October 2013 Commit Log

Number of Commits:
119
Number of Active Developers:
2
westram 2013-10-31 17:52 Rev.: 11012


* misc warnings fixed; others suppressed

6 lines of code changed in 4 files:

westram 2013-10-31 17:51 Rev.: 11011


* remove unused code

0 lines of code changed in 1 file:

westram 2013-10-31 17:51 Rev.: 11010


* useless code commented out
* added an assertion to trigger future inspection

4 lines of code changed in 1 file:

westram 2013-10-31 17:49 Rev.: 11009


* use arb_assert code

15 lines of code changed in 2 files:

westram 2013-10-31 17:46 Rev.: 11008


* omg clang!
- first warns about self assignment
- if self-assignment is removed, it warns about unused parameters, but parameter-names cant be omitted (this is C)

1 lines of code changed in 1 file:

westram 2013-10-31 17:14 Rev.: 11007


* prototype for GBK_terminate differed between arb_core.h and arb_msg.h

30 lines of code changed in 11 files:

westram 2013-10-31 16:29 Rev.: 11006


* fix possible uses of uninitialized values

9 lines of code changed in 2 files:

westram 2013-10-31 16:15 Rev.: 11005


* fixed unused private members reported by clang
* turned off 'unused private members'-warnings (2 of 3 were false positives)

9 lines of code changed in 4 files:

westram 2013-10-31 15:51 Rev.: 11004


* unused parameter warnings

4 lines of code changed in 4 files:

westram 2013-10-31 15:42 Rev.: 11003


* 'struct { private' -> class

7 lines of code changed in 4 files:

westram 2013-10-31 15:40 Rev.: 11002


* 'class { public' -> struct

96 lines of code changed in 38 files:

westram 2013-10-31 15:23 Rev.: 11001


* undo todays clang-inspired bogus-patches concerning char-indices

10 lines of code changed in 5 files:

westram 2013-10-31 15:10 Rev.: 11000


* auto-rename flagfile old->new (to avoid cleaning all checkouts)

24 lines of code changed in 1 file:

westram 2013-10-31 14:59 Rev.: 10999


* disable clang bogus-warnings

9 lines of code changed in 1 file:

westram 2013-10-31 14:21 Rev.: 10998


* cflags were completely unused (untested)

1 lines of code changed in 1 file:

westram 2013-10-31 14:18 Rev.: 10997


* use cflags before cxxflags (where locally modified)

6 lines of code changed in 2 files:

westram 2013-10-31 14:10 Rev.: 10996


* use cflags before cxxflags

80 lines of code changed in 79 files:

westram 2013-10-31 14:01 Rev.: 10995


* fix compiler detection for 'Apple LLVM'

4 lines of code changed in 1 file:

westram 2013-10-31 13:48 Rev.: 10994


* directly use cflags

1 lines of code changed in 1 file:

westram 2013-10-31 13:37 Rev.: 10993


* added detection for gcc vs clang
- separated allowed version for both compilers
- renamed a bunch of gcc-specific make variables
- dumps compiler version output (-dumpversion and --version) to compile log in case of failure

149 lines of code changed in 9 files:

westram 2013-10-31 11:46 Rev.: 10992


* fix misc warnings (char index, extra parens, trap via NULL ptr indirection, ...)

14 lines of code changed in 6 files:

westram 2013-10-31 11:44 Rev.: 10991


- fix struct/class mismatches

18 lines of code changed in 7 files:

westram 2013-10-31 10:49 Rev.: 10989


- renamed AW_device_size::clear and AW_size_tracker::clear
- make clear they are not related to AW_device::clear()
- silence clang warnings about possible wrong overload

9 lines of code changed in 4 files:

westram 2013-10-31 10:45 Rev.: 10988


- remove unused function 'clear_text' from AW_device + AW_device_Xm
(might be unused because overload was broken)

0 lines of code changed in 4 files:

westram 2013-10-31 10:01 Rev.: 10986


- fix char-index warnings

2 lines of code changed in 1 file:

westram 2013-10-31 10:01 Rev.: 10985


- use GBK_terminate instead of provoking trap manually

2 lines of code changed in 1 file:

westram 2013-10-31 09:54 Rev.: 10983


- fix some struct vs class warnings (clang)

7 lines of code changed in 4 files:

westram 2013-10-31 09:53 Rev.: 10982


- remove self-assignments of unused parameters

10 lines of code changed in 2 files:

westram 2013-10-30 17:43 Rev.: 10981


- comment out leftover expectation (failing for clang)

