[med-svn] [SCM] vegan annotated tag, debian/2.0-7-1, created. debian/2.0-7-1

2013-04-07 Thread Charles Plessy 
The annotated tag, debian/2.0-7-1 has been created
at  4cd4f8fb434926fe6744298c712428f226aa7d12 (tag)
   tagging  0dac5a00cbf95e0ded8959f50e0d4fb11dc5177b (commit)
  replaces  debian/2.0-3-1
 tagged by  Charles Plessy
on  Mon Apr 8 13:24:43 2013 +0900

- Shortlog 
r-cran-vegan (2.0-7-1) unstable; urgency=low

  8136fa9 Imported Upstream version 2.0-7
  049dcc3 No new license not copyright notice in the new upstream release.
  d291a8a Removed obsolete DM-Upload-Allowed field.
  267d818 Normalised VCS URLs following Lintian's standard.
  4601587 Using Debhelper 9.
  45db17d Conforms to Policy 3.9.4.

 -- Charles Plessy   Mon, 08 Apr 2013 13:18:12 +0900
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-END PGP SIGNATURE-

Charles Plessy (15):
  Imported Upstream version 2.0-4
  Merge tag 'upstream/2.0-4'
  Imported Upstream version 2.0-5
  Merge tag 'upstream/2.0-5'
  Imported Upstream version 2.0-6
  Merge tag 'upstream/2.0-6'
  Imported Upstream version 2.0-7
  Merge tag 'upstream/2.0-7'
  No new license not copyright notice in the new upstream release.
  Removed obsolete DM-Upload-Allowed field.
  Normalised VCS URLs following Lintian's standard.
  Using Debhelper 9.
  Conforms to Policy 3.9.4.
  Waiting for the next mirror push to build vegan in a clean chroot.
  r-cran-vegan (2.0-7-1) unstable; urgency=low

---

-- 
Community Ecology Package for R

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[med-svn] [SCM] vegan branch, upload, updated. 83eaddb0ff45a931882dbeed8646825c8c73e2c4

2013-04-07 Thread Charles Plessy 
The following commit has been merged in the upload branch:
commit 83eaddb0ff45a931882dbeed8646825c8c73e2c4
Author: Charles Plessy 
Date:   Mon Apr 8 13:24:23 2013 +0900

r-cran-vegan (2.0-7-1) unstable; urgency=low

  8136fa9 Imported Upstream version 2.0-7
  049dcc3 No new license not copyright notice in the new upstream release.
  d291a8a Removed obsolete DM-Upload-Allowed field.
  267d818 Normalised VCS URLs following Lintian's standard.
  4601587 Using Debhelper 9.
  45db17d Conforms to Policy 3.9.4.

 -- Charles Plessy   Mon, 08 Apr 2013 13:18:12 +0900

diff --git a/changes b/changes
index 1a1a38c..c9766bf 100644
--- a/changes
+++ b/changes
@@ -2,11 +2,11 @@
 Hash: SHA256
 
 Format: 1.8
-Date: Mon, 19 Mar 2012 13:12:23 +0900
+Date: Mon, 08 Apr 2013 13:18:12 +0900
 Source: r-cran-vegan
 Binary: r-cran-vegan
 Architecture: source amd64
-Version: 2.0-3-1
+Version: 2.0-7-1
 Distribution: unstable
 Urgency: low
 Maintainer: Debian Med Packaging Team 

