[med-svn] [aghermann] 23/23: prepare for 1.1.2
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
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
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 20/23: trivial id renames and emendations
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:
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:: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 16/23: prettify stale session lock message
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 09/23: don't forget to update vars to widgets in d/rk1968
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:: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 19/23: sweep up deprecated gtk_ and gdk_ functions
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
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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 18/23: better figure rk1968 window size
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 11/23: undisappear buttons, generally tidy up rk1968.glade
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
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; } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 12/23: correctly anchor menu for Alt+N on SF montage
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
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 13/23: complete e44f65354b
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); } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 06/23: patterns: more accurate sscanf to unbreak load()
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 08/23: don't let current_profile dangle in SDirlevelStorableAdapter::discard_c_p
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); } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 07/23: assignments within declaration broke set_profile_manage_buttons_visibility
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 04/23: icm
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 01/23: handle SIGBUS on unreadable edfs
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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 03/23: avoid passing a non-const ref of thing to be modified
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)
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 The 23 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 05/23: populate: correctly calculate tl_width
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); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 02/23: whitespace and ICM
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() -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (880de88 -> 4c94ec3)
This is an automated email from the git hooks/post-receive script. 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 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 6 ++ debian/control | 5 +++-- 2 files changed, 9 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (880de88 -> 4c94ec3)
This is an automated email from the git hooks/post-receive script. 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 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 6 ++ debian/control | 5 +++-- 2 files changed, 9 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: follow Debian Med policy in debian/control
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] tag 2.1.0 created (now 880de88)
This is an automated email from the git hooks/post-receive script. hmmr-guest pushed a change to tag 2.1.0 in repository cnrun. at 880de88 (commit) No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (9cbeb6b -> 880de88)
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 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 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (9cbeb6b -> 880de88)
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 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 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: fix Build-Depends
This is an automated email from the git hooks/post-receive script. 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 05/05: do any writing in make test in ./_test
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 ( -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (4527d2c -> 9cbeb6b)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 04/05: make it cme-clean
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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/05: implement NML export
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
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
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"); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (86e5810 -> 9cbeb6b)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (feabc20 -> 86e5810)
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 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 +++ 1 file changed, 7 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: update debian/changelog
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). -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 02/02: Merge branch 'WIP' of ssh://git.debian.org/git/debian-med/cnrun into WIP
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/02: debian/*: fix to comply with cme recommendations
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (0321539 -> feabc20)
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 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 | 36 upstream/compile | 2 +- 2 files changed, 25 insertions(+), 13 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (4527d2c -> 0321539)
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 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 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again; bump Standards-Version to 3.9.7
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] tag 1.1.1 created (now 945862e)
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 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] tag 1.1.0 created (now 4ce0f7e)
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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 04/05: commit or no commit?
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 { -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 05/05: don't bother setting or printing built_by
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
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 } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] tag 1.0.9 created (now 1387ab5)
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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 02/05: enable multiple instances, drop libunique; lock sessions in use
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)
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 03/07: add a 'hint' widget on main window
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
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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 01/07: mind your pointers
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 07/07: update changelogs for 1.0.9 again
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"> -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] branch master updated (4ea92cc -> 1387ab5)
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 02/07: prepare 1.0.9
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). -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 04/07: petty whitespace cleanup
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() ) { -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 05/07: don't expect profile scale to be == 0.
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(); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] branch WIP updated (76dcfc9 -> 1387ab5)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 14/14: prepare 1.0.8
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 09/14: build with gsl-2.0 if found, supporting gsl-1.6
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: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 04/14: tweak .gitignore
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/ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 06/14: refactor sigfile:: definitions wrt types & channel classification
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
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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] branch master updated (6b6d19c -> 4ea92cc)
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
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 02/14: Merge branch 'WIP' of github.com:hmmr/aghermann into WIP
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 10/14: whitespace touch up; remove emacs vars
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
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)); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 03/14: prepare for 1.0.6
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 13/14: remove some dead, c++17-incorrect code
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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 12/14: gentoo: one last update, further changes to be done in gh/gentoo-science
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
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] 08/14: prepare 1.0.7
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aghermann.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [aghermann] branch WIP updated (6b6d19c -> 76dcfc9)
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)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (b4896c9 -> 4527d2c)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (2b66b34 -> b4896c9)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (6576c33 -> b4896c9)
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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 01/01: debian/control: fix Vsc-Git URL again
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 10/11: debian: build with gsl-2.0
This is an automated email from the git hooks/post-receive script. 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 11/11: gentoo: one last update before moving to gh/gentoo-science
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}" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 02/04: debian: build with gsl-2.0
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 04/04: debian/control: fix Vsc-Git URL
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 03/04: Merge branch 'WIP'
This is an automated email from the git hooks/post-receive script. 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 07/11: update changelogs
This is an automated email from the git hooks/post-receive script. 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). -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch master updated (f02ba53 -> 6576c33)
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 06/11: pass --enable-all configure flags from debian/rules to build all packages
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 09/11: prepare 2.0.3
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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 02/11: add a debian-specific target dist-orig-xz
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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] tag 2.0.2 updated (f02ba53 -> 8bf3d6b)
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] tag 2.0.3 created (now 2b66b34)
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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 04/11: update year in debian/copyright
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] branch WIP updated (f02ba53 -> 2b66b34)
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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [cnrun] 05/11: remove unused script make_version
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
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()); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit