from:"Andrei Zavada"

[med-svn] [aghermann] 23/23: prepare for 1.1.2

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit abfd5140da53fefd245495a5f3f4a0ad34626f21
Author: Andrei Zavada 
Date:   Tue Jan 3 15:40:26 2017 +0200

prepare for 1.1.2
---
 debian/changelog  |  6 ++
 debian/control| 29 +
 debian/copyright  |  2 +-
 upstream/ChangeLog|  9 +
 upstream/Makefile.am  |  1 +
 upstream/configure.ac |  2 +-
 upstream/data/ui/mw-dialogs.glade | 22 --
 7 files changed, 51 insertions(+), 20 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index da02029..2257bf2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.1.2-1) unstable; urgency=low
+
+  * New upstream version.
+
+ -- Andrei Zavada   Tue,  3 Jan 2017 15:31:00 +0200
+
 aghermann (1.1.1-1) unstable; urgency=low
 
   * New upstream version (Closes: #833472).
diff --git a/debian/control b/debian/control
index a7c4e83..b3e9139 100644
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,32 @@
 Source: aghermann
+Uploaders: Andrei Zavada 
+Maintainer: Debian Med Packaging Team 

 Section: science
 Priority: optional
-Maintainer: Andrei Zavada 
-Build-Depends: debhelper (>= 9), dh-autoreconf,
- autoconf-archive, pkg-config, libgomp1, libconfig++-dev, libgsl-dev, 
libfftw3-dev,
- libsamplerate0-dev (>= 0.1.7), libgtk-3-dev, libitpp-dev, libvte-2.91-dev,
- liblua5.2-dev, lua5.2, libxml2-utils
+Build-Depends: debhelper (>= 9),
+   dh-autoreconf,
+   autoconf-archive,
+   pkg-config,
+   libgomp1,
+   libconfig++-dev,
+   libgsl-dev,
+   libfftw3-dev,
+   libsamplerate0-dev,
+   libgtk-3-dev,
+   libitpp-dev,
+   libvte-2.91-dev,
+   liblua5.2-dev,
+   lua5.2,
+   libxml2-utils
 Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/aghermann.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/aghermann.git
 Homepage: http://johnhommer.com/academic/code/aghermann
-Vcs-Git: git://git.debian.org/git/debian-med/aghermann.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/aghermann.git
 
 Package: aghermann
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
 Suggests: edfbrowser
 Description: Sleep-research experiment manager
  Aghermann is a program designed around a common workflow in
diff --git a/debian/copyright b/debian/copyright
index 28b1988..db30fe1 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-Name: Aghermann
 Upstream-Contact: Andrei Zavada 
 Source: http://johnhommer.com/academic/code/aghermann/source/
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index a83da18..ff576fa 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,12 @@
+v.1.1.2 (2017-01-03)
+   * Fix: Don't crash on unreadable headers in EDF files.
+   * Fix: Assorted crashes/UX mishaps when managing RK1968 (and
+ possibly other) profiles.
+   * Fix: Saved patterns can be loaded again.
+   * Fix: Correctly calculate sibject timeline (remove days of empty
+ space).
+   * Fix/misc: Keep up with GTK+ deprecations.
+
 v.1.1.1 (2016-08-05)
* Misc: Ensure reproducible build #2.
 
diff --git a/upstream/Makefile.am b/upstream/Makefile.am
index 6be49ab..e49d94c 100644
--- a/upstream/Makefile.am
+++ b/upstream/Makefile.am
@@ -17,6 +17,7 @@ man_MANS = \
 unwanted_files = \
m4/*.m4 \
aclocal.m4 \
+   compile \
config.sub \
ltmain.sh \
depcomp \
diff --git a/upstream/configure.ac b/upstream/configure.ac
index e340c6f..bd3921a 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-16 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.1.1], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.1.2], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index 60420aa..3b9914a 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1,7 +1,7 @@
 
-
+
 
-  
+  
   
 80
 1.5
@@ -1534,7 +1534,7 @@
 start
 5
 15
-<b><big><big>Aghermann 1.1.1 
</big></big></b>
+<b><big><big>Aghermann 1.1.2 
</big></big></b>
 <a 
href=

[med-svn] [aghermann] 22/23: expand profile combobox in sf-patterns.glade

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit cedc7d66c68c14cbcbd80c5c98aa80b8a54b42e9
Author: Andrei Zavada 
Date:   Tue Jan 3 15:39:11 2017 +0200

expand profile combobox in sf-patterns.glade
---
 upstream/data/ui/sf-patterns.glade | 173 ++---
 1 file changed, 84 insertions(+), 89 deletions(-)

diff --git a/upstream/data/ui/sf-patterns.glade 
b/upstream/data/ui/sf-patterns.glade
index b0f8b6a..c213f05 100644
--- a/upstream/data/ui/sf-patterns.glade
+++ b/upstream/data/ui/sf-patterns.glade
@@ -1,6 +1,7 @@
 
+
 
-  
+  
   
 True
 False
@@ -153,10 +154,6 @@
 0.01
 0.10001
   
-  
-True
-False
-  
   
 False
 10
@@ -271,8 +268,8 @@
 Search
 True
 True
-True
 False
+True
   
   
 
@@ -283,9 +280,9 @@
   
 True
 False
-0
 5
  in 

+0
   
   
 1
@@ -391,8 +388,8 @@
 True
 False
 end
-1
 Searching 
…
+1
 
   
 
@@ -440,9 +437,9 @@
   
 True
 False
-0
 5
 Find 
pattern
+0
 
   
   
@@ -478,7 +475,7 @@
 False
   
   
-False
+True
 True
 1
   
@@ -586,7 +583,6 @@
 •
 1
 True
-True
 False
 False
 jSFFDDZCDFSigma
@@ -610,7 +606,6 @@
 •
 1
 True
-True
 False
 False
 jSFFDBandPassFrom
@@ -630,9 +625,9 @@
   
 True
 False
-1
 5
 Between:
+1
   
   
 4
@@ -645,9 +640,9 @@
   
 True
 False
-1
 5
 Sigma:
+1
   
   
 10
@@ -674,9 +669,9 @@
   
 True
 False
-1
 5
 Order:
+1
   
   
 6
@@ -693,7 +688,6 @@
 •
 1
 True
-True
 False
 False
 jSFFDBandPassOrder
@@ -729,10 +723,10 @@
 False
 5
 5
-0
 5
 <b>Derivative ZC density</b>
 True
+0
   
   
 3
@@ -748,10 +742,10 @@
 False
 5
 5
-0
 5
 <b>Target frequency</b>
 True
+0
   
   
 3
@@ -765,9 +759,9 @@
   
 True
 False
-1
 5
 Step:
+

[med-svn] [aghermann] 15/23: replace deprecated gdk_cairo_create

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit fe97655cf03385d9380d14cfc43652b9aa576ecc
Author: Andrei Zavada 
Date:   Tue Jan 3 05:52:58 2017 +0200

replace deprecated gdk_cairo_create
---
 upstream/src/aghermann/ui/mw/populate.cc | 13 -
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/ui/mw/populate.cc 
b/upstream/src/aghermann/ui/mw/populate.cc
index 713fb31..fc3d3fa 100644
--- a/upstream/src/aghermann/ui/mw/populate.cc
+++ b/upstream/src/aghermann/ui/mw/populate.cc
@@ -305,6 +305,17 @@ annotation_type_s( const sigfile::SAnnotation::TType t)
 static const char* types[] = {"", "S", "K", "E"};
 return types[t];
 }
+
+cairo_t*
+gdk_cairo_create_wrapper(agh::ui::SExpDesignUI::SSubjectPresentation& J)
+{
+return cairo_create(
+gdk_window_create_similar_surface(
+gtk_widget_get_window( J.da),
+CAIRO_CONTENT_COLOR_ALPHA,
+J.tl_width(), J.tl_height()));
+
+}
 }
 
 void
@@ -524,7 +535,7 @@ populate_1()
 
 // determine tl_left_margin
 {
-cairo_t *cr = gdk_cairo_create( 
gtk_widget_get_window( J.da));
+cairo_t *cr = gdk_cairo_create_wrapper( J);
 cairo_text_extents_t extents;
 cairo_select_font_face( cr, "serif", 
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_BOLD);
 cairo_set_font_size( cr, 11);

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[med-svn] [aghermann] 20/23: trivial id renames and emendations

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 64e8cce83581c27fb2540104bd6ecae75fc6c52f
Author: Andrei Zavada 
Date:   Tue Jan 3 14:17:49 2017 +0200

trivial id renames and emendations
---
 upstream/src/aghermann/ui/dirlevel-storable-adapter.hh |  2 +-
 upstream/src/aghermann/ui/dirlevel-storable-adapter.ii |  9 +
 upstream/src/aghermann/ui/sf/d/artifacts.cc|  2 +-
 upstream/src/aghermann/ui/sf/d/patterns.cc |  2 +-
 upstream/src/aghermann/ui/sf/d/rk1968.cc   | 14 +++---
 5 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/upstream/src/aghermann/ui/dirlevel-storable-adapter.hh 
b/upstream/src/aghermann/ui/dirlevel-storable-adapter.hh
index efe0097..8b36fa2 100644
--- a/upstream/src/aghermann/ui/dirlevel-storable-adapter.hh
+++ b/upstream/src/aghermann/ui/dirlevel-storable-adapter.hh
@@ -59,7 +59,7 @@ class SDirlevelStorableAdapter {
 
 SUIVarCollection
 W_V;
-void atomic_up()
+void protected_up()
 {
 suppress_w_v = true;
 W_V.up();
diff --git a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii 
b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
index 8bf671a..af8d769 100644
--- a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
+++ b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
@@ -4,7 +4,8 @@
  *  Author:  Andrei Zavada 
  * Initial version:  2013-09-15
  *
- * Purpose:  
+ * Purpose:  handle per-user/experiment/subject storable items
+ *   (sleep waveform patterns, rk1968 scripts)
  *
  * License:  GPL
  */
@@ -173,7 +174,7 @@ eXProfileList_changed_cb()
 if ( ci != -1 ) {
 current_profile = profile_by_idx(ci);
 Pp2 = *current_profile;
-atomic_up();
+protected_up();
 set_profile_manage_buttons_visibility();
 } else {
 current_profile = profiles.end();
@@ -326,7 +327,7 @@ bXProfileDiscard_clicked_cb()
 
 if ( not profiles.empty() ) {
 Pp2 = *current_profile;
-atomic_up();
+protected_up();
 } else {
 profiles.emplace_back( Pp2);
 profiles.back().level = TExpDirLevel::transient;
@@ -347,7 +348,7 @@ bXProfileRevert_clicked_cb()
 
 Pp2 = *current_profile;
 
-atomic_up();
+protected_up();
 
 set_profile_manage_buttons_visibility();
 }
diff --git a/upstream/src/aghermann/ui/sf/d/artifacts.cc 
b/upstream/src/aghermann/ui/sf/d/artifacts.cc
index b318999..7c45547 100644
--- a/upstream/src/aghermann/ui/sf/d/artifacts.cc
+++ b/upstream/src/aghermann/ui/sf/d/artifacts.cc
@@ -174,7 +174,7 @@ SArtifactsDialog (SScoringFacility& p_)
 W_V.reg( eSFADFlatMinRegionSize, &P.flat_min_size);
 W_V.reg( eSFADFlatPad,   &P.flat_pad);
 
-atomic_up();
+protected_up();
 }
 
 
diff --git a/upstream/src/aghermann/ui/sf/d/patterns.cc 
b/upstream/src/aghermann/ui/sf/d/patterns.cc
index a70478f..5d2154f 100644
--- a/upstream/src/aghermann/ui/sf/d/patterns.cc
+++ b/upstream/src/aghermann/ui/sf/d/patterns.cc
@@ -189,7 +189,7 @@ SPatternsDialog (SScoringFacility& p_)
 
 W_V.reg( eSFFDIncrement, &increment);
 
-atomic_up();
+protected_up();
 }
 
 SScoringFacility::SPatternsDialog::
diff --git a/upstream/src/aghermann/ui/sf/d/rk1968.cc 
b/upstream/src/aghermann/ui/sf/d/rk1968.cc
index b93239f..2c78af1 100644
--- a/upstream/src/aghermann/ui/sf/d/rk1968.cc
+++ b/upstream/src/aghermann/ui/sf/d/rk1968.cc
@@ -9,6 +9,7 @@
  * License:  GPL
  */
 
+#include 
 #include "rk1968.hh"
 
 using namespace std;
@@ -68,8 +69,8 @@ SRK1968Dialog (SScoringFacility& p_)
 gtk_combo_box_set_model_properly(
 eSFRKProfileList, mSFRKProfiles);
 
-agh::ui::global::set_mono_font(
-(GtkWidget*)eSFRKScript, agh::ui::global::css_mono10);
+// agh::ui::global::set_mono_font(
+// (GtkWidget*)eSFRKScript, agh::ui::global::css_mono10);
 
 G_CONNECT_1 (wSFRK, show);
 G_CONNECT_1 (wSFRK, hide);
@@ -82,11 +83,10 @@ SRK1968Dialog (SScoringFacility& p_)
 G_CONNECT_1 (bSFRKProfileRevert,  clicked);
 G_CONNECT_1 (bSFRKProfileDiscard, clicked);
 
-for ( auto& W : {tSFRKScript} )
-g_signal_connect(
-W, "changed",
-(GCallback)eSFRK_any_profile_value_changed_cb,
-this);
+g_signal_connect(
+tSFRKScript, "changed",
+(GCallback)eSFRK_any_profile_value_changed_cb,
+this);
 
 G_CONNECT_1 (bSFRK

[med-svn] [aghermann] 21/23: rk1968 profile management fixes:

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit ef4c540d215b53463aec2aba0c526c3f8233e0bc
Author: Andrei Zavada 
Date:   Tue Jan 3 15:35:33 2017 +0200

rk1968 profile management fixes:

* don't try to save deleted rk1968 profiles;
* throw on load failure in ctor;
* allow empty scripts;
* use protected_up() in construct.
---
 upstream/src/aghermann/expdesign/dirlevel.cc |  4 +++-
 upstream/src/aghermann/expdesign/dirlevel.hh |  2 +-
 upstream/src/aghermann/rk1968/rk1968.cc  | 13 ++---
 upstream/src/aghermann/ui/sf/d/rk1968.cc |  2 +-
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/upstream/src/aghermann/expdesign/dirlevel.cc 
b/upstream/src/aghermann/expdesign/dirlevel.cc
index dea8285..38959f5 100644
--- a/upstream/src/aghermann/expdesign/dirlevel.cc
+++ b/upstream/src/aghermann/expdesign/dirlevel.cc
@@ -149,8 +149,10 @@ save()
 
 int
 CStorablePPack::
-delete_file() const
+delete_file()
 {
+APPLOG_INFO ("deleting %s", path().c_str());
+saved = true;
 return unlink( path().c_str());
 }
 
diff --git a/upstream/src/aghermann/expdesign/dirlevel.hh 
b/upstream/src/aghermann/expdesign/dirlevel.hh
index 2ef8929..c5852f2 100644
--- a/upstream/src/aghermann/expdesign/dirlevel.hh
+++ b/upstream/src/aghermann/expdesign/dirlevel.hh
@@ -121,7 +121,7 @@ class CStorablePPack {
 
 virtual int load();
 virtual int save();
-virtual int delete_file() const;
+virtual int delete_file();
 virtual string serialize() const;
 void touch()
 { saved = false; }
diff --git a/upstream/src/aghermann/rk1968/rk1968.cc 
b/upstream/src/aghermann/rk1968/rk1968.cc
index efab606..41bb7e8 100644
--- a/upstream/src/aghermann/rk1968/rk1968.cc
+++ b/upstream/src/aghermann/rk1968/rk1968.cc
@@ -43,8 +43,10 @@ CScoreAssistant (const string& name_,
 status (0),
 lua_state (nullptr)
 {
-if ( load() )
+if ( load() ) {
 APPLOG_WARN ("no script loaded from \"%s\"", path().c_str());
+throw invalid_argument ("no script loaded");
+}
 }
 
 CScoreAssistant::
@@ -83,6 +85,9 @@ int
 CScoreAssistant::
 save() const
 {
+if ( saved || level == TExpDirLevel::transient || level == 
TExpDirLevel::system )
+return 0;
+
 string p = path();
 if ( fs::mkdir_with_parents( fs::dirname(p)) ) {
 APPLOG_WARN ("mkdir(\"%s\") failed: %s", p.c_str(), 
strerror(errno));
@@ -111,12 +116,6 @@ int
 CScoreAssistant::
 compile()
 {
-if ( script_contents.empty() ) {
-APPLOG_WARN ("no script to compile (\"%s\")", path().c_str());
-status |= TFlags::ecompile;
-return -1;
-}
-
 lua_init();
 lua_settop( lua_state, 0);
 int ret1 = luaL_loadbuffer(
diff --git a/upstream/src/aghermann/ui/sf/d/rk1968.cc 
b/upstream/src/aghermann/ui/sf/d/rk1968.cc
index 2c78af1..3a40ef3 100644
--- a/upstream/src/aghermann/ui/sf/d/rk1968.cc
+++ b/upstream/src/aghermann/ui/sf/d/rk1968.cc
@@ -102,7 +102,7 @@ SRK1968Dialog (SScoringFacility& p_)
 
   // 2. dialog
 W_V.reg( tSFRKScript, &Pp2.script_contents);
-W_V.up();
+protected_up();
 }
 
 SScoringFacility::SRK1968Dialog::

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[med-svn] [aghermann] 16/23: prettify stale session lock message

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 796676a0e644ee88b7619799e8507ee40fdf9140
Author: Andrei Zavada 
Date:   Tue Jan 3 05:54:02 2017 +0200

prettify stale session lock message
---
 upstream/src/aghermann/expdesign/expdesign.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/upstream/src/aghermann/expdesign/expdesign.cc 
b/upstream/src/aghermann/expdesign/expdesign.cc
index e466318..1cf7a66 100644
--- a/upstream/src/aghermann/expdesign/expdesign.cc
+++ b/upstream/src/aghermann/expdesign/expdesign.cc
@@ -120,9 +120,9 @@ CExpDesign (const string& session_dir_,
 if ( stst == 0 ) {
 const char *lock_mtime_s = ctime( &stat0.st_mtime);
 throw invalid_argument
-(sasprintf("A lock file 
exists:\n%s,\ncreated %.*s).\n\n"
+(sasprintf("A lock file exists (created 
%.*s):\n\n%s\n\n"
"If this lock is stale, delete it 
and try again.",
-   lock_fname.c_str(), 
(int)strlen(lock_mtime_s)-1, lock_mtime_s));
+   (int)strlen(lock_mtime_s)-1, 
lock_mtime_s, lock_fname.c_str()));
 }
 open( lock_fname.c_str(), O_WRONLY|O_CREAT|O_TRUNC, 0600);
 stst = stat( lock_fname.c_str(), &stat0);

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[med-svn] [aghermann] 09/23: don't forget to update vars to widgets in d/rk1968

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit f9c2aa6d5843112da2ddf27d075995ac0af79acd
Author: Andrei Zavada 
Date:   Tue Jan 3 05:45:37 2017 +0200

don't forget to update vars to widgets in d/rk1968
---
 upstream/src/aghermann/ui/sf/d/rk1968.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/upstream/src/aghermann/ui/sf/d/rk1968.cc 
b/upstream/src/aghermann/ui/sf/d/rk1968.cc
index 5c10991..513cf4f 100644
--- a/upstream/src/aghermann/ui/sf/d/rk1968.cc
+++ b/upstream/src/aghermann/ui/sf/d/rk1968.cc
@@ -100,6 +100,7 @@ SRK1968Dialog (SScoringFacility& p_)
 
   // 2. dialog
 W_V.reg( tSFRKScript, &Pp2.script_contents);
+W_V.up();
 }
 
 SScoringFacility::SRK1968Dialog::

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[med-svn] [aghermann] 19/23: sweep up deprecated gtk_ and gdk_ functions

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit b9c361d23ebe7f96918821e620c40d7f0e636e65
Author: Andrei Zavada 
Date:   Tue Jan 3 14:16:43 2017 +0200

sweep up deprecated gtk_ and gdk_ functions
---
 upstream/src/aghermann/ui/globals.cc  |  4 ++--
 upstream/src/aghermann/ui/mf/mf.cc|  5 +
 upstream/src/aghermann/ui/sf/d/patterns_cb.cc |  4 +---
 upstream/src/aghermann/ui/sf/montage_cb.cc| 17 +
 4 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/upstream/src/aghermann/ui/globals.cc 
b/upstream/src/aghermann/ui/globals.cc
index abd0aae..3e3cd22 100644
--- a/upstream/src/aghermann/ui/globals.cc
+++ b/upstream/src/aghermann/ui/globals.cc
@@ -40,8 +40,8 @@ prepare_for_expdesign()
 {
   // tell me what they are
 client_pointer =
-gdk_device_manager_get_client_pointer(
-gdk_display_get_device_manager( 
gdk_display_get_default()));
+gdk_seat_get_pointer(
+gdk_display_get_default_seat( 
gdk_display_get_default()));
 
 GResource
 *gresource
diff --git a/upstream/src/aghermann/ui/mf/mf.cc 
b/upstream/src/aghermann/ui/mf/mf.cc
index 0db8769..6d8e6bd 100644
--- a/upstream/src/aghermann/ui/mf/mf.cc
+++ b/upstream/src/aghermann/ui/mf/mf.cc
@@ -68,10 +68,7 @@ SModelrunFacility (agh::ach::CModelRun& csim, SExpDesignUI& 
parent)
 "Simulation: %s (%s) in %s (%s)",
 csim.subject(), csim.session(), csim.channel(),
 csim.P().display_name().c_str()));
-gtk_window_set_default_size(
-wModelrunFacility,
-gdk_screen_get_width( gdk_screen_get_default()) * .80,
-gdk_screen_get_height( gdk_screen_get_default()) * .55);
+set_window_size_as_screen_fraction( wModelrunFacility, .80, .55);
 
 gtk_toggle_button_set_active( (GtkToggleButton*)eMFDB1, 
csim.ctl_params.DBAmendment1);
 gtk_toggle_button_set_active( (GtkToggleButton*)eMFDB2, 
csim.ctl_params.DBAmendment2);
diff --git a/upstream/src/aghermann/ui/sf/d/patterns_cb.cc 
b/upstream/src/aghermann/ui/sf/d/patterns_cb.cc
index 03eabf9..75bf37e 100644
--- a/upstream/src/aghermann/ui/sf/d/patterns_cb.cc
+++ b/upstream/src/aghermann/ui/sf/d/patterns_cb.cc
@@ -128,9 +128,7 @@ daSFFDField_button_press_event_cb(
 break;
 case 3:
 FD.update_field_check_menu_items();
-gtk_menu_popup(
-FD.iiSFFDField,
-NULL, NULL, NULL, NULL, 3, event->time);
+gtk_menu_popup_at_pointer( FD.iiSFFDField, (GdkEvent*)event);
 break;
 }
 
diff --git a/upstream/src/aghermann/ui/sf/montage_cb.cc 
b/upstream/src/aghermann/ui/sf/montage_cb.cc
index 68b071a..b46d608 100644
--- a/upstream/src/aghermann/ui/sf/montage_cb.cc
+++ b/upstream/src/aghermann/ui/sf/montage_cb.cc
@@ -99,8 +99,7 @@ daSFMontage_button_press_event_cb(
 (GtkContainer*)SF.iiSFICAPage,
 radio_item_setter, (gpointer)mapped);
 SF.suppress_redraw = false;
-gtk_menu_popup( SF.iiSFICAPage,
-NULL, NULL, NULL, NULL, 3, 
event->time);
+gtk_menu_popup_at_pointer( SF.iiSFICAPage, 
(GdkEvent*)event);
 }
 return TRUE;
 }
@@ -141,9 +140,7 @@ daSFMontage_button_press_event_cb(
 break;
 case 3:
 Ch->update_power_menu_items();
-gtk_menu_popup(
-SF.iiSFPower,
-NULL, NULL, NULL, NULL, 3, event->time);
+gtk_menu_popup_at_pointer( SF.iiSFPower, 
(GdkEvent*)event);
 break;
 }
 