@@ -14,39 +14,44 @@ Changed-By: Charles Plessy 
 Description: 
  r-cran-vegan - Community Ecology Package for R
 Changes: 
- r-cran-vegan (2.0-3-1) unstable; urgency=low
+ r-cran-vegan (2.0-7-1) unstable; urgency=low
  .
-   b6a9868 Imported Upstream version 2.0-3
+   8136fa9 Imported Upstream version 2.0-7
+   049dcc3 No new license not copyright notice in the new upstream release.
+   d291a8a Removed obsolete DM-Upload-Allowed field.
+   267d818 Normalised VCS URLs following Lintian's standard.
+   4601587 Using Debhelper 9.
+   45db17d Conforms to Policy 3.9.4.
 Checksums-Sha1: 
- 43d1a0a17b465c03d83f0ec6f7d154f7d54fa240 2022 r-cran-vegan_2.0-3-1.dsc
- 45974bad9f0c869fb85983bdded50c261bfe3a55 1540468 
r-cran-vegan_2.0-3.orig.tar.gz
- 561fad479f1301f7ef68ea7f337477fe75755c13 8322 r-cran-vegan_2.0-3-1.diff.gz
- d675cba4c4559f95fff7aa91ca004f4d703a998f 2167320 
r-cran-vegan_2.0-3-1_amd64.deb
+ ba118366a3c05998cde3aad2de5a22ab2031fe68 2014 r-cran-vegan_2.0-7-1.dsc
+ 92ea9b57b9f97f0b1c9f093bedcd2d1f38046a4d 157 
r-cran-vegan_2.0-7.orig.tar.gz
+ 83280e6a3571264cda0f793eefb790a17ad5caaf 8472 r-cran-vegan_2.0-7-1.diff.gz
+ cb4b9b215fb439945bf45d269f6c2a8aaebefa5c 2217056 
r-cran-vegan_2.0-7-1_amd64.deb
 Checksums-Sha256: 
- 60a37f2c8b340cf98f9ace0f5afc45610cffb23d83f93a9e3d1055e78f7d6ac4 2022 
r-cran-vegan_2.0-3-1.dsc
- fa06df47a9681e4c045dfe55870ec1a10e4c6404150e9b4797f64e05848dd91c 1540468 
r-cran-vegan_2.0-3.orig.tar.gz
- 68a722bf59f9c5ecd6b2bdca7a60faad95748498881b7e69088b2730b5ff5a87 8322 
r-cran-vegan_2.0-3-1.diff.gz
- 8f0c2b8716eb2d58ca4c38a06a36d149de79811fdd6961802fa5a13961151fb9 2167320 
r-cran-vegan_2.0-3-1_amd64.deb
+ 34a5ec49463e344ed35acc232eace7e4da2d7fe37a6428fdc21875bed11eb88f 2014 
r-cran-vegan_2.0-7-1.dsc
+ 28e6587329c08ae22e85b77afaa0fa2d966e33bb57e52eb4b2ade987c32a31eb 157 
r-cran-vegan_2.0-7.orig.tar.gz
+ 1b2266a45879aca517d16e1b6f27377c5a36f50c187cd8224841b0236dda273f 8472 
r-cran-vegan_2.0-7-1.diff.gz
+ df76f3786ca25937e992d2798292cd68396e9b326c8d5a07b161a1120c305471 2217056 
r-cran-vegan_2.0-7-1_amd64.deb
 Files: 
- b3ef3c6b223bb42abd745c4241afc437 2022 gnu-r optional r-cran-vegan_2.0-3-1.dsc
- 0bf54508bd04de611a9f3633d1759cee 1540468 gnu-r optional 
r-cran-vegan_2.0-3.orig.tar.gz
- 223905ebc1a86186507d7fbd09718b63 8322 gnu-r optional 
r-cran-vegan_2.0-3-1.diff.gz
- 3138c0dd0d8677e13560963dc553cc18 2167320 gnu-r optional 
r-cran-vegan_2.0-3-1_amd64.deb
+ 590a95f252207f274f6d044c37d01386 2014 gnu-r optional r-cran-vegan_2.0-7-1.dsc
+ 314bedb7018d09e3f52edc3bb09b9369 157 gnu-r optional 
r-cran-vegan_2.0-7.orig.tar.gz
+ d26d75b9cdad2ddc92a3c41bad9ad64b 8472 gnu-r optional 
r-cran-vegan_2.0-7-1.diff.gz
+ e8340c2b3fc30c7b42b69ec85cf249cb 2217056 gnu-r optional 
r-cran-vegan_2.0-7-1_amd64.deb
 
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+X8zNKnDMOBr1kQpfZcRXXxscK6R1DST1

[med-svn] [SCM] vegan branch, master, updated. debian/2.0-3-1-16-g0dac5a0

2013-04-07 Thread Charles Plessy 
The following commit has been merged in the master branch:
commit 0dac5a00cbf95e0ded8959f50e0d4fb11dc5177b
Author: Charles Plessy 
Date:   Mon Apr 8 13:18:34 2013 +0900

r-cran-vegan (2.0-7-1) unstable; urgency=low

  8136fa9 Imported Upstream version 2.0-7
  049dcc3 No new license not copyright notice in the new upstream release.
  d291a8a Removed obsolete DM-Upload-Allowed field.
  267d818 Normalised VCS URLs following Lintian's standard.
  4601587 Using Debhelper 9.
  45db17d Conforms to Policy 3.9.4.

