3482 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-coils (2002-5) UNRELEASED; urgency=low
+coils (2002-5) unstable; urgency=low
 
   [ Steffen Moeller ]
   * debian/upstream/metadata:
@@ -13,7 +13,7 @@ coils (2002-5) UNRELEASED; urgency=low
   * Fix DEP5 issues
   * Add fake watch file
 
- -- Andreas Tille   Mon, 18 Sep 2017 09:07:04 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 09:14:46 +0200
 
 coils (2002-4) unstable; urgency=low
 

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[med-svn] [coils] 03/06: hardening=+all

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository coils.

commit 7f0945dc0405d85ca33e612851bb9c8da28b8b98
Author: Andreas Tille 
Date:   Mon Sep 18 09:08:29 2017 +0200

hardening=+all
---
 debian/changelog | 5 +++--
 debian/rules | 2 ++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fbfca97..b487e3c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-coils (2002-6) UNRELEASED; urgency=low
+coils (2002-5) UNRELEASED; urgency=low
 
   [ Steffen Moeller ]
   * debian/upstream/metadata:
@@ -9,8 +9,9 @@ coils (2002-6) UNRELEASED; urgency=low
   * Moved packaging from SVN to Git
   * debhelper 10
   * Standards-Version: 4.1.0 (no changes needed)
+  * hardening=+all
 
- -- Andreas Tille   Mon, 18 Sep 2017 09:03:04 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 09:07:04 +0200
 
 coils (2002-4) unstable; urgency=low
 
diff --git a/debian/rules b/debian/rules
old mode 100644
new mode 100755
index 0fa44c7..2557986
--- a/debian/rules
+++ b/debian/rules
@@ -4,6 +4,8 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
dh $@
 

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[med-svn] [coils] 01/06: debhelper 10

2017-09-18 Thread Andreas Tille

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tille pushed a commit to branch master
in repository coils.

commit b754289dbc901b271cecc150bf9f4c2faa27c49a
Author: Andreas Tille 
Date:   Mon Sep 18 09:05:41 2017 +0200

debhelper 10
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 5b86102..2d0ac06 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ coils (2002-6) UNRELEASED; urgency=low
 
   [ Andreas Tille ]
   * Moved packaging from SVN to Git
+  * debhelper 10
 
  -- Andreas Tille   Mon, 18 Sep 2017 09:03:04 +0200
 
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 89aeaf2..fa93679 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille ,
Laszlo Kajan 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
perl
 Standards-Version: 3.9.4
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/coils.git

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[med-svn] [dicompyler] 02/04: Updated version 0.4.2.0 from 'upstream/0.4.2.0'

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit 2229466133df1c6a3081911099370e8be8a8291c
Merge: 08e0e30 4f2ebd3
Author: Andreas Tille 
Date:   Mon Sep 18 10:15:19 2017 +0200

Updated version 0.4.2.0 from 'upstream/0.4.2.0'

with Debian dir 6ca99345ad107b585020abe74760a164d966329f

 .hgignore|  9 +
 PKG-INFO | 57 ---
 dicompyler.egg-info/PKG-INFO | 57 ---
 dicompyler.egg-info/SOURCES.txt  | 67 
 dicompyler.egg-info/dependency_links.txt |  1 -
 dicompyler.egg-info/entry_points.txt |  3 --
 dicompyler.egg-info/not-zip-safe |  1 -
 dicompyler.egg-info/requires.txt |  4 --
 dicompyler.egg-info/top_level.txt|  1 -
 README.txt => readme.txt |  0
 scripts/dicompyler   | 12 ++
 setup.cfg|  5 ---
 12 files changed, 21 insertions(+), 196 deletions(-)

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[med-svn] [dicompyler] 01/04: New upstream version 0.4.2.0

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit 4f2ebd3c9e2a643a5930d292aa860357ddcba90e
Author: Andreas Tille 
Date:   Mon Sep 18 10:15:18 2017 +0200

New upstream version 0.4.2.0
---
 .hgignore|  9 +
 PKG-INFO | 57 ---
 dicompyler.egg-info/PKG-INFO | 57 ---
 dicompyler.egg-info/SOURCES.txt  | 67 
 dicompyler.egg-info/dependency_links.txt |  1 -
 dicompyler.egg-info/entry_points.txt |  3 --
 dicompyler.egg-info/not-zip-safe |  1 -
 dicompyler.egg-info/requires.txt |  4 --
 dicompyler.egg-info/top_level.txt|  1 -
 README.txt => readme.txt |  0
 scripts/dicompyler   | 12 ++
 setup.cfg|  5 ---
 12 files changed, 21 insertions(+), 196 deletions(-)

diff --git a/.hgignore b/.hgignore
new file mode 100644
index 000..390e69f
--- /dev/null
+++ b/.hgignore
@@ -0,0 +1,9 @@
+syntax: glob
+*.pyc
+*~
+.*.swp
+.DS_Store
+.AppleDouble
+._*
+dist
+build
diff --git a/PKG-INFO b/PKG-INFO
deleted file mode 100644
index 89308ab..000
--- a/PKG-INFO
+++ /dev/null
@@ -1,57 +0,0 @@
-Metadata-Version: 1.1
-Name: dicompyler
-Version: 0.4.2
-Summary: Extensible radiation therapy research platform and viewer for DICOM 
and DICOM RT.
-Home-page: http://code.google.com/p/dicompyler/
-Author: Aditya Panchal
-Author-email: apanc...@bastula.org
-License: BSD License
-Description: 
-dicompyler
-==
-
-dicompyler is an extensible open source radiation therapy research 
-platform based on the DICOM standard. It also functions as a 
-cross-platform DICOM RT viewer.
-
-dicompyler runs on Windows, Mac and Linux systems and is available 
in 
-source and binary versions. Since dicompyler is based on modular 
-architecture, it is easy to extend it with 3rd party plugins.
-
-Visit the dicompyler _`home page`:
-http://code.google.com/p/dicompyler/ for how-to information and 
guides.
-
-Getting Help
-
-
-To get help with dicompyler, visit the _`mailing list`: 
-http://groups.google.com/group/dicompyler/ or follow us on 
_`twitter`: 
-http://twitter.com/dicompyler
-
-Requirements
-
-
-dicompyler requires the following packages to run from source:
-
-- Python 2.5 or higher (not tested on Python 3)
-- wxPython 2.8.8.1 to 2.8.10.1
-- matplotlib 0.99 to 1.10
-- numpy 1.2.1 or higher
-- PIL 1.1.7 or any version of Pillow
-- pydicom 0.9.5 or 0.9.6
-- simplejson (only for Python 2.5, Python 2.6+ includes JSON 
support)
-Keywords: radiation therapy research python dicom dicom-rt
-Platform: UNKNOWN
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: Intended Audience :: Science/Research
-Classifier: Development Status :: 4 - Beta
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2.5
-Classifier: Programming Language :: Python :: 2.6
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: Topic :: Scientific/Engineering :: Visualization
diff --git a/dicompyler.egg-info/PKG-INFO b/dicompyler.egg-info/PKG-INFO
deleted file mode 100644
index 89308ab..000
--- a/dicompyler.egg-info/PKG-INFO
+++ /dev/null
@@ -1,57 +0,0 @@
-Metadata-Version: 1.1
-Name: dicompyler
-Version: 0.4.2
-Summary: Extensible radiation therapy research platform and viewer for DICOM 
and DICOM RT.
-Home-page: http://code.google.com/p/dicompyler/
-Author: Aditya Panchal
-Author-email: apanc...@bastula.org
-License: BSD License
-Description: 
-dicompyler
-==
-
-dicompyler is an extensible open source radiation therapy research 
-platform based on the DICOM standard. It also functions as a 
-cross-platform DICOM RT viewer.
-
-dicompyler runs on Windows, Mac and Linux systems and is available 
in 
-source and binary versions. Since dicompyler is based on modular 
-architecture, it is easy to extend it with 3rd party plugins.
-
-Visit the dicompyler _`home page`:
-http://code.google.com/p/dicompyler/ for how-to information and 
guide

[med-svn] [dicompyler] branch master updated (08e0e30 -> a762a37)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository dicompyler.

  from  08e0e30   More patches to finally work with wx 3.0
   new  4f2ebd3   New upstream version 0.4.2.0
   new  2229466   Updated version 0.4.2.0 from 'upstream/0.4.2.0'
   new  c0dbaa5   Not really new upstream version but content of upstream 
source archive on Github has changed
   new  a762a37   In new source tarball README.txt was renamed to readme.txt

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .hgignore|  9 
 PKG-INFO | 57 ---
 debian/changelog |  4 +-
 debian/docs  |  2 +-
 dicompyler.egg-info/PKG-INFO | 57 ---
 dicompyler.egg-info/SOURCES.txt  | 67 
 dicompyler.egg-info/dependency_links.txt |  1 -
 dicompyler.egg-info/entry_points.txt |  3 --
 dicompyler.egg-info/not-zip-safe |  1 -
 dicompyler.egg-info/requires.txt |  4 --
 dicompyler.egg-info/top_level.txt|  1 -
 README.txt => readme.txt |  0
 dicompyler/__init__.py => scripts/dicompyler | 10 ++---
 setup.cfg|  5 ---
 14 files changed, 17 insertions(+), 204 deletions(-)
 create mode 100644 .hgignore
 delete mode 100644 PKG-INFO
 delete mode 100644 dicompyler.egg-info/PKG-INFO
 delete mode 100644 dicompyler.egg-info/SOURCES.txt
 delete mode 100644 dicompyler.egg-info/dependency_links.txt
 delete mode 100644 dicompyler.egg-info/entry_points.txt
 delete mode 100644 dicompyler.egg-info/not-zip-safe
 delete mode 100644 dicompyler.egg-info/requires.txt
 delete mode 100644 dicompyler.egg-info/top_level.txt
 rename README.txt => readme.txt (100%)
 copy dicompyler/__init__.py => scripts/dicompyler (61%)
 mode change 100644 => 100755
 delete mode 100644 setup.cfg

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[med-svn] [dicompyler] 03/04: Not really new upstream version but content of upstream source archive on Github has changed

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit c0dbaa58ac01c5924a061452036ea7f866047a35
Author: Andreas Tille 
Date:   Mon Sep 18 10:16:23 2017 +0200

Not really new upstream version but content of upstream source archive on 
Github has changed
---
 debian/changelog | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index c212ffe..8fe181d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,9 @@
-dicompyler (0.4.2-5) UNRELEASED; urgency=medium
+dicompyler (0.4.2.0-1) UNRELEASED; urgency=medium
 
   * Team upload
   * More patches to finally work with wx 3.0
+  * Not really new upstream version but content of upstream source archive
+on Github has changed
 
  -- Vojtech Kulvait   Mon, 18 Sep 2017 09:54:37 +0200
 

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[med-svn] [dicompyler] 01/01: pristine-tar data for dicompyler_0.4.2.0.orig.tar.gz

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository dicompyler.

commit b071327047335c7d2d56c8988e5800b2a1c1c80b
Author: Andreas Tille 
Date:   Mon Sep 18 10:15:19 2017 +0200

pristine-tar data for dicompyler_0.4.2.0.orig.tar.gz
---
 dicompyler_0.4.2.0.orig.tar.gz.delta | Bin 0 -> 2718 bytes
 dicompyler_0.4.2.0.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/dicompyler_0.4.2.0.orig.tar.gz.delta 
b/dicompyler_0.4.2.0.orig.tar.gz.delta
new file mode 100644
index 000..c027439
Binary files /dev/null and b/dicompyler_0.4.2.0.orig.tar.gz.delta differ
diff --git a/dicompyler_0.4.2.0.orig.tar.gz.id 
b/dicompyler_0.4.2.0.orig.tar.gz.id
new file mode 100644
index 000..eaf47e9
--- /dev/null
+++ b/dicompyler_0.4.2.0.orig.tar.gz.id
@@ -0,0 +1 @@
+8158c8604128c02859edd6424c2f983403bded0d

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[med-svn] [dicompyler] branch upstream updated (07f34b4 -> 4f2ebd3)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository dicompyler.

  from  07f34b4   New upstream version 0.4.2
   new  4f2ebd3   New upstream version 0.4.2.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .hgignore|  9 
 PKG-INFO | 57 ---
 dicompyler.egg-info/PKG-INFO | 57 ---
 dicompyler.egg-info/SOURCES.txt  | 67 
 dicompyler.egg-info/dependency_links.txt |  1 -
 dicompyler.egg-info/entry_points.txt |  3 --
 dicompyler.egg-info/not-zip-safe |  1 -
 dicompyler.egg-info/requires.txt |  4 --
 dicompyler.egg-info/top_level.txt|  1 -
 README.txt => readme.txt |  0
 dicompyler/__init__.py => scripts/dicompyler | 10 ++---
 setup.cfg|  5 ---
 12 files changed, 13 insertions(+), 202 deletions(-)
 create mode 100644 .hgignore
 delete mode 100644 PKG-INFO
 delete mode 100644 dicompyler.egg-info/PKG-INFO
 delete mode 100644 dicompyler.egg-info/SOURCES.txt
 delete mode 100644 dicompyler.egg-info/dependency_links.txt
 delete mode 100644 dicompyler.egg-info/entry_points.txt
 delete mode 100644 dicompyler.egg-info/not-zip-safe
 delete mode 100644 dicompyler.egg-info/requires.txt
 delete mode 100644 dicompyler.egg-info/top_level.txt
 rename README.txt => readme.txt (100%)
 copy dicompyler/__init__.py => scripts/dicompyler (61%)
 mode change 100644 => 100755
 delete mode 100644 setup.cfg