@@ -181,14 +178,11 @@ daSFMontage_button_press_event_cb(
 case 3:
 if ( (event->state & GDK_MOD1_MASK && SF.n_hidden > 0) 
||
  !(SF.n_hidden < (int)SF.channels.size()) )
-gtk_menu_popup( SF.iiSFPageHidden,
-NULL, NULL, NULL, NULL, 3, 
event->time);
+gtk_menu_popup_at_pointer( SF.iiSFPageHidden, 
(GdkEvent*)event);
 else {
 Ch->update_channel_menu_items( event->x);
 Ch->update_power_menu_items();
-gtk_menu_popup(
-in_selection ? SF.iiSFPageSelection : 
SF.iiSFPage,
-NULL, NULL, NULL, NULL, 3, 
event->

[med-svn] [aghermann] 17/23: replace some calls of deprecated gtk_menu_popup

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit d91616f9af9d98da42cd1fee035c1f21372330d4
Author: Andrei Zavada 
Date:   Tue Jan 3 05:55:12 2017 +0200

replace some calls of deprecated gtk_menu_popup
---
 upstream/src/aghermann/ui/mw/measurements_cb.cc | 3 +--
 upstream/src/aghermann/ui/sf/hypnogram_cb.cc| 5 ++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/measurements_cb.cc 
b/upstream/src/aghermann/ui/mw/measurements_cb.cc
index 104e05d..0928a38 100644
--- a/upstream/src/aghermann/ui/mw/measurements_cb.cc
+++ b/upstream/src/aghermann/ui/mw/measurements_cb.cc
@@ -122,8 +122,7 @@ daSubjectTimeline_button_press_event_cb(
 gtk_widget_set_visible( (GtkWidget*)ED.iSubjectTimelineScore, 
episode_ops);
 gtk_widget_set_visible( 
(GtkWidget*)ED.iSubjectTimelineDetectUltradianCycle, episode_ops);
 gtk_widget_set_visible( 
(GtkWidget*)ED.iSubjectTimelineEDFInfo, episode_ops);
-gtk_menu_popup( ED.iiSubjectTimeline,
-NULL, NULL, NULL, NULL, 3, event->time);
+gtk_menu_popup_at_pointer( ED.iiSubjectTimeline, 
(GdkEvent*)event);
 break;
 }
 
diff --git a/upstream/src/aghermann/ui/sf/hypnogram_cb.cc 
b/upstream/src/aghermann/ui/sf/hypnogram_cb.cc
index df9c443..eab6850 100644
--- a/upstream/src/aghermann/ui/sf/hypnogram_cb.cc
+++ b/upstream/src/aghermann/ui/sf/hypnogram_cb.cc
@@ -54,9 +54,8 @@ daSFHypnogram_button_press_event_cb(
 gtk_widget_queue_draw( wid);
 break;
 case 3:
-gtk_menu_popup(
-SF.iiSFScore,
-NULL, NULL, NULL, NULL, 3, event->time);
+gtk_menu_popup_at_pointer(
+SF.iiSFScore, NULL);
 break;
 }
 return TRUE;

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[med-svn] [aghermann] 18/23: better figure rk1968 window size

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit cc4f557a1d7bc2cf634261965755025ace0b5641
Author: Andrei Zavada 
Date:   Tue Jan 3 05:56:10 2017 +0200

better figure rk1968 window size
---
 upstream/src/aghermann/ui/sf/d/rk1968.cc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/upstream/src/aghermann/ui/sf/d/rk1968.cc 
b/upstream/src/aghermann/ui/sf/d/rk1968.cc
index 513cf4f..b93239f 100644
--- a/upstream/src/aghermann/ui/sf/d/rk1968.cc
+++ b/upstream/src/aghermann/ui/sf/d/rk1968.cc
@@ -74,6 +74,8 @@ SRK1968Dialog (SScoringFacility& p_)
 G_CONNECT_1 (wSFRK, show);
 G_CONNECT_1 (wSFRK, hide);
 
+set_window_size_as_screen_fraction( (GtkWindow*)wSFRK, .4, .7);
+
 eSFRKProfileList_changed_cb_handler_id =
 G_CONNECT_1 (eSFRKProfileList, changed);
 G_CONNECT_1 (bSFRKProfileSave,clicked);

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[med-svn] [aghermann] 11/23: undisappear buttons, generally tidy up rk1968.glade

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit e44f65354ba2f633c54f7549988c345b35a5fc2e
Author: Andrei Zavada 
Date:   Tue Jan 3 05:47:51 2017 +0200

undisappear buttons, generally tidy up rk1968.glade
---
 upstream/data/ui/sf-rk1968.glade | 129 +--
 1 file changed, 69 insertions(+), 60 deletions(-)

diff --git a/upstream/data/ui/sf-rk1968.glade b/upstream/data/ui/sf-rk1968.glade
index c322037..2a6a22d 100644
--- a/upstream/data/ui/sf-rk1968.glade
+++ b/upstream/data/ui/sf-rk1968.glade
@@ -1,6 +1,7 @@
 
+
 
-  
+  
   
 0.01
 30
@@ -101,7 +102,6 @@
   
 True
 False
-0
 RK (n 
channels)
 True
   
@@ -135,7 +135,7 @@
 False
   
   
-False
+True
 True
 1
   
@@ -172,7 +172,7 @@
 
   
   
-False
+True
 True
 1
   
@@ -196,46 +196,57 @@
   
 
 
-  
+  
 True
 False
-2
-5
-5
+True
+True
 
   
 True
 False
-0
+start
+True
 Script:
+True
   
   
-GTK_FILL
+0
+0
   
 
 
   
 True
 True
+True
+True
 in
+False
+False
 
   
+-1
+-1
 True
 True
+True
+True
 3
 tSFRKScript
 GTK_INPUT_HINT_NO_SPELLCHECK | GTK_INPUT_HINT_NONE
+True
   
 
   
   
+0
 1
-2
   
 
   
   
-True
+False
 True
 2
   
@@ -244,7 +255,6 @@
   
 True
 False
-0
   
   
 False
@@ -303,6 +313,52 @@
 5
 vertical
 10
+
+  
+True
+False
+end
+
+  
+gtk-cancel
+True
+True
+False
+True
+True
+  
+  
+False
+False
+0
+  
+
+
+  
+gtk-ok
+True
+True
+False
+True
+True
+True
+True
+
+  
+  
+False
+False
+1
+  
+
+  
+  
+False
+True
+end
+3
+  
+
 
   
 True
@@ -319,7 +375,6 @@
 5
 •
 True
-True
 False
 False
   
@@ -423,52 +478,6 @@
 2
   
 
-
-  
-True
-False
-end
-
-  
-gtk-cancel
-True
-True
-True
-True
-False
-  
-  
-False
-False
-0
-  
-
-
-  
-gtk-ok
-True
-True
-True
-True
-True
-True
-False
-
-  
-  
-False
-False
-1
-  
-
-  
-  
-False
-True

[med-svn] [aghermann] 14/23: log rk1968 script name if empty

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit f42dce96c52b68ce08d75077cbe535242b8306ae
Author: Andrei Zavada 
Date:   Tue Jan 3 05:51:13 2017 +0200

log rk1968 script name if empty
---
 upstream/src/aghermann/rk1968/rk1968.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/rk1968/rk1968.cc 
b/upstream/src/aghermann/rk1968/rk1968.cc
index 66ec05c..efab606 100644
--- a/upstream/src/aghermann/rk1968/rk1968.cc
+++ b/upstream/src/aghermann/rk1968/rk1968.cc
@@ -112,7 +112,7 @@ CScoreAssistant::
 compile()
 {
 if ( script_contents.empty() ) {
-APPLOG_WARN ("no script to compile");
+APPLOG_WARN ("no script to compile (\"%s\")", path().c_str());
 status |= TFlags::ecompile;
 return -1;
 }

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[med-svn] [aghermann] 12/23: correctly anchor menu for Alt+N on SF montage

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 6abff5488cc76c52240deec63b8a394553004a9e
Author: Andrei Zavada 
Date:   Tue Jan 3 05:49:55 2017 +0200

correctly anchor menu for Alt+N on SF montage
---
 upstream/src/aghermann/ui/sf/mainmenu_cb.cc | 34 -
 upstream/src/aghermann/ui/sf/sf.cc  |  6 +++--
 upstream/src/aghermann/ui/ui.cc | 21 ++
 upstream/src/aghermann/ui/ui.hh |  6 ++---
 4 files changed, 47 insertions(+), 20 deletions(-)

diff --git a/upstream/src/aghermann/ui/sf/mainmenu_cb.cc 
b/upstream/src/aghermann/ui/sf/mainmenu_cb.cc
index c196d0d..73e2c04 100644
--- a/upstream/src/aghermann/ui/sf/mainmenu_cb.cc
+++ b/upstream/src/aghermann/ui/sf/mainmenu_cb.cc
@@ -260,23 +260,21 @@ iSFMontageCloseAndNext_activate_cb(
 
 namespace {
 
-#define EVENT_X 30
-
+const double EVENT_X = 40;
 size_t position_for_channel = -1;
+
 void channel_menu_position(
 GtkMenu*,
 gint *x,
 gint *y,
-gboolean*, //push_in,
 const gpointer userdata)
 {
 auto& SF = *(SScoringFacility*)userdata;
-int mwx, mwy, rwx, rwy;
-gtk_window_get_position( SF.wSF, &mwx, &mwy);
+int rwx, rwy;
 gdk_window_get_position( gtk_widget_get_window( 
(GtkWidget*)SF.daSFMontage), &rwx, &rwy);
 if ( position_for_channel < SF.channels.size() ) {
-*x = mwx + rwx + EVENT_X;
-*y = mwy + rwx + SF[position_for_channel].zeroy-20;
+*x = rwx + EVENT_X;
+*y = rwy + SF[position_for_channel].zeroy-20;
 } else
 *x = *y = 0;
 }
@@ -284,7 +282,7 @@ void channel_menu_position(
 }
 
 gboolean
-wSF_key_press_event_cb( GtkWidget*, const GdkEventKey *event, const gpointer 
userdata)
+wSF_key_press_event_cb( GtkWidget* window, const GdkEventKey *event, const 
gpointer userdata)
 {
 auto& SF = *(SScoringFacility*)userdata;
 
@@ -293,13 +291,19 @@ wSF_key_press_event_cb( GtkWidget*, const GdkEventKey 
*event, const gpointer use
 return FALSE;
 
 #define KEKE(N) \
-position_for_channel = N-1;\
-if ( position_for_channel < SF.channels.size() ) {\
-SF.using_channel = &SF[position_for_channel];\
-SF.using_channel->update_channel_menu_items( EVENT_X);\
-gtk_menu_popup( SF.iiSFPage, NULL, NULL, 
channel_menu_position, userdata, 3, event->time); \
-} else\
-gdk_beep();\
+position_for_channel = N-1; \
+if ( position_for_channel < SF.channels.size() ) {  \
+SF.using_channel = &SF[position_for_channel];   \
+SF.using_channel->update_channel_menu_items( EVENT_X);  \
+GdkRectangle rect;  \
+channel_menu_position( SF.iiSFPage, &rect.x, &rect.y, 
userdata); \
+rect.width = rect.height = 1;   \
+gtk_menu_popup_at_rect( SF.iiSFPage, 
gtk_widget_get_window(window), &rect, \
+GDK_GRAVITY_SOUTH_WEST, 
GDK_GRAVITY_NORTH_WEST, NULL); \
+gtk_label_set_text( SF.lSFOverChannel, 
SF.using_channel->name()); \
+gtk_widget_queue_draw( window); \
+} else  \
+gdk_beep(); \
 return TRUE;
 
 switch ( event->keyval ) {
diff --git a/upstream/src/aghermann/ui/sf/sf.cc 
b/upstream/src/aghermann/ui/sf/sf.cc
index 87083a6..170eca1 100644
--- a/upstream/src/aghermann/ui/sf/sf.cc
+++ b/upstream/src/aghermann/ui/sf/sf.cc
@@ -279,14 +279,16 @@ SScoringFacility (agh::CSubject& J,
 "You can hide some using appropriate channel context 
menus.", channels.size() - n_hidden);
 
 {
+GdkRectangle rect;
+get_monitor_geometry( gtk_widget_get_window((GtkWidget*)wSF), 
&rect);
 int bar_height;
 gtk_widget_get_size_request( (GtkWidget*)cSFControlBar, NULL, 
&bar_height);
 int optimal_win_height = min(
 (int)(HypnogramHeight + bar_height + da_ht + 100),
-(int)(gdk_screen_get_height( gdk_screen_get_default()) 
* .95));
+(int)(rect.height * .95));
 gtk_window_set_default_size(
 wSF,
-gdk_sc

[med-svn] [aghermann] 10/23: work around non-utf8 terminating \0, unbreak lua scripts loading in rk1968

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 2f6c5f8ef3bc68fda90ade98250779de88ff320e
Author: Andrei Zavada 
Date:   Tue Jan 3 05:46:52 2017 +0200

work around non-utf8 terminating \0, unbreak lua scripts loading in rk1968
---
 upstream/src/aghermann/ui/ui++.hh | 5 -
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/ui/ui++.hh 
b/upstream/src/aghermann/ui/ui++.hh
index 6827ed8..51a3e28 100644
--- a/upstream/src/aghermann/ui/ui++.hh
+++ b/upstream/src/aghermann/ui/ui++.hh
@@ -245,7 +245,10 @@ SUIVar_::down()const { 
v->assign( gtk_entry_get_text(
 template <> inline void
 SUIVar_::up() const
 {
-gtk_text_buffer_set_text( w, v->c_str(), -1);
+// v->c_str() fails g_utf8_validate. It has a non-utf8 terminating \0, 
apparently.
+gchar* s2 = g_strdup(v->c_str());
+gtk_text_buffer_set_text( w, s2, v->size());
+g_free(s2);
 }
 template <> inline void
 SUIVar_::down()const

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[med-svn] [aghermann] 13/23: complete e44f65354b

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 47b1d431567a52b78f0b6f5302097f7cfabf6490
Author: Andrei Zavada 
Date:   Tue Jan 3 05:50:31 2017 +0200

complete e44f65354b
---
 upstream/src/aghermann/ui/dirlevel-storable-adapter.ii | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii 
b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
index 2892361..8bf671a 100644
--- a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
+++ b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
@@ -154,9 +154,9 @@ set_profile_manage_buttons_visibility()
 boolis_immutable = have_active && current_profile->level == 
agh::TExpDirLevel::system;
 // printf( "active %d %s %d\n", have_active, have_active ? 
agh::exp_dir_level_s(current_profile->level) : "-", have_active ? not 
(*current_profile == Pp2) : -1);
 // printf( "%s\n-vs-\n%s\n", have_active ? 
current_profile->serialize().c_str() : "??", Pp2.serialize().c_str());
-gtk_widget_set_visible( (GtkWidget*)bXProfileSave, have_active);
-gtk_widget_set_visible( (GtkWidget*)bXProfileRevert, have_active and 
not is_transient and is_modified);
-gtk_widget_set_visible( (GtkWidget*)bXProfileDiscard, have_active and 
not is_transient and not is_immutable);
+gtk_widget_set_sensitive( (GtkWidget*)bXProfileSave, have_active);
+gtk_widget_set_sensitive( (GtkWidget*)bXProfileRevert, have_active and 
not is_transient and is_modified);
+gtk_widget_set_sensitive( (GtkWidget*)bXProfileDiscard, have_active 
and not is_transient and not is_immutable);
 gtk_widget_set_sensitive( (GtkWidget*)eXProfileList, not is_modified);
 }
 

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[med-svn] [aghermann] 06/23: patterns: more accurate sscanf to unbreak load()

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit f7cacc4b977cf4bea59e51bb1f6608dda3ffbe21
Author: Andrei Zavada 
Date:   Tue Jan 3 05:39:13 2017 +0200

patterns: more accurate sscanf to unbreak load()
---
 upstream/src/aghermann/patterns/patterns.cc | 7 ++-
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/upstream/src/aghermann/patterns/patterns.cc 
b/upstream/src/aghermann/patterns/patterns.cc
index 44ad74f..fc77de8 100644
--- a/upstream/src/aghermann/patterns/patterns.cc
+++ b/upstream/src/aghermann/patterns/patterns.cc
@@ -126,8 +126,7 @@ load()
 double  t1, t2, t3, t4;
 if ( 15 != fscanf(
  fd,
- "%lg  %u %lg %lg  %lg %lg %u"
- " %lg %lg %lg %lg"
+ "%lg  %u %lg %lg  %lg %lg %u  %lg %lg %lg %lg\n"
  " %zu %zu %zu %zu\n"
  "--DATA--\n",
  &Pp.env_scope,
@@ -175,7 +174,7 @@ load()
 else
 fprintf( stderr, "load_pattern(\"%s\"): tried, but 
failed, to rename as *~\n", fname);
 
-return -2;
+throw;
 }
 }
 
@@ -237,7 +236,5 @@ SPattern (const string& name_, TExpDirLevel level_, 
CExpDesign& ED_, const SExpD
 }
 
 
-
-
 }
 } // namespace agh::pattern

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[med-svn] [aghermann] 08/23: don't let current_profile dangle in SDirlevelStorableAdapter::discard_c_p

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 1343cc5444b8a7b5d5af206f3048404b2c49e755
Author: Andrei Zavada 
Date:   Tue Jan 3 05:43:42 2017 +0200

don't let current_profile dangle in SDirlevelStorableAdapter::discard_c_p
---
 upstream/src/aghermann/ui/dirlevel-storable-adapter.ii | 9 -
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii 
b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
index 7d108d1..2892361 100644
--- a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
+++ b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
@@ -130,7 +130,14 @@ discard_current_profile()
 return;
 
 auto todelete = current_profile;
-current_profile = next(current_profile);
+auto prec = prev(current_profile);
+auto foll = next(current_profile);
+current_profile =
+(foll != profiles.end())
+? foll
+: (current_profile != profiles.begin())
+? prec
+: profiles.end();
 todelete->delete_file();
 profiles.erase( todelete);
 }

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[med-svn] [aghermann] 07/23: assignments within declaration broke set_profile_manage_buttons_visibility

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit bb953fcf03949eee2fd739bd037b4371f45f0c78
Author: Andrei Zavada 
Date:   Tue Jan 3 05:42:27 2017 +0200

assignments within declaration broke set_profile_manage_buttons_visibility
---
 upstream/src/aghermann/ui/dirlevel-storable-adapter.ii | 8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii 
b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
index e7be6a7..7d108d1 100644
--- a/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
+++ b/upstream/src/aghermann/ui/dirlevel-storable-adapter.ii
@@ -141,10 +141,10 @@ void
 SDirlevelStorableAdapter::
 set_profile_manage_buttons_visibility()
 {
-boolhave_active  = current_profile != profiles.end(),
-is_transient = have_active && current_profile->level == 
agh::TExpDirLevel::transient,
-is_modified  = have_active && not (*current_profile == Pp2),
-is_immutable = have_active && current_profile->level == 
agh::TExpDirLevel::system;
+boolhave_active  = current_profile != profiles.end();
+boolis_transient = have_active && current_profile->level == 
agh::TExpDirLevel::transient;
+boolis_modified  = have_active && not (*current_profile == Pp2);
+boolis_immutable = have_active && current_profile->level == 
agh::TExpDirLevel::system;
 // printf( "active %d %s %d\n", have_active, have_active ? 
agh::exp_dir_level_s(current_profile->level) : "-", have_active ? not 
(*current_profile == Pp2) : -1);
 // printf( "%s\n-vs-\n%s\n", have_active ? 
current_profile->serialize().c_str() : "??", Pp2.serialize().c_str());
 gtk_widget_set_visible( (GtkWidget*)bXProfileSave, have_active);

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[med-svn] [aghermann] 04/23: icm

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 96e37bd2d7e344643b76591379ed2095d4127b07
Author: Andrei Zavada 
Date:   Mon Jan 2 05:58:41 2017 +0200

icm
---
 upstream/src/aghermann/globals.hh | 1 +
 upstream/src/libsigfile/edf.cc| 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/globals.hh 
b/upstream/src/aghermann/globals.hh
index a311245..d3ee68b 100644
--- a/upstream/src/aghermann/globals.hh
+++ b/upstream/src/aghermann/globals.hh
@@ -28,6 +28,7 @@ extern gsl_rng *rng;
 
 extern int num_procs;
 
+
 extern agh::log::CLogFacility* default_log_facility;
 void log( agh::log::TLevel, const char* issuer, const char* fmt, ...) 
__attribute__ ((format (printf, 3, 4)));
 
diff --git a/upstream/src/libsigfile/edf.cc b/upstream/src/libsigfile/edf.cc
index 9f71891..2888d1d 100644
--- a/upstream/src/libsigfile/edf.cc
+++ b/upstream/src/libsigfile/edf.cc
@@ -483,7 +483,7 @@ _parse_header()
 ? TSubtype::edfplus_d
 : TSubtype::edf;
 
-size_theader_length;
+size_t  header_length;
 
 header_length = n_data_records = data_record_size = n_channels 
= 0;
 sscanf( header.header_length,"%8zu", &header_length);

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[med-svn] [aghermann] 01/23: handle SIGBUS on unreadable edfs

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit e4b3933aba5b2a8a24e7271266bf9743f67f8a17
Author: Andrei Zavada 
Date:   Mon Jan 2 05:55:06 2017 +0200

handle SIGBUS on unreadable edfs

assuming it will get triggered in _parse_header or not at all, which can
well be wrong.
---
 upstream/src/common/lang.hh  | 13 +++--
 upstream/src/common/libcommon.cc | 16 +++-
 upstream/src/libsigfile/edf.cc   | 35 +--
 3 files changed, 51 insertions(+), 13 deletions(-)

diff --git a/upstream/src/common/lang.hh b/upstream/src/common/lang.hh
index 34e04b6..e8fe3ef 100644
--- a/upstream/src/common/lang.hh
+++ b/upstream/src/common/lang.hh
@@ -16,13 +16,22 @@
 #  include "config.h"
 #endif
 
-#include 
-#include 
 #include 
 #include 
+#include 
+#include 
+#include 
+#include 
 
 using namespace std;
 
+extern "C" {
+extern sigjmp_buf sj_env;
+
+void trip_SIGBUS(int sig, siginfo_t *siginfo, void *context);
+}
+
+
 namespace agh {
 
 // for functions to suppress some possibly benign exceptions:
diff --git a/upstream/src/common/libcommon.cc b/upstream/src/common/libcommon.cc
index cd8d896..4637d87 100644
--- a/upstream/src/common/libcommon.cc
+++ b/upstream/src/common/libcommon.cc
@@ -19,7 +19,7 @@
 #include 
 #include 
 #include 
-#include 
+#include 
 
 #include "string.hh"
 #include "alg.hh"
@@ -33,6 +33,20 @@
 using namespace std;
 
 
+extern "C" {
+
+sigjmp_buf sj_env;
+
+void trip_SIGBUS(int sig, siginfo_t *siginfo, void *context)
+{
+// "The behaviour of a process is undefined after it returns
+// normally from a signal-catching function for a SIGBUS,..."
+// That said:
+
+siglongjmp( sj_env, 1);
+}
+}
+
 string
 agh::str::
 svasprintf( const char* fmt, va_list ap)
diff --git a/upstream/src/libsigfile/edf.cc b/upstream/src/libsigfile/edf.cc
index ab01141..0f392c0 100644
--- a/upstream/src/libsigfile/edf.cc
+++ b/upstream/src/libsigfile/edf.cc
@@ -10,10 +10,11 @@
  */
 
 
-#include 
-#include 
 #include 
 #include 
+#include 
+#include 
+#include 
 #include 
 #include 
 #include 
@@ -103,11 +104,6 @@ set_recording_time( const string& s)
 
 
 
-
-
-
-
-
 #define EOA '$'
 
 namespace {
@@ -136,11 +132,16 @@ CEDFFile (const string& fname_, const int flags_, 
agh::log::CLogFacility* log_fa
 _mmapping =
 mmap( NULL,
   _fsize,
-  PROT_READ | PROT_WRITE, MAP_SHARED,
+  PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_POPULATE,
   _fd, 0);
 if ( _mmapping == (void*)-1 ) {
 close( _fd);
-throw length_error ("CEDFFile::CEDFFile(): mmap error");
+throw invalid_argument (explain_status(_status |= 
TStatus::mmap_error));
+}
+if ( sigsetjmp(sj_env, 1) ) {
+munmap( _mmapping, _fsize);
+close( _fd);
+throw invalid_argument (explain_status(_status |= 
TStatus::mmap_error));
 }
 