 -- Charles Plessy   Mon, 08 Apr 2013 13:18:12 +0900

diff --git a/debian/changelog b/debian/changelog
index 942bfcc..e203417 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-r-cran-vegan (2.0-7-1) UNRELEASED; urgency=low
+r-cran-vegan (2.0-7-1) unstable; urgency=low
 
   8136fa9 Imported Upstream version 2.0-7
   049dcc3 No new license not copyright notice in the new upstream release.
@@ -7,7 +7,7 @@ r-cran-vegan (2.0-7-1) UNRELEASED; urgency=low
   4601587 Using Debhelper 9.
   45db17d Conforms to Policy 3.9.4.
 
- -- Charles Plessy   Thu, 04 Apr 2013 14:47:44 +0900
+ -- Charles Plessy   Mon, 08 Apr 2013 13:18:12 +0900
 
 r-cran-vegan (2.0-3-1) unstable; urgency=low
 

-- 
Community Ecology Package for R

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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 65add7a81ffcf60b3e754aadd631a766286c9c6a
Author: Andrei Zavada 
Date:   Sun Apr 7 19:41:47 2013 +0300

make it 0.8.2

diff --git a/ChangeLog b/ChangeLog
index 7054617..67a0ba6 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+v.0.8.2 (2013-04-07)
+   * Fix GtkScrolledWindow issue in Annotations dialog.
+   * Fix those random omp-related freezes on tree rescan.
+   * Make main window busy if profile regeneration needs to happen.
+   * URL fix for SWU page on jh.com/aghermann.
+   * Enable subject sort.
+
 v.0.8.1 (2013-02-24)
* Calculate SWU metric over time.
* SF: ensure signal line remains visible at high page sizes.
diff --git a/configure.ac b/configure.ac
index 1303bf0..994fa72 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-13 Andrei Zavada ])
 
-AC_INIT([Aghermann], [0.8.2_rc], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [0.8.2], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade
index b6e91ea..f733630 100644
--- a/data/mw-dialogs.glade
+++ b/data/mw-dialogs.glade
@@ -1,19 +1,6 @@
 
 
   
-  
-80
-1.5
-0.25
-10
-  
-  
-0.01
-5
-0.5
-0.25
-1
-  
   
 1
 100
@@ -28,6 +15,19 @@
 0.25
 1
   
+  
+80
+1.5
+0.25
+10
+  
+  
+0.01
+5
+0.5
+0.25
+1
+  
   
 5
 300
@@ -328,7 +328,8 @@
 0
 5
 15
-Aghermann 0.8.2 
rcjohnhommer.com/academic/code/aghermann;
+Aghermann 0.8.2  
MacBaren 
+johnhommer.com/academic/code/aghermann;
 True
   
   
@@ -423,7 +424,16 @@ With bug reports, either send yours to 
+   * Fix GtkScrolledWindow issue in Annotations dialog.
+   * Fix those random omp-related freezes on tree rescan.
+   * Make main window busy if profile regeneration
+ needs to happen.
+   * URL fix for SWU page on jh.com/aghermann.
+   * Enable subject sort.
+
+v. 0.8.1 (2013-02-24)
 
* Calculate SWU metric over time.
* SF: ensure signal line remains visible at high page
@@ -431,31 +441,6 @@ With bug reports, either send yours to 
-   * edfcat: proper handling of overshooting signal
- portions.
-   * SF: mark flat signal portions as artifacts.
-   * Fix envelope function.
-   * Fix dzcdf function.
-   * SF: reingeneered Patterns/Find dialog:
- o use band-pass for target frequency matching;
- o system, user, experiment and subject-wide patterns:
- o obtain match index once, for instantaneous finding
-   against variable criteria;
- o mark matches as annotations, incl. as phasic events
-  such as spikes;
-   * Differentiate and make use of subject full/short name.
-   * SF: Ensure all annotations are shown (some inserted in
- non-linear order were dropped).
-   * Clamp MC metric to 0 to prevent occasional negative
- values spoil the profile plot.
-   * SF: Alt+1..9 to pop up channel menu.
-   * Fix many crashes when subjects have exclusive sets
- of channels.
-   * Various smaller fixes.
-
-
 (for older entries, see full 
changelog)
 True
 True
diff --git a/debian/changelog b/debian/changelog
index 6da5f76..80ee514 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+aghermann (0.8.2-1) experimental; urgency=low
+
+  * New upstream version.
+
+ -- Andrei Zavada   Sun, 07 Apr 2013 19:21:16 +0200
+
 aghermann (0.8.1-1) experimental; urgency=low
 
   * New upstream version.