2 lines of code changed in 1 file:

westram 2013-10-30 17:42 Rev.: 10980


- filter out some (harmless) Dwarf Error

3 lines of code changed in 1 file:

westram 2013-10-30 17:38 Rev.: 10979


- fix undefined behavior (called a function with side-effect twice w/o sequence point; caused test-failure with clang on linux)

6 lines of code changed in 1 file:

westram 2013-10-30 16:13 Rev.: 10978


* test code

4 lines of code changed in 1 file:

westram 2013-10-30 16:06 Rev.: 10976


* DRY

1 lines of code changed in 1 file:

westram 2013-10-30 16:04 Rev.: 10975


* fixed wrong include variables (CC-CXX-mix). Harmless since includes do not differ atm

11 lines of code changed in 11 files:

westram 2013-10-30 15:58 Rev.: 10974


* renamed include variables

121 lines of code changed in 88 files:

westram 2013-10-30 15:26 Rev.: 10973


* merge makefile-generation scripts (creating perl-makefile no longer differed between OSX and LINUX)

56 lines of code changed in 5 files:

westram 2013-10-30 14:58 Rev.: 10971


* use compiler settings from ARB-Makefile (A_CXX)

4 lines of code changed in 2 files:

westram 2013-10-30 14:49 Rev.: 10970


* define A_CC and A_CXX at top
* directly pass A_CXX to arb_gcc_version.pl (worksaround make-bug http://savannah.gnu.org/bugs/?10593)

11 lines of code changed in 2 files:

westram 2013-10-30 14:13 Rev.: 10969


* vtable hack is used unconditionally

3 lines of code changed in 1 file:

westram 2013-10-30 13:51 Rev.: 10968


* remove variables GCC and GPP (ARB now expects CC and CXX)

28 lines of code changed in 3 files:

westram 2013-10-30 13:05 Rev.: 10965


* reduce minor differences between trunk and gtk branches

8 lines of code changed in 1 file:

westram 2013-10-30 12:31 Rev.: 10962


* moved some parts of ARB-main-Makefile to make sure all variables
- have been defined before exported
- have been exported before being used (by submakefiles or called scripts)

81 lines of code changed in 1 file:

westram 2013-10-29 13:19 Rev.: 10959


* inlined and eliminated 'CPPLIB'
* instead pass down 'shared_cflags'

8 lines of code changed in 7 files:

westram 2013-10-29 13:16 Rev.: 10958


* another clang "fix" (as [10952] and [10942])

1 lines of code changed in 1 file:

westram 2013-10-29 13:01 Rev.: 10957


* removed ACCLIB (effectively unused)

3 lines of code changed in 4 files:

westram 2013-10-29 12:55 Rev.: 10956


* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

97 lines of code changed in 82 files:

westram 2013-10-29 12:23 Rev.: 10955


- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

182 lines of code changed in 93 files:

westram 2013-10-29 11:43 Rev.: 10954


- document mechanism used by ARB to export variables to submakefiles
- document most important variables

108 lines of code changed in 73 files:

westram 2013-10-29 10:44 Rev.: 10953


* do not depend on '_GLIBCXX_STRING' for definition of inline helper functions (should fix another clang error)

36 lines of code changed in 8 files:

westram 2013-10-28 22:08 Rev.: 10952


- fix another clang "error"

1 lines of code changed in 1 file:

westram 2013-10-28 19:29 Rev.: 10951


* fix cppcheck warnings

13 lines of code changed in 4 files:

westram 2013-10-28 19:09 Rev.: 10950


* fix cppcheck warnings
- renamed enum members hiding variables
- reintroduced suppressions removed in [10946]
- renamed function index()

63 lines of code changed in 4 files:

westram 2013-10-28 18:38 Rev.: 10949


- fix cppcheck warnings

19 lines of code changed in 9 files:

westram 2013-10-28 18:37 Rev.: 10948


- added some missing remake-dependencies

11 lines of code changed in 1 file:

westram 2013-10-28 18:36 Rev.: 10947


- new cppcheck suppressions

2 lines of code changed in 2 files:

westram 2013-10-28 17:39 Rev.: 10946


- remove outdated cppcheck-suppressions

1 lines of code changed in 14 files:

westram 2013-10-28 11:45 Rev.: 10943


- fixes for remake-script

6 lines of code changed in 2 files:

westram 2013-10-28 11:15 Rev.: 10942


- clang complains about the non-constness of a compare-objects operator() with an error (imo a clang-bug)