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[med-svn] [dicompyler] branch pristine-tar updated (f770759 -> b071327)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch pristine-tar
in repository dicompyler.

  from  f770759   pristine-tar data for dicompyler_0.4.2.orig.tar.gz
   new  b071327   pristine-tar data for dicompyler_0.4.2.0.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 dicompyler_0.4.2.0.orig.tar.gz.delta | Bin 0 -> 2718 bytes
 dicompyler_0.4.2.0.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 dicompyler_0.4.2.0.orig.tar.gz.delta
 create mode 100644 dicompyler_0.4.2.0.orig.tar.gz.id

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[med-svn] [dicompyler] 04/04: In new source tarball README.txt was renamed to readme.txt

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit a762a37b9cdce45d006f792b23e1b501bb2c5e89
Author: Andreas Tille 
Date:   Mon Sep 18 10:16:42 2017 +0200

In new source tarball README.txt was renamed to readme.txt
---
 debian/docs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/docs b/debian/docs
index 71dfd5b..b2b2a78 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1 @@
-README.txt
+readme.txt

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[med-svn] [dicompyler] annotated tag upstream/0.4.2.0 created (now e0bd37a)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to annotated tag upstream/0.4.2.0
in repository dicompyler.

at  e0bd37a   (tag)
   tagging  4f2ebd3c9e2a643a5930d292aa860357ddcba90e (commit)
  replaces  upstream/0.4.2
 tagged by  Andreas Tille
on  Mon Sep 18 10:15:19 2017 +0200

- Log -
Upstream version 0.4.2.0

Andreas Tille (1):
  New upstream version 0.4.2.0

---

This annotated tag includes the following new commits:

   new  4f2ebd3   New upstream version 0.4.2.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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[med-svn] [rdp-classifier] branch master updated (a7d4f53 -> bd9c4ea)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository rdp-classifier.

  from  a7d4f53   Fix changelog
   new  bd9c4ea   Upload to unstable

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repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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[med-svn] [rdp-classifier] 01/01: Upload to unstable

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository rdp-classifier.

commit bd9c4ea7bf2f1374a1f00b5590b33b0dd167ace0
Author: Andreas Tille 
Date:   Mon Sep 18 11:09:13 2017 +0200

Upload to unstable
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index ec68928..68fd496 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium
+rdp-classifier (2.10.2-2) unstable; urgency=medium
 
   * Team upload
 

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[med-svn] [rdp-classifier] tag debian/2.10.2-2 created (now bd9c4ea)

2017-09-18 Thread Andreas Tille

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tille pushed a change to tag debian/2.10.2-2
in repository rdp-classifier.

at  bd9c4ea   (commit)
No new revisions were added by this update.

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[med-svn] [edfbrowser] 01/05: Builds now with Qt5

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository edfbrowser.

commit 03d116053a6e9f094d6979614c54fb9f19cd0102
Author: Andreas Tille 
Date:   Sun Sep 10 19:55:39 2017 +0200

Builds now with Qt5
---
 debian/rules | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/debian/rules b/debian/rules
index f3effba..d854343 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,11 +21,13 @@ else
   QMAKE_CXXFLAGS_RELEASE = -O2
 endif
 
+export QT_SELECT=qt5
+
 %:
dh $@
 
 override_dh_auto_build:
-   qmake-qt4 -makefile -after \
+   qmake -makefile -after \
QMAKE_CXXFLAGS="$(QMAKE_CXXFLAGS)" \
QMAKE_CXXFLAGS_RELEASE="$(QMAKE_CXXFLAGS_RELEASE)" \
QMAKE_LFLAGS="$(Q_LDFLAGS)"

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[med-svn] [edfbrowser] branch master updated (d268967 -> 6ca02b5)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch master
in repository edfbrowser.

  from  d268967   Hints by Nicolas Guilbert  - but it does 
not build yet.
   new  03d1160   Builds now with Qt5
   new  1383aca   Close bug, upload to unstable
   new  5e83817   New upstream version 1.60
   new  54591f0   Updated version 1.60 from 'upstream/1.60'
   new  6ca02b5   New upstream version

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 README.txt |  71 +++-
 ascii2edf.cpp  |  23 +-
 averager_dialog.cpp|  17 +
 biosemi2bdfplus.cpp|   1 +
 check_edf_file.cpp |  13 +-
 debian/changelog   |  11 +-
 debian/rules   |   4 +-
 doc/manual.html|  48 ++-
 edf_annot_list.c   |  82 
 edf_annot_list.h   |   3 +
 edf_annotations.cpp|  12 +-
 edfbrowser.pro |  18 +-
 edflib.c   |  20 +-
 edit_annotation_dock.cpp   |  12 +-
 edit_annotation_dock.h |   1 +
 filteredblockread.cpp  |   5 +
 global.h   |   9 +-
 header_editor.cpp  | 103 -
 images/splash.png  | Bin 9305 -> 9306 bytes
 import_annotations.cpp |   5 +
 load_montage_dialog.cpp| 138 ++-
 load_montage_dialog.h  |   1 +
 mainwindow.cpp | 108 +-
 mainwindow.h   |   5 +
 mainwindow_constr.cpp  |  35 +-
 mit2edf.cpp|  75 +++-
 mit2edf.h  |   1 +
 options_dialog.cpp |  83 +++-
 options_dialog.h   |   3 +
 plif_ecg_subtract_filter.c | 416 +
 plif_ecg_subtract_filter.h |  89 +
 plif_ecg_subtract_filter_dialog.cpp| 301 +++
 ...r_dialog.h => plif_ecg_subtract_filter_dialog.h |  29 +-
 print_to_bdf.cpp   |  21 +-
 print_to_edf.cpp   |  19 +-
 read_write_settings.cpp|  45 ++-
 save_montage_dialog.cpp|   9 +
 show_actual_montage_dialog.cpp |   8 +
 signal_chooser.cpp |  14 +
 signals_dialog.cpp |   2 +-
 spectrum_dock.cpp  |  17 +
 spectrumanalyzer.cpp   |  17 +
 version.txt|  25 ++
 view_montage_dialog.cpp|  63 +++-
 viewbuf.cpp|  24 +-
 viewcurve.cpp  | 135 ++-
 viewcurve.h|   2 +
 47 files changed, 2011 insertions(+), 132 deletions(-)
 create mode 100644 plif_ecg_subtract_filter.c
 create mode 100644 plif_ecg_subtract_filter.h
 create mode 100644 plif_ecg_subtract_filter_dialog.cpp
 copy spike_filter_dialog.h => plif_ecg_subtract_filter_dialog.h (76%)

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[med-svn] [edfbrowser] 05/05: New upstream version

2017-09-18 Thread Andreas Tille

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in repository edfbrowser.

commit 6ca02b52a25da7b2e0a7f3cb82388d1e84696bd6
Author: Andreas Tille 
Date:   Mon Sep 18 11:35:25 2017 +0200

New upstream version
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index dda8b35..ebfdf48 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+edfbrowser (1.60-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille   Mon, 18 Sep 2017 11:24:47 +0200
+
 edfbrowser (1.59-2) unstable; urgency=medium
 
   * Switch build to Qt5

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[med-svn] [edfbrowser] branch pristine-tar updated (04bb0f8 -> f22ee4c)

2017-09-18 Thread Andreas Tille

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  from  04bb0f8   pristine-tar data for edfbrowser_1.59.orig.tar.gz
   new  f22ee4c   pristine-tar data for edfbrowser_1.60.orig.tar.gz

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listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 edfbrowser_1.60.orig.tar.gz.delta | Bin 0 -> 10954 bytes
 edfbrowser_1.60.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 edfbrowser_1.60.orig.tar.gz.delta
 create mode 100644 edfbrowser_1.60.orig.tar.gz.id

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[med-svn] [edfbrowser] 03/05: New upstream version 1.60

2017-09-18 Thread Andreas Tille

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in repository edfbrowser.

commit 5e83817f3e82c7fe450def9077313fce4fe755fc
Author: Andreas Tille 
Date:   Mon Sep 18 11:23:42 2017 +0200

New upstream version 1.60
---
 README.txt |  71 +++-
 ascii2edf.cpp  |  23 +-
 averager_dialog.cpp|  17 +
 biosemi2bdfplus.cpp|   1 +
 check_edf_file.cpp |  13 +-
 doc/manual.html|  48 ++-
 edf_annot_list.c   |  82 
 edf_annot_list.h   |   3 +
 edf_annotations.cpp|  12 +-
 edfbrowser.pro |  18 +-
 edflib.c   |  20 +-
 edit_annotation_dock.cpp   |  12 +-
 edit_annotation_dock.h |   1 +
 filteredblockread.cpp  |   5 +
 global.h   |   9 +-
 header_editor.cpp  | 103 -
 images/splash.png  | Bin 9305 -> 9306 bytes
 import_annotations.cpp |   5 +
 load_montage_dialog.cpp| 138 ++-
 load_montage_dialog.h  |   1 +
 mainwindow.cpp | 108 +-
 mainwindow.h   |   5 +
 mainwindow_constr.cpp  |  35 +-
 mit2edf.cpp|  75 +++-
 mit2edf.h  |   1 +
 options_dialog.cpp |  83 +++-
 options_dialog.h   |   3 +
 plif_ecg_subtract_filter.c | 416 +
 plif_ecg_subtract_filter.h |  89 +
 plif_ecg_subtract_filter_dialog.cpp| 301 +++
 ...e_dialog.h => plif_ecg_subtract_filter_dialog.h |  63 ++--
 print_to_bdf.cpp   |  21 +-
 print_to_edf.cpp   |  19 +-
 read_write_settings.cpp|  45 ++-
 save_montage_dialog.cpp|   9 +
 show_actual_montage_dialog.cpp |   8 +
 signal_chooser.cpp |  14 +
 signals_dialog.cpp |   2 +-
 spectrum_dock.cpp  |  17 +
 spectrumanalyzer.cpp   |  17 +
 version.txt|  25 ++
 view_montage_dialog.cpp|  63 +++-
 viewbuf.cpp|  24 +-
 viewcurve.cpp  | 135 ++-
 viewcurve.h|   2 +
 45 files changed, 2018 insertions(+), 144 deletions(-)

diff --git a/README.txt b/README.txt
index f1ecc56..2a72c23 100644
--- a/README.txt
+++ b/README.txt
@@ -5,7 +5,8 @@ Qt  http://www.qt.io/
 
 Minimum version 4.7.1 or later, preferable 4.8.7
 
-Do not use Qt 5.x.x to compile EDFbrowser, Qt5 is not yet ready for production 
use. It contains still bugs that affects EDFbrowser.
+If you insist on using Qt5 (which I don't recommend), it must be version >= 
5.9.1.
+For info how to compile Qt5 from source, scroll down.
 
 
 The GCC compiler on Linux or Mingw-w64 on windows. 