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 5655b46a99d4b91f21a68f237b9eb5c00ec42d11
Author: Andrei Zavada 
Date:   Sun Apr 7 18:58:24 2013 +0300

subject sorting in main window

diff --git a/data/mw.glade b/data/mw.glade
index f475474..830bc3c 100644
--- a/data/mw.glade
+++ b/data/mw.glade
@@ -1,6 +1,12 @@
 
 
   
+  
+1
+0.94996
+0.01
+0.10001
+  
   
 True
 False
@@ -81,12 +87,6 @@
 False
 reload
   
-  
-1
-0.94996
-0.01
-0.10001
-  
   
 6
 10
@@ -711,6 +711,83 @@ rm */*/*/.*.{psd,mc,swu}
   
 
 
+  
+True
+False
+Subject _order
+True
+
+  
+True
+False
+
+  
+True
+False
+_Name
+True
+True
+True
+  
+
+
+  
+True
+False
+_Age
+True
+True
+iExpSubjectSortName
+  
+
+
+  
+True
+False
+Ad_mission date
+True
+True
+iExpSubjectSortName
+  
+
+
+  
+True
+False
+Average _profile power
+True
+True
+iExpSubjectSortName
+  
+
+
+  
+True
+False
+  
+
+
+  
+True
+False
+A_scending
+True
+True
+  
+
+
+  
+True
+False
+S_egregate by gender
+True
+  
+
+  
+
+  
+
+
   
 True
 False
diff --git a/src/ui/mw/construct.cc b/src/ui/mw/construct.cc
index f5e6f67..72d2658 100644
--- a/src/ui/mw/construct.cc
+++ b/src/ui/mw/construct.cc
@@ -96,6 +96,12 @@ SExpDesignUIWidgets

[med-svn] [SCM] aghermann tag, 0.8.2, created. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The tag, 0.8.2 has been created
at  65add7a81ffcf60b3e754aadd631a766286c9c6a (commit)

- Shortlog 
commit 65add7a81ffcf60b3e754aadd631a766286c9c6a
Author: Andrei Zavada 
Date:   Sun Apr 7 19:41:47 2013 +0300

make it 0.8.2
---

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit ff010d9f838af38e00e2e8b9dea1b3bbe3936c25
Author: Andrei Zavada 
Date:   Sun Apr 7 12:05:47 2013 +0300

leave __buf__ alone in sb_main_progress_indicator

diff --git a/src/ui/mw/mw.cc b/src/ui/mw/mw.cc
index 7236242..5af78bd 100644
--- a/src/ui/mw/mw.cc
+++ b/src/ui/mw/mw.cc
@@ -552,8 +552,9 @@ void
 aghui::SExpDesignUI::
 sb_main_progress_indicator( const char* current, size_t n, size_t i, 
aghui::TGtkRefreshMode mode)
 {
-   snprintf_buf( "(%zu of %zu) %s", i, n, current);
-   sb_message( __buf__);
+   DEF_UNIQUE_CHARP (b);
+   ASPRINTF( &b, "(%zu of %zu) %s", i, n, current);
+   sb_message( b);
 
switch ( mode ) {
case TGtkRefreshMode::gtk:

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit e10ecb6fc0128baf8fdce3e8a7f5b038a60ff36c
Author: Andrei Zavada 
Date:   Sun Apr 7 18:57:25 2013 +0300

more accurate messages in main window status bar

diff --git a/src/ui/mw/mainmenu_cb.cc b/src/ui/mw/mainmenu_cb.cc
index 805a47e..425bc66 100644
--- a/src/ui/mw/mainmenu_cb.cc
+++ b/src/ui/mw/mainmenu_cb.cc
@@ -123,16 +123,15 @@ iExpBasicSADetectUltradianCycles_activate_cb( 
GtkMenuItem*, gpointer userdata)
   size_t i, size_t n)
{
snprintf_buf(
-   "(%zu of %zu) %s/%s/%s", i, n,
+   "Detect ultradian cycle %s/%s/%s",
ED.ED->group_of(J), J.short_name.c_str(), E.name());
-   ED.sb_message( __buf__);
+   ED.sb_main_progress_indicator( __buf__, n, i, 
TGtkRefreshMode::gtk);
gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
-   gdk_window_process_updates(
-   gtk_widget_get_parent_window( 
(GtkWidget*)ED.cMeasurements),
-   TRUE);
};
 