   // parse header
@@ -213,13 +214,18 @@ CEDFFile (const string& fname_, const TSubtype subtype_, 
const int flags_,
 _mmapping =
 mmap( NULL,
   _fsize,
-  PROT_READ | PROT_WRITE, MAP_SHARED,
+  PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_POPULATE,
   _fd,
   0);
 if ( _mmapping == (void*)-1 ) {
 close( _fd);
 throw invalid_argument (explain_status(_status |= 
TStatus::mmap_error));
 }
+if ( sigsetjmp(sj_env, 1) ) {
+munmap( _mmapping, _fsize);
+close( _fd);
+throw invalid_argument (explain_status(_status |= 
TStatus::mmap_error));
+}
 
   // fill out some essential header fields
 channels.resize( channels_.size());
@@ -446,6 +452,15 @@ int
 CEDFFile::
 _parse_header()
 {
+{
+struct sigaction lsa;
+memset( (void*)&lsa, 0, sizeof(lsa));
+lsa.sa_sigaction = trip_SIGBUS;
+sigemptyset( &lsa.sa_mask);
+sigaddset( &lsa.sa_mask, SIGBUS);
+lsa.sa_flags = SA_SIGINFO;
+sigaction(SIGBUS, &lsa, NULL);
+}
 size_t  n_channels;
 try {
 _fld_pos = 0;

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[med-svn] [aghermann] 03/23: avoid passing a non-const ref of thing to be modified

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 1ff6b424d7475714ce3fe1dcafd2e65b31a640c5
Author: Andrei Zavada 
Date:   Mon Jan 2 05:57:21 2017 +0200

avoid passing a non-const ref of thing to be modified
---
 upstream/src/libsigfile/edf.cc | 47 +-
 upstream/src/libsigfile/edf.hh |  2 +-
 2 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/upstream/src/libsigfile/edf.cc b/upstream/src/libsigfile/edf.cc
index 04b6151..9f71891 100644
--- a/upstream/src/libsigfile/edf.cc
+++ b/upstream/src/libsigfile/edf.cc
@@ -426,20 +426,19 @@ _lay_out_header()
 
 
 
-
 char*
 CEDFFile::
-_get_next_field( char *&field, const size_t fld_size) throw (TStatus)
+_get_next_field( char **field, const size_t fld_size) throw (TStatus)
 {
 if ( _fld_pos + fld_size > _fsize ) {
 _status |= bad_header;
 throw bad_header;
 }
 
-field = (char*)_mmapping + _fld_pos;
+*field = (char*)_mmapping + _fld_pos;
 _fld_pos += fld_size;
 
-return field;
+return *field;
 }
 
 
@@ -461,16 +460,16 @@ _parse_header()
 size_t  n_channels;
 try {
 _fld_pos = 0;
-_get_next_field( header.version_number,   8);
-_get_next_field( header.patient_id,  80);
-_get_next_field( header.recording_id,80);
-_get_next_field( header.recording_date,   8);
-_get_next_field( header.recording_time,   8);
-_get_next_field( header.header_length,8);
-_get_next_field( header.reserved,44);
-_get_next_field( header.n_data_records,   8);
-_get_next_field( header.data_record_size, 8);
-_get_next_field( header.n_channels,   4);
+_get_next_field( &header.version_number,   8);
+_get_next_field( &header.patient_id,  80);
+_get_next_field( &header.recording_id,80);
+_get_next_field( &header.recording_date,   8);
+_get_next_field( &header.recording_time,   8);
+_get_next_field( &header.header_length,8);
+_get_next_field( &header.reserved,44);
+_get_next_field( &header.n_data_records,   8);
+_get_next_field( &header.data_record_size, 8);
+_get_next_field( &header.n_channels,   4);
 
 if ( strncmp( header.version_number, version_string, 8) ) {
 _status |= (bad_version | inoperable);
@@ -536,20 +535,20 @@ _parse_header()
 
   // determine & validate signal types
 for ( auto &H : channels ) {
-_get_next_field( H.header.label, 16);
+_get_next_field( &H.header.label, 16);
 // let libsigfile::SChannel ctor figure
 H.ucd = {trim( string (H.header.label, 16))};
 }
 for ( auto &H : channels )
 H.transducer_type =
-trim( string (_get_next_field( 
H.header.transducer_type, 80), 80));
+trim( string (_get_next_field( 
&H.header.transducer_type, 80), 80));
 
 for ( auto &H : channels )
 H.physical_dim =
-trim( string (_get_next_field( 
H.header.physical_dim, 8), 8));
+trim( string (_get_next_field( 
&H.header.physical_dim, 8), 8));
 
 for ( auto &H : channels ) {
-_get_next_field( H.header.physical_min, 8);
+_get_next_field( &H.header.physical_min, 8);
 if ( H.ucd.type() == 
sigfile::definitions::types::edf_annotation )
 continue;
 if ( sscanf( H.header.physical_min, "%8lg",
@@ -560,7 +559,7 @@ _parse_header()
 }
 }
 for ( auto &H : channels ) {
-_get_next_field( H.header.physical_max, 8);
+_get_next_field( &H.header.physical_max, 8);
 if ( H.ucd.type() == 
sigfile::definitions::types::edf_annotation )
 continue;
 if ( sscanf( H.header.physical_max, "%8lg",
@@ -572,7 +571,7 @@ _parse_header()
 }

[med-svn] [aghermann] tag 1.1.2 created (now abfd514)

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a change to tag 1.1.2
in repository aghermann.

at  abfd514   (commit)
This tag includes the following new commits:

   new  e4b3933   handle SIGBUS on unreadable edfs
   new  4f9e037   whitespace and ICM
   new  1ff6b42   avoid passing a non-const ref of thing to be modified
   new  96e37bd   icm
   new  b34066d   populate: correctly calculate tl_width
   new  f7cacc4   patterns: more accurate sscanf to unbreak load()
   new  bb953fc   assignments within declaration broke 
set_profile_manage_buttons_visibility
   new  1343cc5   don't let current_profile dangle in 
SDirlevelStorableAdapter::discard_c_p
   new  f9c2aa6   don't forget to update vars to widgets in d/rk1968
   new  2f6c5f8   work around non-utf8 terminating \0, unbreak lua scripts 
loading in rk1968
   new  e44f653   undisappear buttons, generally tidy up rk1968.glade
   new  6abff54   correctly anchor menu for Alt+N on SF montage
   new  47b1d43   complete e44f65354b
   new  f42dce9   log rk1968 script name if empty
   new  fe97655   replace deprecated gdk_cairo_create
   new  796676a   prettify stale session lock message
   new  d91616f   replace some calls of deprecated gtk_menu_popup
   new  cc4f557   better figure rk1968 window size
   new  b9c361d   sweep up deprecated gtk_ and gdk_ functions
   new  64e8cce   trivial id renames and emendations
   new  ef4c540   rk1968 profile management fixes:
   new  cedc7d6   expand profile combobox in sf-patterns.glade
   new  abfd514   prepare for 1.1.2

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[med-svn] [aghermann] 05/23: populate: correctly calculate tl_width

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit b34066d991a8905b0359b74332b712f0f8ebc89c
Author: Andrei Zavada 
Date:   Mon Jan 2 05:59:26 2017 +0200

populate: correctly calculate tl_width
---
 upstream/src/aghermann/ui/mw/populate.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/ui/mw/populate.cc 
b/upstream/src/aghermann/ui/mw/populate.cc
index 03dea12..713fb31 100644
--- a/upstream/src/aghermann/ui/mw/populate.cc
+++ b/upstream/src/aghermann/ui/mw/populate.cc
@@ -449,7 +449,7 @@ populate_1()
 timeline_end - timeline_start;
 if ( full_secs < 3600 )
 full_secs = 3600;
-tl_width = full_secs * tl_pph;
+tl_width = full_secs * tl_pph / 3600;
 tl_pages = full_secs / ED->psd_params.pagesize;
 
 APPLOG_INFO ("populate_1(): common timeline is %zu pages:", tl_pages);

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[med-svn] [aghermann] 02/23: whitespace and ICM

2017-01-04 Thread andrei zavada

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

hmmr-guest pushed a commit to tag 1.1.2
in repository aghermann.

commit 4f9e037e4ee09b9ec5b3be78874a60cd1691f468
Author: Andrei Zavada 
Date:   Mon Jan 2 05:56:18 2017 +0200

whitespace and ICM
---
 upstream/src/aghermann/globals.cc | 1 -
 upstream/src/libsigfile/edf.cc| 9 +++--
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/upstream/src/aghermann/globals.cc 
b/upstream/src/aghermann/globals.cc
index fe43580..902881f 100644
--- a/upstream/src/aghermann/globals.cc
+++ b/upstream/src/aghermann/globals.cc
@@ -27,7 +27,6 @@
 #endif
 
 using namespace std;
-using namespace agh::global;
 
 
 gsl_rng *agh::global::rng = nullptr;
diff --git a/upstream/src/libsigfile/edf.cc b/upstream/src/libsigfile/edf.cc
index 0f392c0..04b6151 100644
--- a/upstream/src/libsigfile/edf.cc
+++ b/upstream/src/libsigfile/edf.cc
@@ -390,12 +390,6 @@ CEDFFile::
 
 
 
-
-
-
-
-
-
 void
 CEDFFile::
 _lay_out_header()
@@ -448,6 +442,9 @@ _get_next_field( char *&field, const size_t fld_size) throw 
(TStatus)
 return field;
 }
 
+
+
+
 int
 CEDFFile::
 _parse_header()

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[med-svn] [cnrun] branch WIP updated (880de88 -> 4c94ec3)

2017-01-03 Thread andrei zavada

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hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  880de88   fix Build-Depends
   new  4c94ec3   follow Debian Med policy in debian/control

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Summary of changes:
 debian/changelog | 6 ++
 debian/control   | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

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[med-svn] [cnrun] branch master updated (880de88 -> 4c94ec3)

2017-01-03 Thread andrei zavada

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hmmr-guest pushed a change to branch master
in repository cnrun.

  from  880de88   fix Build-Depends
   new  4c94ec3   follow Debian Med policy in debian/control

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Summary of changes:
 debian/changelog | 6 ++
 debian/control   | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

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[med-svn] [cnrun] 01/01: follow Debian Med policy in debian/control

2017-01-03 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 4c94ec3bdb798314ee790e6a42cdaa1dbea87930
Author: Andrei Zavada 
Date:   Tue Jan 3 17:37:14 2017 +0200

follow Debian Med policy in debian/control
---
 debian/changelog | 6 ++
 debian/control   | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d90f34e..8dc2ab9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+cnrun (2.1.0-2) experimental; urgency=low
+
+  * debian/control: fix Maintainer and Uploaders per Debian Med policy.
+
+ -- Andrei Zavada   Tue,  3 Jan 2017 16:52:00 +0200
+
 cnrun (2.1.0-1) experimental; urgency=low
 
   * debian/control: fix Vcs-* fields, depend on liblua5.1-0,
diff --git a/debian/control b/debian/control
index 4424e3b..c7e2b0f 100644
--- a/debian/control
+++ b/debian/control
@@ -1,5 +1,6 @@
 Source: cnrun
-Maintainer: Andrei Zavada 
+Uploaders: Andrei Zavada 
+Maintainer: Debian Med Packaging Team 

 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
@@ -14,7 +15,7 @@ Build-Depends: debhelper (>= 9),
lua5.2 | lua5.3
 Standards-Version: 3.9.8
 Vcs-Git: https://anonscm.debian.org/git/debian-med/cnrun.git
-Vcs-Browser: https://anonscm.debian.org/cgit/cnrun.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cnrun.git
 Homepage: http://johnhommer.com/academic/code/cnrun
 
 Package: libcnrun2

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[med-svn] [cnrun] tag 2.1.0 created (now 880de88)

2016-12-30 Thread andrei zavada

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hmmr-guest pushed a change to tag 2.1.0
in repository cnrun.

at  880de88   (commit)
No new revisions were added by this update.

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[med-svn] [cnrun] branch master updated (9cbeb6b -> 880de88)

2016-12-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository cnrun.

  from  9cbeb6b   do any writing in make test in ./_test
   new  880de88   fix Build-Depends

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Summary of changes:
 debian/control | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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[med-svn] [cnrun] branch WIP updated (9cbeb6b -> 880de88)

2016-12-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  9cbeb6b   do any writing in make test in ./_test
   new  880de88   fix Build-Depends

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Summary of changes:
 debian/control | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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[med-svn] [cnrun] 01/01: fix Build-Depends

2016-12-30 Thread andrei zavada

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hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 880de88e7505ffd82b832d716412ec7f3df8d548
Author: Andrei Zavada 
Date:   Thu Dec 29 15:31:43 2016 +0200

fix Build-Depends
---
 debian/control | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index 7cfaddf..4424e3b 100644
--- a/debian/control
+++ b/debian/control
@@ -10,8 +10,8 @@ Build-Depends: debhelper (>= 9),
pkg-config,
libgsl-dev | libgsl0-dev,
libxml2-dev,
-   liblua5.1-0-dev | liblua5.2-dev,
-   liblua5.1-0 | lua5.2
+   liblua5.2-dev | liblua5.3-dev,
+   lua5.2 | lua5.3
 Standards-Version: 3.9.8
 Vcs-Git: https://anonscm.debian.org/git/debian-med/cnrun.git
 Vcs-Browser: https://anonscm.debian.org/cgit/cnrun.git

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[med-svn] [cnrun] 05/05: do any writing in make test in ./_test

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 9cbeb6bc7a1c75eb8c1e4ade15142f23e29cf065
Author: Andrei Zavada 
Date:   Wed Dec 28 19:42:18 2016 +0200

do any writing in make test in ./_test
---
 upstream/doc/examples/example1.lua | 5 -
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/upstream/doc/examples/example1.lua 
b/upstream/doc/examples/example1.lua
index e991f44..ae4efac 100644
--- a/upstream/doc/examples/example1.lua
+++ b/upstream/doc/examples/example1.lua
@@ -131,13 +131,16 @@ do
print ()
 end
 
+Pw ("Import NML")
 ASSERT (M.import_nml (C, mname, "m.nml"))
 
 
 do
Pw ("Testing NML export")
local mname2 = "FAFA2"
-   local f2 = "/tmp/m2.nml"
+   -- cwd is specially created for us in test target: ./ is entirely
+   -- at our disposal
+   local f2 = "./m2.nml"
 
Pw ("Exporting to " .. f2)
ASSERT (

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[med-svn] [cnrun] branch master updated (4527d2c -> 9cbeb6b)

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository cnrun.

  from  4527d2c   debian/control: fix Vsc-Git URL again
  adds  adcd787   debian/*: fix to comply with cme recommendations
  adds  0321539   debian/control: fix Vsc-Git URL again; bump 
Standards-Version to 3.9.7
  adds  feabc20   Merge branch 'WIP' of 
ssh://git.debian.org/git/debian-med/cnrun into WIP
  adds  86e5810   update debian/changelog
   new  b2837eb   implement NML export
   new  42f66df   have CHost::del_model return false on nx model args
   new  9ca4a60   rework example1.lua
   new  6069b6b   make it cme-clean
   new  9cbeb6b   do any writing in make test in ./_test

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:
 debian/changelog  |   8 +
 debian/control|  36 ++-
 debian/copyright  |   4 +-
 upstream/ChangeLog|   4 +
 upstream/Makefile.am  |   1 +
 upstream/compile  |   2 +-
 upstream/configure.ac |   8 +-
 upstream/doc/examples/example1.lua| 368 ++
 upstream/doc/lua-api/cnrun-lua-api.texi   |   2 +-
 upstream/src/libcnrun/model/cycle.cc  |   5 +-
 upstream/src/libcnrun/model/model.hh  |  19 +-
 upstream/src/libcnrun/model/nmlio.cc  | 211 +
 upstream/src/libcnrun/model/struct.cc |  57 ++--
 upstream/src/libcnrun/units/base-neuron.hh|  10 +-
 upstream/src/libcnrun/units/base-synapse.hh   |   3 +-
 upstream/src/libcnrun/units/base-unit.cc  | 102 --
 upstream/src/libcnrun/units/base-unit.hh  |  47 +--
 upstream/src/libcnrun/units/hosted-neurons.cc |   8 +-
 upstream/src/libcnrun/units/hosted-neurons.hh |  84 ++---
 upstream/src/libcnrun/units/standalone-neurons.cc |  20 +-
 upstream/src/libcnrun/units/standalone-neurons.hh |  53 ++--
 upstream/src/lua-cnrun/cnhost.hh  |   9 +-
 upstream/src/lua-cnrun/commands.cc|  28 +-
 upstream/src/tools/hh-latency-estimator.cc|  18 +-
 24 files changed, 695 insertions(+), 412 deletions(-)

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[med-svn] [cnrun] 04/05: make it cme-clean

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 6069b6b0abbaae093dbf9545b157cbdd046d0774
Author: Andrei Zavada 
Date:   Wed Dec 28 03:25:14 2016 +0200

make it cme-clean
---
 debian/changelog   | 5 +++--
 debian/copyright   | 4 ++--
 upstream/ChangeLog | 2 +-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 703134d..d90f34e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,10 @@
-cnrun (2.0.3-2) experimental; urgency=low
+cnrun (2.1.0-1) experimental; urgency=low
 
   * debian/control: fix Vcs-* fields, depend on liblua5.1-0,
 bump Standards-Version.
+  * New upstream version.
 
- -- Andrei Zavada   Wed, 09 Nov 2016 19:49:00 +0200
+ -- Andrei Zavada   Wed, 28 Dec 2016 02:19:00 +0200
 
 cnrun (2.0.3-1) experimental; urgency=low
 
diff --git a/debian/copyright b/debian/copyright
index 3bc97c2..ecb0a44 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-Name: cnrun
 Upstream-Contact: Andrei Zavada 
 Source: http://johnhommer.com/academic/code/cnrun/source/
@@ -9,7 +9,7 @@ License: GPL-2+
 
 Files: src/libcnrun/*.cc
 Copyright: 2008 Thomas Nowotny 
-  2008-2012 Andrei Zavada 
+2008-2012 Andrei Zavada 
 License: GPL-2+
 
 License: GPL-2+
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 7f5fe8f..a1a2876 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,4 +1,4 @@
-2016-12-25  andrei zavada  
+2016-12-28  andrei zavada  
* Implement NML export.
* Release 2.1.
 

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[med-svn] [cnrun] 01/05: implement NML export

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit b2837ebc10cd07be444f729982ac45d8c9d45939
Author: Andrei Zavada 
Date:   Tue Dec 27 05:57:59 2016 +0200

implement NML export
---
 upstream/ChangeLog|   4 +
 upstream/Makefile.am  |   1 +
 upstream/configure.ac |   8 +-
 upstream/doc/examples/example1.lua| 117 ++--
 upstream/doc/lua-api/cnrun-lua-api.texi   |   2 +-
 upstream/src/libcnrun/model/cycle.cc  |   5 +-
 upstream/src/libcnrun/model/model.hh  |  19 +-
 upstream/src/libcnrun/model/nmlio.cc  | 211 --
 upstream/src/libcnrun/model/struct.cc |  57 +++---
 upstream/src/libcnrun/units/base-neuron.hh|  10 +-
 upstream/src/libcnrun/units/base-synapse.hh   |   3 +-
 upstream/src/libcnrun/units/base-unit.cc  | 102 +--
 upstream/src/libcnrun/units/base-unit.hh  |  47 +++--
 upstream/src/libcnrun/units/hosted-neurons.cc |   8 +-
 upstream/src/libcnrun/units/hosted-neurons.hh |  84 -
 upstream/src/libcnrun/units/standalone-neurons.cc |  20 +-
 upstream/src/libcnrun/units/standalone-neurons.hh |  53 +++---
 upstream/src/lua-cnrun/commands.cc|   4 +-
 upstream/src/tools/hh-latency-estimator.cc|  18 +-
 19 files changed, 507 insertions(+), 266 deletions(-)

diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 6f20a86..7f5fe8f 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,7 @@
+2016-12-25  andrei zavada  
+   * Implement NML export.
+   * Release 2.1.
+
 2016-01-12  andrei zavada  
* Fix decimate and putout.
* Release 2.0.3.
diff --git a/upstream/Makefile.am b/upstream/Makefile.am
index 98cfaed..4789435 100644
--- a/upstream/Makefile.am
+++ b/upstream/Makefile.am
@@ -33,6 +33,7 @@ unwanted_files = \
m4/ltsugar.m4 \
m4/ltversion.m4 \
aclocal.m4 \
+   compile \
config.sub \
ltmain.sh \
depcomp \
diff --git a/upstream/configure.ac b/upstream/configure.ac
index d945eb0..b335672 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-15 Andrei Zavada ])
 
-AC_INIT([cnrun], [2.0.3], [johnhom...@gmail.com])
+AC_INIT([cnrun], [2.1.0], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/libcnrun/model/model.hh])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
@@ -65,14 +65,12 @@ AX_LUA_HEADERS2014
 dnl we cannot do strcmp in cpp, so here's bash to the rescue
 if test x"$LUA_VERSION" = x"5.2"; then
AC_DEFINE([HAVE_LUA_52], [], ["Do we have lua 5.2?"])
-else
-   AC_DEFINE([HAVE_LUA_51], [], ["Do we have lua 5.1?"])
 fi
 
 AC_ARG_ENABLE(
[tools],
-   AS_HELP_STRING( [--enable-tools], [build spike2sdf, varfold & 
hh-latency-estimator (default = no)]),
-   [do_tools=$enableval], [do_tools=no])
+   AS_HELP_STRING( [--enable-tools], [build spike2sdf, varfold & 
hh-latency-estimator (default = yes)]),
+   [do_tools=$enableval], [do_tools=yes])
 AM_CONDITIONAL(DO_TOOLS, [test x"$do_tools" = xyes])
 
 AC_ARG_ENABLE(
diff --git a/upstream/doc/examples/example1.lua 
b/upstream/doc/examples/example1.lua
index 3f91c82..bf4900c 100644
--- a/upstream/doc/examples/example1.lua
+++ b/upstream/doc/examples/example1.lua
@@ -35,6 +35,55 @@ if res == nil then
 end
 C = ult
 
+function print_units (model_name, ult, unit_regex)
+   print ("There are " .. #ult .. " unit(s) matching \"" .. unit_regex .. "\"")
+   local unit_list = ult
+   local fmt = " %-10s %-16s %-16s %-12s %-16s %-6s"
+   print (string.format(
+ fmt,
+ "label", "class", "family", "species", "has_sources", 
"is_altered"))
+   print (string.rep('-', 87))
+   for _, u in ipairs(unit_list) do
+  result = {M.get_unit_properties (C, model_name, u)}
+  res, ult = result[1], {effective_unpack(result, 2)}
+  local b = function (x) if x then return "yes" else return "no" end end
+  print (string.format(
+fmt,
+ult[1], ult[2], ult[3], ult[4], b(ult[5]), b(ult[6])))
+   end
+   print()
+end
+
+function compare_models (model_name1, model_name2)
+   local result1 = {M.get_units_matching(C, model_name1, ".*")}
+   local result2 = {M.get_units_matching(C, model_name2, ".*")}
+   res, ult1 = result[1], {effective_unpack(result1, 2)}
+   if res == nil then
+  print (ult1)
+  return
+   end
+   res, ult2 = result[1], {effective_unpack(result2, 2)}
+   if res == nil then
+  print (ult2)
+  return
+   end
+   local relevant_list1 = get_relevant_unit_params (model_name1

[med-svn] [cnrun] 03/05: rework example1.lua

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 9ca4a6010fd2ebb9ae5bbd0d958b9df666324695
Author: Andrei Zavada 
Date:   Wed Dec 28 02:14:22 2016 +0200

rework example1.lua
---
 upstream/doc/examples/example1.lua | 360 +++--
 1 file changed, 186 insertions(+), 174 deletions(-)

diff --git a/upstream/doc/examples/example1.lua 
b/upstream/doc/examples/example1.lua
index bf4900c..e991f44 100644
--- a/upstream/doc/examples/example1.lua
+++ b/upstream/doc/examples/example1.lua
@@ -26,53 +26,70 @@ local M = require("cnrun")
 local res, ult, result
 local C, model
 
-M.dump_available_units ()
+function Pw (str) print ("\027[01;1m" .. str  .. "\027[00m") end
+function Pg (str) print ("\027[01;32m" .. str  .. "\027[00m") end
+function Pr (str) print ("\027[01;31m" .. str  .. "\027[00m") end
+function Pok ()
+   print ("\027[01;34m" .. "ok" .. "\027[00m")
+   print ()
+end
 