@@ -72,5 +73,73 @@ How to compile (step by step)
 Now you can run the program by typing: edfbrowser
 
 
+In case you insist on using Qt5, the recommended way is not to use the Qt5 
libraries that comes with your distro.
+Instead, download and compile the Qt5 source and use that to compile 
EDFbrowser.
+Here's a step by step list of instuctions:
+
+First, fulfill the requirements for Qt:
+
+http://doc.qt.io/qt-5/linux.html
+
+Debian/Ubuntu: sudo apt-get install build-essential libgl1-mesa-dev 
libcups2-dev libx11-dev
+
+Fedora: sudo dnf groupinstall "C Development Tools and Libraries"
+sudo dnf install mesa-libGL-devel cups-devel libx11-dev
+
+openSUSE: sudo zypper install -t pattern devel_basis
+  sudo zypper install xorg-x11-devel cups-devel freetype-devel 
fontconfig-devel
+
+#
+#  
 #
+# Compile a static version of the Qt5 libraries excluding all modules that are 
not needed.  #
+#  
 #
+# This will not mess with your system libraries. The new compiled libraries 
will be stored  #
+#

[med-svn] [edfbrowser] branch upstream updated (82babf1 -> 5e83817)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository edfbrowser.

  from  82babf1   New upstream version 1.59
   new  5e83817   New upstream version 1.60

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 README.txt |  71 +++-
 ascii2edf.cpp  |  23 +-
 averager_dialog.cpp|  17 +
 biosemi2bdfplus.cpp|   1 +
 check_edf_file.cpp |  13 +-
 doc/manual.html|  48 ++-
 edf_annot_list.c   |  82 
 edf_annot_list.h   |   3 +
 edf_annotations.cpp|  12 +-
 edfbrowser.pro |  18 +-
 edflib.c   |  20 +-
 edit_annotation_dock.cpp   |  12 +-
 edit_annotation_dock.h |   1 +
 filteredblockread.cpp  |   5 +
 global.h   |   9 +-
 header_editor.cpp  | 103 -
 images/splash.png  | Bin 9305 -> 9306 bytes
 import_annotations.cpp |   5 +
 load_montage_dialog.cpp| 138 ++-
 load_montage_dialog.h  |   1 +
 mainwindow.cpp | 108 +-
 mainwindow.h   |   5 +
 mainwindow_constr.cpp  |  35 +-
 mit2edf.cpp|  75 +++-
 mit2edf.h  |   1 +
 options_dialog.cpp |  83 +++-
 options_dialog.h   |   3 +
 plif_ecg_subtract_filter.c | 416 +
 plif_ecg_subtract_filter.h |  89 +
 plif_ecg_subtract_filter_dialog.cpp| 301 +++
 ...r_dialog.h => plif_ecg_subtract_filter_dialog.h |  29 +-
 print_to_bdf.cpp   |  21 +-
 print_to_edf.cpp   |  19 +-
 read_write_settings.cpp|  45 ++-
 save_montage_dialog.cpp|   9 +
 show_actual_montage_dialog.cpp |   8 +
 signal_chooser.cpp |  14 +
 signals_dialog.cpp |   2 +-
 spectrum_dock.cpp  |  17 +
 spectrumanalyzer.cpp   |  17 +
 version.txt|  25 ++
 view_montage_dialog.cpp|  63 +++-
 viewbuf.cpp|  24 +-
 viewcurve.cpp  | 135 ++-
 viewcurve.h|   2 +
 45 files changed, 1999 insertions(+), 129 deletions(-)
 create mode 100644 plif_ecg_subtract_filter.c
 create mode 100644 plif_ecg_subtract_filter.h
 create mode 100644 plif_ecg_subtract_filter_dialog.cpp
 copy spike_filter_dialog.h => plif_ecg_subtract_filter_dialog.h (76%)

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[med-svn] [edfbrowser] 01/01: pristine-tar data for edfbrowser_1.60.orig.tar.gz

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository edfbrowser.

commit f22ee4c0a61678a801b582a4cb928ba65c7bbff5
Author: Andreas Tille 
Date:   Mon Sep 18 11:23:44 2017 +0200

pristine-tar data for edfbrowser_1.60.orig.tar.gz
---
 edfbrowser_1.60.orig.tar.gz.delta | Bin 0 -> 10954 bytes
 edfbrowser_1.60.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/edfbrowser_1.60.orig.tar.gz.delta 
b/edfbrowser_1.60.orig.tar.gz.delta
new file mode 100644
index 000..fd30c20
Binary files /dev/null and b/edfbrowser_1.60.orig.tar.gz.delta differ
diff --git a/edfbrowser_1.60.orig.tar.gz.id b/edfbrowser_1.60.orig.tar.gz.id
new file mode 100644
index 000..579091b
--- /dev/null
+++ b/edfbrowser_1.60.orig.tar.gz.id
@@ -0,0 +1 @@
+1af6f7cc20160608c36f8bba466eae7882f10a66

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[med-svn] [edfbrowser] 04/05: Updated version 1.60 from 'upstream/1.60'

2017-09-18 Thread Andreas Tille

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tille pushed a commit to branch master
in repository edfbrowser.

commit 54591f055c1cafefe0a83f499f840ceea976257e
Merge: 1383aca 5e83817
Author: Andreas Tille 
Date:   Mon Sep 18 11:23:44 2017 +0200

Updated version 1.60 from 'upstream/1.60'

with Debian dir 70befd141e7c250fb36841791aa79259713649b5

 README.txt |  71 +++-
 ascii2edf.cpp  |  23 +-
 averager_dialog.cpp|  17 +
 biosemi2bdfplus.cpp|   1 +
 check_edf_file.cpp |  13 +-
 doc/manual.html|  48 ++-
 edf_annot_list.c   |  82 
 edf_annot_list.h   |   3 +
 edf_annotations.cpp|  12 +-
 edfbrowser.pro |  18 +-
 edflib.c   |  20 +-
 edit_annotation_dock.cpp   |  12 +-
 edit_annotation_dock.h |   1 +
 filteredblockread.cpp  |   5 +
 global.h   |   9 +-
 header_editor.cpp  | 103 -
 images/splash.png  | Bin 9305 -> 9306 bytes
 import_annotations.cpp |   5 +
 load_montage_dialog.cpp| 138 ++-
 load_montage_dialog.h  |   1 +
 mainwindow.cpp | 108 +-
 mainwindow.h   |   5 +
 mainwindow_constr.cpp  |  35 +-
 mit2edf.cpp|  75 +++-
 mit2edf.h  |   1 +
 options_dialog.cpp |  83 +++-
 options_dialog.h   |   3 +
 plif_ecg_subtract_filter.c | 416 +
 plif_ecg_subtract_filter.h |  89 +
 plif_ecg_subtract_filter_dialog.cpp| 301 +++
 ...e_dialog.h => plif_ecg_subtract_filter_dialog.h |  63 ++--
 print_to_bdf.cpp   |  21 +-
 print_to_edf.cpp   |  19 +-
 read_write_settings.cpp|  45 ++-
 save_montage_dialog.cpp|   9 +
 show_actual_montage_dialog.cpp |   8 +
 signal_chooser.cpp |  14 +
 signals_dialog.cpp |   2 +-
 spectrum_dock.cpp  |  17 +
 spectrumanalyzer.cpp   |  17 +
 version.txt|  25 ++
 view_montage_dialog.cpp|  63 +++-
 viewbuf.cpp|  24 +-
 viewcurve.cpp  | 135 ++-
 viewcurve.h|   2 +
 45 files changed, 2018 insertions(+), 144 deletions(-)

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[med-svn] [edfbrowser] 02/05: Close bug, upload to unstable

2017-09-18 Thread Andreas Tille

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tille pushed a commit to branch master
in repository edfbrowser.

commit 1383aca7e28a6d78738f6dfb52b122e2751905f1
Author: Andreas Tille 
Date:   Sun Sep 10 20:09:22 2017 +0200

Close bug, upload to unstable
---
 debian/changelog | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 266260f..dda8b35 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-edfbrowser (1.59-2) UNRELEASED; urgency=medium
+edfbrowser (1.59-2) unstable; urgency=medium
 
   * Switch build to Qt5
+Closes: #874858
 
- -- Andreas Tille   Sun, 10 Sep 2017 00:08:57 +0200
+ -- Andreas Tille   Sun, 10 Sep 2017 20:08:43 +0200
 
 edfbrowser (1.59-1) unstable; urgency=medium
 

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[med-svn] [edfbrowser] tag debian/1.60-1 created (now 6ca02b5)

2017-09-18 Thread Andreas Tille

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in repository edfbrowser.

at  6ca02b5   (commit)
No new revisions were added by this update.

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[med-svn] [edfbrowser] annotated tag upstream/1.60 created (now 94d0e59)

2017-09-18 Thread Andreas Tille

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tille pushed a change to annotated tag upstream/1.60
in repository edfbrowser.

at  94d0e59   (tag)
   tagging  5e83817f3e82c7fe450def9077313fce4fe755fc (commit)
  replaces  upstream/1.59
 tagged by  Andreas Tille
on  Mon Sep 18 11:23:44 2017 +0200

- Log -
Upstream version 1.60

Andreas Tille (1):
  New upstream version 1.60

---

This annotated tag includes the following new commits:

   new  5e83817   New upstream version 1.60

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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[med-svn] r24056 - in trunk/packages/autodocksuite/trunk/debian: . upstream

2017-09-18 Thread Steffen Möller

Author: moeller
Date: 2017-09-18 10:04:00 + (Mon, 18 Sep 2017)
New Revision: 24056

Modified:
   trunk/packages/autodocksuite/trunk/debian/changelog
   trunk/packages/autodocksuite/trunk/debian/control
   trunk/packages/autodocksuite/trunk/debian/upstream/metadata
Log:
Added references to registries.


Modified: trunk/packages/autodocksuite/trunk/debian/changelog
===
--- trunk/packages/autodocksuite/trunk/debian/changelog 2017-09-18 07:11:21 UTC 
(rev 24055)
+++ trunk/packages/autodocksuite/trunk/debian/changelog 2017-09-18 10:04:00 UTC 
(rev 24056)
@@ -1,3 +1,13 @@
+autodocksuite (4.2.6-4) UNRELEASED; urgency=medium
+
+  * debian/upstream/metadata:
+- Added Nat. Prot. paper
+- Added references to registries
+- yamllint cleanliness - mostly
+  * Bumped policy to 4.1.0 (no changes)
+
+ -- Steffen Moeller   Mon, 18 Sep 2017 12:02:27 +0200 
+
 autodocksuite (4.2.6-3) unstable; urgency=medium
 
   * cme fix dpkg-control

Modified: trunk/packages/autodocksuite/trunk/debian/control
===
--- trunk/packages/autodocksuite/trunk/debian/control   2017-09-18 07:11:21 UTC 
(rev 24055)
+++ trunk/packages/autodocksuite/trunk/debian/control   2017-09-18 10:04:00 UTC 
(rev 24056)
@@ -11,7 +11,7 @@
automake,
python,
autotools-dev
-Standards-Version: 3.9.6
+Standards-Version: 4.1.0
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/autodocksuite/trunk/
 Vcs-Svn: 
svn://anonscm.debian.org/debian-med/trunk/packages/autodocksuite/trunk/
 Homepage: http://autodock.scripps.edu/

Modified: trunk/packages/autodocksuite/trunk/debian/upstream/metadata
===
--- trunk/packages/autodocksuite/trunk/debian/upstream/metadata 2017-09-18 
07:11:21 UTC (rev 24055)
+++ trunk/packages/autodocksuite/trunk/debian/upstream/metadata 2017-09-18 
10:04:00 UTC (rev 24056)
@@ -1,10 +1,15 @@
-Donation: 
http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+Donation: "http://autodock.scripps.edu/downloads/\
+ autodock-registration/autodock-4-2-download-page/"
 Homepage: http://autodock.scripps.edu/
 Name: AutoDock
 Reference:
- - Author: Garrett M. Morris and Ruth Huey and William Lindstrom and Michel F. 
Sanner and Richard K. Belew and David S. Goodsell and Arthur J. Olson
+ - Author: >
+Garrett M. Morris and Ruth Huey and William Lindstrom and Michel
+F. Sanner and Richard K. Belew and David S. Goodsell and Arthur
+J. Olson
Title: >
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor 
flexibility
+AutoDock4 and AutoDockTools4: Automated docking with selective
+receptor flexibility
Journal: Journal of Computational Chemistry
Volume: 30
Number: 16
@@ -13,18 +18,26 @@
PMID: 19399780
DOI: 10.1002/jcc.21256
URL: http://www3.interscience.wiley.com/journal/122365050/abstract
- - Debian-package: autodock-getdata
-   Author: John J. Irwin and Brian K. Shoichet
-   Title: "ZINC – A Free Database of Commercially Available Compounds for 
Virtual Screening"
-   Journal: J Chem Inf Model.
-   Volume: 45
-   Number: 1
-   Pages: 177-182
-   Year: 2005
-   DOI: 10.1021/ci049714
-   PMID: 15667143
-   URL: http://pubs.acs.org/doi/abs/10.1021/ci049714%2B
-   eprint: http://pubs.acs.org/doi/pdf/10.1021/ci049714%2B
+ - Author: >
+Stefano Forli and Ruth Huey and Michael E Pique and Michel F Sanner
+and David S Goodsell and Arthur J Olson
+   Journal: Nature Protocols
+   Title: >
+Computational protein–ligand docking and virtual drug screening
+with the AutoDock suite
+   Volume: 11
+   Pages: 905–919
+   Year: 2016
+   DOI: 10.1038/nprot.2016.051
+   PMID: 27077332
+   URL: http://www.nature.com/nprot/journal/v11/n5/full/nprot.2016.051.html
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_19997
+ - Name: RRID
+   Entry: SCR_012746
+ - Name: bio.tools
+   Entry: NA
 Registration: http://autodock.scripps.edu/downloads/autodock-registration
 Watch: |
  opts="dversionmangle=s/\+rc/~rc/" \


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[med-svn] r24057 - in trunk/packages/autodock-vina/trunk/debian: . upstream

2017-09-18 Thread Steffen Möller

Author: moeller
Date: 2017-09-18 10:46:30 + (Mon, 18 Sep 2017)
New Revision: 24057

Modified:
   trunk/packages/autodock-vina/trunk/debian/changelog
   trunk/packages/autodock-vina/trunk/debian/upstream/metadata
Log:
Added references to registries.