1 lines of code changed in 1 file:

westram 2013-10-25 14:32 Rev.: 10933


* define ARB_PATH_MAX
- uses PATH_MAX if provided/found
- limits to reasonable range (256-10000)
- use FILENAME_MAX to double check

80 lines of code changed in 8 files:

westram 2013-10-25 13:00 Rev.: 10932


- move misleading typedef away from wrong place

32 lines of code changed in 3 files:

westram 2013-10-25 11:14 Rev.: 10928


* cleaned up targets
- 'realclean' removed
- ensure 'cleanlinks' is only once in dep-chain
* force creation of mafft-links (as already was done for other links)
* declare targets PHONY

39 lines of code changed in 1 file:

westram 2013-10-24 18:46 Rev.: 10926


- elim some magics

32 lines of code changed in 1 file:

westram 2013-10-24 18:33 Rev.: 10925


- completely switched to safe cb interface

62 lines of code changed in 1 file:

westram 2013-10-24 18:12 Rev.: 10923


* examples for popup callback interface [10922]

8 lines of code changed in 1 file:

westram 2013-10-24 18:11 Rev.: 10922


* safer interface for popup callbacks
- allow to pass !CreateWindowCallback directly to AW_window::callback and AW_window::insert_menu_topic
- decl AW_POPUP deprecated (new interface uses private AW_window::popper instead)

24 lines of code changed in 2 files:

westram 2013-10-24 17:53 Rev.: 10921


* !WindowCreatorCallback -> !CreateWindowCallback (as long as it's unused)

54 lines of code changed in 2 files:

westram 2013-10-24 15:32 Rev.: 10920


- doubled unittest timeouts

5 lines of code changed in 1 file:

westram 2013-10-24 09:43 Rev.: 10916


* use AW_POPUP version from gtk-branch
- eliminated pop_up_window from AW_cb

35 lines of code changed in 4 files:

epruesse 2013-10-24 09:06 Rev.: 10915

mark for later check

1 lines of code changed in 1 file:

westram 2013-10-24 08:38 Rev.: 10914


- added full support for mixed const/non-const callback parameters

37 lines of code changed in 2 files:

westram 2013-10-23 16:00 Rev.: 10913


* remove unused deprecated callback interface from aw_window_Xm

0 lines of code changed in 1 file:

westram 2013-10-23 15:52 Rev.: 10911


* hide motif relict inside AW_window

4 lines of code changed in 1 file:

westram 2013-10-23 15:45 Rev.: 10910


* eliminate old interface for
- set_expose_callback
- set_resize_callback
- create_mode
- d_callback

1 lines of code changed in 2 files:

westram 2013-10-23 15:21 Rev.: 10909


* macro id..

1 lines of code changed in 1 file:

westram 2013-10-23 14:43 Rev.: 10907


* use typesafe expose/resize callbacks
* some renames (callbacks in ARB normally have '_cb'-suffix)

32 lines of code changed in 4 files:

westram 2013-10-23 13:46 Rev.: 10906


* typesafed AWT_expose_cb and AWT_resize_cb

36 lines of code changed in 7 files:

westram 2013-10-23 13:44 Rev.: 10905


* remove unusable parameter name

1 lines of code changed in 1 file:

westram 2013-10-23 13:00 Rev.: 10904


* added "UNFIXED" callback builders allowing to hide the fixed argument
- does not really hide the argument, but hides its type
- allows to use one callback as !RootCallback and as !WindowCallback, e.g.
{{{
void fun(UNFIXED, usertype x) {}

usertype val;
makeWindowCallback(fun,val);
makeRootCallback(fun,val);
}}}
- added tests for unfixed callbacks

45 lines of code changed in 2 files:

westram 2013-10-23 12:28 Rev.: 10903


* DRYed comment

0 lines of code changed in 1 file:

westram 2013-10-23 12:02 Rev.: 10902


* elim unused parameter from AWT_expose_cb and AWT_resize_cb

19 lines of code changed in 9 files:

westram 2013-10-23 11:53 Rev.: 10901


* remove useless user parameter from init_devices
- only one caller passing AW_CL(0), which is never used anywhere

20 lines of code changed in 14 files:

westram 2013-10-23 10:39 Rev.: 10900


* enhances [10444]
- updated species information help
- show specific help for "detached" infowindow
- fixed a reference to renamed 'GET' button

53 lines of code changed in 4 files:

westram 2013-10-22 16:29 Rev.: 10892


- fixed deprecated calls to AW_window::set_resize_callback/set_expose_callback

24 lines of code changed in 1 file:

westram 2013-10-22 15:59 Rev.: 10891


- replace deprecated calls to AW_window::create_mode

50 lines of code changed in 6 files:

epruesse 2013-10-22 02:20 Rev.: 10883

tell aww about the changed picture size before updating the folding lines
In Motif, this has no effect. In GTK, it is required because it may cause
a scroll to keep the scroll-position within bounds. Doing this after
calc_bottomRight_folding_dimension would result in double-correction of
top_dim().