-res, ult = M.get_context ()
-if res == nil then
-   print (ult)
-   return
+function ASSERT (a1, a2)
+   res, ult = a1, a2
+   if res == nil then
+  Pr (ult)
+  os.exit (2)
+   end
+   Pok ()
+end
+
+function ASSERT_FALSE (a1, a2)
+   res, ult = a1, a2
+   if res ~= nil then
+  Pr (res)
+  Pr (ult)
+  os.exit (2)
+   end
+   Pg ("ok (" .. ult .. ")")
+   print ()
 end
-C = ult
+
 
 function print_units (model_name, ult, unit_regex)
-   print ("There are " .. #ult .. " unit(s) matching \"" .. unit_regex .. "\"")
+   Pg ("There are " .. #ult .. " unit(s) matching \"" .. unit_regex .. "\"")
local unit_list = ult
local fmt = " %-10s %-16s %-16s %-12s %-16s %-6s"
-   print (string.format(
- fmt,
- "label", "class", "family", "species", "has_sources", 
"is_altered"))
-   print (string.rep('-', 87))
+   Pg (string.format(
+  fmt,
+  "label", "class", "family", "species", "has_sources", "is_altered"))
+   Pg (string.rep('-', 87))
for _, u in ipairs(unit_list) do
   result = {M.get_unit_properties (C, model_name, u)}
   res, ult = result[1], {effective_unpack(result, 2)}
   local b = function (x) if x then return "yes" else return "no" end end
-  print (string.format(
-fmt,
-ult[1], ult[2], ult[3], ult[4], b(ult[5]), b(ult[6])))
+  Pg (string.format(
+ fmt,
+ ult[1], ult[2], ult[3], ult[4], b(ult[5]), b(ult[6])))
end
print()
 end
 
+
 function compare_models (model_name1, model_name2)
local result1 = {M.get_units_matching(C, model_name1, ".*")}
local result2 = {M.get_units_matching(C, model_name2, ".*")}
res, ult1 = result[1], {effective_unpack(result1, 2)}
-   if res == nil then
-  print (ult1)
-  return
-   end
+   ASSERT (res, ult1)
res, ult2 = result[1], {effective_unpack(result2, 2)}
-   if res == nil then
-  print (ult2)
-  return
-   end
+   ASSERT (res, ult2)
+
local relevant_list1 = get_relevant_unit_params (model_name1, ult1)
local relevant_list2 = get_relevant_unit_params (model_name2, ult2)
 
return relevant_list1 == relevant_list2
 end
 
+
 function get_relevant_unit_params (model_name, unit_list)
local rup = {}
for _, u in ipairs(unit_list) do
@@ -84,201 +101,196 @@ function get_relevant_unit_params (model_name, unit_list)
 end
 
 
+-- main
+
 local mname = "FAFA"
-res, ult = M.new_model (C, mname)
-if res == nil then
-   print (ult)
-   return
+local verbosely = 3
+
+do
+   Pw ("Dump units")
+   M.dump_available_units ()
 end
+
+Pw ("Obtain context")
+ASSERT (M.get_context ())
+C = ult
+
+Pw ("Create model")
+ASSERT (M.new_model (C, mname))
 model = ult
-print ("Created model")
 
-local verbosely = 3
-print ("Setting verbosely to " .. verbosely)
 M.set_model_parameter (C, mname, "verbosely", verbosely)
 
 result = {M.list_models (C)}
-res, ult = result[1], {effective_unpack(result, 2)}
-if res == nil then
-   print (ult)
-   return
+ASSERT (result[1], {effective_unpack(result, 2)})
+
+do
+   Pg ("Model(s):")
+   local model_list = ult
+   Pg (table.concat(model_list))
+   print ()
 end
-print ()
 
-print ("Model(s):")
-local model_list = ult
-print (table.concat(model_list))
-print ()
+ASSERT (M.import_nml (C, mname, "m.nml"))
 
 
-res, ult = M.import_nml (C, mname, "m.nml")
-if res == nil then
-   print (ult)
-   -- return
-end
-print ()
+do
+   Pw ("Testing NML export")
+   local mname2 = "FAFA2"

[med-svn] [cnrun] 02/05: have CHost::del_model return false on nx model args

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 42f66dfcd73fbcdb37905c558af60e73d812491e
Author: Andrei Zavada 
Date:   Wed Dec 28 02:14:01 2016 +0200

have CHost::del_model return false on nx model args
---
 upstream/src/lua-cnrun/cnhost.hh   |  9 ++---
 upstream/src/lua-cnrun/commands.cc | 24 ++--
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/upstream/src/lua-cnrun/cnhost.hh b/upstream/src/lua-cnrun/cnhost.hh
index 84d9418..c674b31 100644
--- a/upstream/src/lua-cnrun/cnhost.hh
+++ b/upstream/src/lua-cnrun/cnhost.hh
@@ -81,11 +81,14 @@ class CHost
 } else
 return -1;
 }
-void del_model( const string& name)
+bool del_model( const string& name)
 {
-if ( models.find(name) != models.end() )
+if ( models.find(name) != models.end() ) {
 delete models[name];
-models.erase( name);
+models.erase( name);
+return true;
+} else
+return false;
 }
 // cmd_new_model( const TArgs&);
 // cmd_delete_model( const TArgs&);
diff --git a/upstream/src/lua-cnrun/commands.cc 
b/upstream/src/lua-cnrun/commands.cc
index c91386e..8b3390f 100644
--- a/upstream/src/lua-cnrun/commands.cc
+++ b/upstream/src/lua-cnrun/commands.cc
@@ -176,16 +176,6 @@ int new_model( lua_State *L)
 }
 
 
-int delete_model( lua_State *L)
-{
-INTRO_WITH_MODEL_NAME("ps");
-
-C.del_model( model_name);
-
-VOID_RETURN;
-}
-
-
 int list_models( lua_State *L)
 {
 INTRO_WITH_CONTEXT("p");
@@ -207,6 +197,20 @@ int list_models( lua_State *L)
 __FUNCTION__, model_name); \
 auto& M = *C.get_model(model_name);
 
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wunused-variable"
+int delete_model( lua_State *L)
+{
+INTRO_WITH_MODEL("ps");
+
+C.del_model( model_name);
+
+VOID_RETURN;
+}
+#pragma GCC diagnostic pop
+
+
 int import_nml( lua_State *L)
 {
 INTRO_WITH_MODEL("pss");

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[med-svn] [cnrun] branch WIP updated (86e5810 -> 9cbeb6b)

2016-12-28 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  86e5810   update debian/changelog
   new  b2837eb   implement NML export
   new  42f66df   have CHost::del_model return false on nx model args
   new  9ca4a60   rework example1.lua
   new  6069b6b   make it cme-clean
   new  9cbeb6b   do any writing in make test in ./_test

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:
 debian/changelog  |   5 +-
 debian/copyright  |   4 +-
 upstream/ChangeLog|   4 +
 upstream/Makefile.am  |   1 +
 upstream/configure.ac |   8 +-
 upstream/doc/examples/example1.lua| 368 ++
 upstream/doc/lua-api/cnrun-lua-api.texi   |   2 +-
 upstream/src/libcnrun/model/cycle.cc  |   5 +-
 upstream/src/libcnrun/model/model.hh  |  19 +-
 upstream/src/libcnrun/model/nmlio.cc  | 211 +
 upstream/src/libcnrun/model/struct.cc |  57 ++--
 upstream/src/libcnrun/units/base-neuron.hh|  10 +-
 upstream/src/libcnrun/units/base-synapse.hh   |   3 +-
 upstream/src/libcnrun/units/base-unit.cc  | 102 --
 upstream/src/libcnrun/units/base-unit.hh  |  47 +--
 upstream/src/libcnrun/units/hosted-neurons.cc |   8 +-
 upstream/src/libcnrun/units/hosted-neurons.hh |  84 ++---
 upstream/src/libcnrun/units/standalone-neurons.cc |  20 +-
 upstream/src/libcnrun/units/standalone-neurons.hh |  53 ++--
 upstream/src/lua-cnrun/cnhost.hh  |   9 +-
 upstream/src/lua-cnrun/commands.cc|  28 +-
 upstream/src/tools/hh-latency-estimator.cc|  18 +-
 22 files changed, 665 insertions(+), 401 deletions(-)

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[med-svn] [cnrun] branch WIP updated (feabc20 -> 86e5810)

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  feabc20   Merge branch 'WIP' of 
ssh://git.debian.org/git/debian-med/cnrun into WIP
   new  86e5810   update debian/changelog

The 1 revisions listed above as "new" are entirely new to this
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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 | 7 +++
 1 file changed, 7 insertions(+)

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[med-svn] [cnrun] 01/01: update debian/changelog

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 86e5810801f7086b5ad4b69c8b3697468e7ead20
Author: Andrei Zavada 
Date:   Wed Nov 9 21:37:10 2016 +0200

update debian/changelog
---
 debian/changelog | 7 +++
 1 file changed, 7 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index e4e2b2a..703134d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+cnrun (2.0.3-2) experimental; urgency=low
+
+  * debian/control: fix Vcs-* fields, depend on liblua5.1-0,
+bump Standards-Version.
+
+ -- Andrei Zavada   Wed, 09 Nov 2016 19:49:00 +0200
+
 cnrun (2.0.3-1) experimental; urgency=low
 
   * Build with gsl-2.0 (Closes: #807190).

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[med-svn] [cnrun] 02/02: Merge branch 'WIP' of ssh://git.debian.org/git/debian-med/cnrun into WIP

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit feabc20b1fedc543a36e53d82d809696211c173e
Merge: adcd787 0321539
Author: Andrei Zavada 
Date:   Wed Nov 9 19:24:10 2016 +0200

Merge branch 'WIP' of ssh://git.debian.org/git/debian-med/cnrun into WIP

# Conflicts:
#   debian/control


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[med-svn] [cnrun] 01/02: debian/*: fix to comply with cme recommendations

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit adcd787221b2e0a0ae4bfda817a0609dae1f7d3c
Author: Andrei Zavada 
Date:   Wed Nov 9 19:22:36 2016 +0200

debian/*: fix to comply with cme recommendations

* Vsc-* fields;
* bump Standards-Version to 3.9.8;
* liblua5.1 is now called liblua5.1-0;
* bump copyright year in updtream/compile.
---
 debian/control   | 36 
 upstream/compile |  2 +-
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/debian/control b/debian/control
index 7eb9abe..7cfaddf 100644
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,27 @@
 Source: cnrun
+Maintainer: Andrei Zavada 
 Section: science
 Priority: optional
-Maintainer: Andrei Zavada 
-Build-Depends: debhelper (>= 9), dh-autoreconf, autoconf-archive, texinfo,
- libgomp1, pkg-config, libgsl-dev | libgsl0-dev, libxml2-dev,
- liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
-Standards-Version: 3.9.6
+Build-Depends: debhelper (>= 9),
+   dh-autoreconf,
+   autoconf-archive,
+   texinfo,
+   libgomp1,
+   pkg-config,
+   libgsl-dev | libgsl0-dev,
+   libxml2-dev,
+   liblua5.1-0-dev | liblua5.2-dev,
+   liblua5.1-0 | lua5.2
+Standards-Version: 3.9.8
+Vcs-Git: https://anonscm.debian.org/git/debian-med/cnrun.git
+Vcs-Browser: https://anonscm.debian.org/cgit/cnrun.git
 Homepage: http://johnhommer.com/academic/code/cnrun
-Vcs-Git: git://anonscm.debian.org/debian-med/cnrun.git
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/cnrun.git/
 
 Package: libcnrun2
 Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
 Pre-Depends: ${misc:Pre-Depends}
-Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: NeuroML-capable neuronal network simulator (shared lib)
  CNrun is a neuronal network simulator implemented as a Lua package.
  This package contains shared libraries.
@@ -21,9 +29,10 @@ Description: NeuroML-capable neuronal network simulator 
(shared lib)
  See lua-cnrun description for extended description.
 
 Package: libcnrun2-dev
-Section: libdevel
 Architecture: any
-Depends: libcnrun2 (= ${binary:Version}), ${misc:Depends}
+Section: libdevel
+Depends: libcnrun2 (= ${binary:Version}),
+ ${misc:Depends}
 Suggests: pkg-config
 Description: NeuroML-capable neuronal network simulator (development files)
  CNrun is a neuronal network simulator implemented as a Lua package.
@@ -33,7 +42,8 @@ Description: NeuroML-capable neuronal network simulator 
(development files)
 
 Package: cnrun-tools
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
 Description: NeuroML-capable neuronal network simulator (tools)
  CNrun is a neuronal network simulator implemented as a Lua package.
  This package contains two standalone tools (hh-latency-estimator and
@@ -43,7 +53,9 @@ Description: NeuroML-capable neuronal network simulator 
(tools)
 
 Package: lua-cnrun
 Architecture: any
-Depends: libcnrun2, lua5.1 | lua5.2, ${misc:Depends}
+Depends: libcnrun2,
+ lua5.1 | lua5.2,
+ ${misc:Depends}
 Suggests: gnuplot
 Description: NeuroML-capable neuronal network simulator (Lua package)
  CNrun is a neuronal network simulator, with these features:
diff --git a/upstream/compile b/upstream/compile
index 531136b..a85b723 100755
--- a/upstream/compile
+++ b/upstream/compile
@@ -3,7 +3,7 @@
 
 scriptversion=2012-10-14.11; # UTC
 
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 # Written by Tom Tromey .
 #
 # This program is free software; you can redistribute it and/or modify

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[med-svn] [cnrun] branch WIP updated (0321539 -> feabc20)

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  0321539   debian/control: fix Vsc-Git URL again; bump 
Standards-Version to 3.9.7
   new  adcd787   debian/*: fix to comply with cme recommendations
   new  feabc20   Merge branch 'WIP' of 
ssh://git.debian.org/git/debian-med/cnrun into WIP

The 2 revisions listed above as "new" are entirely new to this
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been added to this reference.


Summary of changes:
 debian/control   | 36 
 upstream/compile |  2 +-
 2 files changed, 25 insertions(+), 13 deletions(-)

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[med-svn] [cnrun] branch WIP updated (4527d2c -> 0321539)

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  4527d2c   debian/control: fix Vsc-Git URL again
   new  0321539   debian/control: fix Vsc-Git URL again; bump 
Standards-Version to 3.9.7

The 1 revisions listed above as "new" are entirely new to this
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been added to this reference.


Summary of changes:
 debian/control | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again; bump Standards-Version to 3.9.7

2016-11-09 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 0321539e040e10fd3dd38eecf993bfdec77bc30d
Author: Andrei Zavada 
Date:   Wed Nov 9 18:24:11 2016 +0200

debian/control: fix Vsc-Git URL again; bump Standards-Version to 3.9.7
---
 debian/control | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index 7eb9abe..33f9cce 100644
--- a/debian/control
+++ b/debian/control
@@ -5,10 +5,10 @@ Maintainer: Andrei Zavada 
 Build-Depends: debhelper (>= 9), dh-autoreconf, autoconf-archive, texinfo,
  libgomp1, pkg-config, libgsl-dev | libgsl0-dev, libxml2-dev,
  liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
 Homepage: http://johnhommer.com/academic/code/cnrun
-Vcs-Git: git://anonscm.debian.org/debian-med/cnrun.git
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/cnrun.git/
+Vcx-Git: git://anonscm.debian.org/debian-med/cnrun.git
+Vcs-Browser: https://anonscm.debian.org/gitweb/?p=debian-med/cnrun.git
 
 Package: libcnrun2
 Architecture: any

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[med-svn] [aghermann] tag 1.1.1 created (now 945862e)

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a change to tag 1.1.1
in repository aghermann.

at  945862e   (commit)
This tag includes the following new commits:

   new  bb606b7   follow debian recipe to properly ensure reproducible 
builds
   new  47cff8b   enable multiple instances, drop libunique; lock sessions 
in use
   new  c376f06   update changelogs, prepare for 1.1.0
   new  4ce0f7e   commit or no commit?
   new  945862e   don't bother setting or printing built_by

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


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[med-svn] [aghermann] tag 1.1.0 created (now 4ce0f7e)

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a change to tag 1.1.0
in repository aghermann.

at  4ce0f7e   (commit)
This tag includes the following new commits:

   new  bb606b7   follow debian recipe to properly ensure reproducible 
builds
   new  47cff8b   enable multiple instances, drop libunique; lock sessions 
in use
   new  c376f06   update changelogs, prepare for 1.1.0
   new  4ce0f7e   commit or no commit?

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.


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[med-svn] [aghermann] 04/05: commit or no commit?

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository aghermann.

commit 4ce0f7e0c54e443e743f165e2c7455c600cb2c22
Author: Andrei Zavada 
Date:   Sun Jun 26 02:16:44 2016 +0300

commit or no commit?
---
 upstream/data/experiment-dl.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/upstream/data/experiment-dl.sh b/upstream/data/experiment-dl.sh
index 2aec981..35eb345 100755
--- a/upstream/data/experiment-dl.sh
+++ b/upstream/data/experiment-dl.sh
@@ -3,7 +3,7 @@ 
URL="http://johnhommer.com/academic/code/aghermann/Experiment.tar.bz2";
 TARBALL=Experiment.tar.bz2
 echo "
 Now downloading sample data.
-Press Ctl-C to interrupt.
+Press Ctrl+C to interrupt.
 "
 function kill_wget
 {

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[med-svn] [aghermann] 05/05: don't bother setting or printing built_by

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository aghermann.

commit 945862e77844e3d65cfa597e999160b45a89c584
Author: Andrei Zavada 
Date:   Fri Aug 5 01:58:06 2016 +0300

don't bother setting or printing built_by

this is to make builds (very) reproducible, per Debian policy.
---
 debian/changelog|  6 ++
 upstream/ChangeLog  |  3 +++
 upstream/configure.ac   |  3 +--
 upstream/data/ui/mw-dialogs.glade   |  7 ++-
 upstream/src/aghermann/Makefile.am  |  4 
 upstream/src/aghermann/main.cc  |  3 ++-
 upstream/src/aghermann/print_version.cc | 19 ---
 7 files changed, 18 insertions(+), 27 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index f986b63..da02029 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.1.1-1) unstable; urgency=low
+
+  * New upstream version (Closes: #833472).
+
+ -- Andrei Zavada   Fri,  5 Aug 2016 00:35:00 +0200
+
 aghermann (1.1.0-1) unstable; urgency=low
 
   * New upstream version (Closes: #824574).
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index b88a4f9..a83da18 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,6 @@
+v.1.1.1 (2016-08-05)
+   * Misc: Ensure reproducible build #2.
+
 v.1.1.0 (2016-06-24)
* New: Allow multiple instances, and use session lock files.
 
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 4893a30..e340c6f 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-16 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.1.0], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.1.1], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
@@ -190,7 +190,6 @@ if test x$enable_update_mime_database = xyes ; then
 fi
 
 dnl Any private defines
-AC_SUBST(user, [`whoami`@`hostname`])
 AC_SUBST(build_date, [`date --utc --date=@${SOURCE_DATE_EPOCH:-$(date +%s)} 
+"%F"`])
 AC_SUBST(build_datetime, [`date --utc --date=@${SOURCE_DATE_EPOCH:-$(date 
+%s)}`])
 
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index 27b71c0..60420aa 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1534,7 +1534,7 @@
 start
 5
 15
-<b><big><big>Aghermann 1.1.0 
</big></big></b>
+<b><big><big>Aghermann 1.1.1 
</big></big></b>
 <a 
href="http://johnhommer.com/academic/code/aghermann">johnhommer.com/academic/code/aghermann</a>;
 True
 0
@@ -1631,6 +1631,11 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 10
 10
 
+<b>v. 1.1.1</b> (2016-08-05)
+<span font="monospace" size="small">
+   * Misc: Remove built_by define to ensure reproducible build
+ (required by Debian).
+</span>
 <b>v. 1.1.0</b> (2016-06-24)
 <span font="monospace" size="small">
* New: Allow multiple instances, and use session lock files.
diff --git a/upstream/src/aghermann/Makefile.am 
b/upstream/src/aghermann/Makefile.am
index af0f43b..8ec8ed6 100644
--- a/upstream/src/aghermann/Makefile.am
+++ b/upstream/src/aghermann/Makefile.am
@@ -123,14 +123,10 @@ aghermann_SOURCES := \
ui/ui.cc \
ui/ui.hh \
ui/ui-itpp.hh \
-   print_version.cc \
main.cc \
globals.cc \
globals.hh
 
-print_version.o: FORCE
-FORCE:
-
 aghermann_LDADD := \
../libmetrics/libmetrics.la \
../libsigproc/libsigproc.la \
diff --git a/upstream/src/aghermann/main.cc b/upstream/src/aghermann/main.cc
index 62b436d..1fb8386 100644
--- a/upstream/src/aghermann/main.cc
+++ b/upstream/src/aghermann/main.cc
@@ -10,6 +10,7 @@
  */
 
 
+#include 
 
 #ifdef _OPENMP
 # include 
@@ -37,7 +38,7 @@ void print_usage( const char*);
 int
 main( int argc, char **argv)
 {
-print_version();
+puts( PACKAGE_STRING "\n");
 
 bool headless = false;
 string lf_fname = "";
diff --git a/upstream/src/aghermann/print_version.cc 
b/upstream/src/aghermann/print_version.cc
deleted file mode 100644
index c3c2d6c..000
--- a/upstream/src/aghermann/print_version.cc
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- *   File name:  aghermann/print_version.cc
- * Project:  Aghermann
- *  Author:  Andrei Zavada 
- * Initial version:  2013-05-28
- *
- * Purpose:  print version (separate file for every make to always 
touch it)
- *
- * Li

[med-svn] [aghermann] 01/05: follow debian recipe to properly ensure reproducible builds

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository aghermann.

commit bb606b7be0be35697ab786fe32c747e74bfcc645
Author: Andrei Zavada 
Date:   Sun Jun 26 02:10:52 2016 +0300

follow debian recipe to properly ensure reproducible builds

which is, look at SOURCE_DATE_EPOCH in configure.ac
---
 debian/rules| 2 --
 upstream/configure.ac   | 4 ++--
 upstream/src/aghermann/print_version.cc | 4 
 3 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/debian/rules b/debian/rules
index 60a9db7..9f3491f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,8 +4,6 @@
 DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/buildflags.mk
 
-CXXFLAGS += -D__REPRODUCIBLE_BUILD
-
 %:
dh $@ --with autoreconf
 
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 3000402..b96c254 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -192,8 +192,8 @@ fi
 
 dnl Any private defines
 AC_SUBST(user, [`whoami`@`hostname`])
-AC_SUBST(build_date, [`date +"%F"`])
-AC_SUBST(build_datetime, [`date`])
+AC_SUBST(build_date, [`date --utc --date=@${SOURCE_DATE_EPOCH:-$(date +%s)} 
+"%F"`])
+AC_SUBST(build_datetime, [`date --utc --date=@${SOURCE_DATE_EPOCH:-$(date 
+%s)}`])
 
 AC_OUTPUT([
Makefile
diff --git a/upstream/src/aghermann/print_version.cc 
b/upstream/src/aghermann/print_version.cc
index 5573ddc..c3c2d6c 100644
--- a/upstream/src/aghermann/print_version.cc
+++ b/upstream/src/aghermann/print_version.cc
@@ -15,9 +15,5 @@
 void
 print_version()
 {
-#ifdef __REPRODUCIBLE_BUILD
-printf( PACKAGE_STRING "\n");
-#else
 printf( PACKAGE_STRING " built " __DATE__ " " __TIME__ " by " BUILT_BY 
"\n");
-#endif
 }

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[med-svn] [aghermann] tag 1.0.9 created (now 1387ab5)

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a change to tag 1.0.9
in repository aghermann.

at  1387ab5   (commit)
No new revisions were added by this update.