Modified: trunk/packages/autodock-vina/trunk/debian/changelog
===
--- trunk/packages/autodock-vina/trunk/debian/changelog 2017-09-18 10:04:00 UTC 
(rev 24056)
+++ trunk/packages/autodock-vina/trunk/debian/changelog 2017-09-18 10:46:30 UTC 
(rev 24057)
@@ -1,3 +1,11 @@
+autodock-vina (1.1.2-4) UNRELEASED; urgency=low
+
+  * debian/upstream/metadata
+- yamllint cleanliness
+- Added references to registries
+
+ -- Steffen Moeller   Mon, 18 Sep 2017 12:36:01 +0200
+
 autodock-vina (1.1.2-3) unstable; urgency=low
 
   [ Andreas Tille ]

Modified: trunk/packages/autodock-vina/trunk/debian/upstream/metadata
===
--- trunk/packages/autodock-vina/trunk/debian/upstream/metadata 2017-09-18 
10:04:00 UTC (rev 24056)
+++ trunk/packages/autodock-vina/trunk/debian/upstream/metadata 2017-09-18 
10:46:30 UTC (rev 24057)
@@ -4,7 +4,8 @@
 Reference:
   author: Oleg Trott and Arthur J. Olson
   title: >
-AutoDock Vina: Improving the speed and accuracy of docking with a new 
scoring function, efficient optimization, and multithreading
+AutoDock Vina: Improving the speed and accuracy of docking with a
+new scoring function, efficient optimization, and multithreading
   journal: Journal of Computational Chemistry
   volume: 31
   number: 2
@@ -13,3 +14,10 @@
   DOI: 10.1002/jcc.21334
   URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract
   eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/full
+Registry:
+  - Name: OMICtools
+Entry: OMICS_03790
+  - Name: RRID
+Entry: SCR_011958
+  - Name: bio.tools
+Entry: NA


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[med-svn] [probabel] 03/03: Drop autoconf dependency (redundant for debhelper 10), upload to unstable

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository probabel.

commit 83d5eaa9d35326e78c304e78b4dc4f8438ade8c2
Author: Andreas Tille 
Date:   Mon Sep 18 13:02:43 2017 +0200

Drop autoconf dependency (redundant for debhelper 10), upload to unstable
---
 debian/changelog | 5 +++--
 debian/control   | 2 --
 debian/rules | 8 +---
 3 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 4decec3..08d664d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,11 @@
-probabel (0.4.5-5) UNRELEASED; urgency=medium
+probabel (0.4.5-5) unstable; urgency=medium
 
   * Ignore errors in test suite for big endian architectures
 Closes: #865191
   * Standards-Version: 4.1.0
+  * Drop autoconf dependency (redundant for debhelper 10)
 
- -- Andreas Tille   Mon, 18 Sep 2017 12:54:20 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 12:55:39 +0200
 
 probabel (0.4.5-4) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index 3962ded..d91bc93 100644
--- a/debian/control
+++ b/debian/control
@@ -5,8 +5,6 @@ Uploaders: Andreas Tille ,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
-   autotools-dev,
-   dh-autoreconf,
texlive-latex-base,
texlive-latex-extra,
texlive-latex-recommended,
diff --git a/debian/rules b/debian/rules
index 99b2126..fec66c5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,14 +12,8 @@ include /usr/share/dpkg/default.mk
 # probabel-examples package
 DEBEXAMPLES:=$(DEB_SOURCE)-examples
 
-
-# alternatively to manually set those variables you can
-#  include /usr/share/cdbs/1/rules/buildvars.mk
-# and use what is set there.  Any hint whether dh might set variables in
-# a similar manner are welcome.
-
 %:
-   dh $@ --with autoreconf
+   dh $@
 
 override_dh_auto_configure:
dh_auto_configure -- --disable-silent-rules

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[med-svn] [probabel] 02/03: Standards-Version: 4.1.0

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository probabel.

commit a8d61db851ac5f8f05881de8ec38b4a67c572c2e
Author: Andreas Tille 
Date:   Mon Sep 18 12:55:33 2017 +0200

Standards-Version: 4.1.0
---
 debian/changelog | 1 +
 debian/control   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 480abea..4decec3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ probabel (0.4.5-5) UNRELEASED; urgency=medium
 
   * Ignore errors in test suite for big endian architectures
 Closes: #865191
+  * Standards-Version: 4.1.0
 
  -- Andreas Tille   Mon, 18 Sep 2017 12:54:20 +0200
 
diff --git a/debian/control b/debian/control
index 8963e9a..3962ded 100644
--- a/debian/control
+++ b/debian/control
@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 10),
texlive-latex-recommended,
texlive-fonts-recommended,
libeigen3-dev
-Standards-Version: 4.0.0
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/probabel.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/probabel.git
 Homepage: http://www.genabel.org

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[med-svn] [probabel] 01/03: Ignore errors in test suite for big endian architectures

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository probabel.

commit b48a6d5db021fb16ad61056499eff9839375842e
Author: Andreas Tille 
Date:   Mon Sep 18 12:55:06 2017 +0200

Ignore errors in test suite for big endian architectures
---
 debian/changelog |  7 +++
 debian/rules | 13 +
 2 files changed, 20 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index dcd95cb..480abea 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+probabel (0.4.5-5) UNRELEASED; urgency=medium
+
+  * Ignore errors in test suite for big endian architectures
+Closes: #865191
+
+ -- Andreas Tille   Mon, 18 Sep 2017 12:54:20 +0200
+
 probabel (0.4.5-4) unstable; urgency=medium
 
   * debhelper 10
diff --git a/debian/rules b/debian/rules
index 9ff057d..99b2126 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,8 @@
 
 # DH_VERBOSE := 1
 
+BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
+
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 include /usr/share/dpkg/default.mk
@@ -39,3 +41,14 @@ override_dh_install-arch:
dh_install -a --fail-missing
rm debian/$(DEB_SOURCE)/usr/bin/probabel.pl
mv debian/$(DEB_SOURCE)/etc/probabel_config.cfg.example 
debian/$(DEB_SOURCE)/etc/probabel_config.cfg
+
+ifeq ($(BUILDARCH),$(filter $(BUILDARCH), mips s390x hppa powerpc ppc64 
sparc64))
+# On big endian architectures the tests are failing due to
+# some binary format output that is compared with a file that
+# was created on a low endian architecture and those files
+# are dependent from the architecture (with no influence on
+# the final result.  See
+#   https://github.com/GenABEL-Project/ProbABEL/issues/45
+override_dh_auto_test:
+   dh_auto_test || true
+endif

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[med-svn] [probabel] branch master updated (d9eafbc -> 83d5eaa)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository probabel.

  from  d9eafbc   d/rules: make use of DEB_SOURCE, hardening=+all, upload 
to unstable
   new  b48a6d5   Ignore errors in test suite for big endian architectures
   new  a8d61db   Standards-Version: 4.1.0
   new  83d5eaa   Drop autoconf dependency (redundant for debhelper 10), 
upload to unstable

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog |  9 +
 debian/control   |  4 +---
 debian/rules | 21 ++---
 3 files changed, 24 insertions(+), 10 deletions(-)

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[med-svn] [probabel] tag debian/0.4.5-5 created (now 83d5eaa)

2017-09-18 Thread Andreas Tille

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tille pushed a change to tag debian/0.4.5-5
in repository probabel.

at  83d5eaa   (commit)
No new revisions were added by this update.

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[med-svn] [dicompyler] 01/03: Adding Kulvait as an uploader to debian/control

2017-09-18 Thread Vojtech Kulvait

This is an automated email from the git hooks/post-receive script.

kulvait-guest pushed a commit to branch master
in repository dicompyler.

commit c0b50a61b277d47d7029366b2ba4fcd5209e3b06
Author: Vojtěch Kulvait 
Date:   Mon Sep 18 12:30:17 2017 +0200

Adding Kulvait as an uploader to debian/control
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index b70703a..eedc073 100644
--- a/debian/control
+++ b/debian/control
@@ -1,6 +1,6 @@
 Source: dicompyler
 Maintainer: Debian Med Packaging Team 

-Uploaders: Andreas Tille 
+Uploaders: Andreas Tille , Vojtěch Kulvait 

 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),

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[med-svn] [dicompyler] 03/03: Solving bug #854837

2017-09-18 Thread Vojtech Kulvait

This is an automated email from the git hooks/post-receive script.

kulvait-guest pushed a commit to branch master
in repository dicompyler.

commit 5894bb2e11eb156d5cfd329b43770bb99bdb035e
Author: Vojtěch Kulvait 
Date:   Mon Sep 18 14:52:53 2017 +0200

Solving bug #854837

Adding 01.patch, which added support for pillow >=3.0.0 addressing changes 
due to commit

https://github.com/python-pillow/Pillow/commit/71c95c8e5f3bba1845444a246d04646825e6bab3,
small indentation fix. This commit enables one to explore RT data, tested 
in stretch.
---
 debian/control  |  2 +-
 debian/patches/01.patch | 38 ++
 debian/patches/series   |  1 +
 3 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index eedc073..8f783ac 100644
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Architecture: all
 Depends: ${misc:Depends},
  ${python:Depends},
  python-wxgtk3.0,
- python-pil,
+ python-pil (>=3.0.0),
  python-numpy,
  python-matplotlib,
  python-dicom,
diff --git a/debian/patches/01.patch b/debian/patches/01.patch
new file mode 100644
index 000..6244747
--- /dev/null
+++ b/debian/patches/01.patch
@@ -0,0 +1,38 @@
+Author: Vojtěch Kulvait 
+Last-Update: Mon Sep 18 14:44:01 CEST 2017
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854837
+Description: Added support for pillow >=3.0.0 addressing changes due to commit 
https://github.com/python-pillow/Pillow/commit/71c95c8e5f3bba1845444a246d04646825e6bab3,
 small indentation fix.
+
+Index: dicompyler/dicompyler/dvhcalc.py
+===
+--- dicompyler.orig/dicompyler/dvhcalc.py
 dicompyler/dicompyler/dvhcalc.py
+@@ -160,7 +160,7 @@ def calculate_contour_areas(plane):
+ def get_contour_mask(doselut, dosegridpoints, contour):
+ """Get the mask for the contour with respect to the dose plane."""
+ 
+-grid = nx.points_inside_poly(dosegridpoints, contour)
++grid = nx.points_inside_poly(dosegridpoints, contour)
+ grid = grid.reshape((len(doselut[1]), len(doselut[0])))
+ 
+ return grid
+Index: dicompyler/dicompyler/guiutil.py
+===
+--- dicompyler.orig/dicompyler/guiutil.py
 dicompyler/dicompyler/guiutil.py
+@@ -78,12 +78,12 @@ def convert_pil_to_wx(pil, alpha=True):
+ Code taken from Dave Witten's imViewer-Simple.py in pydicom 
contrib."""
+ if alpha:
+ image = apply(wx.EmptyImage, pil.size)
+-image.SetData(pil.convert("RGB").tostring())
+-image.SetAlphaData(pil.convert("RGBA").tostring()[3::4])
++image.SetData(pil.convert("RGB").tobytes())#Pillow >= 3.0.0
++image.SetAlphaData(pil.convert("RGBA").tobytes()[3::4])#Pillow >= 
3.0.0
+ else:
+ image = wx.EmptyImage(pil.size[0], pil.size[1])
+ new_image = pil.convert('RGB')
+-data = new_image.tostring()
++data = new_image.tobytes()#Fixes this commit 
https://github.com/python-pillow/Pillow/commit/71c95c8e5f3bba1845444a246d04646825e6bab3
+ image.SetData(data)
+ return image
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 3d2c56f..5b1d765 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ enable_later_versions_of_matplotlib.patch
 fix-xrc-errors.patch
 fix_DicomImporterDialog.patch
 more_wx30_patches.patch
+01.patch

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[med-svn] [dicompyler] branch master updated (a762a37 -> 5894bb2)

2017-09-18 Thread Vojtech Kulvait

This is an automated email from the git hooks/post-receive script.

kulvait-guest pushed a change to branch master
in repository dicompyler.

  from  a762a37   In new source tarball README.txt was renamed to readme.txt
   new  c0b50a6   Adding Kulvait as an uploader to debian/control
   new  eda7df0   In changelog I have corrected Vojtech to Vojtěch
   new  5894bb2   Solving bug #854837

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog|  2 +-
 debian/control  |  4 ++--
 debian/patches/01.patch | 38 ++
 debian/patches/series   |  1 +
 4 files changed, 42 insertions(+), 3 deletions(-)
 create mode 100644 debian/patches/01.patch

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[med-svn] [dicompyler] 02/03: In changelog I have corrected Vojtech to Vojtěch

2017-09-18 Thread Vojtech Kulvait

This is an automated email from the git hooks/post-receive script.

kulvait-guest pushed a commit to branch master
in repository dicompyler.

commit eda7df0a1f472094ded1bd16097baa74950412f2
Author: Vojtěch Kulvait 
Date:   Mon Sep 18 12:47:31 2017 +0200