ED.ED->for_all_episodes( F, reporter, filter);
+
+   ED.sb_clear();
 }
 
 
@@ -181,10 +180,9 @@ iExpGloballyDetectArtifacts_activate_cb( GtkMenuItem*, 
gpointer userdata)
 size_t i, size_t total)
{
snprintf_buf(
-   "(%zu of %zu) Detect artifacts in 
%s/%s/%s/%s:%s", i, total,
+   "Detect artifacts in %s/%s/%s/%s:%s",
ED.ED->group_of(J), J.short_name.c_str(), 
D.c_str(), E.name(), R.F().channel_by_id(R.h()));
-   ED.sb_message( __buf__);
-   gtk_flush();
+   ED.sb_main_progress_indicator( __buf__, total, i, 
TGtkRefreshMode::gtk);
};
switch ( response ) {
case GTK_RESPONSE_OK:
@@ -235,6 +233,7 @@ iExpGloballyDetectArtifacts_activate_cb( GtkMenuItem*, 
gpointer userdata)
bbl.push_front( new aghui::SBusyBlock (SFp->wSF));
 
ED.ED -> for_all_recordings( op, reporter, filter);
+   ED.sb_clear();
 
for ( auto& SF : ED.open_scoring_facilities ) {
for ( auto& H : SF->channels )

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit f977748f09627e001c43630a4932eb4dff19f70c
Author: Andrei Zavada 
Date:   Sun Apr 7 11:38:22 2013 +0300

cosmetic strings touchup

diff --git a/data/mw.glade b/data/mw.glade
index 620945a..f475474 100644
--- a/data/mw.glade
+++ b/data/mw.glade
@@ -887,7 +887,7 @@ rm */*/*/.*.{psd,mc,swu}
 False
 center
 1
-freq range: 
+F: 
 True
   
   
@@ -1002,7 +1002,7 @@ rm */*/*/.*.{psd,mc,swu}
 False
 center
 1
-f0: 
+F0: 
 True
 True
   
@@ -1091,7 +1091,7 @@ rm */*/*/.*.{psd,mc,swu}
 True
 center
 1
-f0: 
+F0: 
 True
 True
   
@@ -7259,6 +7259,12 @@ dragging individual signals with 
Alt.
   
 
+
+  
+
+
+  
+
   
 
 
diff --git a/src/ui/mw/simulations.cc b/src/ui/mw/simulations.cc
index 07d0411..b6af5d2 100644
--- a/src/ui/mw/simulations.cc
+++ b/src/ui/mw/simulations.cc
@@ -110,7 +110,7 @@ populate_2()
-1);
} else {
gtk_tree_store_set( mSimulations, 
&iter_h,
-   1, "(untried — 
click to run)",
+   1, "(untried — 
dbl-click to run)",

msimulations_modref_col, virgin,
-1);
}

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 10a0cc903d32694d7c33dca930ac2e0da0758226
Author: Andrei Zavada 
Date:   Sun Apr 7 11:24:13 2013 +0300

endow on-demand profile recompute with omp goodness

diff --git a/src/ui/mw/mw_cb.cc b/src/ui/mw/mw_cb.cc
index 80c97ca..e3fb4d3 100644
--- a/src/ui/mw/mw_cb.cc
+++ b/src/ui/mw/mw_cb.cc
@@ -126,23 +126,47 @@ eMsmtProfileType_changed_cb( GtkComboBox* b, gpointer 
userdata)
 
auto params = ED.make_active_profile_paramset();
// don't let it throw on insufficiently scored recordings
-   params.req_percent_scored   = 0.;
+   params.req_percent_scored   = 0.;
params.swa_laden_pages_before_SWA_0 = 0u;
 
+   // collect profiles that need to be re-created
aghui::SBusyBlock *bb = nullptr;
+   vector redo_profiles;
for ( auto &G : ED.groups )
for ( auto &J : G )
if ( J.cprofile and J.cprofile->need_compute( params) ) 
{
-   bb = new aghui::SBusyBlock (ED.wMainWindow);
-   goto proceed;
+   if ( !bb )
+   bb = new aghui::SBusyBlock 
(ED.wMainWindow);
+   redo_profiles.push_back( J.cprofile);
}
-proceed:
 