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[med-svn] [aghermann] 02/05: enable multiple instances, drop libunique; lock sessions in use

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository aghermann.

commit 47cff8bdcaba494302947b5633928f25bca7c489
Author: Andrei Zavada 
Date:   Sun Jun 26 02:14:34 2016 +0300

enable multiple instances, drop libunique; lock sessions in use
---
 debian/control|  4 +-
 upstream/configure.ac |  1 -
 upstream/src/Makefile.am  |  2 +-
 upstream/src/aghermann/Makefile.am|  4 +-
 upstream/src/aghermann/expdesign/expdesign.cc | 38 -
 upstream/src/aghermann/expdesign/expdesign.hh |  5 +-
 upstream/src/aghermann/main.cc| 79 +--
 upstream/src/aghermann/ui/globals.cc  | 15 -
 upstream/src/aghermann/ui/globals.hh  |  6 --
 upstream/src/aghermann/ui/sm/sm.cc| 51 ++---
 upstream/src/tools/Makefile.am|  2 +-
 11 files changed, 75 insertions(+), 132 deletions(-)

diff --git a/debian/control b/debian/control
index 2cd8c80..a7c4e83 100644
--- a/debian/control
+++ b/debian/control
@@ -4,9 +4,9 @@ Priority: optional
 Maintainer: Andrei Zavada 
 Build-Depends: debhelper (>= 9), dh-autoreconf,
  autoconf-archive, pkg-config, libgomp1, libconfig++-dev, libgsl-dev, 
libfftw3-dev,
- libsamplerate0-dev (>= 0.1.7), libgtk-3-dev, libitpp-dev, libunique-3.0-dev, 
libvte-2.91-dev,
+ libsamplerate0-dev (>= 0.1.7), libgtk-3-dev, libitpp-dev, libvte-2.91-dev,
  liblua5.2-dev, lua5.2, libxml2-utils
-Standards-Version: 3.9.6
+Standards-Version: 3.9.8
 Homepage: http://johnhommer.com/academic/code/aghermann
 Vcs-Git: git://git.debian.org/git/debian-med/aghermann.git
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/aghermann.git
diff --git a/upstream/configure.ac b/upstream/configure.ac
index b96c254..a83816a 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -64,7 +64,6 @@ PKG_CHECK_MODULES([FFTW3], [fftw3])
 PKG_CHECK_MODULES([ITPP], [itpp])
 PKG_CHECK_MODULES([GTK], [gtk+-3.0 >= 3.4 glib-2.0 gthread-2.0 gio-unix-2.0 
gmodule-export-2.0])
 PKG_CHECK_MODULES([CAIRO], [cairo >= 1.8.10])
-PKG_CHECK_MODULES([UNIQUE], [unique-3.0])
 PKG_CHECK_MODULES([VTE], [vte-2.91])
 
 AX_PATH_GSL([2.0], [AC_DEFINE([HAVE_GSL_20], [], [we have gsl >= 2.0])], [])
diff --git a/upstream/src/Makefile.am b/upstream/src/Makefile.am
index b49f04a..0035780 100644
--- a/upstream/src/Makefile.am
+++ b/upstream/src/Makefile.am
@@ -10,7 +10,7 @@ EXTRA_DIST := \
 # by trial and error, the _CFLAGS mentioned are the minimum required to 
pre-build all headers
 AM_CXXFLAGS := \
-Wall -std=c++0x -fno-rtti \
-   $(GTK_CFLAGS)  $(UNIQUE_CFLAGS) \
+   $(GTK_CFLAGS) \
$(OPENMP_CXXFLAGS) \
-I$(top_srcdir)/src -I.. \
-DHAVE_CONFIG_H \
diff --git a/upstream/src/aghermann/Makefile.am 
b/upstream/src/aghermann/Makefile.am
index 3ff0fa1..af0f43b 100644
--- a/upstream/src/aghermann/Makefile.am
+++ b/upstream/src/aghermann/Makefile.am
@@ -1,6 +1,6 @@
 AM_CXXFLAGS := \
-Wall -Werror=format-security -Wdeprecated-declarations -std=c++0x 
-fno-rtti \
-   $(GTK_CFLAGS) $(VTE_CFLAGS) $(CAIRO_CFLAGS) $(LIBCONFIGXX_CFLAGS) 
$(UNIQUE_CFLAGS) \
+   $(GTK_CFLAGS) $(VTE_CFLAGS) $(CAIRO_CFLAGS) $(LIBCONFIGXX_CFLAGS) \
$(OPENMP_CXXFLAGS) \
$(LUA_INCLUDE) \
-I$(top_srcdir)/src \
@@ -137,7 +137,7 @@ aghermann_LDADD := \
../common/liba.a \
../libsigfile/libsigfile.la \
$(FFTW3_LIBS) $(ITPP_LIBS) $(SAMPLERATE_LIBS) $(GSL_LIBS) \
-   $(GTK_LIBS) $(CAIRO_LIBS) $(UNIQUE_LIBS) $(VTE_LIBS) \
+   $(GTK_LIBS) $(CAIRO_LIBS) $(VTE_LIBS) \
$(LIBCONFIGXX_LIBS) \
$(LIBFFTW3_LDADD) $(OPENMP_CXXFLAGS) \
$(LUA_LIB)
diff --git a/upstream/src/aghermann/expdesign/expdesign.cc 
b/upstream/src/aghermann/expdesign/expdesign.cc
index 713ed34..e466318 100644
--- a/upstream/src/aghermann/expdesign/expdesign.cc
+++ b/upstream/src/aghermann/expdesign/expdesign.cc
@@ -11,6 +11,8 @@
 
 
 #include 
+#include 
+#include 
 #include 
 
 #ifdef _OPENMP
@@ -93,7 +95,7 @@ CExpDesign (const string& session_dir_,
 throw invalid_argument (string ("Failed to canonicalize dir: 
") + session_dir_);
 
 if ( session_dir_ != tmp ) {
-APPLOG_INFO( "canonicalized session_dir \"%s\" to \"%s\"", 
session_dir_.c_str(), tmp);
+APPLOG_INFO ("canonicalized session_dir \"%s\" to \"%s\"", 
session_dir_.c_str(), tmp);
 _session_dir.assign( tmp);
 } else
 _session_dir = session_dir_;
@@ -102,11 +104,34 @@ CExpDesign (const string& session_dir_,
 if ( _session_dir.size() > 1 && _session_dir[_session_dir.size()-1] == 
'/' )
 _session_dir.erase( _session_dir.size()-1, 1);
 
+using agh::str::s

[med-svn] [aghermann] branch master updated (1387ab5 -> 945862e)

2016-08-04 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository aghermann.

  from  1387ab5   update changelogs for 1.0.9 again
   new  bb606b7   follow debian recipe to properly ensure reproducible 
builds
   new  47cff8b   enable multiple instances, drop libunique; lock sessions 
in use
   new  c376f06   update changelogs, prepare for 1.1.0
   new  4ce0f7e   commit or no commit?
   new  945862e   don't bother setting or printing built_by

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:
 debian/changelog  | 13 +
 debian/control|  4 +-
 debian/rules  |  2 -
 upstream/ChangeLog|  6 ++
 upstream/configure.ac |  8 +--
 upstream/data/experiment-dl.sh|  2 +-
 upstream/data/ui/mw-dialogs.glade | 14 -
 upstream/src/Makefile.am  |  2 +-
 upstream/src/aghermann/Makefile.am|  8 +--
 upstream/src/aghermann/expdesign/expdesign.cc | 38 -
 upstream/src/aghermann/expdesign/expdesign.hh |  5 +-
 upstream/src/aghermann/main.cc| 82 ++-
 upstream/src/aghermann/print_version.cc   | 23 
 upstream/src/aghermann/ui/globals.cc  | 15 -
 upstream/src/aghermann/ui/globals.hh  |  6 --
 upstream/src/aghermann/ui/sm/sm.cc| 51 ++---
 upstream/src/tools/Makefile.am|  2 +-
 17 files changed, 112 insertions(+), 169 deletions(-)
 delete mode 100644 upstream/src/aghermann/print_version.cc

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[med-svn] [aghermann] 03/07: add a 'hint' widget on main window

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 536fa6a0b131f7f3322a54488a4ef3eb2d04b8ec
Author: Andrei Zavada 
Date:   Mon Apr 25 04:35:48 2016 +0300

add a 'hint' widget on main window
---
 upstream/data/ui/mw.glade | 54 +--
 1 file changed, 38 insertions(+), 16 deletions(-)

diff --git a/upstream/data/ui/mw.glade b/upstream/data/ui/mw.glade
index e574b29..6fa51f6 100644
--- a/upstream/data/ui/mw.glade
+++ b/upstream/data/ui/mw.glade
@@ -4027,7 +4027,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 EMG
-rgba(25,180,213,0.91663)
+rgba(25,180,213,0.916667)
   
   
 0
@@ -4092,7 +4092,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 EEG Microcontinuity
-rgba(26,190,140,0.84057971014492749)
+rgba(26,190,140,0.84058)
   
   
 0
@@ -4107,7 +4107,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 EEG PSD
-rgba(80,107,177,0.8188405797101449)
+rgba(80,107,177,0.818841)
   
   
 0
@@ -4122,7 +4122,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 SWU
-rgba(216,13,75,0.89130434782608692)
+rgba(216,13,75,0.891304)
   
   
 0
@@ -4278,7 +4278,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 Artifacts
-rgba(204,0,0,0.62681159420289856)
+rgba(204,0,0,0.626812)
   
   
 0
@@ -4293,7 +4293,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 Annotations
-rgba(128,139,113,0.62318840579710144)
+rgba(128,139,113,0.623188)
   
   
 0
@@ -4308,7 +4308,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 Embedded annotations
-rgba(109,144,62,0.62318840579710144)
+rgba(109,144,62,0.623188)
   
   
 0
@@ -4323,7 +4323,7 @@ dragging individual signals with 
<i>Alt</i>.</small>none
 True
 Cursor
-

[med-svn] [aghermann] 06/07: only change active profile scale with Ctrl+Wheel on mw

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit cd28f6a424246a80856598fcce3a84040c40f4e3
Author: Andrei Zavada 
Date:   Mon Apr 25 15:15:56 2016 +0300

only change active profile scale with Ctrl+Wheel on mw
---
 upstream/src/aghermann/ui/mw/measurements_cb.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/upstream/src/aghermann/ui/mw/measurements_cb.cc 
b/upstream/src/aghermann/ui/mw/measurements_cb.cc
index 5fcb56b..104e05d 100644
--- a/upstream/src/aghermann/ui/mw/measurements_cb.cc
+++ b/upstream/src/aghermann/ui/mw/measurements_cb.cc
@@ -159,7 +159,7 @@ daSubjectTimeline_scroll_event_cb(
 return TRUE;
 
 } else if ( event->state & GDK_CONTROL_MASK ) {
-ED.modify_profile_scales( event->direction);
+ED.modify_active_profile_scale( event->direction);
 gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
 return TRUE;
 

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[med-svn] [aghermann] 01/07: mind your pointers

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 974930f6ecd26565cd57704ad482b8aeb40285e0
Author: Andrei Zavada 
Date:   Mon Apr 25 02:58:03 2016 +0300

mind your pointers
---
 upstream/src/common/config-validate.hh | 6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/upstream/src/common/config-validate.hh 
b/upstream/src/common/config-validate.hh
index 9cc9419..bb24bbf 100644
--- a/upstream/src/common/config-validate.hh
+++ b/upstream/src/common/config-validate.hh
@@ -146,7 +146,8 @@ struct SValidator : IValidator {
 return; // leave at default
 }
 if ( not valf(tmp) ) {
-lo->msg( agh::log::TLevel::warning, 
LOG_SOURCE_ISSUER, "Bad value for key \"%s\"", key.c_str());
+if ( lo )
+lo->msg( agh::log::TLevel::warning, 
LOG_SOURCE_ISSUER, "Bad value for key \"%s\"", key.c_str());
 if ( throw_option == TThrowOption::do_throw )
 throw invalid_argument( string("Bad 
value for \"") + key + "\"");
 } else
@@ -193,7 +194,8 @@ get( const libconfig::Config& C,
 return; // leave at default
 }
 if ( tmp < 0 || not valf((size_t)tmp) ) {
-lo->msg( agh::log::TLevel::warning, LOG_SOURCE_ISSUER, "Bad 
value for key \"%s\"", key.c_str());
+if (lo)
+lo->msg( agh::log::TLevel::warning, LOG_SOURCE_ISSUER, 
"Bad value for key \"%s\"", key.c_str());
 if ( throw_option == TThrowOption::do_throw )
 throw invalid_argument( string("Bad value for \"") + 
key + "\"");
 } else

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[med-svn] [aghermann] 07/07: update changelogs for 1.0.9 again

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 1387ab5255430f30b3cf9e0ef0dd38a9bf60cce0
Author: Andrei Zavada 
Date:   Tue Apr 26 03:13:02 2016 +0300

update changelogs for 1.0.9 again
---
 debian/changelog  | 2 +-
 upstream/ChangeLog| 4 
 upstream/data/ui/mw-dialogs.glade | 4 
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index d9c906c..6d7c377 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,7 +2,7 @@ aghermann (1.0.9-1) unstable; urgency=low
 
   * New upstream version.
 
- -- Andrei Zavada   Mon, 25 Apr 2016 03:49:00 +0200
+ -- Andrei Zavada   Mon, 25 Apr 2016 15:23:00 +0200
 
 aghermann (1.0.8-1) unstable; urgency=low
 
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 66347e8..a565ae6 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,6 +1,10 @@
 v.1.0.9 (2016-04-25)
* Fix: Don't try to use uninitialized logging facility on
  config validation failures.
+   * Fix: Only change active scale with Ctrl+Wheel on MW, leave other
+ scale values alone.
+   * New: Put a 'hint' widget in MW corner to explain how to change
+ profile vert and horiz scales.
 
 v.1.0.8 (2016-01-23)
* Fix: Remove code that was not up to c++-17 (which turned out to
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index 1a8e862..edb1f36 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1634,6 +1634,10 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 <span font="monospace" size="small">
* Fix: Don't try to use uninitialized logging facility on
  config validation failures.
+   * Fix: Only change active scale with Ctrl+Wheel on MW, leave other
+ scale values alone.
+   * New: Put a 'hint' widget in MW corner to explain how to change
+ profile vert and horiz scales.
 </span>
 <b>v. 1.0.8</b> (2016-01-23)
 <span font="monospace" size="small">

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[med-svn] [aghermann] branch master updated (4ea92cc -> 1387ab5)

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository aghermann.

  from  4ea92cc   update debian/ files for 1.0.7
  adds  47d4282   gentoo: one last update, further changes to be done in 
gh/gentoo-science
  adds  356b03d   remove some dead, c++17-incorrect code
  adds  76dcfc9   prepare 1.0.8
   new  974930f   mind your pointers
   new  0b9a2b6   prepare 1.0.9
   new  536fa6a   add a 'hint' widget on main window
   new  3411909   petty whitespace cleanup
   new  6b10e28   don't expect profile scale to be == 0.
   new  cd28f6a   only change active profile scale with Ctrl+Wheel on mw
   new  1387ab5   update changelogs for 1.0.9 again

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:
 debian/changelog| 12 ++
 debian/copyright|  2 +-
 gentoo/ChangeLog| 11 +++--
 gentoo/README   |  3 ++
 gentoo/aghermann-1.0.3-r1.ebuild| 30 --
 gentoo/aghermann-1.0.3.ebuild   | 30 --
 gentoo/aghermann-1.0.4.ebuild   | 30 --
 gentoo/aghermann.ebuild | 29 +++--
 upstream/ChangeLog  | 12 ++
 upstream/configure.ac   |  8 ++--
 upstream/data/ui/mw-dialogs.glade   | 18 -
 upstream/data/ui/mw.glade   | 54 +
 upstream/src/aghermann/ui/mw/measurements.cc|  2 +-
 upstream/src/aghermann/ui/mw/measurements_cb.cc |  2 +-
 upstream/src/aghermann/ui/mw/mw.cc  |  4 +-
 upstream/src/aghermann/ui/mw/mw.hh  |  7 
 upstream/src/aghermann/ui/mw/mw_cb.cc   |  3 +-
 upstream/src/common/config-validate.hh  |  6 ++-
 18 files changed, 116 insertions(+), 147 deletions(-)
 create mode 100644 gentoo/README
 delete mode 100644 gentoo/aghermann-1.0.3-r1.ebuild
 delete mode 100644 gentoo/aghermann-1.0.3.ebuild
 delete mode 100644 gentoo/aghermann-1.0.4.ebuild

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[med-svn] [aghermann] 02/07: prepare 1.0.9

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 0b9a2b670fa934d753a5315e994455c293092bf1
Author: Andrei Zavada 
Date:   Mon Apr 25 03:51:46 2016 +0300

prepare 1.0.9
---
 debian/changelog  | 6 ++
 upstream/ChangeLog| 4 
 upstream/configure.ac | 2 +-
 upstream/data/ui/mw-dialogs.glade | 7 ++-
 4 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e925ffc..d9c906c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.0.9-1) unstable; urgency=low
+
+  * New upstream version.
+
+ -- Andrei Zavada   Mon, 25 Apr 2016 03:49:00 +0200
+
 aghermann (1.0.8-1) unstable; urgency=low
 
   * New upstream version (Closes: #812024).
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 048fe75..66347e8 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,7 @@
+v.1.0.9 (2016-04-25)
+   * Fix: Don't try to use uninitialized logging facility on
+ config validation failures.
+
 v.1.0.8 (2016-01-23)
* Fix: Remove code that was not up to c++-17 (which turned out to
  be dead anyway).
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 260ea79..3000402 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-16 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.0.8], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.0.9], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index 812187e..1a8e862 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1630,7 +1630,12 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 5
 10
 10
-<b>v. 1.0.8</b> 
(2016-01-23)
+<b>v. 1.0.9</b> 
(2016-04-25)
+<span font="monospace" size="small">
+   * Fix: Don't try to use uninitialized logging facility on
+ config validation failures.
+</span>
+<b>v. 1.0.8</b> (2016-01-23)
 <span font="monospace" size="small">
* Fix: Remove code that was not up to c++-17 (which turned out to
  be dead anyway).

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[med-svn] [aghermann] 04/07: petty whitespace cleanup

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 341190988dee0a5689419d188a3d33a436116f41
Author: Andrei Zavada 
Date:   Mon Apr 25 15:13:41 2016 +0300

petty whitespace cleanup
---
 upstream/src/aghermann/ui/mw/measurements.cc | 2 +-
 upstream/src/aghermann/ui/mw/mw.cc   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/measurements.cc 
b/upstream/src/aghermann/ui/mw/measurements.cc
index bd66d39..8aab776 100644
--- a/upstream/src/aghermann/ui/mw/measurements.cc
+++ b/upstream/src/aghermann/ui/mw/measurements.cc
@@ -102,7 +102,7 @@ draw_timeline( cairo_t *cr) const
 time_t tl_start_fixed = mktime( &tl_start_fixed_tm);
 
 double  scale = 0.;
-switch (_p._p.display_profile_type ) {
+switch ( _p._p.display_profile_type ) {
 case metrics::TType::psd: scale = _p._p.profile_scale_psd; 
break;
 case metrics::TType::swu: scale = _p._p.profile_scale_swu; 
break;
 case metrics::TType::mc : scale = _p._p.profile_scale_mc;  
break;
diff --git a/upstream/src/aghermann/ui/mw/mw.cc 
b/upstream/src/aghermann/ui/mw/mw.cc
index efadf73..acf4c0c 100644
--- a/upstream/src/aghermann/ui/mw/mw.cc
+++ b/upstream/src/aghermann/ui/mw/mw.cc
@@ -451,8 +451,8 @@ double
 SExpDesignUI::
 calculate_profile_scale()
 {
-doubleavg_profile_height = 0.;
-size_tvalid_episodes = 0;
+double  avg_profile_height = 0.;
+size_t  valid_episodes = 0;
 for ( auto& G : groups )
 for ( auto &J : G )
 if ( J.cprofile && !J.cprofile->mm_list().empty() ) {

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[med-svn] [aghermann] 05/07: don't expect profile scale to be == 0.

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 6b10e28b6baac3db19efd2cfcfbe3f49fc731362
Author: Andrei Zavada 
Date:   Mon Apr 25 15:15:04 2016 +0300

don't expect profile scale to be == 0.
---
 upstream/src/aghermann/ui/mw/mw_cb.cc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/mw_cb.cc 
b/upstream/src/aghermann/ui/mw/mw_cb.cc
index 02d05cb..7a670b5 100644
--- a/upstream/src/aghermann/ui/mw/mw_cb.cc
+++ b/upstream/src/aghermann/ui/mw/mw_cb.cc
@@ -234,8 +234,7 @@ eMsmtProfileType_changed_cb(
 J.cprofile->create_timeline( params);
 
 
-if ( ED.profile_scale_psd == 0. || ED.profile_scale_swu == 0. || 
ED.profile_scale_mc == 0. ||  // don't know which
-ED.autoscale )
+if ( ED.autoscale )
 ED.calculate_profile_scale();
 
 ED.adjust_op_freq_spinbuttons();

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[med-svn] [aghermann] branch WIP updated (76dcfc9 -> 1387ab5)

2016-04-25 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository aghermann.

  from  76dcfc9   prepare 1.0.8
   new  974930f   mind your pointers
   new  0b9a2b6   prepare 1.0.9
   new  536fa6a   add a 'hint' widget on main window
   new  3411909   petty whitespace cleanup
   new  6b10e28   don't expect profile scale to be == 0.
   new  cd28f6a   only change active profile scale with Ctrl+Wheel on mw
   new  1387ab5   update changelogs for 1.0.9 again

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:
 debian/changelog|  6 +++
 upstream/ChangeLog  |  8 
 upstream/configure.ac   |  2 +-
 upstream/data/ui/mw-dialogs.glade   | 11 -
 upstream/data/ui/mw.glade   | 54 +
 upstream/src/aghermann/ui/mw/measurements.cc|  2 +-
 upstream/src/aghermann/ui/mw/measurements_cb.cc |  2 +-
 upstream/src/aghermann/ui/mw/mw.cc  |  4 +-
 upstream/src/aghermann/ui/mw/mw_cb.cc   |  3 +-
 upstream/src/common/config-validate.hh  |  6 ++-
 10 files changed, 72 insertions(+), 26 deletions(-)

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[med-svn] [aghermann] 14/14: prepare 1.0.8

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 76dcfc95414a90d868ce058c00d10ef59f892114
Author: Andrei Zavada 
Date:   Sat Jan 23 12:57:45 2016 +0200

prepare 1.0.8
---
 debian/changelog  | 6 ++
 debian/copyright  | 2 +-
 upstream/ChangeLog| 4 
 upstream/configure.ac | 8 
 upstream/data/ui/mw-dialogs.glade | 9 +++--
 5 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index f1c6785..e925ffc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.0.8-1) unstable; urgency=low
+
+  * New upstream version (Closes: #812024).
+
+ -- Andrei Zavada   Sat, 23 Jan 2016 11:22:00 +0200
+
 aghermann (1.0.7-1) unstable; urgency=low
 
   * New upstream version (Closes: #805746).
diff --git a/debian/copyright b/debian/copyright
index 8c7e950..28b1988 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Andrei Zavada 
 Source: http://johnhommer.com/academic/code/aghermann/source/
 
 Files: *
-Copyright: 2008-2015 Andrei Zavada 
+Copyright: 2008-2016 Andrei Zavada 
 License: GPL-2+
 
 Files: src/libsigproc/exstrom.hh
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 94b809f..048fe75 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,7 @@
+v.1.0.8 (2016-01-23)
+   * Fix: Remove code that was not up to c++-17 (which turned out to
+ be dead anyway).
+
 v.1.0.7 (2015-12-11)
* Fix: Ensure profile overview timeline is at least 1h long.
* Fix: Correctly identify channels by a matching prefix (like
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 65f350a..260ea79 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
-AC_COPYRIGHT([Copyright (c) 2008-15 Andrei Zavada ])
+AC_COPYRIGHT([Copyright (c) 2008-16 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.0.7], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.0.8], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
@@ -50,7 +50,7 @@ ac_cv_cxx_cpp11_features,
 ])
 AC_CXX_STDCPP11_FEATURES()
 test $ac_cv_cxx_cpp11_features = no && \
-   AC_MSG_ERROR([g++ >= 4.7 is required to build $PACKAGE as we must use 
-std=c++11 features your compiler doesn't seem to support], 1)
+   AC_MSG_ERROR([Incomplete support of -std=c++11], 1)
 cxx_version=`$CXX --version | head -n1`
 