In changelog I have corrected Vojtech to Vojtěch
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 8fe181d..c45c8f2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,7 +5,7 @@ dicompyler (0.4.2.0-1) UNRELEASED; urgency=medium
   * Not really new upstream version but content of upstream source archive
 on Github has changed
 
- -- Vojtech Kulvait   Mon, 18 Sep 2017 09:54:37 +0200
+ -- Vojtěch Kulvait   Mon, 18 Sep 2017 09:54:37 +0200
 
 dicompyler (0.4.2-4) unstable; urgency=medium
 

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[med-svn] r24058 - trunk/helper-scripts

2017-09-18 Thread Andreas Tille

Author: tille
Date: 2017-09-18 13:15:02 + (Mon, 18 Sep 2017)
New Revision: 24058

Modified:
   trunk/helper-scripts/debian-med-authors
Log:
Add Yask Gupta


Modified: trunk/helper-scripts/debian-med-authors
===
--- trunk/helper-scripts/debian-med-authors 2017-09-18 10:46:30 UTC (rev 
24057)
+++ trunk/helper-scripts/debian-med-authors 2017-09-18 13:15:02 UTC (rev 
24058)
@@ -63,6 +63,7 @@
 lkajan-guest = Laszlo Kajan 
 malat = Mathieu Malaterre 
 malat-guest = Mathieu Malaterre 
+malex-guest = Alexandre Mestiashvili 
 manuel = Manuel Prinz 
 mattia = Mattia Rizzolo 
 mbanck = Michael Banck 
@@ -114,6 +115,6 @@
 ucko = Aaron M. Ucko 
 varun = Varun Hiremath 
 xnox = Dimitri Ledkov 
+yask-guest = Yask Gupta 
 yoh = Yaroslav Halchenko 
 yoh-guest = Yaroslav Halchenko 
-malex-guest = Alexandre Mestiashvili 


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[med-svn] [diamond-aligner] 01/07: New upstream version 0.9.10+dfsg

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit baec593e94cc4cfd918fa334eb9493a638abdc70
Author: Andreas Tille 
Date:   Mon Sep 18 13:30:39 2017 +0200

New upstream version 0.9.10+dfsg
---
 CMakeLists.txt   |   4 +
 README.rst   |   2 +-
 build_simple.sh  |   4 +
 src/ChangeLog|  14 +-
 src/align/align.cpp  | 288 +--
 src/align/align.h|  64 +
 src/align/align_queries.h|  67 --
 src/align/align_target.cpp   |   4 +
 src/align/query_mapper.cpp   | 133 ++-
 src/align/query_mapper.h |  16 ++
 src/basic/basic.cpp  |   4 +-
 src/basic/config.cpp |  28 ++-
 src/basic/config.h   |   6 +-
 src/basic/const.h|   2 +-
 src/basic/hssp.cpp   |  30 ++-
 src/basic/match.h|   2 +
 src/basic/sequence.h |   9 +-
 src/basic/value.h|   2 +-
 src/data/load_seqs.h |  12 +-
 src/data/reference.cpp   |  22 ++
 src/data/reference.h |   9 +-
 src/data/taxonomy.cpp|  81 ++-
 src/data/taxonomy.h  |  15 ++
 src/dp/dp.h  |   7 +-
 src/dp/swipe.cpp |   2 +-
 src/extra/match_file.h   |   1 +
 src/output/blast_pairwise_format.cpp |   5 +-
 src/output/blast_tab_format.cpp  |   8 +-
 src/output/join_blocks.cpp   |  51 +++-
 src/output/output.h  |  39 ++-
 src/output/output_format.cpp |  25 +-
 src/output/output_format.h   |  69 +-
 src/output/output_sink.cpp   |  86 +++
 src/output/sam_format.cpp|   2 +-
 src/{basic/const.h => output/target_culling.cpp} |  30 +--
 src/output/target_culling.h  |  73 ++
 src/output/taxon_format.cpp  |  51 
 src/output/{view.h => view.cpp}  |  67 +++---
 src/run/double_indexed.cpp   |  10 +-
 src/run/main.cpp |   7 +-
 src/run/tools.cpp|   6 +-
 src/util/log_stream.h|   5 +
 src/{basic/const.h => util/queue.h}  |  59 +++--
 43 files changed, 830 insertions(+), 591 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 05d6c12..35ee8bf 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -85,6 +85,10 @@ add_executable(diamond src/run/main.cpp
   src/data/seed_set.cpp
   src/util/binary_file.cpp
   src/util/simd.cpp
+  src/output/taxon_format.cpp
+  src/output/view.cpp
+  src/output/output_sink.cpp
+  src/output/target_culling.cpp
 )
 
 target_link_libraries(diamond ${ZLIB_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})
diff --git a/README.rst b/README.rst
index 7d043f3..40c77f1 100644
--- a/README.rst
+++ b/README.rst
@@ -8,7 +8,7 @@ Please read the `manual

[med-svn] [diamond-aligner] branch master updated (d2d3a75 -> eaa0274)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository diamond-aligner.

  from  d2d3a75   New upstream version
   new  baec593   New upstream version 0.9.10+dfsg
   new  c5e9593   Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'
   new  aa9a12b   New upstream version
   new  c87ab56   Force the symbol with c++ explicit function template 
instantiation for the latter prototype instead of relying on implicit 
instantiation Upload and see, whether this will help to fix bug   #865132
   new  2c10a77   Standards-Version: 4.1.0 (no changes needed)
   new  608f5e6   Do not parse d/changelog
   new  eaa0274   Fix typo in d/rules and upload to unstable

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 CMakeLists.txt |   4 +
 README.rst |   2 +-
 build_simple.sh|   4 +
 debian/changelog   |  10 +
 debian/control |   2 +-
 debian/patches/avoid_unwanted_optimisation.patch   |  17 ++
 debian/patches/series  |   1 +
 debian/rules   |  14 +-
 src/ChangeLog  |  14 +-
 src/align/align.cpp| 288 -
 src/align/align.h  |  64 +
 src/align/align_queries.h  |  67 -
 src/align/align_target.cpp |   4 +
 src/align/query_mapper.cpp | 133 +-
 src/align/query_mapper.h   |  16 ++
 src/basic/basic.cpp|   4 +-
 src/basic/config.cpp   |  28 +-
 src/basic/config.h |   6 +-
 src/basic/const.h  |   2 +-
 src/basic/hssp.cpp |  30 ++-
 src/basic/match.h  |   2 +
 src/basic/sequence.h   |   9 +-
 src/basic/value.h  |   2 +-
 src/data/load_seqs.h   |  12 +-
 src/data/reference.cpp |  22 ++
 src/data/reference.h   |   9 +-
 src/data/taxonomy.cpp  |  81 +-
 src/data/taxonomy.h|  15 ++
 src/dp/dp.h|   7 +-
 src/dp/swipe.cpp   |   2 +-
 src/extra/match_file.h |   1 +
 src/output/blast_pairwise_format.cpp   |   5 +-
 src/output/blast_tab_format.cpp|   8 +-
 src/output/join_blocks.cpp |  51 +++-
 src/output/output.h|  39 ++-
 src/output/output_format.cpp   |  25 +-
 src/output/output_format.h |  69 -
 src/output/output_sink.cpp |  86 ++
 src/output/sam_format.cpp  |   2 +-
 src/{util/system_c.h => output/target_culling.cpp} |  14 +-
 src/output/target_culling.h|  73 ++
 src/output/taxon_format.cpp|  51 
 src/output/{view.h => view.cpp}|  67 ++---
 src/run/double_indexed.cpp |  10 +-
 src/run/main.cpp   |   7 +-
 src/run/tools.cpp  |   6 +-
 src/util/log_stream.h  |   5 +
 src/util/{high_res_timer.h => queue.h} |  62 ++---
 48 files changed, 861 insertions(+), 591 deletions(-)
 create mode 100644 debian/patches/avoid_unwanted_optimisation.patch
 delete mode 100644 src/align/align_queries.h
 create mode 100644 src/output/output_sink.cpp
 copy src/{util/system_c.h => output/target_culling.cpp} (80%)
 create mode 100644 src/output/target_culling.h
 create mode 100644 src/output/taxon_format.cpp
 rename src/output/{view.h => view.cpp} (73%)
 copy src/util/{high_res_timer.h => queue.h} (62%)

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[med-svn] [diamond-aligner] 03/07: New upstream version

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit aa9a12b4c200d332b9f4be3f6b5561c15dd813ff
Author: Andreas Tille 
Date:   Mon Sep 18 13:31:00 2017 +0200

New upstream version
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 0db3ee0..d29a6cd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille   Mon, 18 Sep 2017 13:30:44 +0200
+
 diamond-aligner (0.9.8+dfsg-1) unstable; urgency=medium
 
   * New upstream version

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[med-svn] [diamond-aligner] branch pristine-tar updated (6af4561 -> d98569e)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch pristine-tar
in repository diamond-aligner.

  from  6af4561   pristine-tar data for 
diamond-aligner_0.9.8+dfsg.orig.tar.xz
   new  d98569e   pristine-tar data for 
diamond-aligner_0.9.10+dfsg.orig.tar.xz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta | Bin 0 -> 4912 bytes
 diamond-aligner_0.9.10+dfsg.orig.tar.xz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta
 create mode 100644 diamond-aligner_0.9.10+dfsg.orig.tar.xz.id

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[med-svn] [diamond-aligner] 05/07: Standards-Version: 4.1.0 (no changes needed)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit 2c10a77fdea468c8a9f6f985063b9ed36fb99c94
Author: Andreas Tille 
Date:   Mon Sep 18 14:49:52 2017 +0200

Standards-Version: 4.1.0 (no changes needed)
---
 debian/changelog | 3 ++-
 debian/control   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0a98c20..6f3bc84 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,8 +3,9 @@ diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
   * New upstream version
   * Force the symbol with c++ explicit function template instantiation for the
 latter prototype instead of relying on implicit instantiation
+  * Standards-Version: 4.1.0 (no changes needed)
 
- -- Andreas Tille   Mon, 18 Sep 2017 13:30:44 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 13:34:51 +0200
 
 diamond-aligner (0.9.8+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index 23a328a..58f44d2 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper (>= 10),
cmake,
zlib1g-dev
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/diamond-aligner.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/diamond-aligner.git
 Homepage: https://github.com/bbuchfink/diamond

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[med-svn] [diamond-aligner] tag debian/0.9.10+dfsg-1 created (now eaa0274)

2017-09-18 Thread Andreas Tille

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tille pushed a change to tag debian/0.9.10+dfsg-1
in repository diamond-aligner.

at  eaa0274   (commit)
No new revisions were added by this update.

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[med-svn] [diamond-aligner] annotated tag upstream/0.9.10+dfsg created (now 6f2ad2a)

2017-09-18 Thread Andreas Tille

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tille pushed a change to annotated tag upstream/0.9.10+dfsg
in repository diamond-aligner.

at  6f2ad2a   (tag)
   tagging  baec593e94cc4cfd918fa334eb9493a638abdc70 (commit)
  replaces  upstream/0.9.8+dfsg
 tagged by  Andreas Tille
on  Mon Sep 18 13:30:40 2017 +0200

- Log -
Upstream version 0.9.10+dfsg

Andreas Tille (1):
  New upstream version 0.9.10+dfsg

---

This annotated tag includes the following new commits:

   new  baec593   New upstream version 0.9.10+dfsg

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[med-svn] [diamond-aligner] 02/07: Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit c5e9593e49b8ca59317dc3ea11de82ab284f723e
Merge: d2d3a75 baec593
Author: Andreas Tille 
Date:   Mon Sep 18 13:30:40 2017 +0200

Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'

with Debian dir d7e6526cc3f25884323dd55b00e1052088978fa5

 CMakeLists.txt   |   4 +
 README.rst   |   2 +-
 build_simple.sh  |   4 +
 src/ChangeLog|  14 +-
 src/align/align.cpp  | 288 +--
 src/align/align.h|  64 +
 src/align/align_queries.h|  67 --
 src/align/align_target.cpp   |   4 +
 src/align/query_mapper.cpp   | 133 ++-
 src/align/query_mapper.h |  16 ++
 src/basic/basic.cpp  |   4 +-
 src/basic/config.cpp |  28 ++-
 src/basic/config.h   |   6 +-
 src/basic/const.h|   2 +-
 src/basic/hssp.cpp   |  30 ++-
 src/basic/match.h|   2 +
 src/basic/sequence.h |   9 +-
 src/basic/value.h|   2 +-
 src/data/load_seqs.h |  12 +-
 src/data/reference.cpp   |  22 ++
 src/data/reference.h |   9 +-
 src/data/taxonomy.cpp|  81 ++-
 src/data/taxonomy.h  |  15 ++
 src/dp/dp.h  |   7 +-
 src/dp/swipe.cpp |   2 +-
 src/extra/match_file.h   |   1 +
 src/output/blast_pairwise_format.cpp |   5 +-
 src/output/blast_tab_format.cpp  |   8 +-
 src/output/join_blocks.cpp   |  51 +++-
 src/output/output.h  |  39 ++-
 src/output/output_format.cpp |  25 +-
 src/output/output_format.h   |  69 +-
 src/output/output_sink.cpp   |  86 +++
 src/output/sam_format.cpp|   2 +-
 src/{basic/const.h => output/target_culling.cpp} |  30 +--
 src/output/target_culling.h  |  73 ++
 src/output/taxon_format.cpp  |  51 
 src/output/{view.h => view.cpp}  |  67 +++---
 src/run/double_indexed.cpp   |  10 +-
 src/run/main.cpp |   7 +-
 src/run/tools.cpp|   6 +-
 src/util/log_stream.h|   5 +
 src/{basic/const.h => util/queue.h}  |  59 +++--
 43 files changed, 830 insertions(+), 591 deletions(-)