(All of this is a mess...)

3 lines of code changed in 1 file:

epruesse 2013-10-21 19:35 Rev.: 10881

~~remove double clear of spacers in editor~~

(reverted by [11074])

7 lines of code changed in 1 file:

westram 2013-10-21 18:25 Rev.: 10877


* eliminate all deprecated callback-installer-calls(!) from WINDOW
- mostly useless work (code only exists in motif version)

74 lines of code changed in 8 files:

westram 2013-10-21 17:30 Rev.: 10875


* use typesafe callbacks

15 lines of code changed in 7 files:

westram 2013-10-21 16:50 Rev.: 10873


* sync with gtk-branch

4 lines of code changed in 2 files:

westram 2013-10-21 16:24 Rev.: 10871


* added non-deprecated flavors of callback-installers (accepting functions w/o AW_CL)
* inlined deprecated wrappers

34 lines of code changed in 6 files:

westram 2013-10-21 13:47 Rev.: 10869


* get rid of format warning

5 lines of code changed in 1 file:

westram 2013-10-21 13:40 Rev.: 10867


* typesafe advice cbs

15 lines of code changed in 7 files:

westram 2013-10-21 13:22 Rev.: 10865


* eliminate AW_POPUP_HELP

1 lines of code changed in 2 files:

westram 2013-10-21 13:16 Rev.: 10863


* replaced usage of untyped AW_POPUP_HELP

167 lines of code changed in 85 files:

westram 2013-10-21 12:58 Rev.: 10861


* added typesafe replacement AW_help_popup (for AW_POPUP_HELP)
- provide tmp compatibility wrapper AW_POPUP_HELP
- added makeHelpCallback (shortcut for {{{makeWindowCallback(AW_help_popup,...)}}})

20 lines of code changed in 8 files:

westram 2013-10-21 11:01 Rev.: 10857


* accept changed rootdir mergeinfo

3 lines of code changed in 1 file:

westram 2013-10-21 10:21 Rev.: 10856


* added typed callbacks to WINDOW interface where still missing
- still used in 'is_.*_callback' (only used WINDOW-internally, already extinct in gtk)
* marked old interface as deprecated (set SHOWTODO=1 in config.makefile to trigger warnings)

42 lines of code changed in 4 files:

epruesse 2013-10-19 02:49 Rev.: 10852

fix changes to EDIT4 NDS settings not always updating (see #381)
ED4_expose_recalculations was needed to pass the new widths around.
ED4_trigger_instant_refresh was needed to get the update time down.
All of those are called by ED4_request_relayout

2 lines of code changed in 1 file:

westram 2013-10-18 13:22 Rev.: 10842


* reintegrates 'help' into 'trunk':
* adds:
- log:branches/help@10647:10841
- log:branches/helptest@10704:10720

2248 lines of code changed in 68 files:

westram 2013-10-18 09:39 Rev.: 10835


* directly build $ARBHOME/bin/muscle
* fixed problematic subdir generation
1. create subdir if needed
2. recall make on target
* moved unused source files out of sight

569 lines of code changed in 7 files:

westram 2013-10-17 12:00 Rev.: 10827


* changed cb-tests back to text-trace (readability)
* added tests for plain-callbacks (functions w/o the fixed argument)

50 lines of code changed in 1 file:

westram 2013-10-09 15:24 Rev.: 10771


* {{{GB_concat_path("/", "file")}}} produces "/file" now (prev: "//file")
* GB_canonical_path no longer fails on nonexistant entries in / (fixes #383)

33 lines of code changed in 1 file:

westram 2013-10-09 11:08 Rev.: 10766


* ARB_textfiles_have_difflines now fails if files differ and one of them is binary
- does not fail if both are binary and identical [sic]

48 lines of code changed in 2 files:

westram 2013-10-09 10:26 Rev.: 10765


* add tests showing broken behavior of ARB_textfiles_have_difflines (always returns true when one of the compared file is a binary file)

19 lines of code changed in 1 file:

westram 2013-10-09 10:07 Rev.: 10764


* renamed file- and mem-cmp-functions
* added parameter 'blockStartAddress' to ARB_test_mem_equal
- use it to show correct file-offset when called from ARB_files_are_equal
* removed unused function files_are_equal()

52 lines of code changed in 6 files:

westram 2013-10-09 09:15 Rev.: 10763


- mark test as slow

1 lines of code changed in 1 file:

epruesse 2013-10-06 11:27 Rev.: 10745

remove use of AW_cb outside of WINDOW (scheduled for removal in gtkport).
this is a hack, I know. I'm open to suggestions.