 
@@ -230,7 +230,7 @@ AC_MSG_RESULT([
 
PREFIX:  $prefix
 
-   CXX:$CXX (${cxx_version})
+   CXX: $CXX (${cxx_version})
CXXFLAGS:$CXXFLAGS
LDFLAGS: $LDFLAGS
OPENMP_CXXFLAGS: $OPENMP_CXXFLAGS
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index f2741e1..812187e 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1534,7 +1534,7 @@
 start
 5
 15
-<b><big><big>Aghermann 1.0.7 
</big></big></b>
+<b><big><big>Aghermann 1.0.8 
</big></big></b>
 <a 
href="http://johnhommer.com/academic/code/aghermann">johnhommer.com/academic/code/aghermann</a>;
 True
 0
@@ -1630,7 +1630,12 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 5
 10
 10
-<b>v. 1.0.7</b> 
(2015-11-21)
+<b>v. 1.0.8</b> 
(2016-01-23)
+<span font="monospace" size="small">
+   * Fix: Remove code that was not up to c++-17 (which turned out to
+ be dead anyway).
+</span>
+<b>v. 1.0.7</b> (2015-11-21)
 <span font="monospace" size="small">
* Fix: Ensure profile overview timeline is at least 1h long.
* Fix: Correctly identify channels by a matching prefix (like

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[med-svn] [aghermann] 09/14: build with gsl-2.0 if found, supporting gsl-1.6

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 0dc94a334ae373831b760c617995ab3acce18533
Author: Andrei Zavada 
Date:   Fri Dec 11 00:42:37 2015 +

build with gsl-2.0 if found, supporting gsl-1.6
---
 upstream/ChangeLog  |  3 +-
 upstream/configure.ac   |  2 ++
 upstream/src/aghermann/model/borbely.cc | 60 +++--
 3 files changed, 32 insertions(+), 33 deletions(-)

diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 36a2d1f..94b809f 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,7 +1,8 @@
-v.1.0.7 (2015-11-21)
+v.1.0.7 (2015-12-11)
* Fix: Ensure profile overview timeline is at least 1h long.
* Fix: Correctly identify channels by a matching prefix (like
  "F3-AV"); also rework data structures in libsigfile/channel.*.
+   * New: Support building with gsl-2.0.
 
 v.1.0.6 (2015-08-13)
* Fix: Make widgets reappear on Empty Experiment splash.
diff --git a/upstream/configure.ac b/upstream/configure.ac
index dbfe2cd..65f350a 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -67,6 +67,8 @@ PKG_CHECK_MODULES([CAIRO], [cairo >= 1.8.10])
 PKG_CHECK_MODULES([UNIQUE], [unique-3.0])
 PKG_CHECK_MODULES([VTE], [vte-2.91])
 
+AX_PATH_GSL([2.0], [AC_DEFINE([HAVE_GSL_20], [], [we have gsl >= 2.0])], [])
+
 AC_CHECK_LIB(
fftw3_omp, fftw_init_threads,
[AC_DEFINE([HAVE_LIBFFTW3_OMP], [], [we have fftw3 omp-enabled])
diff --git a/upstream/src/aghermann/model/borbely.cc 
b/upstream/src/aghermann/model/borbely.cc
index 04d0ded..b6b5fd8 100644
--- a/upstream/src/aghermann/model/borbely.cc
+++ b/upstream/src/aghermann/model/borbely.cc
@@ -85,16 +85,6 @@ expb_fdf( const gsl_vector* x, void *data,
 return GSL_SUCCESS;
 }
 
-
-void
-print_state( size_t iter, gsl_multifit_fdfsolver* s)
-{
-APPLOG_DEBUG ("iter: %3zu x = % 15.8f |f(x)| = %g",
-  iter,
-  gsl_vector_get (s->x, 0),
-  gsl_blas_dnrm2 (s->f));
-}
-
 } // namespace
 
 agh::beersma::SClassicFit
@@ -155,14 +145,28 @@ classic_fit( agh::CRecording& M,
 pp, 1);
 gsl_multifit_fdfsolver_set( S, &F, &X.vector);
 
-  // find it
-int status;
+#ifdef HAVE_GSL_20
+const double xtol = 1e-8;
+const double gtol = 1e-8;
+const double ftol = 0.0;
+
+int info;
+gsl_multifit_fdfsolver_driver(S, 20, xtol, gtol, ftol, &info);
+
+gsl_matrix *J = gsl_matrix_alloc(pp, 1);
+gsl_multifit_fdfsolver_jac(S, J);
+gsl_multifit_covar( J, 0.0, covar);
+
+gsl_matrix_free (J);
+
+#else  // HAVE_GSL_16
 unsigned int iter = 0;
+int status;
+
 do {
 ++iter;
 status = gsl_multifit_fdfsolver_iterate( S);
 
-print_state( iter, S);
 if ( status ) {
 APPLOG_WARN ("status = %s", gsl_strerror( status));
 break;
@@ -174,18 +178,18 @@ classic_fit( agh::CRecording& M,
 
 gsl_multifit_covar( S->J, 0.0, covar);
 
-#define FIT(i) gsl_vector_get( S->x, i)
-#define ERR(i) sqrt(gsl_matrix_get( covar, i, i))
-{
-double chi = gsl_blas_dnrm2(S->f);
-double dof = pp - 1;
-double c = GSL_MAX_DBL(1, chi / sqrt(dof));
-
-APPLOG_DEBUG ("chisq/dof = %g",  gsl_pow_2(chi) / dof);
-APPLOG_DEBUG ("r = %.5f +/- %.5f", FIT(0), c*ERR(0));
-}
+// #define FIT(i) gsl_vector_get( S->x, i)
+// #define ERR(i) sqrt(gsl_matrix_get( covar, i, i))
+// {
+// double chi = gsl_blas_dnrm2(S->f);
+// double dof = pp - 1;
+// double c = GSL_MAX_DBL(1, chi / sqrt(dof));
 
-double  rate = gsl_vector_get( S->x, 0);
+// APPLOG_DEBUG ("chisq/dof = %g",  gsl_pow_2(chi) / dof);
+// APPLOG_DEBUG ("r = %.5f +/- %.5f", FIT(0), c*ERR(0));
+// }
+#endif
+const double  rate = gsl_vector_get( S->x, 0);
 
 gsl_multifit_fdfsolver_free( S);
 gsl_matrix_free( covar);
@@ -193,11 +197,3 @@ classic_fit( agh::CRecording& M,
 return {rate};
 
 }
-
-
-// Local Variables:
-// Mode: c++
-// indent-tabs-mode: nil
-// tab-width: 8
-// c-basic-offset: 8
-// End:

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[med-svn] [aghermann] 04/14: tweak .gitignore

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit af4068ba66c72eb79ddd1a8eead62b1d13dd726f
Author: Andrei Zavada 
Date:   Fri Aug 14 02:51:37 2015 +0400

tweak .gitignore
---
 .gitignore  | 2 --
 upstream/.gitignore | 2 ++
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index bf35827..c15ec90 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1 @@
 .DirIcon
-.backups/
-*~
diff --git a/upstream/.gitignore b/upstream/.gitignore
index ca8724f..1948f06 100644
--- a/upstream/.gitignore
+++ b/upstream/.gitignore
@@ -10,6 +10,8 @@ cscope.*
 *.lo
 *.pc
 /*.tar.bz2
+/*.tar.gz
+/*.tar.xz
 
 # autotools
 .deps/

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[med-svn] [aghermann] 06/14: refactor sigfile:: definitions wrt types & channel classification

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 014de4b283298218dbbb1bea3a78059d479ed4d2
Author: Andrei Zavada 
Date:   Tue Nov 17 11:02:57 2015 +0200

refactor sigfile:: definitions wrt types & channel classification

Work towards accommodating prefixed channel names like "FZ-AV",
seen in the wild (that Ivan's EEG from oberig.ua).

* use enum class for signal types;
* have channel represented in static registry as {"Fz", types::eeg}, thus
  avoiding enum channels that can/should/may have or not have comparable
  elements;
* sigfile::SChannel::TType -> sigfile::definitions::types throughout.
---
 upstream/src/aghermann/artifact-detection/3in1.cc  |  17 +-
 upstream/src/aghermann/expdesign/dirlevel.cc   |   8 -
 upstream/src/aghermann/expdesign/expdesign.cc  |  13 +-
 upstream/src/aghermann/expdesign/expdesign.hh  |   9 +-
 upstream/src/aghermann/expdesign/profile.hh|   7 -
 upstream/src/aghermann/expdesign/recording.hh  |  11 +-
 upstream/src/aghermann/expdesign/subject.hh|   9 +-
 upstream/src/aghermann/expdesign/tree-scanner.cc   |  11 +-
 upstream/src/aghermann/globals.hh  |   7 -
 upstream/src/aghermann/model/achermann.hh  |   7 -
 upstream/src/aghermann/rk1968/rk1968.cc|  11 +-
 upstream/src/aghermann/ui/mw/mainmenu_cb.cc|  17 +-
 upstream/src/aghermann/ui/mw/mw.hh |   4 +-
 upstream/src/aghermann/ui/mw/mw_cb.cc  |  14 +-
 upstream/src/aghermann/ui/mw/populate.cc   |  13 +-
 upstream/src/aghermann/ui/sf/channel.cc|  22 +--
 upstream/src/aghermann/ui/sf/channel.hh|  11 +-
 .../src/aghermann/ui/sf/d/phasediff-construct.cc   |  11 +-
 upstream/src/aghermann/ui/sf/ica.cc|  10 +-
 upstream/src/aghermann/ui/sf/montage-menus_cb.cc   |  13 +-
 upstream/src/aghermann/ui/sf/montage-overlays.cc   |  16 +-
 upstream/src/aghermann/ui/sf/montage.cc|  12 +-
 upstream/src/aghermann/ui/sf/montage_cb.cc |  21 +--
 upstream/src/aghermann/ui/sf/sf.cc |  41 ++---
 upstream/src/aghermann/ui/sm/sm.cc |   7 -
 upstream/src/common/log-facility.hh|   7 -
 upstream/src/common/subject_id.cc  |   9 -
 upstream/src/libmetrics/mc.cc  |  16 +-
 upstream/src/libmetrics/page-metrics-base.cc   |  11 +-
 upstream/src/libmetrics/psd.cc |  17 +-
 upstream/src/libmetrics/swu.cc |  18 +-
 upstream/src/libsigfile/channel.cc | 200 ++---
 upstream/src/libsigfile/channel.hh | 192 ++--
 upstream/src/libsigfile/edf-io.cc  |  11 +-
 upstream/src/libsigfile/edf.cc |  47 ++---
 upstream/src/libsigfile/edf.hh |  15 +-
 upstream/src/libsigfile/source-base.hh |  13 +-
 upstream/src/libsigfile/tsv.cc |  10 +-
 upstream/src/libsigfile/tsv.hh |  21 +--
 upstream/src/libsigfile/typed-source.cc|   8 -
 upstream/src/libsigfile/typed-source.hh|   7 -
 upstream/src/tools/edfhed-gtk.cc   |   8 -
 upstream/src/tools/edfhed.cc   |  14 +-
 43 files changed, 259 insertions(+), 687 deletions(-)

diff --git a/upstream/src/aghermann/artifact-detection/3in1.cc 
b/upstream/src/aghermann/artifact-detection/3in1.cc
index 853c23f..12c35e3 100644
--- a/upstream/src/aghermann/artifact-detection/3in1.cc
+++ b/upstream/src/aghermann/artifact-detection/3in1.cc
@@ -106,15 +106,16 @@ detect_artifacts( sigfile::SNamedChannel& N,
 
   // 2. EMG perturbations
 if ( P.do_emg_perturbations &&
- N.source.signal_type(N.sig_no) != sigfile::SChannel::TType::emg ) 
{
+ N.source.signal_type(N.sig_no) != 
sigfile::definitions::types::emg ) {
 // which EMG channels are there?
 list emgRR;
 for ( int h = 0; h < (int)N.source.n_channels(); ++h )
-if ( N.source.signal_type(h) == 
sigfile::SChannel::TType::emg )
+if ( N.source.signal_type(h) == 
sigfile::definitions::types::emg )
 emgRR.push_front( h);
 
 if ( emgRR.empty() )
-APPLOG_INFO ("No EMG recordings in %s:%s, skipping EMG 
perturbation-bound artifact detection", N.source.filename(), 
N.source.channel_by_id(N.sig_no).name());
+APPLOG_INFO ("No EMG recordings in %s:%s, skipping EMG 
perturbation-bound artifact detection",
+ N.source.filename(), 
N.source.channel_by_id(N.sig_no).custom_name());
 
 for ( const int h : emgRR ) {

[med-svn] [aghermann] 01/14: make widgets reappear on Empty Experiment splash

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit abdc0ee716c5cc7f031b12116dda600c7be71a8b
Author: andrei zavada 
Date:   Fri Jul 17 04:56:38 2015 +0300

make widgets reappear on Empty Experiment splash
---
 upstream/src/aghermann/ui/mw/splash.cc  | 38 ++---
 upstream/src/aghermann/ui/mw/widgets.hh |  2 +-
 2 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/splash.cc 
b/upstream/src/aghermann/ui/mw/splash.cc
index 641b260..c38a0cc 100644
--- a/upstream/src/aghermann/ui/mw/splash.cc
+++ b/upstream/src/aghermann/ui/mw/splash.cc
@@ -67,6 +67,12 @@ show_empty_experiment_blurb()
 (GtkContainer*)cMeasurements,
 (GtkCallback) gtk_widget_destroy,
 NULL);
+
+g_object_set( (GObject*)cMeasurements,
+  "margin", 20,
+  NULL);
+gtk_grid_set_row_spacing(cMeasurements, 20);
+
 const char *blurb =
 "Empty experiment\n\n"
 "When you have your recordings ready as a set of .edf files,\n"
@@ -84,10 +90,12 @@ show_empty_experiment_blurb()
 GtkLabel *blurb_label = (GtkLabel*)gtk_label_new( "");
 gtk_label_set_markup( blurb_label, blurb);
 
-gtk_box_pack_start(
-(GtkBox*)cMeasurements,
+gtk_grid_insert_row(
+cMeasurements, 0);
+gtk_grid_attach(
+cMeasurements,
 (GtkWidget*)blurb_label,
-TRUE, TRUE, 10);
+0, 0, 1, 1);
 GtkWidget *bDownload = gtk_button_new_with_label("  Get sample dataset 
 ");
 g_object_set(
 (GObject*)bDownload,
@@ -98,16 +106,21 @@ show_empty_experiment_blurb()
 bDownload, "clicked",
 (GCallback)bDownload_clicked_cb,
 this);
-gtk_box_pack_start(
-(GtkBox*)cMeasurements,
+
+gtk_grid_insert_row(
+cMeasurements, 1);
+gtk_grid_attach(
+cMeasurements,
 bDownload,
-FALSE, FALSE, 0);
+0, 1, 1, 1);
 
-gtk_box_pack_start(
-(GtkBox*)cMeasurements,
+gtk_grid_insert_row(
+(GtkGrid*)cMeasurements, 2);
+gtk_grid_attach(
+cMeasurements,
 (GtkWidget*)gtk_image_new_from_file(
 PACKAGE_DATADIR "/aghermann/idle-bg.svg"),
-TRUE, FALSE, 0);
+0, 2, 1, 1);
 
 gtk_widget_show_all( (GtkWidget*)cMeasurements);
 }
@@ -128,10 +141,11 @@ try_download()
 tTerm, "child-exited",
 (GCallback)download_process_child_exited_cb,
 this);
-gtk_box_pack_start(
-(GtkBox*)cMeasurements,
+gtk_grid_insert_row(cMeasurements, 0);
+gtk_grid_attach(
+cMeasurements,
 (GtkWidget*)tTerm,
-TRUE, FALSE, 0);
+0, 0, 1, 1);
 set_wMainWindow_interactive( false, true);
 // punch a hole for VteTerminal for any user ^C
 gtk_widget_set_sensitive( (GtkWidget*)cMeasurements, TRUE);
diff --git a/upstream/src/aghermann/ui/mw/widgets.hh 
b/upstream/src/aghermann/ui/mw/widgets.hh
index 47b734a..6308d0e 100644
--- a/upstream/src/aghermann/ui/mw/widgets.hh
+++ b/upstream/src/aghermann/ui/mw/widgets.hh
@@ -154,7 +154,7 @@ struct SExpDesignUIWidgets {
 *eMsmtSession;
 
 // main area
-GtkVBox
+GtkGrid
 *cMeasurements;
 GtkStatusbar
 *sbMainStatusBar;

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[med-svn] [aghermann] branch master updated (6b6d19c -> 4ea92cc)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository aghermann.

  from  6b6d19c   make dist-orig-xz for bare-autoconf, debian-friendly 
tarball
   new  abdc0ee   make widgets reappear on Empty Experiment splash
   new  8ec0ccf   Merge branch 'WIP' of github.com:hmmr/aghermann into WIP
   new  21b157e   prepare for 1.0.6
   new  af4068b   tweak .gitignore
   new  3987b71   retract "Closes: #794703" from debina/changelog
   new  014de4b   refactor sigfile:: definitions wrt types & channel 
classification
   new  c580fb2   ensure there is at least one hour in overview profile
   new  2a0bcf4   prepare 1.0.7
   new  0dc94a3   build with gsl-2.0 if found, supporting gsl-1.6
   new  7f947e0   whitespace touch up; remove emacs vars
   new  4ea92cc   update debian/ files for 1.0.7

The 11 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:
 .gitignore |   2 -
 debian/changelog   |  12 ++
 debian/control |   2 +-
 upstream/.gitignore|   2 +
 upstream/ChangeLog |   9 +
 upstream/configure.ac  |   4 +-
 upstream/data/ui/mw-dialogs.glade  |  20 ++-
 upstream/src/aghermann/artifact-detection/3in1.cc  |  17 +-
 upstream/src/aghermann/artifact-detection/3in1.hh  |   6 -
 .../aghermann/artifact-detection/forward-decls.hh  |   7 -
 upstream/src/aghermann/expdesign/dirlevel.cc   |   8 -
 upstream/src/aghermann/expdesign/dirlevel.hh   |   7 -
 upstream/src/aghermann/expdesign/expdesign.cc  |  13 +-
 upstream/src/aghermann/expdesign/expdesign.hh  |   9 +-
 upstream/src/aghermann/expdesign/forward-decls.hh  |   7 -
 upstream/src/aghermann/expdesign/loadsave.cc   |   8 -
 upstream/src/aghermann/expdesign/profile.hh|   9 -
 upstream/src/aghermann/expdesign/recording.cc  |   8 -
 upstream/src/aghermann/expdesign/recording.hh  |  11 +-
 upstream/src/aghermann/expdesign/subject.cc|  10 --
 upstream/src/aghermann/expdesign/subject.hh|   9 +-
 upstream/src/aghermann/expdesign/tree-scanner.cc   |  11 +-
 upstream/src/aghermann/globals.cc  |   9 -
 upstream/src/aghermann/globals.hh  |   7 -
 upstream/src/aghermann/ica/forward-decls.hh|   7 -
 upstream/src/aghermann/ica/ica.hh  |   8 -
 upstream/src/aghermann/main.cc |   7 -
 upstream/src/aghermann/model/achermann-siman.cc|  10 --
 upstream/src/aghermann/model/achermann-tunable.cc  |   8 -
 upstream/src/aghermann/model/achermann-tunable.hh  |   7 -
 upstream/src/aghermann/model/achermann.cc  | 102 +--
 upstream/src/aghermann/model/achermann.hh  |   7 -
 upstream/src/aghermann/model/beersma.hh|  15 +-
 upstream/src/aghermann/model/borbely.cc|  58 +++---
 upstream/src/aghermann/model/forward-decls.hh  |   7 -
 upstream/src/aghermann/model/ultradian-cycle.cc|   8 -
 upstream/src/aghermann/patterns/forward-decls.hh   |   8 -
 upstream/src/aghermann/patterns/patterns.cc|  21 ++-
 upstream/src/aghermann/patterns/patterns.hh|   8 -
 upstream/src/aghermann/patterns/patterns.ii|  19 +-
 upstream/src/aghermann/print_version.cc|   7 -
 upstream/src/aghermann/rk1968/rk1968-profiles.cc   |  10 --
 upstream/src/aghermann/rk1968/rk1968.cc|  11 +-
 upstream/src/aghermann/rk1968/rk1968.hh|   7 -
 .../src/aghermann/ui/dirlevel-storable-adapter.hh  |   8 -
 .../src/aghermann/ui/dirlevel-storable-adapter.ii  |   6 -
 upstream/src/aghermann/ui/forward-decls.hh |   9 +-
 upstream/src/aghermann/ui/globals.cc   |   9 -
 upstream/src/aghermann/ui/globals.hh   |   7 -
 upstream/src/aghermann/ui/mf/construct.cc  |   8 -
 upstream/src/aghermann/ui/mf/mf.cc |  12 --
 upstream/src/aghermann/ui/mf/mf.hh |   9 +-
 upstream/src/aghermann/ui/mf/mf_cb.cc  |   7 -
 upstream/src/aghermann/ui/mf/mf_cb.hh  |   9 +-
 upstream/src/aghermann/ui/misc.cc  |   8 -
 upstream/src/aghermann/ui/misc.hh  |   7 -
 upstream/src/aghermann/ui/mw/admit-one.cc  |   9 -
 upstream/src/aghermann/ui/mw/admit-one_cb.cc   |   8 -
 upstream/src/aghermann/ui/mw/construct.cc  |   8 -
 upstream/src/aghermann/ui/mw/loadsave.cc   |  60 +++
 upstream/src/aghermann/ui/mw/mainmenu_cb.cc|  17 +-
 upstream/src/aghermann/ui/mw/measurements.cc   |   7 -
 upstream/src/aghermann/ui/mw/measurements_cb.cc|  10 +-
 upstream/sr

[med-svn] [aghermann] 05/14: retract "Closes: #794703" from debina/changelog

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 3987b71b44aabe8c066d2178199a1c886db588cf
Author: Andrei Zavada 
Date:   Sat Aug 15 04:26:29 2015 +0400

retract "Closes: #794703" from debina/changelog

because that bug proved to be a false alarm
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index cba962e..f4de824 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 aghermann (1.0.6-1) unstable; urgency=low
 
-  * New upstream version (Closes: #794703).
+  * New upstream version.
 