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[med-svn] [diamond-aligner] 04/07: Force the symbol with c++ explicit function template instantiation for the latter prototype instead of relying on implicit instantiation Upload and see, whether this

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit c87ab5636fecc62986a16653e7d3868a09897dda
Author: Andreas Tille 
Date:   Mon Sep 18 13:34:03 2017 +0200

Force the symbol with c++ explicit function template instantiation for the 
latter prototype instead of relying on implicit instantiation
Upload and see, whether this will help to fix bug   #865132
---
 debian/changelog |  2 ++
 debian/patches/avoid_unwanted_optimisation.patch | 17 +
 debian/patches/series|  1 +
 3 files changed, 20 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index d29a6cd..0a98c20 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,8 @@
 diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
+  * Force the symbol with c++ explicit function template instantiation for the
+latter prototype instead of relying on implicit instantiation
 
  -- Andreas Tille   Mon, 18 Sep 2017 13:30:44 +0200
 
diff --git a/debian/patches/avoid_unwanted_optimisation.patch 
b/debian/patches/avoid_unwanted_optimisation.patch
new file mode 100644
index 000..75e25b3
--- /dev/null
+++ b/debian/patches/avoid_unwanted_optimisation.patch
@@ -0,0 +1,17 @@
+Author: Frédéric Bonnard 
+Bug-Debian: https://bugs.debian.org/865132
+Last-Update: Wed, 28 Jun 2017 13:56:39 +0200
+Description: Force the symbol with c++ explicit function template 
instantiation for the latter
+  prototype instead of relying on implicit instantiation in 
needleman_wunsch.cpp
+
+--- a/src/dp/needleman_wunsch.cpp
 b/src/dp/needleman_wunsch.cpp
+@@ -322,4 +322,6 @@ void smith_waterman(sequence q, sequence
+   }
+   print_diag(i0, j0, l, score, diags, q, s);
+   print_hsp(hsp, q);
+-}
+\ No newline at end of file
++}
++
++template Fixed_score_buffer const& needleman_wunsch(sequence, sequence, int&, Local const&, int const&);
diff --git a/debian/patches/series b/debian/patches/series
index 7261679..fca5787 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 drop_march_native_flag.patch
+avoid_unwanted_optimisation.patch

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[med-svn] [diamond-aligner] 06/07: Do not parse d/changelog

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit 608f5e6c1ac56794c03b2744fa6eccc8e41ca3d8
Author: Andreas Tille 
Date:   Mon Sep 18 14:51:16 2017 +0200

Do not parse d/changelog
---
 debian/changelog |  1 +
 debian/rules | 14 +++---
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 6f3bc84..d27faf2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
   * Force the symbol with c++ explicit function template instantiation for the
 latter prototype instead of relying on implicit instantiation
   * Standards-Version: 4.1.0 (no changes needed)
+  * Do not parse d/changelog
 
  -- Andreas Tille   Mon, 18 Sep 2017 13:34:51 +0200
 
diff --git a/debian/rules b/debian/rules
index ec55a35..cec9635 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,7 @@ export LC_ALL=C.UTF-8
 # for hardening you might like to uncomment this:
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
-DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+include /usr/share/dpkg/default.mk
 
 ME3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then 
echo "-mssse3" ; fi)
 
@@ -16,15 +16,15 @@ ME3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 
'amd64' ] ; then ech
 override_dh_install:
dh_install
# due to a file name conflict diamond is moved out of the way
-   mkdir -p debian/$(DEBPKGNAME)/usr/lib/debian-med/bin/
-   mv debian/$(DEBPKGNAME)/usr/bin/diamond 
debian/$(DEBPKGNAME)/usr/lib/debian-med/bin/
+   mkdir -p debian/$(DEB_SOURCE)/gusr/lib/debian-med/bin/
+   mv debian/$(DEB_SOURCE)/gusr/bin/diamond 
debian/$(DEBPKGNAME)/usr/lib/debian-med/bin/
 
 override_dh_installman:
dh_installman
# due to a file name conflict diamond.1 is moved out of the way
-   mkdir -p debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/
-   mv debian/$(DEBPKGNAME)/usr/share/man/man1/diamond.1 
debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/
-   gzip -9 debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/diamond.1
+   mkdir -p debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/
+   mv debian/$(DEB_SOURCE)/gusr/share/man/man1/diamond.1 
debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/
+   gzip -9 
debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/diamond.1
 
 override_dh_compress:
dh_compress --exclude=.pdf
@@ -32,7 +32,7 @@ override_dh_compress:
 override_dh_fixperms:
dh_fixperms
# strangely the manpage becomes executable ... hmmm
-   chmod -x debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/*
+   chmod -x debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/*
 
 build_simple:
ME3=$(ME3) build_simple.sh

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[med-svn] [diamond-aligner] branch upstream updated (e37193d -> baec593)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository diamond-aligner.

  from  e37193d   New upstream version 0.9.8+dfsg
   new  baec593   New upstream version 0.9.10+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 CMakeLists.txt |   4 +
 README.rst |   2 +-
 build_simple.sh|   4 +
 src/ChangeLog  |  14 +-
 src/align/align.cpp| 288 -
 src/align/align.h  |  64 +
 src/align/align_queries.h  |  67 -
 src/align/align_target.cpp |   4 +
 src/align/query_mapper.cpp | 133 +-
 src/align/query_mapper.h   |  16 ++
 src/basic/basic.cpp|   4 +-
 src/basic/config.cpp   |  28 +-
 src/basic/config.h |   6 +-
 src/basic/const.h  |   2 +-
 src/basic/hssp.cpp |  30 ++-
 src/basic/match.h  |   2 +
 src/basic/sequence.h   |   9 +-
 src/basic/value.h  |   2 +-
 src/data/load_seqs.h   |  12 +-
 src/data/reference.cpp |  22 ++
 src/data/reference.h   |   9 +-
 src/data/taxonomy.cpp  |  81 +-
 src/data/taxonomy.h|  15 ++
 src/dp/dp.h|   7 +-
 src/dp/swipe.cpp   |   2 +-
 src/extra/match_file.h |   1 +
 src/output/blast_pairwise_format.cpp   |   5 +-
 src/output/blast_tab_format.cpp|   8 +-
 src/output/join_blocks.cpp |  51 +++-
 src/output/output.h|  39 ++-
 src/output/output_format.cpp   |  25 +-
 src/output/output_format.h |  69 -
 src/output/output_sink.cpp |  86 ++
 src/output/sam_format.cpp  |   2 +-
 src/{util/system_c.h => output/target_culling.cpp} |  14 +-
 src/output/target_culling.h|  73 ++
 src/output/taxon_format.cpp|  51 
 src/output/{view.h => view.cpp}|  67 ++---
 src/run/double_indexed.cpp |  10 +-
 src/run/main.cpp   |   7 +-
 src/run/tools.cpp  |   6 +-
 src/util/log_stream.h  |   5 +
 src/util/{high_res_timer.h => queue.h} |  62 ++---
 43 files changed, 825 insertions(+), 583 deletions(-)
 delete mode 100644 src/align/align_queries.h
 create mode 100644 src/output/output_sink.cpp
 copy src/{util/system_c.h => output/target_culling.cpp} (80%)
 create mode 100644 src/output/target_culling.h
 create mode 100644 src/output/taxon_format.cpp
 rename src/output/{view.h => view.cpp} (73%)
 copy src/util/{high_res_timer.h => queue.h} (62%)

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[med-svn] [diamond-aligner] 01/01: pristine-tar data for diamond-aligner_0.9.10+dfsg.orig.tar.xz

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository diamond-aligner.

commit d98569e64c0e037df21bb80e1457219d9ffe174f
Author: Andreas Tille 
Date:   Mon Sep 18 13:30:40 2017 +0200

pristine-tar data for diamond-aligner_0.9.10+dfsg.orig.tar.xz
---
 diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta | Bin 0 -> 4912 bytes
 diamond-aligner_0.9.10+dfsg.orig.tar.xz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta 
b/diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta
new file mode 100644
index 000..b28e6e7
Binary files /dev/null and b/diamond-aligner_0.9.10+dfsg.orig.tar.xz.delta 
differ
diff --git a/diamond-aligner_0.9.10+dfsg.orig.tar.xz.id 
b/diamond-aligner_0.9.10+dfsg.orig.tar.xz.id
new file mode 100644
index 000..d2f1053
--- /dev/null
+++ b/diamond-aligner_0.9.10+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+3ee5314d1fcdea6977a5c2484fcb56f8526a7d11

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[med-svn] [diamond-aligner] 07/07: Fix typo in d/rules and upload to unstable

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository diamond-aligner.

commit eaa02742b0f5512eccee3db52b580bf63998b909
Author: Andreas Tille 
Date:   Mon Sep 18 15:15:11 2017 +0200

Fix typo in d/rules and upload to unstable
---
 debian/changelog |  4 ++--
 debian/rules | 12 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d27faf2..dd1fdae 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
+diamond-aligner (0.9.10+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Force the symbol with c++ explicit function template instantiation for the
@@ -6,7 +6,7 @@ diamond-aligner (0.9.10+dfsg-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.1.0 (no changes needed)
   * Do not parse d/changelog
 
- -- Andreas Tille   Mon, 18 Sep 2017 13:34:51 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 14:51:21 +0200
 
 diamond-aligner (0.9.8+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/rules b/debian/rules
index cec9635..f0b9e01 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,15 +16,15 @@ ME3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 
'amd64' ] ; then ech
 override_dh_install:
dh_install
# due to a file name conflict diamond is moved out of the way
-   mkdir -p debian/$(DEB_SOURCE)/gusr/lib/debian-med/bin/
-   mv debian/$(DEB_SOURCE)/gusr/bin/diamond 
debian/$(DEBPKGNAME)/usr/lib/debian-med/bin/
+   mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
+   mv debian/$(DEB_SOURCE)/usr/bin/diamond 
debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
 
 override_dh_installman:
dh_installman
# due to a file name conflict diamond.1 is moved out of the way
-   mkdir -p debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/
-   mv debian/$(DEB_SOURCE)/gusr/share/man/man1/diamond.1 
debian/$(DEBPKGNAME)/usr/lib/debian-med/share/man/man1/
-   gzip -9 
debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/diamond.1
+   mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
+   mv debian/$(DEB_SOURCE)/usr/share/man/man1/diamond.1 
debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
+   gzip -9 debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/diamond.1
 
 override_dh_compress:
dh_compress --exclude=.pdf
@@ -32,7 +32,7 @@ override_dh_compress:
 override_dh_fixperms:
dh_fixperms
# strangely the manpage becomes executable ... hmmm
-   chmod -x debian/$(DEB_SOURCE)/gusr/lib/debian-med/share/man/man1/*
+   chmod -x debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/*
 
 build_simple:
ME3=$(ME3) build_simple.sh

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[med-svn] [dicompyler] 01/01: Do not fix problems in one patch in a subsequent one.

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository dicompyler.

commit 737c28f05cb87f13e52519a6c3164be7a94cb8d4
Author: Andreas Tille 
Date:   Mon Sep 18 16:09:04 2017 +0200

Do not fix problems in one patch in a subsequent one.
---
 debian/patches/01.patch| 19 ++-
 debian/patches/more_wx30_patches.patch |  6 --
 2 files changed, 6 insertions(+), 19 deletions(-)

diff --git a/debian/patches/01.patch b/debian/patches/01.patch
index 6244747..4613dbf 100644
--- a/debian/patches/01.patch
+++ b/debian/patches/01.patch
@@ -3,23 +3,8 @@ Last-Update: Mon Sep 18 14:44:01 CEST 2017
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854837
 Description: Added support for pillow >=3.0.0 addressing changes due to commit 
https://github.com/python-pillow/Pillow/commit/71c95c8e5f3bba1845444a246d04646825e6bab3,
 small indentation fix.
 
