September 2014 Commit Log

Number of Commits:
50
Number of Active Developers:
2
epruesse 2014-09-30 15:40 Rev.: 12976

don't use -Wl,-no-inhibit-exec on Darwin (clang doesn't need/understand this)

6 lines of code changed in 1 file:

epruesse 2014-09-30 14:28 Rev.: 12975

rewrote parsimony combine loop to be vectorizable by gcc
speedup through use of SSE instructions should be on the order of 2x-4x

85 lines of code changed in 1 file:

westram 2014-09-30 13:24 Rev.: 12973


* [12967] got reverted by 'make proto'. fixed.

61 lines of code changed in 10 files:

epruesse 2014-09-30 12:59 Rev.: 12972

add -Wl,-noinhibit-exec flag to make launchpad binutils continue to build ARB
(this should be removed once the "overlapping FDEs" error new new binutils
detect has been fixed)

6 lines of code changed in 1 file:

epruesse 2014-09-30 11:08 Rev.: 12970

(performance) use filteredpos to alignment pos table to pick bases from alignment for
un-bootstrapped parsimony instead of scanning the entire alignment. speeds up set up
time a lot.

7 lines of code changed in 1 file:

epruesse 2014-09-30 11:02 Rev.: 12969

use arb_alloc_aligned to allocate seq_pars char*

7 lines of code changed in 1 file:

epruesse 2014-09-30 10:45 Rev.: 12968

- cheat around using array if filter is unweighted (i.e. all = 1)
- use aligned memory for weights
- add function to access this directly (for vectorized access)

24 lines of code changed in 2 files:

epruesse 2014-09-30 10:44 Rev.: 12967

add arb_alloc_alligned(someptr, num_elements)
- allocates num_elements into someptr aligned to 16 byte boundary
- exports error if posix_memalign fails

17 lines of code changed in 2 files:

westram 2014-09-29 18:27 Rev.: 12963


* ~~re-enable TEST_open_socket in jenkins~~
- ~~i do not really believe [12962] fixes anything, but who knows..~~
- ~~revert again if unittest keeps failing~~

(reverted by [12981])

0 lines of code changed in 1 file:

westram 2014-09-29 18:25 Rev.: 12962


* arb_open_unix_socket/arb_open_tcp_socket:
- one exit point
- after a call to {{{socket()}}} has succeeded, close socket (and set 'fd' to -1) on further errors (e.g. failing {{{connect()}}})
- postcondition: if NULL is returned, caller is responsible to close the socket
* close socket in {{{echo_server()}}}

126 lines of code changed in 1 file:

westram 2014-09-29 17:37 Rev.: 12961


- stuff leak in arb_shell_expand

21 lines of code changed in 1 file:

westram 2014-09-24 17:51 Rev.: 12936


* remove artificial stack-limit (500000 pushs)
- no idea what this was good for - maybe only to detect infinite loops or similar
- fixes #608

2 lines of code changed in 2 files:

westram 2014-09-23 14:05 Rev.: 12931


* fix label ('#...' means gfx)

1 lines of code changed in 1 file:

westram 2014-09-23 13:59 Rev.: 12930


* sync behavior with gtk
- allow gfx-labels before input- and text-fields
- force text in option menus
* fail assertion if gfx used for option-menu-label (afaik unused; can't use in motif)

12 lines of code changed in 1 file:

westram 2014-09-23 12:19 Rev.: 12928


* clone AW_IS_IMAGEREF from gtk (and replace hardcoded tests)

15 lines of code changed in 4 files:

westram 2014-09-23 11:10 Rev.: 12926


* remove {{{at_set_min_size()}}} (unused)
* remove last (external) call to {{{set_window_size()}}} (from GDE; already implicitely called via {{{load_xfig}}} just above)
* sync in {{{load_xfig}}}
* mark more functions of AW_window as local (IN_ARB_WINDOW)

15 lines of code changed in 4 files:

westram 2014-09-23 09:14 Rev.: 12925


- mention raxml8 + expand zombies

3 lines of code changed in 1 file:

westram 2014-09-22 15:23 Rev.: 12923


* mark {{{get_at()}}} motif-only

5 lines of code changed in 1 file:

westram 2014-09-22 13:35 Rev.: 12920


* abstract AW_at-storage-classes
- create via factory
- ask window to restore
* again hide aw_at.hxx in WINDOW
* undef {{{get_at()}}} for non-WINDOW users of aw_window.hxx

106 lines of code changed in 13 files:

westram 2014-09-22 10:32 Rev.: 12916


* AW_window
- {{{_at}}} + {{{xfig_data}}} -> private section
- mark read-only section as motif-only

6 lines of code changed in 1 file:

westram 2014-09-22 10:18 Rev.: 12914


* AW_window
- make {{{at_}}} private
- collect motif only functions (make some private)
- collect should-be-private members
- calculate_label_size -> {{{AW_window::calculate_label_size}}} (to access at_)
- use get_at() for rest

48 lines of code changed in 3 files:

westram 2014-09-22 09:40 Rev.: 12912


* sync classes {{{AW_at_size}}}, {{{AW_at_maxsize}}} and {{{AW_at_auto}}} with gtk
- uses refs when passing AW_at
* use get_at() to pass AW_at in global code

67 lines of code changed in 6 files:

westram 2014-09-22 09:18 Rev.: 12910


* add temp. public accessor {{{get_at()}}} to AW_window

6 lines of code changed in 1 file:

westram 2014-09-22 08:59 Rev.: 12908


* aw_at.hxx:
- move AW_at-storage-classes there
- temp. publish and include where needed
- sync with gtk