  -- Andrei Zavada   Fri, 14 Aug 2015 00:03:00 +0400
 

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[med-svn] [aghermann] 02/14: Merge branch 'WIP' of github.com:hmmr/aghermann into WIP

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 8ec0ccf082501dc12e7222c84f8913075f9d3c19
Merge: abdc0ee 6b6d19c
Author: andrei zavada 
Date:   Fri Jul 17 04:58:32 2015 +0300

Merge branch 'WIP' of github.com:hmmr/aghermann into WIP

 debian/unwanted-files | 22 --
 upstream/Makefile.am  | 28 
 2 files changed, 28 insertions(+), 22 deletions(-)

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[med-svn] [aghermann] 10/14: whitespace touch up; remove emacs vars

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 7f947e08df2061f0ffa183492ce3dcdc9288cc53
Author: Andrei Zavada 
Date:   Fri Dec 11 01:41:28 2015 +

whitespace touch up; remove emacs vars
---
 upstream/src/aghermann/artifact-detection/3in1.hh  |   6 --
 .../aghermann/artifact-detection/forward-decls.hh  |   7 --
 upstream/src/aghermann/expdesign/dirlevel.hh   |   7 --
 upstream/src/aghermann/expdesign/forward-decls.hh  |   7 --
 upstream/src/aghermann/expdesign/loadsave.cc   |   8 --
 upstream/src/aghermann/expdesign/profile.hh|   2 -
 upstream/src/aghermann/expdesign/recording.cc  |   8 --
 upstream/src/aghermann/expdesign/subject.cc|  10 --
 upstream/src/aghermann/globals.cc  |   9 --
 upstream/src/aghermann/ica/forward-decls.hh|   7 --
 upstream/src/aghermann/ica/ica.hh  |   8 --
 upstream/src/aghermann/main.cc |   7 --
 upstream/src/aghermann/model/achermann-siman.cc|  10 --
 upstream/src/aghermann/model/achermann-tunable.cc  |   8 --
 upstream/src/aghermann/model/achermann-tunable.hh  |   7 --
 upstream/src/aghermann/model/achermann.cc  | 102 ++---
 upstream/src/aghermann/model/beersma.hh|  15 +--
 upstream/src/aghermann/model/borbely.cc|  16 +---
 upstream/src/aghermann/model/forward-decls.hh  |   7 --
 upstream/src/aghermann/model/ultradian-cycle.cc|   8 --
 upstream/src/aghermann/patterns/forward-decls.hh   |   8 --
 upstream/src/aghermann/patterns/patterns.cc|  21 ++---
 upstream/src/aghermann/patterns/patterns.hh|   8 --
 upstream/src/aghermann/patterns/patterns.ii|  19 ++--
 upstream/src/aghermann/print_version.cc|   7 --
 upstream/src/aghermann/rk1968/rk1968-profiles.cc   |  10 --
 upstream/src/aghermann/rk1968/rk1968.hh|   7 --
 .../src/aghermann/ui/dirlevel-storable-adapter.hh  |   8 --
 .../src/aghermann/ui/dirlevel-storable-adapter.ii  |   6 --
 upstream/src/aghermann/ui/forward-decls.hh |   9 +-
 upstream/src/aghermann/ui/globals.cc   |   9 --
 upstream/src/aghermann/ui/globals.hh   |   7 --
 upstream/src/aghermann/ui/mf/construct.cc  |   8 --
 upstream/src/aghermann/ui/mf/mf.cc |  12 ---
 upstream/src/aghermann/ui/mf/mf.hh |   9 +-
 upstream/src/aghermann/ui/mf/mf_cb.cc  |   7 --
 upstream/src/aghermann/ui/mf/mf_cb.hh  |   9 +-
 upstream/src/aghermann/ui/misc.cc  |   8 --
 upstream/src/aghermann/ui/misc.hh  |   7 --
 upstream/src/aghermann/ui/mw/admit-one.cc  |   9 --
 upstream/src/aghermann/ui/mw/admit-one_cb.cc   |   8 --
 upstream/src/aghermann/ui/mw/construct.cc  |   8 --
 upstream/src/aghermann/ui/mw/loadsave.cc   |  60 ++--
 upstream/src/aghermann/ui/mw/measurements.cc   |   7 --
 upstream/src/aghermann/ui/mw/measurements_cb.cc|   7 --
 upstream/src/aghermann/ui/mw/mw.cc |   9 --
 upstream/src/aghermann/ui/mw/mw.hh |   7 --
 upstream/src/aghermann/ui/mw/mw_cb.hh  |   8 --
 upstream/src/aghermann/ui/mw/populate.cc   |   6 +-
 upstream/src/aghermann/ui/mw/settings_cb.cc|   7 --
 upstream/src/aghermann/ui/mw/simulations.cc|   8 --
 upstream/src/aghermann/ui/mw/simulations_cb.cc |   7 --
 upstream/src/aghermann/ui/mw/splash.cc |   7 --
 upstream/src/aghermann/ui/mw/widgets.hh|   7 --
 upstream/src/aghermann/ui/sf/construct.cc  |   6 --
 upstream/src/aghermann/ui/sf/controls_cb.cc|   7 --
 .../src/aghermann/ui/sf/d/artifacts-profiles_cb.cc |   6 --
 upstream/src/aghermann/ui/sf/d/artifacts.cc|   8 --
 upstream/src/aghermann/ui/sf/d/artifacts.hh|   6 --
 upstream/src/aghermann/ui/sf/d/artifacts_cb.cc |   6 --
 .../src/aghermann/ui/sf/d/filters-construct.cc |   7 --
 upstream/src/aghermann/ui/sf/d/filters.cc  |   7 --
 upstream/src/aghermann/ui/sf/d/filters.hh  |   6 --
 upstream/src/aghermann/ui/sf/d/filters_cb.cc   |   7 --
 upstream/src/aghermann/ui/sf/d/patterns-draw.cc|   8 --
 .../src/aghermann/ui/sf/d/patterns-profiles.cc |   7 --
 .../src/aghermann/ui/sf/d/patterns-profiles_cb.cc  |   9 --
 upstream/src/aghermann/ui/sf/d/patterns.cc |   7 --
 upstream/src/aghermann/ui/sf/d/patterns.hh |   7 --
 upstream/src/aghermann/ui/sf/d/patterns_cb.cc  |   9 --
 upstream/src/aghermann/ui/sf/d/phasediff.cc|   8 --
 upstream/src/aghermann/ui/sf/d/phasediff.hh|   7 --
 upstream/src/aghermann/ui/sf/d/phasediff_cb.cc |   8 --
 upstream/src/aghermann/ui/sf/d/rk1968-profiles.cc  |   8 --
 .../src/aghermann/ui/sf/d/rk1968-profiles_cb.cc|   6 --
 upstream/src/aghermann/ui/sf/d/rk1968.cc   |   9 --
 upstream/src/aghermann/ui/sf/d

[med-svn] [aghermann] 07/14: ensure there is at least one hour in overview profile

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit c580fb28a2f49f7f242007148058e2d4c8aa1311
Author: Andrei Zavada 
Date:   Sat Nov 21 13:02:32 2015 +0200

ensure there is at least one hour in overview profile
---
 upstream/src/aghermann/ui/mw/measurements_cb.cc |  3 ++-
 upstream/src/aghermann/ui/mw/populate.cc| 12 
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/measurements_cb.cc 
b/upstream/src/aghermann/ui/mw/measurements_cb.cc
index 1fcbac1..19fea62 100644
--- a/upstream/src/aghermann/ui/mw/measurements_cb.cc
+++ b/upstream/src/aghermann/ui/mw/measurements_cb.cc
@@ -146,7 +146,8 @@ daSubjectTimeline_scroll_event_cb(
 default: break;
 }
 
-ED.tl_width = (ED.timeline_end - ED.timeline_start) / 3600 * 
ED.tl_pph;
+auto hours = (ED.timeline_end - ED.timeline_start) / 3600;
+ED.tl_width = (hours < 1 ? 1 : hours) * ED.tl_pph;
 for ( auto &G : ED.groups )
 for ( auto &J : G )
 g_object_set(
diff --git a/upstream/src/aghermann/ui/mw/populate.cc 
b/upstream/src/aghermann/ui/mw/populate.cc
index 93e0672..f47b73f 100644
--- a/upstream/src/aghermann/ui/mw/populate.cc
+++ b/upstream/src/aghermann/ui/mw/populate.cc
@@ -445,10 +445,14 @@ populate_1()
 
 timeline_start = earliest_start;
 timeline_end   = latest_end;
-tl_width = (timeline_end - timeline_start) / 3600 * tl_pph;
-tl_pages = (timeline_end - timeline_start) / ED->psd_params.pagesize;
-
-APPLOG_INFO ("populate_1(): common timeline:");
+decltype(timeline_end) full_secs =
+timeline_end - timeline_start;
+if ( full_secs < 3600 )
+full_secs = 3600;
+tl_width = full_secs * tl_pph;
+tl_pages = full_secs / ED->psd_params.pagesize;
+
+APPLOG_INFO ("populate_1(): common timeline is %zu pages:", tl_pages);
 {
 string t {asctime( localtime(&earliest_start))};
 t += asctime( localtime(&latest_end));

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[med-svn] [aghermann] 03/14: prepare for 1.0.6

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 21b157ee2d7ed4056b562ee3e357614f1c3d35fc
Author: Andrei Zavada 
Date:   Fri Aug 14 02:51:22 2015 +0400

prepare for 1.0.6
---
 debian/changelog  | 6 ++
 upstream/ChangeLog| 3 +++
 upstream/configure.ac | 2 +-
 upstream/data/ui/mw-dialogs.glade | 8 ++--
 4 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 1e69160..cba962e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.0.6-1) unstable; urgency=low
+
+  * New upstream version (Closes: #794703).
+
+ -- Andrei Zavada   Fri, 14 Aug 2015 00:03:00 +0400
+
 aghermann (1.0.5-1) unstable; urgency=low
 
   * New upstream version (Closes: #788025).
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index ec368f2..f32528c 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,6 @@
+v.1.0.6 (2015-08-13)
+   * Fix: Make widgets reappear on Empty Experiment splash.
+
 v.1.0.5 (2015-06-15)
* Fix: Depend on vte-2.91.
* Fix: Deal with GTK deprecations in glade resources of MW, SF
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 6d3027d..99e0003 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-15 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.0.5], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.0.6], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index e9969e6..7bef407 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1534,7 +1534,7 @@
 start
 5
 15
-<b><big><big>Aghermann 1.0.5 
</big></big></b>
+<b><big><big>Aghermann 1.0.6 
</big></big></b>
 <a 
href="http://johnhommer.com/academic/code/aghermann">johnhommer.com/academic/code/aghermann</a>;
 True
 0
@@ -1630,7 +1630,11 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 5
 10
 10
-<b>v. 1.0.5</b> 
(2015-06-15)
+<b>v. 1.0.6</b> 
(2015-08-14)
+<span font="monospace" size="small">
+   * Fix: Make widgets reappear on Empty Experiment splash.
+</span>
+<b>v. 1.0.5</b> (2015-06-15)
 <span font="monospace" size="small">
* Fix: Depend on vte-2.91.
* Fix: Deal with GTK deprecations in glade resources of MW, SF

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[med-svn] [aghermann] 13/14: remove some dead, c++17-incorrect code

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 356b03d803283d9e55a90ca18c0076479d834dc7
Author: Andrei Zavada 
Date:   Sat Jan 23 12:57:23 2016 +0200

remove some dead, c++17-incorrect code
---
 upstream/src/aghermann/ui/mw/mw.hh | 7 ---
 1 file changed, 7 deletions(-)

diff --git a/upstream/src/aghermann/ui/mw/mw.hh 
b/upstream/src/aghermann/ui/mw/mw.hh
index 723f4a2..5835a7f 100644
--- a/upstream/src/aghermann/ui/mw/mw.hh
+++ b/upstream/src/aghermann/ui/mw/mw.hh
@@ -327,13 +327,6 @@ class SExpDesignUI
  agh::ui::TGtkRefreshMode);
 
   // dnd
-struct SDndIface {
-GtkTargetEntry
-target_list[];
-size_t  n_targets;
-};
-SDndIface
-dnd;
 int dnd_maybe_admit_one( const char* fname);
 
 string  browse_command;

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[med-svn] [aghermann] 12/14: gentoo: one last update, further changes to be done in gh/gentoo-science

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 47d428229556bd42484c0c7c3b49955e17b7df5e
Author: Andrei Zavada 
Date:   Thu Jan 21 17:56:09 2016 +0200

gentoo: one last update, further changes to be done in gh/gentoo-science
---
 gentoo/ChangeLog | 11 +++
 gentoo/README|  3 +++
 gentoo/aghermann-1.0.3-r1.ebuild | 30 --
 gentoo/aghermann-1.0.3.ebuild| 30 --
 gentoo/aghermann-1.0.4.ebuild| 30 --
 gentoo/aghermann.ebuild  | 29 ++---
 6 files changed, 24 insertions(+), 109 deletions(-)

diff --git a/gentoo/ChangeLog b/gentoo/ChangeLog
index 9936cbb..05373ff 100644
--- a/gentoo/ChangeLog
+++ b/gentoo/ChangeLog
@@ -1,15 +1,18 @@
 # ChangeLog for sci-biology/aghermann
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Jan 2015; Andrei Zavada  aghermann-1.0.7.ebuild:
+  sci-biology/aghermann: New upstream version.
+
   15 Jun 2015; Andrei Zavada  aghermann-1.0.5.ebuild:
-  New upstream version.
+  sci-biology/aghermann: New upstream version.
 
   10 Apr 2015; Andrei Zavada  aghermann-1.0.4.ebuild:
-  New upstream version.
+  sci-biology/aghermann: New upstream version.
 
   28 Mar 2015; Andrei Zavada  aghermann-1.0.3-r1.ebuild:
-  Install binaries into /usr/bin not /bin.
+  sci-biology/aghermann: Install binaries into /usr/bin not /bin.
 
   18 Feb 2015; Justin Lecher  aghermann-1.0.3.ebuild:
   sci-biology/aghermann: Fix slot operators
diff --git a/gentoo/README b/gentoo/README
new file mode 100644
index 000..660d4cd
--- /dev/null
+++ b/gentoo/README
@@ -0,0 +1,3 @@
+Gentoo ebuilds exist separately in the 'gentoo-science' overlay
+(github.com/gentoo-science), under sci-biology.  The files in this
+directory have been last updated in Jan 2016 for upstream version 1.0.7,
diff --git a/gentoo/aghermann-1.0.3-r1.ebuild b/gentoo/aghermann-1.0.3-r1.ebuild
deleted file mode 100644
index 2e1b52a..000
--- a/gentoo/aghermann-1.0.3-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="5"
-
-DESCRIPTION="A sleep-research experiment manager, EDF viewer & Achermann's 
Process S model runner"
-HOMEPAGE="http://johnhommer.com/academic/code/aghermann";
-SRC_URI="http://johnhommer.com/academic/code/aghermann/source/${P}.tar.xz";
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/lua:*
-   dev-libs/libconfig
-   dev-libs/libunique:3
-   media-libs/libsamplerate
-   sci-libs/fftw:3.0
-   sci-libs/gsl
-   sci-libs/itpp
-   x11-libs/gtk+:3
-   x11-libs/vte:2.90"
-
-DEPEND="${RDEPEND}
-   virtual/pkgconfig"
-
-src_configure() {
-   econf --bindir="${EPREFIX}"/usr/bin
-}
diff --git a/gentoo/aghermann-1.0.3.ebuild b/gentoo/aghermann-1.0.3.ebuild
deleted file mode 100644
index 58eaa8d..000
--- a/gentoo/aghermann-1.0.3.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="5"
-
-DESCRIPTION="A sleep-research experiment manager, EDF viewer & Achermann's 
Process S model runner"
-HOMEPAGE="http://johnhommer.com/academic/code/aghermann";
-SRC_URI="http://johnhommer.com/academic/code/aghermann/source/${P}.tar.xz";
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/lua:*
-   dev-libs/libconfig
-   dev-libs/libunique:3
-   media-libs/libsamplerate
-   sci-libs/fftw:3.0
-   sci-libs/gsl
-   sci-libs/itpp
-   x11-libs/gtk+:3
-   x11-libs/vte:2.90"
-
-DEPEND="${RDEPEND}
-   virtual/pkgconfig"
-
-src_configure() {
-   econf --bindir="${EPREFIX}"/bin
-}
diff --git a/gentoo/aghermann-1.0.4.ebuild b/gentoo/aghermann-1.0.4.ebuild
deleted file mode 100644
index 2e1b52a..000
--- a/gentoo/aghermann-1.0.4.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="5"
-
-DESCRIPTION="A sleep-research experiment manager, EDF viewer & Achermann's 
Process S model runner"
-HOMEPAGE="http://johnhommer.com/academic/code/aghermann";
-SRC_URI="http://johnhommer.com/academic/code/aghermann/source/${P}.tar.xz";
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/lua:*
-   dev-libs/l

[med-svn] [aghermann] 11/14: update debian/ files for 1.0.7

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 4ea92cc2f867bef035e48b75cd365f50691b570f
Author: Andrei Zavada 
Date:   Sat Dec 12 00:40:47 2015 +

update debian/ files for 1.0.7
---
 debian/changelog | 4 ++--
 debian/control   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 2a5744c..f1c6785 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,8 @@
 aghermann (1.0.7-1) unstable; urgency=low
 
-  * New upstream version.
+  * New upstream version (Closes: #805746).
 
- -- Andrei Zavada   Sat, 21 Nov 2015 13:33:00 +0200
+ -- Andrei Zavada   Fri, 11 Dec 2015 15:58:00 +
 
 aghermann (1.0.6-1) unstable; urgency=low
 
diff --git a/debian/control b/debian/control
index a783e21..2cd8c80 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Maintainer: Andrei Zavada 
 Build-Depends: debhelper (>= 9), dh-autoreconf,
- autoconf-archive, pkg-config, libgomp1, libconfig++-dev, libgsl0-dev, 
libfftw3-dev,
+ autoconf-archive, pkg-config, libgomp1, libconfig++-dev, libgsl-dev, 
libfftw3-dev,
  libsamplerate0-dev (>= 0.1.7), libgtk-3-dev, libitpp-dev, libunique-3.0-dev, 
libvte-2.91-dev,
  liblua5.2-dev, lua5.2, libxml2-utils
 Standards-Version: 3.9.6

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[med-svn] [aghermann] 08/14: prepare 1.0.7

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository aghermann.

commit 2a0bcf4dfc1a8d9133b85a6fd731d83d613c9e9f
Author: Andrei Zavada 
Date:   Wed Dec 2 01:52:44 2015 +0200

prepare 1.0.7
---
 debian/changelog  |  6 ++
 upstream/ChangeLog|  5 +
 upstream/configure.ac |  2 +-
 upstream/data/ui/mw-dialogs.glade | 16 
 4 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index f4de824..2a5744c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (1.0.7-1) unstable; urgency=low
+
+  * New upstream version.
+
+ -- Andrei Zavada   Sat, 21 Nov 2015 13:33:00 +0200
+
 aghermann (1.0.6-1) unstable; urgency=low
 
   * New upstream version.
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index f32528c..36a2d1f 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,8 @@
+v.1.0.7 (2015-11-21)
+   * Fix: Ensure profile overview timeline is at least 1h long.
+   * Fix: Correctly identify channels by a matching prefix (like
+ "F3-AV"); also rework data structures in libsigfile/channel.*.
+
 v.1.0.6 (2015-08-13)
* Fix: Make widgets reappear on Empty Experiment splash.
 
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 99e0003..dbfe2cd 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-15 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.0.6], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [1.0.7], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/upstream/data/ui/mw-dialogs.glade 
b/upstream/data/ui/mw-dialogs.glade
index 7bef407..f2741e1 100644
--- a/upstream/data/ui/mw-dialogs.glade
+++ b/upstream/data/ui/mw-dialogs.glade
@@ -1534,7 +1534,7 @@
 start
 5
 15
-<b><big><big>Aghermann 1.0.6 
</big></big></b>
+<b><big><big>Aghermann 1.0.7 
</big></big></b>
 <a 
href="http://johnhommer.com/academic/code/aghermann">johnhommer.com/academic/code/aghermann</a>;
 True
 0
@@ -1630,7 +1630,13 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
 5
 10
 10
-<b>v. 1.0.6</b> 
(2015-08-14)
+<b>v. 1.0.7</b> 
(2015-11-21)
+<span font="monospace" size="small">
+   * Fix: Ensure profile overview timeline is at least 1h long.
+   * Fix: Correctly identify channels by a matching prefix (like
+ "F3-AV"); also rework data structures in libsigfile/channel.*.
+</span>
+<b>v. 1.0.6</b> (2015-08-14)
 <span font="monospace" size="small">
* Fix: Make widgets reappear on Empty Experiment splash.
 </span>
@@ -1693,12 +1699,6 @@ With bug reports, open an issue on <a 
href="http://github.com/hmmr/aghermann/
* Misc: Separate upstream tree from distribution-related files.
* Misc: Do away with aghermann/**/liba.a files.
 </span>
-<b>v. 0.9.1.1</b> (2013-07-24)
-<span font="monospace" size="small">
-   * Fix 32-bit builds where sizeof(size_t) != sizeof(unsigned long).
-   * MW: take care to recalculate profile drawing area width
- on Shift+Scroll.
-</span>
 
 (for older entries, see <a 
href="http://johnhommer.com/academic/code/aghermann">full 
changelog</a>)
 True

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[med-svn] [aghermann] branch WIP updated (6b6d19c -> 76dcfc9)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository aghermann.

  from  6b6d19c   make dist-orig-xz for bare-autoconf, debian-friendly 
tarball
   new  abdc0ee   make widgets reappear on Empty Experiment splash
   new  8ec0ccf   Merge branch 'WIP' of github.com:hmmr/aghermann into WIP
   new  21b157e   prepare for 1.0.6
   new  af4068b   tweak .gitignore
   new  3987b71   retract "Closes: #794703" from debina/changelog
   new  014de4b   refactor sigfile:: definitions wrt types & channel 
classification
   new  c580fb2   ensure there is at least one hour in overview profile
   new  2a0bcf4   prepare 1.0.7
   new  0dc94a3   build with gsl-2.0 if found, supporting gsl-1.6
   new  7f947e0   whitespace touch up; remove emacs vars
   new  4ea92cc   update debian/ files for 1.0.7
   new  47d4282   gentoo: one last update, further changes to be done in 
gh/gentoo-science
   new  356b03d   remove some dead, c++17-incorrect code
   new  76dcfc9   prepare 1.0.8

The 14 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:
 .gitignore |   2 -
 debian/changelog   |  18 ++
 debian/control |   2 +-
 debian/copyright   |   2 +-
 gentoo/ChangeLog   |  11 +-
 gentoo/README  |   3 +
 gentoo/aghermann-1.0.3-r1.ebuild   |  30 
 gentoo/aghermann-1.0.3.ebuild  |  30 
 gentoo/aghermann-1.0.4.ebuild  |  30 
 gentoo/aghermann.ebuild|  29 ++-
 upstream/.gitignore|   2 +
 upstream/ChangeLog |  13 ++
 upstream/configure.ac  |  10 +-
 upstream/data/ui/mw-dialogs.glade  |  25 ++-
 upstream/src/aghermann/artifact-detection/3in1.cc  |  17 +-
 upstream/src/aghermann/artifact-detection/3in1.hh  |   6 -
 .../aghermann/artifact-detection/forward-decls.hh  |   7 -
 upstream/src/aghermann/expdesign/dirlevel.cc   |   8 -
 upstream/src/aghermann/expdesign/dirlevel.hh   |   7 -
 upstream/src/aghermann/expdesign/expdesign.cc  |  13 +-
 upstream/src/aghermann/expdesign/expdesign.hh  |   9 +-
 upstream/src/aghermann/expdesign/forward-decls.hh  |   7 -
 upstream/src/aghermann/expdesign/loadsave.cc   |   8 -
 upstream/src/aghermann/expdesign/profile.hh|   9 -
 upstream/src/aghermann/expdesign/recording.cc  |   8 -
 upstream/src/aghermann/expdesign/recording.hh  |  11 +-
 upstream/src/aghermann/expdesign/subject.cc|  10 --
 upstream/src/aghermann/expdesign/subject.hh|   9 +-
 upstream/src/aghermann/expdesign/tree-scanner.cc   |  11 +-
 upstream/src/aghermann/globals.cc  |   9 -
 upstream/src/aghermann/globals.hh  |   7 -
 upstream/src/aghermann/ica/forward-decls.hh|   7 -
 upstream/src/aghermann/ica/ica.hh  |   8 -
 upstream/src/aghermann/main.cc |   7 -
 upstream/src/aghermann/model/achermann-siman.cc|  10 --
 upstream/src/aghermann/model/achermann-tunable.cc  |   8 -
 upstream/src/aghermann/model/achermann-tunable.hh  |   7 -
 upstream/src/aghermann/model/achermann.cc  | 102 +--
 upstream/src/aghermann/model/achermann.hh  |   7 -
 upstream/src/aghermann/model/beersma.hh|  15 +-
 upstream/src/aghermann/model/borbely.cc|  58 +++---
 upstream/src/aghermann/model/forward-decls.hh  |   7 -
 upstream/src/aghermann/model/ultradian-cycle.cc|   8 -
 upstream/src/aghermann/patterns/forward-decls.hh   |   8 -
 upstream/src/aghermann/patterns/patterns.cc|  21 ++-
 upstream/src/aghermann/patterns/patterns.hh|   8 -
 upstream/src/aghermann/patterns/patterns.ii|  19 +-
 upstream/src/aghermann/print_version.cc|   7 -
 upstream/src/aghermann/rk1968/rk1968-profiles.cc   |  10 --
 upstream/src/aghermann/rk1968/rk1968.cc|  11 +-
 upstream/src/aghermann/rk1968/rk1968.hh|   7 -
 .../src/aghermann/ui/dirlevel-storable-adapter.hh  |   8 -
 .../src/aghermann/ui/dirlevel-storable-adapter.ii  |   6 -
 upstream/src/aghermann/ui/forward-decls.hh |   9 +-
 upstream/src/aghermann/ui/globals.cc   |   9 -
 upstream/src/aghermann/ui/globals.hh   |   7 -
 upstream/src/aghermann/ui/mf/construct.cc  |   8 -
 upstream/src/aghermann/ui/mf/mf.cc |  12 --
 upstream/src/aghermann/ui/mf/mf.hh |   9 +-
 upstream/src/aghermann/ui/mf/mf_cb.cc  |   7

[med-svn] [cnrun] branch WIP updated (b4896c9 -> 4527d2c)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  b4896c9   debian/control: fix Vsc-Git URL again
   new  4527d2c   debian/control: fix Vsc-Git URL again

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/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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[med-svn] [cnrun] branch master updated (b4896c9 -> 4527d2c)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository cnrun.

  from  b4896c9   debian/control: fix Vsc-Git URL again
   new  4527d2c   debian/control: fix Vsc-Git URL again

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/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 4527d2cb3a656e7167c41506ac4296b8b4a876e5
Author: Andrei Zavada 
Date:   Sat Jan 30 19:48:29 2016 +0200

debian/control: fix Vsc-Git URL again
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 795d65d..7eb9abe 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 9), dh-autoreconf, 
autoconf-archive, texinfo,
  liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
 Standards-Version: 3.9.6
 Homepage: http://johnhommer.com/academic/code/cnrun
-Vcs-Git: 
ssh://hmmr-gu...@cnrun.alioth.debian.org/~hmmr-guest/public_git/cnrun.git
+Vcs-Git: git://anonscm.debian.org/debian-med/cnrun.git
 Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/cnrun.git/
 
 Package: libcnrun2

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[med-svn] [cnrun] branch WIP updated (2b66b34 -> b4896c9)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  2b66b34   gentoo: one last update before moving to gh/gentoo-science
  adds  79abd17   prepare 2.0.3
  adds  fe11239   debian: build with gsl-2.0
  adds  833a1b4   Merge branch 'WIP'
  adds  6576c33   debian/control: fix Vsc-Git URL
  adds  b4896c9   debian/control: fix Vsc-Git URL again

No new revisions were added by this update.