-Index: dicompyler/dicompyler/dvhcalc.py
-===
 dicompyler.orig/dicompyler/dvhcalc.py
-+++ dicompyler/dicompyler/dvhcalc.py
-@@ -160,7 +160,7 @@ def calculate_contour_areas(plane):
- def get_contour_mask(doselut, dosegridpoints, contour):
- """Get the mask for the contour with respect to the dose plane."""
- 
--grid = nx.points_inside_poly(dosegridpoints, contour)
-+grid = nx.points_inside_poly(dosegridpoints, contour)
- grid = grid.reshape((len(doselut[1]), len(doselut[0])))
- 
- return grid
-Index: dicompyler/dicompyler/guiutil.py
-===
 dicompyler.orig/dicompyler/guiutil.py
-+++ dicompyler/dicompyler/guiutil.py
+--- a/dicompyler/guiutil.py
 b/dicompyler/guiutil.py
 @@ -78,12 +78,12 @@ def convert_pil_to_wx(pil, alpha=True):
  Code taken from Dave Witten's imViewer-Simple.py in pydicom 
contrib."""
  if alpha:
diff --git a/debian/patches/more_wx30_patches.patch 
b/debian/patches/more_wx30_patches.patch
index 955cb3b..d3cd106 100644
--- a/debian/patches/more_wx30_patches.patch
+++ b/debian/patches/more_wx30_patches.patch
@@ -205,16 +205,18 @@ Description: More wx3.0 patches to make dicompyler run
  if nx.pnpoly(point[0], point[1],
   np.array(contours[largestIndex]['data'])):
  contour['inside'] = True
-@@ -171,9 +160,6 @@ def calculate_contour_areas(plane):
+@@ -171,10 +160,7 @@ def calculate_contour_areas(plane):
  def get_contour_mask(doselut, dosegridpoints, contour):
  """Get the mask for the contour with respect to the dose plane."""
  
 -if matplotlib.__version__ > '1.2':
 -grid = mpl_Path(contour).contains_points(dosegridpoints)
 -else:
- grid = nx.points_inside_poly(dosegridpoints, contour)
+-grid = nx.points_inside_poly(dosegridpoints, contour)
++grid = nx.points_inside_poly(dosegridpoints, contour)
  grid = grid.reshape((len(doselut[1]), len(doselut[0])))
  
+ return grid
 --- a/dicompyler/guiutil.py
 +++ b/dicompyler/guiutil.py
 @@ -10,9 +10,7 @@

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[med-svn] [dicompyler] branch master updated (5894bb2 -> 737c28f)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository dicompyler.

  from  5894bb2   Solving bug #854837
   new  737c28f   Do not fix problems in one patch in a subsequent one.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 debian/patches/01.patch| 19 ++-
 debian/patches/more_wx30_patches.patch |  6 --
 2 files changed, 6 insertions(+), 19 deletions(-)

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[med-svn] r24059 - in trunk/packages/mgltools/autodocktools/trunk/debian: . upstream

2017-09-18 Thread Steffen Möller

Author: moeller
Date: 2017-09-18 14:31:03 + (Mon, 18 Sep 2017)
New Revision: 24059

Modified:
   trunk/packages/mgltools/autodocktools/trunk/debian/changelog
   trunk/packages/mgltools/autodocktools/trunk/debian/upstream/metadata
Log:
Added (missing) references to registries.


Modified: trunk/packages/mgltools/autodocktools/trunk/debian/changelog
===
--- trunk/packages/mgltools/autodocktools/trunk/debian/changelog
2017-09-18 13:15:02 UTC (rev 24058)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/changelog
2017-09-18 14:31:03 UTC (rev 24059)
@@ -2,6 +2,11 @@
 
   * cme fix dpkg-control (to fix Vcs fields)
 
+  [ Steffen Moeller ]
+  * debian/upstream/metadata:
+- yamllint cleanliness
+- indicted that there are no entries in software registries
+
  -- Andreas Tille   Thu, 29 Dec 2016 22:28:01 +0100
 
 autodocktools (1.5.7-1) unstable; urgency=medium

Modified: trunk/packages/mgltools/autodocktools/trunk/debian/upstream/metadata
===
--- trunk/packages/mgltools/autodocktools/trunk/debian/upstream/metadata
2017-09-18 13:15:02 UTC (rev 24058)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/upstream/metadata
2017-09-18 14:31:03 UTC (rev 24059)
@@ -2,9 +2,13 @@
 Homepage: http://autodock.scripps.edu/
 Name: AutoDockTools
 Reference:
- - Author: Garrett M. Morris and Ruth Huey and William Lindstrom and Michel F. 
Sanner and Richard K. Belew and David S. Goodsell and Arthur J. Olson
+ - Author: >
+Garrett M. Morris and Ruth Huey and William Lindstrom and Michel
+F. Sanner and Richard K. Belew and David S. Goodsell and Arthur
+J. Olson
Title: >
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor 
flexibility
+AutoDock4 and AutoDockTools4: Automated docking with selective
+receptor flexibility
Journal: Journal of Computational Chemistry
Volume: 30
Number: 16
@@ -15,7 +19,7 @@
URL: http://www3.interscience.wiley.com/journal/122365050/abstract
  - Author: Rodney Harris and Arthur J Olson and David S Goodsell
Title: >
- Automated prediction of ligand-binding sites in proteins.
+Automated prediction of ligand-binding sites in proteins.
Journal: Proteins
Year: 2008
Volume: 70
@@ -24,13 +28,24 @@
PMID: 17910060
DOI: 10.1002/prot.21645
URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.21645/abstract
- - Author: Stefano Forli and Ruth Huey and Michael E Pique and Michel F Sanner 
and David S Goodsell and Arthur J Olson
+ - Author: >
+Stefano Forli and Ruth Huey and Michael E Pique and Michel F Sanner
+and David S Goodsell and Arthur J Olson
Title: >
- Computational protein–ligand docking and virtual drug screening with the 
AutoDock suite
+Computational protein–ligand docking and virtual drug screening
+with the AutoDock suite
Journal: Nature Protocols
Volume: 11
Pages: 905–919
Year: 2016
+   PMID: 27077332
Doi: 10.1038/nprot.2016.051 
 Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Registry:
+ - Name: OMICtools
+   Entry: NA
+ - Name: RRID
+   Entry: NA
+ - Name: bio.tools
+   Entry: NA
 Watch: 
http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz


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[med-svn] [autodock-vina] branch upstream created (now dded90d)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch upstream
in repository autodock-vina.

at  dded90d   New upstream version 1.1.2

No new revisions were added by this update.

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[med-svn] [autodock-vina] 01/01: pristine-tar data for autodock-vina_1.1.2.orig.tar.gz

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository autodock-vina.

commit 64fdce38d08d1112a9d8dde5da78ea31657307aa
Author: Andreas Tille 
Date:   Mon Sep 18 17:05:48 2017 +0200

pristine-tar data for autodock-vina_1.1.2.orig.tar.gz
---
 autodock-vina_1.1.2.orig.tar.gz.delta | Bin 0 -> 3267 bytes
 autodock-vina_1.1.2.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/autodock-vina_1.1.2.orig.tar.gz.delta 
b/autodock-vina_1.1.2.orig.tar.gz.delta
new file mode 100644
index 000..ffb989b
Binary files /dev/null and b/autodock-vina_1.1.2.orig.tar.gz.delta differ
diff --git a/autodock-vina_1.1.2.orig.tar.gz.id 
b/autodock-vina_1.1.2.orig.tar.gz.id
new file mode 100644
index 000..a51a77f
--- /dev/null
+++ b/autodock-vina_1.1.2.orig.tar.gz.id
@@ -0,0 +1 @@
+64021c6931e0c6b678bb9c06af2395a50103b9f2

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[med-svn] [autodock-vina] branch master created (now 0ec23cb)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository autodock-vina.

at  0ec23cb   Moved packaging from SVN to Git

This branch includes the following new commits:

   new  034a114   Preparing for upload of new autodock-vina package for 
experimental.
   new  2c20ad2   Added man pages.
   new  fc8a287   Removing changes that should not be part of the svn.
   new  4e6b6df   Added Michael to Uploaders.
   new  724ce97   added get-orig-source target, someone please fix 
debian/watch for us.
   new  e610d52   bork.
   new  0677290   The ITP arrived.
   new  e7df14d   autodock-vina moving to unstable, some fixed to the man 
pages.
   new  5eaad4d   Please do not drop content like "Some good soul please 
help with the right watch line, please." but rather ask for help on the list.  
Chances are really good that you get help much faster instead of trusting that 
somebody finds it by chance.
   new  5016d95   Added Vcs Fields, Team maintenance in Debian Med team, 
added myself to uploaders
   new  cefe1d9   Choose a technical implementation (Recommends: autodock, 
autogrid) instead of asking the user to install some packages in README.Debian
   new  3295d85   Do not link against unused libraries; remove empty file 
debian/docs
   new  60681d7   Replace dh-make template by somewhat useful comment; 
Remove missleading get-orig-source target - there is no need at all to repack 
upstream source and the next version should be obtained simply by uscan
   new  9444ede   Added upstream-metadata.yaml
   new  1cbac20   Preparing for upload of 1.1.2
   new  5cc15be   Added missing patch
   new  520c87e   Fixing incompatibility with latest boost library
   new  d861542   Remove --static from build instructions.
   new  5731190   Uploaded version 1.1.2 of autodock-vina
   new  8980b62   Start fixing boost issues to close #642697 but not 
finished (new errors occured after fixing the first one
   new  43d7506   Fixed build problems thanks to Sebastian Ramacher 
; usual packaging updates
   new  9f21366   Upstream-Contact changed and DEP5
   new  7509175   Desciption of patch
   new  3259e80   Series of local changes accidentially left uncommitted 
before.  * somewhat neat but unnecessary formatting changes  * adding uploader 
from upstream to vina  * rosetta build instructions  * pynast more verbose 
README.Debian  * snap changelog mentions upload to PPA
   new  afcf901   Renamed debian/upstream-metadata.yaml to debian/upstream.
   new  a42c240   use uscan in get-orig-source target
   new  6fc982e   debian/upstream: Moved DOI and PMID to the Reference 
namespace.
   new  3969a51   Corrected the files that did not validate with YAML::XS.
   new  cc76013 * debian/upstream:  - Separate authors by ' and ' 
rather by ','  - Moved DOI to references
   new  d2df998   Tagged 1.1.2-3
   new  6b21168   Really delete unneeded patch
   new  f4105a8   Move debian/upstream to debian/upstream/metadata
   new  e05ce32   Added references to registries.
   new  dded90d   New upstream version 1.1.2
   new  5a44143   Updated version 1.1.2 from 'upstream/1.1.2'
   new  0ec23cb   Moved packaging from SVN to Git

The 36 revisions listed above as "new" are entirely new to this
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[med-svn] [autodock-vina] branch pristine-tar created (now 64fdce3)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch pristine-tar
in repository autodock-vina.

at  64fdce3   pristine-tar data for autodock-vina_1.1.2.orig.tar.gz

This branch includes the following new commits:

   new  64fdce3   pristine-tar data for autodock-vina_1.1.2.orig.tar.gz

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[med-svn] [python-pysam] 01/02: Apply upstream patch to fix test suite

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-pysam.

commit 0d0ada34f84dc559b70bf0bb2714d3f9a7edc8aa
Author: Andreas Tille 
Date:   Mon Sep 18 17:02:46 2017 +0200

Apply upstream patch to fix test suite
---
 debian/changelog   |  2 +
 ...linking-tests-only-when-explicitely-reque.patch | 66 ++
 debian/patches/series  |  1 +
 3 files changed, 69 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 709bb0d..a079605 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,8 @@ python-pysam (0.12.0.1+ds-1) UNRELEASED; urgency=medium
   [ Andreas Tille ]
   * Drop patch applied upstream
   * Standards-Version: 4.1.0 (no changes needed)
+  * Apply upstream patch to fix test suite
+Closes: #871083
 
   [ Afif Elghraoui ]
   * New upstream version
diff --git 
a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch 
b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
new file mode 100644
index 000..9520111
--- /dev/null
+++ b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
@@ -0,0 +1,66 @@
+From: Andreas Heger 
+Date: Mon, 18 Sep 2017 11:19:28 +0100
+Bug-Debian: https://bugs.debian.org/871083
+Subject: {AH} execute linking tests only when explicitely
+ requested via PYSAM_LINKING_TESTS env var. Keep on travis. Fixes #534
+
+---
+ .travis.yml   |  2 ++
+ tests/TestUtils.py|  1 +
+ tests/linking_test.py | 10 ++
+ 3 files changed, 13 insertions(+)
+
+--- a/.travis.yml
 b/.travis.yml
+@@ -11,6 +11,8 @@ env:
+ - CONDA_PY=3.4
+ - CONDA_PY=3.5
+ - CONDA_PY=3.6
++  global:
++- PYSAM_LINKING_TEST=1
+ 
+ addons:
+   apt:
+--- a/tests/TestUtils.py
 b/tests/TestUtils.py
+@@ -23,6 +23,7 @@ LINKDIR = os.path.abspath(os.path.join(o
+ 
+ IS_PYTHON3 = sys.version_info[0] >= 3
+ 
++
+ if IS_PYTHON3:
+ from itertools import zip_longest
+ from urllib.request import urlopen
+--- a/tests/linking_test.py
 b/tests/linking_test.py
+@@ -31,6 +31,9 @@ def check_tests_pass(statement):
+ return True
+ 
+ 
++@unittest.skipUnless(
++os.environ.get("PYSAM_LINKING_TESTS", None),
++"enable linking tests by setting PYSAM_LINKING_TESTS environment 
variable")
+ class TestLinking(unittest.TestCase):
+ 
+ package_name = "link_with_rpath"
+@@ -43,6 +46,10 @@ class TestLinking(unittest.TestCase):
+ "cd {} && rm -rf build && python setup.py 
install".format(self.workdir),
+ shell=True)
+ 
++
++@unittest.skipUnless(
++os.environ.get("PYSAM_LINKING_TESTS", None),
++"enable linking tests by setting PYSAM_LINKING_TESTS environment 
variable")
+ class TestLinkWithRpath(TestLinking):
+ 
+ package_name = "link_with_rpath"
+@@ -52,6 +59,9 @@ class TestLinkWithRpath(TestLinking):
+ "cd {} && python 
test_module.py".format(os.path.join(self.workdir, "tests"
+ 
+ 
++@unittest.skipUnless(
++os.environ.get("PYSAM_LINKING_TESTS", None),
++"enable linking tests by setting PYSAM_LINKING_TESTS environment 
variable")
+ class TestLinkWithoutRpath(TestLinking):
+ 
+ package_name = "link_without_rpath"
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 000..f250698
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+execute-linking-tests-only-when-explicitely-reque.patch