+   size_t global_i = 0;
+#ifdef _OPENMP
+#pragma omp parallel for schedule(guided)
+#endif
+   for ( size_t i = 0; i < redo_profiles.size(); ++i ) {
+#ifdef _OPENMP
+#pragma omp critical
+#endif
+   {
+   auto& P = *redo_profiles[i];
+   ED.sb_main_progress_indicator(
+   (string ("Compute ") + P.subject() + "/" + 
P.session() + "/" + P.channel()).c_str(),
+   redo_profiles.size(), ++global_i,
+   TGtkRefreshMode::gtk);
+   }
+
+   redo_profiles[i]->create_timeline( params);
+   }
+   ED.sb_clear();
+
+   // do it for all the rest (those needing heavy recompute will be 
fetched from cache)
for ( auto &G : ED.groups )
for ( auto &J : G )
if ( J.cprofile )
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 )
ED.calculate_profile_scale();

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit bf74b77edac4a3e346d920a7c7be3518d9128f6c
Author: Andrei Zavada 
Date:   Sun Apr 7 02:46:11 2013 +0300

probe profile regeneration, make main window busy when it needs to happen

diff --git a/src/expdesign/profile.hh b/src/expdesign/profile.hh
index bb27606..0771e9d 100644
--- a/src/expdesign/profile.hh
+++ b/src/expdesign/profile.hh
@@ -36,6 +36,7 @@ class CProfile
create_timeline();
}
void create_timeline();
+   bool need_compute( const SProfileParamSet&);
 
const SProfileParamSet& P() const
{ return *this; }
diff --git a/src/expdesign/recording.cc b/src/expdesign/recording.cc
index ea43687..3a17112 100644
--- a/src/expdesign/recording.cc
+++ b/src/expdesign/recording.cc
@@ -238,6 +238,16 @@ CProfile (CProfile&& rv)
 
 
 
+bool
+agh::CProfile::
+need_compute( const SProfileParamSet& P)
+{
+   for ( auto Mi = _mm_list.begin(); Mi != _mm_list.end(); ++Mi )
+   if ( (*Mi)->need_compute( P) )
+   return true;
+   return false;
+}
+
 
 void
 agh::CProfile::
diff --git a/src/expdesign/recording.hh b/src/expdesign/recording.hh
index e416809..a0997d3 100644
--- a/src/expdesign/recording.hh
+++ b/src/expdesign/recording.hh
@@ -240,6 +240,21 @@ class CRecording {
}
}
 
+   bool
+   need_compute( const SProfileParamSet& P)
+   {
+   switch ( P.metric ) {
+   case metrics::TType::psd:
+   return psd_profile.need_compute();
+   case metrics::TType::swu:
+   return swu_profile.need_compute();
+   case metrics::TType::mc:
+   return mc_profile.need_compute();
+   default:
+   throw runtime_error ("What metric?");
+   }
+   }
+
metrics::psd::CProfile psd_profile;
metrics::swu::CProfile swu_profile;
metrics::mc::CProfile   mc_profile;
diff --git a/src/metrics/page-metrics-base.cc b/src/metrics/page-metrics-base.cc
index 5c5f165..d7aab1a 100644
--- a/src/metrics/page-metrics-base.cc
+++ b/src/metrics/page-metrics-base.cc
@@ -137,6 +137,26 @@ compute( const SPPack& req_params)
return retval;
 }
 
+bool
+metrics::CProfile::
+need_compute( const SPPack& req_params)
+{
+   auto req_signature = _using_F().dirty_signature( _using_sig_no);
+   if ( have_data()
+and req_signature == _signature_when_mirrored
+and Pp.same_as(req_params) )
+   return false;
+
+   auto old_mirror = mirror_fname();
+   Pp.make_same( req_params);
+   _signature_when_mirrored = req_signature;
+   auto new_mirror = mirror_fname();
+
+   bool got_it = (mirror_back( new_mirror) == 0);
+
+   return not got_it;
+}
+
 
 
 int
diff --git a/src/metrics/page-metrics-base.hh b/src/metrics/page-metrics-base.hh
index 4598e9f..2a315d8 100644
--- a/src/metrics/page-metrics-base.hh
+++ b/src/metrics/page-metrics-base.hh
@@ -155,6 +155,12 @@ class CProfile {
{
return compute( Pp);
}
+   bool need_compute( const SPPack&);  // not const because it does 
mirror_back
+   bool need_compute()
+   {
+   return need_compute( Pp);
+   }
+
 