79 lines of code changed in 11 files:

westram 2014-09-21 15:47 Rev.: 12904


* sync code in AW_at and AW_window (trunk vs gtk; just moves code)

540 lines of code changed in 4 files:

westram 2014-09-20 18:23 Rev.: 12901


* reintegrates 'pars' into 'trunk'
* adds:
- log:branches/pars@12894:12895,12897:12900

40 lines of code changed in 1 file:

westram 2014-09-20 17:33 Rev.: 12898


* merge [12896] from 'pars' into 'trunk'

132 lines of code changed in 13 files:

westram 2014-09-19 14:09 Rev.: 12892


* generally do not link scripts in
- PERL_SCRIPTS/ARBTOOLS/IFTHELP
- PERL_SCRIPTS/ARBTOOLS/TESTS
into bin

12 lines of code changed in 4 files:

westram 2014-09-19 13:34 Rev.: 12891


- do not link manual.pl in $ARBHOME/bin

2 lines of code changed in 1 file:

westram 2014-09-19 13:22 Rev.: 12890


* fix #602
- added manual wrapper for GB_delete

12 lines of code changed in 2 files:

westram 2014-09-19 13:22 Rev.: 12889


* ':' -> '::'

7 lines of code changed in 1 file:

westram 2014-09-19 12:35 Rev.: 12888


* fix #603
- abort all TAs and close all DBs
* in arb-perl death-handler
* on exit (i.e. perl scripts will now abort unclosed TAs - not sure whether they did commit b4)

38 lines of code changed in 6 files:

westram 2014-09-19 09:26 Rev.: 12887


* script to test documented perl-interface vs regression

31 lines of code changed in 1 file:

westram 2014-09-17 13:58 Rev.: 12885


* get rid of TEST_open_socket failures under jenkins

16 lines of code changed in 3 files:

westram 2014-09-17 13:36 Rev.: 12884


* implements #22 ("expand zombies")
- DRYed NT- and PARSIMONY-'collapse/expand'-submenu
* provides 'collapse terminal' to PARSIMONY (missing there)
- merged all helpfiles concerning collapse/expand into one
* fixes missing help for 'collapse terminal'
- added 'expand any color group'
- expand/collapse-callbacks
* renamed
* hide externally unused inside TREEDISP
* other help updates
- zombies -> glossary
- group mode

147 lines of code changed in 21 files:

westram 2014-09-17 12:51 Rev.: 12883


* when SAI groups were defined in DB: opening SAI admin window and clicking on SAI with group crashed (NULL-ptr-deref). fixed.

1 lines of code changed in 1 file:

westram 2014-09-16 19:09 Rev.: 12880


* fix #598 by using a huge default window size
- replaced previously used magics (e.g. 1000 as 'unreachable' window dimension *harhar*)
* AW_xfig: initialize size_x and size_y
* use std::max instead of home-grown

17 lines of code changed in 4 files:

westram 2014-09-16 13:36 Rev.: 12877


* reintegrates 'cluster' into 'trunk'
- implements #259
* adds:
- log:branches/cluster@12869:12876

150 lines of code changed in 5 files:

westram 2014-09-11 13:07 Rev.: 12850


* remove {{{aw_string_selection}}} and related code
* fix signed warnings in {{{new_input_window}}}

10 lines of code changed in 3 files:

westram 2014-09-11 12:27 Rev.: 12848


* reintegrates 'fix' into 'trunk'
- removes calls to {{{aw_string_selection}}} and {{{aw_string_selection2awar}}} (implementing another step for #179)
* adds:
- log:branches/fix@12839:12847

467 lines of code changed in 27 files:

westram 2014-09-04 16:42 Rev.: 12836


- log change (#504)

5 lines of code changed in 1 file:

westram 2014-09-04 16:28 Rev.: 12834


* reintegrates 'fix' into 'trunk'
- fixing #504
* adds:
- log:branches/fix@12806,12812:12818,12820:12822,12828:12833

307 lines of code changed in 13 files:

westram 2014-09-04 16:14 Rev.: 12833


* merge [12811] [12822:12827] from 'fix' into 'trunk'
- separates refactorings done for #504
* adds:
- log:branches/fix@12811,12823:12827

219 lines of code changed in 8 files:

westram 2014-09-04 16:00 Rev.: 12832


* merge [12819] from 'fix' into 'trunk' (probcons update)

7 lines of code changed in 1 file:

westram 2014-09-04 15:59 Rev.: 12831


* merge [12806:12810] from 'fix' into 'trunk'
- eliminates GBT_write_sequence
* adds:
- log:branches/fix@12807:12810

42 lines of code changed in 6 files:

epruesse 2014-09-02 17:44 Rev.: 12816

fix spelling mistake

1 lines of code changed in 1 file:

epruesse 2014-09-02 16:51 Rev.: 12815

fix common typos reported by lintian
- splitted -> split (irregular verb)
- ressources -> resources
- explicitely -> explicitly

33 lines of code changed in 15 files:

epruesse 2014-09-02 16:45 Rev.: 12814

add keywords to arb.desktop file

1 lines of code changed in 1 file:

westram 2014-09-01 14:07 Rev.: 12804


* {{{TEST_EXPECTATION__BROKEN}}} now expects two arguments (WANTED and GOT)
- old behavior available as {{{TEST_EXPECTATION__BROKEN_SIMPLE}}} (and used for bool-alike expectations)

9 lines of code changed in 1 file:

westram 2014-09-01 13:10 Rev.: 12803


* merge from 'alilink' into 'trunk'
* adds:
- log:branches/alilink@12801:12802

94 lines of code changed in 42 files:

August 2014 »

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