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[med-svn] [python-pysam] 02/02: Remaining test suite issue (see upstream #541)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-pysam.

commit 9a7506631dbff91fdff53d8828559e79f0c142c6
Author: Andreas Tille 
Date:   Mon Sep 18 17:33:25 2017 +0200

Remaining test suite issue (see upstream #541)
---
 debian/changelog | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a079605..e5821f2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,7 +4,8 @@ python-pysam (0.12.0.1+ds-1) UNRELEASED; urgency=medium
   * Drop patch applied upstream
   * Standards-Version: 4.1.0 (no changes needed)
   * Apply upstream patch to fix test suite
-Closes: #871083
+Closes: #871083, #834856
+  TODO: not fully solved, see upstream issue 
https://github.com/pysam-developers/pysam/issues/541
 
   [ Afif Elghraoui ]
   * New upstream version
@@ -13,7 +14,7 @@ python-pysam (0.12.0.1+ds-1) UNRELEASED; urgency=medium
   [ Steffen Moeller ]
   * created debian/upstream/metadata: references to registries
 
- -- Afif Elghraoui   Sun, 10 Sep 2017 00:18:20 -0400
+ -- Andreas Tille   Mon, 18 Sep 2017 17:02:54 +0200
 
 python-pysam (0.11.2.2+ds-3) unstable; urgency=medium
 

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[med-svn] [python-pysam] branch master updated (e2a8cbf -> 9a75066)

2017-09-18 Thread Andreas Tille

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tille pushed a change to branch master
in repository python-pysam.

  from  e2a8cbf   Added references to registries
   new  0d0ada3   Apply upstream patch to fix test suite
   new  9a75066   Remaining test suite issue (see upstream #541)

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listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog   |  5 +-
 ...linking-tests-only-when-explicitely-reque.patch | 66 ++
 debian/patches/series  |  1 +
 3 files changed, 71 insertions(+), 1 deletion(-)
 create mode 100644 
debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
 create mode 100644 debian/patches/series

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[med-svn] [imagej] 01/01: d/control: declare imagej dependency on libij-java

2017-09-18 Thread Carnë Draug

This is an automated email from the git hooks/post-receive script.

carandraug-guest pushed a commit to branch master
in repository imagej.

commit c4d06f94306d54e70a30bfd7ea51dac5f1d6281b
Author: Carnë Draug 
Date:   Mon Sep 18 19:57:02 2017 +0100

d/control: declare imagej dependency on libij-java
---
 debian/changelog | 6 ++
 debian/control   | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 3ebae69..028cf91 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+imagej (1.51p+dfsg-2) UNRELEASED; urgency=medium
+
+  * Declare the imagej dependency on the new libij-java package.
+
+ -- Carnë Draug   Mon, 18 Sep 2017 19:54:54 +0100
+
 imagej (1.51p+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
diff --git a/debian/control b/debian/control
index be0df83..91a46ee 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,8 @@ Homepage: https://imagej.nih.gov/ij
 Package: imagej
 Architecture: all
 Depends: ${java:Depends}, ${misc:Depends},
- default-jre | java5-runtime
+ default-jre | java5-runtime,
+ libij-java
 Recommends: ${java:Recommends}
 Description: Image processing program with a focus on microscopy images
  It can display, edit, analyze, process, save and print 8-bit, 16-bit and

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[med-svn] [imagej] branch master updated (1ed7789 -> c4d06f9)

2017-09-18 Thread Carnë Draug

This is an automated email from the git hooks/post-receive script.

carandraug-guest pushed a change to branch master
in repository imagej.

  from  1ed7789   releasing package imagej version 1.51p+dfsg-1
   new  c4d06f9   d/control: declare imagej dependency on libij-java

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 debian/control   | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

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[med-svn] [autodock-vina] tag debian/1.1.2-4 created (now de16f12)

2017-09-18 Thread Andreas Tille

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tille pushed a change to tag debian/1.1.2-4
in repository autodock-vina.

at  de16f12   (commit)
No new revisions were added by this update.

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[med-svn] [autodock-vina] 02/03: debhelper 10

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository autodock-vina.

commit e9976e2fbd452b49f601eb253eeb2b44b4007566
Author: Andreas Tille 
Date:   Mon Sep 18 21:56:15 2017 +0200

debhelper 10
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 1cc91b2..a065d38 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ autodock-vina (1.1.2-4) UNRELEASED; urgency=low
   [ Andreas Tille ]
   * Moved packaging from SVN to Git
   * Standards-Version: 4.1.0
+  * debhelper 10
 
  -- Andreas Tille   Mon, 18 Sep 2017 17:06:31 +0200
 
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 4cc7924..6f381ab 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Uploaders: Steffen Moeller ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
libboost-all-dev
 Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/autodock-vina.git

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[med-svn] [autodock-vina] 03/03: Upload to unstable

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository autodock-vina.

commit de16f1259079c0d796eba502e9f815ff29ca7b1c
Author: Andreas Tille 
Date:   Mon Sep 18 22:04:57 2017 +0200

Upload to unstable
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a065d38..afc024d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-autodock-vina (1.1.2-4) UNRELEASED; urgency=low
+autodock-vina (1.1.2-4) unstable; urgency=low
 
   [ Steffen Moeller ]
   * debian/upstream/metadata
@@ -10,7 +10,7 @@ autodock-vina (1.1.2-4) UNRELEASED; urgency=low
   * Standards-Version: 4.1.0
   * debhelper 10
 
- -- Andreas Tille   Mon, 18 Sep 2017 17:06:31 +0200
+ -- Andreas Tille   Mon, 18 Sep 2017 21:56:36 +0200
 
 autodock-vina (1.1.2-3) unstable; urgency=low
 

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[med-svn] [autodock-vina] branch master updated (0ec23cb -> de16f12)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository autodock-vina.

  from  0ec23cb   Moved packaging from SVN to Git
   new  e767068   Standards-Version: 4.1.0
   new  e9976e2   debhelper 10
   new  de16f12   Upload to unstable

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 --
 debian/compat| 2 +-
 debian/control   | 4 ++--
 3 files changed, 7 insertions(+), 5 deletions(-)

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[med-svn] [autodock-vina] 01/03: Standards-Version: 4.1.0

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository autodock-vina.

commit e76706895ad527a3b4cee38361b6434e1f2c8e06
Author: Andreas Tille 
Date:   Mon Sep 18 21:55:43 2017 +0200

Standards-Version: 4.1.0
---
 debian/changelog | 1 +
 debian/control   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 56306b1..1cc91b2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ autodock-vina (1.1.2-4) UNRELEASED; urgency=low
 
   [ Andreas Tille ]
   * Moved packaging from SVN to Git
+  * Standards-Version: 4.1.0
 
  -- Andreas Tille   Mon, 18 Sep 2017 17:06:31 +0200
 
diff --git a/debian/control b/debian/control
index 3176cca..4cc7924 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
libboost-all-dev
-Standards-Version: 3.9.4
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/autodock-vina.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/autodock-vina.git
 Homepage: http://vina.scripps.edu

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[med-svn] r24060 - trunk/packages/autodock-vina/trunk

2017-09-18 Thread Andreas Tille

Author: tille
Date: 2017-09-18 20:10:51 + (Mon, 18 Sep 2017)
New Revision: 24060

Added:
   trunk/packages/autodock-vina/trunk/README.status
Removed:
   trunk/packages/autodock-vina/trunk/debian/
Log:
Document move to Git


Added: trunk/packages/autodock-vina/trunk/README.status
===
--- trunk/packages/autodock-vina/trunk/README.status
(rev 0)
+++ trunk/packages/autodock-vina/trunk/README.status2017-09-18 20:10:51 UTC 
(rev 24060)
@@ -0,0 +1,7 @@
+---
+Format: 1
+Status: git
+SVNDeleteRevision: 24059
+URL: https://git.debian.org/git/debian-med/autodock-vina.git
+Comment: >
+  This package is now managed in a Git repository.


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[med-svn] [python-pysam] branch master updated (9a75066 -> cfeae8d)

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository python-pysam.

  from  9a75066   Remaining test suite issue (see upstream #541)
   new  cfeae8d   Further patch from upstream should solve final test issue

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog   |  1 -
 ...linking-tests-only-when-explicitely-reque.patch |  2 +-
 ...o-prevent-it-from-being-picked-up-by-nose.patch | 39 ++
 debian/patches/series  |  1 +
 4 files changed, 41 insertions(+), 2 deletions(-)
 create mode 100644 
debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch

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[med-svn] [python-pysam] 01/01: Further patch from upstream should solve final test issue

2017-09-18 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-pysam.

commit cfeae8dc5d07407423e5a93a1995d5dedbc2e036
Author: Andreas Tille 
Date:   Mon Sep 18 22:20:54 2017 +0200

Further patch from upstream should solve final test issue
---
 debian/changelog   |  1 -
 ...linking-tests-only-when-explicitely-reque.patch |  2 +-
 ...o-prevent-it-from-being-picked-up-by-nose.patch | 39 ++
 debian/patches/series  |  1 +
 4 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e5821f2..9d290ad 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,7 +5,6 @@ python-pysam (0.12.0.1+ds-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.1.0 (no changes needed)
   * Apply upstream patch to fix test suite
 Closes: #871083, #834856
-  TODO: not fully solved, see upstream issue 
https://github.com/pysam-developers/pysam/issues/541
 
   [ Afif Elghraoui ]
   * New upstream version
diff --git 
a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch 
b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
index 9520111..185dfbd 100644
--- a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
+++ b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
@@ -1,7 +1,7 @@
 From: Andreas Heger 
 Date: Mon, 18 Sep 2017 11:19:28 +0100
 Bug-Debian: https://bugs.debian.org/871083
-Subject: {AH} execute linking tests only when explicitely
+Subject: execute linking tests only when explicitely
  requested via PYSAM_LINKING_TESTS env var. Keep on travis. Fixes #534
 
 ---
diff --git 
a/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
 
b/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
new file mode 100644
index 000..d96b801
--- /dev/null
+++ 
b/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
@@ -0,0 +1,39 @@
+From: Andreas Heger 
+Date: Mon, 18 Sep 2017 16:48:21 +0100
+Bug-Debian: https://bugs.debian.org/871083
+Subject: rename helper function to prevent it from being picked
+ up by nose, fixes #541
+
+---
+ tests/linking_test.py | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+--- a/tests/linking_test.py
 b/tests/linking_test.py
+@@ -20,7 +20,7 @@ def check_import(statement):
+ raise
+ 
+ 
+-def check_tests_pass(statement):
++def check_pass(statement):
+ try:
+ output = subprocess.check_output(
+ statement, stderr=subprocess.STDOUT, shell=True)
+@@ -55,7 +55,7 @@ class TestLinkWithRpath(TestLinking):
+ package_name = "link_with_rpath"
+ 
+ def test_package_tests_pass(self):
+-self.assertTrue(check_tests_pass(
++self.assertTrue(check_pass(
+ "cd {} && python 
test_module.py".format(os.path.join(self.workdir, "tests"
+ 
+ 
+@@ -79,7 +79,7 @@ class TestLinkWithoutRpath(TestLinking):
+ pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in 
pysam_libraries])
+ pysam_libdir = pysam_libdirs[0]
+ 
+-self.assertTrue(check_tests_pass(
++self.assertTrue(check_pass(
+ "export LD_LIBRARY_PATH={}:$PATH && cd {} && python 
test_module.py".format(
+ pysam_libdir,
+ os.path.join(self.workdir, "tests"
diff --git a/debian/patches/series b/debian/patches/series
index f250698..155615b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 execute-linking-tests-only-when-explicitely-reque.patch
+rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch

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