 protected:
virtual int go_compute() = 0;
diff --git a/src/ui/mw/mw_cb.cc b/src/ui/mw/mw_cb.cc
index 142861e..80c97ca 100644
--- a/src/ui/mw/mw_cb.cc
+++ b/src/ui/mw/mw_cb.cc
@@ -124,12 +124,20 @@ eMsmtProfileType_changed_cb( GtkComboBox* b, gpointer 
userdata)
break;
}
 
-// aghui::SBusyBlock bb (ED.wMainWindow);
auto params = ED.make_active_profile_paramset();
// don't let it throw on insufficiently scored recordings
params.req_percent_scored   = 0.;
params.swa_laden_pages_before_SWA_0 = 0u;
 
+   aghui::SBusyBlock *bb = nullptr;
+   for ( auto &G : ED.groups )
+   for ( auto &J : G )
+   if ( J.cprofile and J.cprofile->need_compute( params) ) 
{
+   bb = new aghui::SBusyBlock (ED.wMainWindow);
+   goto proceed;
+   }
+proceed:
+
for ( auto &G : ED.groups )
for ( auto &J : G )
if ( J.cprofile )
@@ -142,6 +150,9 @@ eMsmtProfileType_changed_cb( GtkComboBox* b, gpointer 
userdata)
ED.adjust_op_freq_spinbuttons();
 
gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
+
+   if ( bb )
+   delete bb;
 }
 
 

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 22e14b1791f0bd63e5d1cdb08c4078e7e66ab166
Author: Andrei Zavada 
Date:   Sun Apr 7 00:43:16 2013 +0300

probably fix those random omp-related hangs

diff --git a/src/metrics/psd.cc b/src/metrics/psd.cc
index 3e35b2c..214b479 100644
--- a/src/metrics/psd.cc
+++ b/src/metrics/psd.cc
@@ -164,7 +164,7 @@ go_compute()
static fftw_plan fft_plan = NULL;
static size_t saved_spp = 0;
 #ifdef _OPENMP
-#pragma omp single
+#pragma omp critical
 #endif
{
 // if ( fft_plan == nullptr ) {

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 84e751cae43ebbe8774db05371abbdbd93490e97
Author: Andrei Zavada 
Date:   Sun Apr 7 02:46:34 2013 +0300

remove unnecessary #pragma omp flush

diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc
index 354081d..b1e9d23 100644
--- a/src/expdesign/tree-scanner.cc
+++ b/src/expdesign/tree-scanner.cc
@@ -312,7 +312,6 @@ scan_tree( TMsmtCollectProgressIndicatorFun 
user_progress_fun)
list complete_episode_set = enumerate_episodes();
size_t  n_episodes = complete_episode_set.size();
 
-#pragma omp flush
for ( auto &G : groups )
for ( auto &J : G.second )
startover:

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a

2013-04-07 Thread Andrei Zavada 
The following commit has been merged in the master branch:
commit 9f4f6cd8d9ec51f6d7976fb4f78ecb529427a834
Author: Andrei Zavada 
Date:   Sun Apr 7 00:53:03 2013 +0300

GtkTreeView nests directly in GtkScrolledWindow in wAnnotations

diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade
index 8233f6b..b6e91ea 100644
--- a/data/mw-dialogs.glade
+++ b/data/mw-dialogs.glade
@@ -1546,21 +1546,14 @@ With bug reports, either send yours to [med-svn] [SCM] aghermann branch, master,	updated. 65add7a81ffcf60b3e754aadd631a766286c9c6a



2013-04-07

Thread
Andrei Zavada



The following commit has been merged in the master branch:
commit 431b51057b0205506b075a5fb7307b79de42b515
Author: Andrei Zavada 
Date:   Wed Apr 3 19:26:36 2013 +0300

properly use move()

diff --git a/src/libsigfile/source.cc b/src/libsigfile/source.cc
index c07bedf..37da818 100644
--- a/src/libsigfile/source.cc
+++ b/src/libsigfile/source.cc
@@ -61,7 +61,7 @@ CTypedSource (CTypedSource&& rv)
case TType::ascii:
throw invalid_argument ("Source type 'ascii' not yet 
supported");
case TType::edf:
-   _obj = new CEDFFile( 
static_cast(*(CEDFFile*)rv._obj));
+   _obj = new CEDFFile( move(*(CEDFFile*)rv._obj));
break;
case TType::edfplus:
//_obj = new CEDFPlusFile( *static_cast(rv._obj);