16 lines of code changed in 5 files:

epruesse 2013-10-05 15:46 Rev.: 10737

- rename menu entries "Distance matrix" and "ARB Neighbor Joining" to
"Distance Matrix + ARB NJ" (both launch arb_dist, so should have the
same name).
- marked species button now shows configurations help (rather than
the nonextistant marked_species.hlp), also has a different action
name (for gtkport action system, same action should have same label,
but the button doesn't)

4 lines of code changed in 1 file:

westram 2013-10-04 08:50 Rev.: 10728


- pack all in UNIT_TESTER/run/help

1 lines of code changed in 1 file:

westram 2013-10-03 13:25 Rev.: 10713


* fix wrong escape code

2 lines of code changed in 1 file:

westram 2013-10-03 13:20 Rev.: 10712


* generated .xml and .hlp both differ by one line (between DEBUG and NDEBUG version)
- ignore difference in NDEBUG mode
* avoid future auto-updates in NDEBUG (would lead to test failures on build server)
* fixed some warnings
* fixed comment for attribute 'edit_warning'

16 lines of code changed in 2 files:

westram 2013-10-03 12:11 Rev.: 10704


- reintegrated branch 'helptest'

1130 lines of code changed in 57 files:

epruesse 2013-10-02 16:52 Rev.: 10696

fix recursive adding of the same CB over and over (did terminate eventually, still)

6 lines of code changed in 1 file:

westram 2013-10-02 13:00 Rev.: 10690


- for some unknown reason calling PHYML-'make install' fails to install the binary under some condition and then even repeated arb-builds do not succeed
- AFAIK this does not happen in clean checkouts (so jenkins did never complain)
- when that happens, do a complete rebuild of PHYML

9 lines of code changed in 1 file:

westram 2013-10-02 11:40 Rev.: 10686


* in gb_make_entry: initialize elements of type GB_STRING with "" (like others are implicitely initialized with 0, 0.0, etc)
* fixes error in merge-tool when running 'Check IDs' w/o changing defaults ({{{ARB ERROR: Expected entry 'ARB_NAME_SERVER_<NONE>' or 'ralf:ARB_NAME_SERVER_<NONE>' in ...}}})

1 lines of code changed in 1 file:

westram 2013-10-01 15:38 Rev.: 10684


* set progress done (needed in error case)

1 lines of code changed in 1 file:

westram 2013-10-01 15:38 Rev.: 10683


* removed macro-ids from two buttons w/o callback

2 lines of code changed in 1 file:

westram 2013-10-01 15:29 Rev.: 10682


* always restart arb_ntree using new ARB_PID [nt_restart]
- fixes "socket ':' in use"-error when quitting merge-tool via 'Quit & start target DB'
* bug was introduced in [10083], originating somewhere around [9873]
- starting arb_ntree [nt_start] is still possible inside current ARB_PID environment
* hack to support debugging (always call arb_launcher with '--async', i.e. "do not block")

24 lines of code changed in 4 files:

westram 2013-10-01 13:38 Rev.: 10681


* use script arb_launcher to launch arb processes
- inside each ARB_PID-environment
* initial call
- opens a named pipe
- starts the command passed via CLI
- listens the pipe, launching new processes
- when all launched processes terminate, the launcher terminates itself
- installs signal handlers for INT, TERM and EXIT
* INT asks whether ARB session shall be terminated
* TERM kills the ARB session (whole process tree)
* EXIT removes the named pipe
* subsequent calls just write launch-requests to the pipe
- when arb_ntree wants to restart itself, it asks arb_launcher to perform that task (synchronously!)
* doing so ensures the initial session stays open until all spawned arb-sub-sessions have terminated
* script 'arb'
- dont use exec for 'arb shell'
- dont use 'sh' use 'bash -i'
- start arb_trace and arb_trace via arb_launcher
- show arb_ntree-help above help for script 'arb'
* should fix #358

236 lines of code changed in 3 files:

September 2013 »

Generated by StatSVN 0.7.0