Summary of changes:
 debian/control | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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[med-svn] [cnrun] branch master updated (6576c33 -> b4896c9)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository cnrun.

  from  6576c33   debian/control: fix Vsc-Git URL
   new  b4896c9   debian/control: fix Vsc-Git URL again

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/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository cnrun.

commit b4896c9ecebea8ced2c5b38c1c64ab0be8c8bc4d
Author: Andrei Zavada 
Date:   Sat Jan 30 19:32:04 2016 +0200

debian/control: fix Vsc-Git URL again
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 53d0bbe..795d65d 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 9), dh-autoreconf, 
autoconf-archive, texinfo,
 Standards-Version: 3.9.6
 Homepage: http://johnhommer.com/academic/code/cnrun
 Vcs-Git: 
ssh://hmmr-gu...@cnrun.alioth.debian.org/~hmmr-guest/public_git/cnrun.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/cnrun.git;a=summary
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/cnrun.git/
 
 Package: libcnrun2
 Architecture: any

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[med-svn] [cnrun] 10/11: debian: build with gsl-2.0

2016-01-30 Thread andrei zavada

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hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 1b10753bb46f8e5a1e483f928240fbed8e1f4862
Author: Andrei Zavada 
Date:   Tue Jan 12 05:22:10 2016 +0200

debian: build with gsl-2.0
---
 debian/changelog | 5 +++--
 debian/control   | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 33f3493..e4e2b2a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-cnrun (2.0.2-1) experimental; urgency=low
+cnrun (2.0.3-1) experimental; urgency=low
 
   * Build with gsl-2.0 (Closes: #807190).
+  * New upstream version (skipping the buggy 2.0.2).
 
- -- Andrei Zavada   Sun, 03 Jan 2016 18:07:00 +0200
+ -- Andrei Zavada   Tue, 12 Jan 2016 05:20:00 +0200
 
 cnrun (2.0.1-1) experimental; urgency=low
 
diff --git a/debian/control b/debian/control
index 3833e5e..3f55315 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Maintainer: Andrei Zavada 
 Build-Depends: debhelper (>= 9), dh-autoreconf, autoconf-archive, texinfo,
- libgomp1, pkg-config, libgsl-dev, libxml2-dev,
+ libgomp1, pkg-config, libgsl-dev | libgsl0-dev, libxml2-dev,
  liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
 Standards-Version: 3.9.6
 Homepage: http://johnhommer.com/academic/code/cnrun

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[med-svn] [cnrun] 11/11: gentoo: one last update before moving to gh/gentoo-science

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 2b66b3429e2110b4ab523084c25cb614b6733694
Author: Andrei Zavada 
Date:   Thu Jan 21 18:00:04 2016 +0200

gentoo: one last update before moving to gh/gentoo-science
---
 gentoo/ChangeLog| 5 -
 gentoo/README   | 3 +++
 gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} | 8 
 gentoo/cnrun.ebuild | 8 
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/gentoo/ChangeLog b/gentoo/ChangeLog
index e1fc305..b9ec8f9 100644
--- a/gentoo/ChangeLog
+++ b/gentoo/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/cnrun
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Jan 2016; Andrei Zavada  cnrun-2.0.3.ebuild:
+  sci-biology/cnrun: New upstream version
+
   19 Feb 2015; Andrei Zavada  cnrun-2.0.2.ebuild:
   sci-biology/cnrun: initial ebuild, repoman clean
diff --git a/gentoo/README b/gentoo/README
new file mode 100644
index 000..c4aaffe
--- /dev/null
+++ b/gentoo/README
@@ -0,0 +1,3 @@
+Gentoo ebuilds exist separately in the 'gentoo-science' overlay
+(github.com/gentoo-science), under sci-biology.  The files in this
+directory have been last updated in Jan 2016 for upstream version 2.0.3,
diff --git a/gentoo/cnrun.ebuild b/gentoo/cnrun-2.0.3.ebuild
similarity index 68%
copy from gentoo/cnrun.ebuild
copy to gentoo/cnrun-2.0.3.ebuild
index dd02af2..862ce28 100644
--- a/gentoo/cnrun.ebuild
+++ b/gentoo/cnrun-2.0.3.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
 EAPI="5"
 
-DESCRIPTION="A NeuroML-enabled, neuronal network simulator w/ conductance- and 
rate-based HH neurons"
+DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
 HOMEPAGE="http://johnhommer.com/academic/code/cnrun";
 SRC_URI="http://johnhommer.com/academic/code/cnrun/source/${P}.tar.xz";
 
@@ -13,7 +13,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
 RDEPEND="dev-libs/libxml2
-dev-lang/lua
+dev-lang/lua:*
 sci-libs/gsl"
 
 DEPEND="${RDEPEND}"
diff --git a/gentoo/cnrun.ebuild b/gentoo/cnrun.ebuild
index dd02af2..862ce28 100644
--- a/gentoo/cnrun.ebuild
+++ b/gentoo/cnrun.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
 EAPI="5"
 
-DESCRIPTION="A NeuroML-enabled, neuronal network simulator w/ conductance- and 
rate-based HH neurons"
+DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
 HOMEPAGE="http://johnhommer.com/academic/code/cnrun";
 SRC_URI="http://johnhommer.com/academic/code/cnrun/source/${P}.tar.xz";
 
@@ -13,7 +13,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
 RDEPEND="dev-libs/libxml2
-dev-lang/lua
+dev-lang/lua:*
 sci-libs/gsl"
 
 DEPEND="${RDEPEND}"

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[med-svn] [cnrun] 02/04: debian: build with gsl-2.0

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository cnrun.

commit fe112394d8bcd1a802685e55694c0c98fdbe2a6d
Author: Andrei Zavada 
Date:   Tue Jan 12 05:22:10 2016 +0200

debian: build with gsl-2.0
---
 debian/changelog | 5 +++--
 debian/control   | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 33f3493..e4e2b2a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-cnrun (2.0.2-1) experimental; urgency=low
+cnrun (2.0.3-1) experimental; urgency=low
 
   * Build with gsl-2.0 (Closes: #807190).
+  * New upstream version (skipping the buggy 2.0.2).
 
- -- Andrei Zavada   Sun, 03 Jan 2016 18:07:00 +0200
+ -- Andrei Zavada   Tue, 12 Jan 2016 05:20:00 +0200
 
 cnrun (2.0.1-1) experimental; urgency=low
 
diff --git a/debian/control b/debian/control
index 3833e5e..3f55315 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Maintainer: Andrei Zavada 
 Build-Depends: debhelper (>= 9), dh-autoreconf, autoconf-archive, texinfo,
- libgomp1, pkg-config, libgsl-dev, libxml2-dev,
+ libgomp1, pkg-config, libgsl-dev | libgsl0-dev, libxml2-dev,
  liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
 Standards-Version: 3.9.6
 Homepage: http://johnhommer.com/academic/code/cnrun

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[med-svn] [cnrun] 04/04: debian/control: fix Vsc-Git URL

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch master
in repository cnrun.

commit 6576c33876a558061e1090d8c3dd0a4ac861e042
Author: Andrei Zavada 
Date:   Sat Jan 30 17:45:37 2016 +0200

debian/control: fix Vsc-Git URL
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 3f55315..53d0bbe 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 9), dh-autoreconf, 
autoconf-archive, texinfo,
  liblua5.1-dev | liblua5.2-dev, lua5.1 | lua5.2
 Standards-Version: 3.9.6
 Homepage: http://johnhommer.com/academic/code/cnrun
-Vcs-Git: git://anonscm.debian.org/cnrun/cnrun.git
+Vcs-Git: 
ssh://hmmr-gu...@cnrun.alioth.debian.org/~hmmr-guest/public_git/cnrun.git
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/cnrun.git;a=summary
 
 Package: libcnrun2

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[med-svn] [cnrun] 03/04: Merge branch 'WIP'

2016-01-30 Thread andrei zavada

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hmmr-guest pushed a commit to branch master
in repository cnrun.

commit 833a1b4b8319d11ed5f4f9917efc4ccb154dd7fa
Merge: fe11239 2b66b34
Author: Andrei Zavada 
Date:   Thu Jan 21 18:01:23 2016 +0200

Merge branch 'WIP'

 gentoo/ChangeLog| 5 -
 gentoo/README   | 3 +++
 gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} | 8 
 gentoo/cnrun.ebuild | 8 
 upstream/configure.ac   | 2 +-
 5 files changed, 16 insertions(+), 10 deletions(-)

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[med-svn] [cnrun] 07/11: update changelogs

2016-01-30 Thread andrei zavada

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hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 8bf3d6bbc97f28788ab108da99345b08552e2d4e
Author: Andrei Zavada 
Date:   Sun Jan 3 18:44:33 2016 +0200

update changelogs
---
 debian/changelog   | 2 +-
 upstream/ChangeLog | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 71786d4..33f3493 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,7 +2,7 @@ cnrun (2.0.2-1) experimental; urgency=low
 
   * Build with gsl-2.0 (Closes: #807190).
 
- -- Andrei Zavada   Sat, 12 Dec 2015 01:01:00 +
+ -- Andrei Zavada   Sun, 03 Jan 2016 18:07:00 +0200
 
 cnrun (2.0.1-1) experimental; urgency=low
 
diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index 0547e74..a21d0f6 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,4 +1,4 @@
-2015-02-18  andrei zavada  
+2016-01-03  andrei zavada  
* Prepare for gentoo.
* Make tools and lua api docs conditionally.
* Make distcheck clean (forgotten libcnrun/model/sources.hh).

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[med-svn] [cnrun] branch master updated (f02ba53 -> 6576c33)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch master
in repository cnrun.

  from  f02ba53   call it 2.0.2
   new  1340993   suppress a couple of -Wformat warnings
   new  f13f3e6   add a debian-specific target dist-orig-xz
   new  c187ea1   debian/control: build with libgsl-dev
   new  3cbb83b   update year in debian/copyright
   new  7c7c3d9   remove unused script make_version
   new  50608bf   pass --enable-all configure flags from debian/rules to 
build all packages
   new  8bf3d6b   update changelogs
   new  b1fdd3a   fix decimate and putout
   new  79abd17   prepare 2.0.3
   new  fe11239   debian: build with gsl-2.0
   new  2bb5e41   prepare 2.0.3
   new  1b10753   debian: build with gsl-2.0
   new  2b66b34   gentoo: one last update before moving to gh/gentoo-science
   new  833a1b4   Merge branch 'WIP'
   new  6576c33   debian/control: fix Vsc-Git URL

The 15 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/control  |  4 ++--
 debian/copyright|  2 +-
 debian/rules|  3 +++
 debian/unwanted-files   | 26 ---
 gentoo/ChangeLog|  5 -
 gentoo/README   |  3 +++
 gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} |  8 +++
 gentoo/cnrun.ebuild |  8 +++
 upstream/ChangeLog  |  6 +-
 upstream/Makefile.am| 33 +
 upstream/configure.ac   |  2 +-
 upstream/make_version   | 17 ---
 upstream/src/libcnrun/model/struct.cc   |  2 +-
 upstream/src/libcnrun/model/tags.cc | 21 +-
 15 files changed, 78 insertions(+), 69 deletions(-)
 delete mode 100644 debian/unwanted-files
 create mode 100644 gentoo/README
 copy gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} (68%)
 delete mode 100755 upstream/make_version

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[med-svn] [cnrun] 06/11: pass --enable-all configure flags from debian/rules to build all packages

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 50608bfb8c5f320ea8939b65f5a3b0313637fd49
Author: Andrei Zavada 
Date:   Sun Jan 3 18:44:20 2016 +0200

pass --enable-all configure flags from debian/rules to build all packages
---
 debian/rules | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/debian/rules b/debian/rules
index 95f91ee..eea62ba 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,9 @@ DEB_BUILD_OPTIONS = parallel=4
dh $@ --with autoreconf --parallel
 #  dh $@ -plua-cnrun --buildsystem=lua --with lua
 
+override_dh_auto_configure:
+   dh_auto_configure -- --enable-tools --enable-lua-api-docs
+
 # Perhaps I didn't try hard enough, but there was a conflict between
 # upstream's own, independent way to install Lua module as
 # /usr/lib/lua/5.x/cnrun.so, and Debian's recommended, using

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[med-svn] [cnrun] 09/11: prepare 2.0.3

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 2bb5e412b3b99c379f943c6bf21c383a5353cd62
Author: Andrei Zavada 
Date:   Tue Jan 12 05:21:42 2016 +0200

prepare 2.0.3
---
 upstream/ChangeLog| 4 
 upstream/configure.ac | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/upstream/ChangeLog b/upstream/ChangeLog
index a21d0f6..6f20a86 100644
--- a/upstream/ChangeLog
+++ b/upstream/ChangeLog
@@ -1,3 +1,7 @@
+2016-01-12  andrei zavada  
+   * Fix decimate and putout.
+   * Release 2.0.3.
+
 2016-01-03  andrei zavada  
* Prepare for gentoo.
* Make tools and lua api docs conditionally.
diff --git a/upstream/configure.ac b/upstream/configure.ac
index 7d73ce4..d945eb0 100644
--- a/upstream/configure.ac
+++ b/upstream/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-15 Andrei Zavada ])
 
-AC_INIT([cnrun], [2.0.2], [johnhom...@gmail.com])
+AC_INIT([cnrun], [2.0.3], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/libcnrun/model/model.hh])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)

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[med-svn] [cnrun] 02/11: add a debian-specific target dist-orig-xz

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit f13f3e62a8c16a8b67a2fc98f32167b555a69edf
Author: Andrei Zavada 
Date:   Sun Jan 3 17:20:31 2016 +0200

add a debian-specific target dist-orig-xz
---
 debian/unwanted-files | 26 --
 upstream/Makefile.am  | 33 +
 2 files changed, 33 insertions(+), 26 deletions(-)

diff --git a/debian/unwanted-files b/debian/unwanted-files
deleted file mode 100644
index 75788c3..000
--- a/debian/unwanted-files
+++ /dev/null
@@ -1,26 +0,0 @@
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-aclocal.m4
-config.sub
-ltmain.sh
-depcomp
-install-sh
-autogen.sh
-configure
-config.guess
-missing
-
-Makefile.in
-src/Makefile.in
-src/*/Makefile.in
-doc/Makefile.in
-doc/lua-api/mdate-sh
-doc/lua-api/texinfo.tex
-doc/lua-api/Makefile.in
-doc/lua-api/mdate-sh
-doc/lua-api/texinfo.tex
-doc/lua-api/stamp-vti
-doc/lua-api/version.texi
-doc/lua-api/cnrun-lua-api.info
diff --git a/upstream/Makefile.am b/upstream/Makefile.am
index 6d15c4c..98cfaed 100644
--- a/upstream/Makefile.am
+++ b/upstream/Makefile.am
@@ -26,3 +26,36 @@ test:
 LUA_CPATH="./?.so;$$LUA_CPATH" \
 LD_PRELOAD=../../../src/libcnrun/.libs/libcnrun.so.2.0.0:$$LD_PRELOAD \
  lua ../example1.lua; e=$$?; cd $$_cwd && rm -rf _test; exit $$e)
+
+unwanted_files = \
+   m4/libtool.m4 \
+   m4/ltoptions.m4 \
+   m4/ltsugar.m4 \
+   m4/ltversion.m4 \
+   aclocal.m4 \
+   config.sub \
+   ltmain.sh \
+   depcomp \
+   install-sh \
+   autogen.sh \
+   configure \
+   config.guess \
+   missing \
+   Makefile.in \
+   src/Makefile.in \
+   src/*/Makefile.in \
+   doc/Makefile.in \
+   doc/lua-api/mdate-sh \
+   doc/lua-api/texinfo.tex \
+   doc/lua-api/Makefile.in \
+   doc/lua-api/mdate-sh \
+   doc/lua-api/texinfo.tex \
+   doc/lua-api/stamp-vti \
+   doc/lua-api/version.texi \
+   doc/lua-api/cnrun-lua-api.info
+
+dist-orig-xz: distdir
+   -rm -f $(distdir).tar.xz
+   (cd $(distdir) && rm -rf $(unwanted_files))
+   tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c 
>$(PACKAGE)_$(VERSION).orig.tar.xz
+   $(am__post_remove_distdir)

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[med-svn] [cnrun] tag 2.0.2 updated (f02ba53 -> 8bf3d6b)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to tag 2.0.2
in repository cnrun.

*** WARNING: tag 2.0.2 was modified! ***

  from  f02ba53   (commit)
to  8bf3d6b   (commit)
  from  f02ba53   call it 2.0.2
  adds  1340993   suppress a couple of -Wformat warnings
  adds  f13f3e6   add a debian-specific target dist-orig-xz
  adds  c187ea1   debian/control: build with libgsl-dev
  adds  3cbb83b   update year in debian/copyright
  adds  7c7c3d9   remove unused script make_version
  adds  50608bf   pass --enable-all configure flags from debian/rules to 
build all packages
  adds  8bf3d6b   update changelogs

No new revisions were added by this update.

Summary of changes:
 debian/changelog  |  6 ++
 debian/control|  2 +-
 debian/copyright  |  2 +-
 debian/rules  |  3 +++
 debian/unwanted-files | 26 --
 upstream/ChangeLog|  2 +-
 upstream/Makefile.am  | 33 +
 upstream/make_version | 17 -
 upstream/src/libcnrun/model/struct.cc |  2 +-
 9 files changed, 46 insertions(+), 47 deletions(-)
 delete mode 100644 debian/unwanted-files
 delete mode 100755 upstream/make_version

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[med-svn] [cnrun] tag 2.0.3 created (now 2b66b34)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to tag 2.0.3
in repository cnrun.

at  2b66b34   (commit)
No new revisions were added by this update.

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[med-svn] [cnrun] 04/11: update year in debian/copyright

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 3cbb83b2a7502315f1a3e8c168d2b610f6763a97
Author: Andrei Zavada 
Date:   Sun Jan 3 18:23:07 2016 +0200

update year in debian/copyright
---
 debian/copyright | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/copyright b/debian/copyright
index 7eaf1af..3bc97c2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Andrei Zavada 
 Source: http://johnhommer.com/academic/code/cnrun/source/
 
 Files: *
-Copyright: 2008-2014 Andrei Zavada 
+Copyright: 2008-2016 Andrei Zavada 
 License: GPL-2+
 
 Files: src/libcnrun/*.cc

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[med-svn] [cnrun] branch WIP updated (f02ba53 -> 2b66b34)

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a change to branch WIP
in repository cnrun.

  from  f02ba53   call it 2.0.2
   new  1340993   suppress a couple of -Wformat warnings
   new  f13f3e6   add a debian-specific target dist-orig-xz
   new  c187ea1   debian/control: build with libgsl-dev
   new  3cbb83b   update year in debian/copyright
   new  7c7c3d9   remove unused script make_version
   new  50608bf   pass --enable-all configure flags from debian/rules to 
build all packages
   new  8bf3d6b   update changelogs
   new  b1fdd3a   fix decimate and putout
   new  2bb5e41   prepare 2.0.3
   new  1b10753   debian: build with gsl-2.0
   new  2b66b34   gentoo: one last update before moving to gh/gentoo-science

The 11 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/control  |  2 +-
 debian/copyright|  2 +-
 debian/rules|  3 +++
 debian/unwanted-files   | 26 ---
 gentoo/ChangeLog|  5 -
 gentoo/README   |  3 +++
 gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} |  8 +++
 gentoo/cnrun.ebuild |  8 +++
 upstream/ChangeLog  |  6 +-
 upstream/Makefile.am| 33 +
 upstream/configure.ac   |  2 +-
 upstream/make_version   | 17 ---
 upstream/src/libcnrun/model/struct.cc   |  2 +-
 upstream/src/libcnrun/model/tags.cc | 21 +-
 15 files changed, 77 insertions(+), 68 deletions(-)
 delete mode 100644 debian/unwanted-files
 create mode 100644 gentoo/README
 copy gentoo/{cnrun.ebuild => cnrun-2.0.3.ebuild} (68%)
 delete mode 100755 upstream/make_version

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[med-svn] [cnrun] 05/11: remove unused script make_version

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit 7c7c3d920a28f589c9dc526fae193f2db8935da4
Author: Andrei Zavada 
Date:   Sun Jan 3 18:33:49 2016 +0200

remove unused script make_version
---
 upstream/make_version | 17 -
 1 file changed, 17 deletions(-)

diff --git a/upstream/make_version b/upstream/make_version
deleted file mode 100755
index f4fb669..000
--- a/upstream/make_version
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/sh
-
-V=$(git describe --tags)
-if [ $? = 0 ]; then
-   echo $V | awk -F"-" '{ print $1"."$2; }'
-   exit 0
-fi
-
-# if git is not installed or we are building from a tarball smuggled
-# from a git repo, fall back to ./VERSION
-if test -r VERSION; then
-   V=$(http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [cnrun] 08/11: fix decimate and putout

2016-01-30 Thread andrei zavada

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

hmmr-guest pushed a commit to branch WIP
in repository cnrun.

commit b1fdd3a24b49f30d378d221b20bdb76031cdf5d0
Author: Andrei Zavada 
Date:   Tue Jan 12 05:18:28 2016 +0200

fix decimate and putout

* don't delete synapses;
* restart iteration over units after delete.
---
 upstream/src/libcnrun/model/tags.cc | 21 ++---
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/upstream/src/libcnrun/model/tags.cc 
b/upstream/src/libcnrun/model/tags.cc
index 847529d..96b32aa 100644
--- a/upstream/src/libcnrun/model/tags.cc
+++ b/upstream/src/libcnrun/model/tags.cc
@@ -142,21 +142,19 @@ process_putout_tags( const list &ToRemove)
 regex_t RE;
 for ( auto& P : ToRemove ) {
 if (0 != regcomp( &RE, P.pattern.c_str(), REG_EXTENDED | 
REG_NOSUB)) {
-vp( 0,  stderr, "Invalid regexp in 
process_putout_tags: \"%s\"\n", P.pattern.c_str());
+vp( 0, stderr, "Invalid regexp in process_putout_tags: 
\"%s\"\n", P.pattern.c_str());
 continue;
 }
-auto Ui = units.rbegin();
-while ( Ui != units.rend() ) {
-++Ui;
-auto& U = **prev(Ui);
-if ( regexec( &RE, U._label, 0, 0, 0) == 0 ) {
-vp( 2, " (put out unit \"%s\")\n", U._label);
-delete &U;
+repeat:
+for ( auto U : units )
+if ( U->is_neuron() and
+ regexec( &RE, U->_label, 0, 0, 0) == 0 ) {
+delete U;
+vp( 2, " (put out unit \"%s\")\n", U->_label);
 ++count;
+goto repeat;
 }
-}
 }
-
 cull_blind_synapses();
 
 return count;
@@ -179,7 +177,8 @@ process_decimate_tags( const list 
&ToDecimate)
   // collect group
 vector dcmgroup;
 for ( auto& U : units )
-if ( regexec( &RE, U->_label, 0, 0, 0) == 0 )
+if ( U->is_neuron() and
+ regexec( &RE, U->_label, 0, 0, 0) == 0 )
 dcmgroup.push_back( U);
 random_shuffle( dcmgroup.begin(), dcmgroup.end());
 

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