-- 
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[med-svn] r13269 - in trunk/packages: . uc-echo uc-echo/trunk	uc-echo/trunk/debian uc-echo/trunk/debian/patches	uc-echo/trunk/debian/script uc-echo/trunk/debian/source




2013-04-07

Thread
Thorsten Alteholz



Author: alteholz
Date: 2013-04-07 14:33:19 + (Sun, 07 Apr 2013)
New Revision: 13269

Added:
   trunk/packages/uc-echo/
   trunk/packages/uc-echo/trunk/
   trunk/packages/uc-echo/trunk/debian/
   trunk/packages/uc-echo/trunk/debian/changelog
   trunk/packages/uc-echo/trunk/debian/compat
   trunk/packages/uc-echo/trunk/debian/control
   trunk/packages/uc-echo/trunk/debian/copyright
   trunk/packages/uc-echo/trunk/debian/patches/
   trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch
   trunk/packages/uc-echo/trunk/debian/patches/include.patch
   trunk/packages/uc-echo/trunk/debian/patches/series
   trunk/packages/uc-echo/trunk/debian/rules
   trunk/packages/uc-echo/trunk/debian/script/
   trunk/packages/uc-echo/trunk/debian/script/uc-echo
   trunk/packages/uc-echo/trunk/debian/source/
   trunk/packages/uc-echo/trunk/debian/source/format
   trunk/packages/uc-echo/trunk/debian/uc-echo.1
   trunk/packages/uc-echo/trunk/debian/uc-echo.install
   trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides
   trunk/packages/uc-echo/trunk/debian/uc-echo.manpages
   trunk/packages/uc-echo/trunk/debian/watch
Log:
initial version of uc-echo


Property changes on: trunk/packages/uc-echo/trunk/debian
___
Added: mergeWithUpstream
   + 1

Added: trunk/packages/uc-echo/trunk/debian/changelog
===
--- trunk/packages/uc-echo/trunk/debian/changelog   
(rev 0)
+++ trunk/packages/uc-echo/trunk/debian/changelog   2013-04-07 14:33:19 UTC 
(rev 13269)
@@ -0,0 +1,6 @@
+uc-echo (1.12-1) unstable; urgency=low
+
+  * initial version (Closes: #704902)
+
+ -- Thorsten Alteholz   Tue, 12 Mar 2013 18:00:07 +0100
+

Added: trunk/packages/uc-echo/trunk/debian/compat
===
--- trunk/packages/uc-echo/trunk/debian/compat  (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/compat  2013-04-07 14:33:19 UTC (rev 
13269)
@@ -0,0 +1 @@
+9

Added: trunk/packages/uc-echo/trunk/debian/control
===
--- trunk/packages/uc-echo/trunk/debian/control (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/control 2013-04-07 14:33:19 UTC (rev 
13269)
@@ -0,0 +1,25 @@
+Source: uc-echo
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team 

+Uploaders: Thorsten Alteholz 
+Build-Depends: debhelper (>= 9), 
+ python-all-dev (>=2.6),
+ python-scipy, 
+ python-numpy,
+ g++-multilib
+Standards-Version: 3.9.4
+Homepage: http://uc-echo.sourceforge.net/
+Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/uc-echo/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/uc-echo/trunk/
+
+Package: uc-echo
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: error correction algorithm designed for short-reads from NGS
+ ECHO is an error correction algorithm designed for short-reads 
+ from next-generation sequencing platforms such as Illumina's 
+ Genome Analyzer II. The algorithm uses a Bayesian framework to 
+ improve the quality of the reads in a given data set by employing 
+ maximum a posteriori estimation.
+

Added: trunk/packages/uc-echo/trunk/debian/copyright
===
--- trunk/packages/uc-echo/trunk/debian/copyright   
(rev 0)
+++ trunk/packages/uc-echo/trunk/debian/copyright   2013-04-07 14:33:19 UTC 
(rev 13269)
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: uc-echo
+Source:  http://uc-echo.sourceforge.net/
+
+Files: *
+Copyright: 2011, Yun S. Song 
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+ .
+Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (