January 2014 Commit Log

Number of Commits:
35
Number of Active Developers:
2
westram 2014-01-31 14:09 Rev.: 11540


- fix target 'savetest'

14 lines of code changed in 1 file:

epruesse 2014-01-30 22:32 Rev.: 11539

fix assertion failure in probe_struct_global::cleanup() on error during startup
psg.com_so is expected to be null on PT_exit

1 lines of code changed in 1 file:

epruesse 2014-01-30 22:19 Rev.: 11538

fixes PT server never updated/built if MEMORY_TEST evalutes to true

This was originally broken in r9242 by removing the "build_map" entry from
struct build_step[], which changed the meaning of testing for index 1
("s == 1") within the loop. To avoid further similar issues, the loop
is unrolled by this patch as this seems to be an example of DRY not
always being the safest option.

(the patch made it into branches/ptsfix in r9447 and into trunk in r11060)

11 lines of code changed in 1 file:

westram 2014-01-30 19:52 Rev.: 11537


- removed obsolete define

1 lines of code changed in 1 file:

westram 2014-01-30 19:51 Rev.: 11536


- revert [11534] (reactivates [11531])

27 lines of code changed in 1 file:

epruesse 2014-01-30 19:44 Rev.: 11535

remove "RESERVED" keyword from arb_tcp.dat template file

1 lines of code changed in 1 file:

westram 2014-01-30 19:18 Rev.: 11534


- revert [11531] (too see [11533] work)

21 lines of code changed in 1 file:

westram 2014-01-30 19:17 Rev.: 11533


- avoid ARBDB again gets incompatible with SINA compilation (or other configure driven compilations)

116 lines of code changed in 4 files:

westram 2014-01-30 17:27 Rev.: 11531


- use content of !__cplusplus to detect whether compilation uses C++11 language standard
- if used => define (full) Cxx11 for gcc 4.8++; allow to use CONSTEXPR and OVERRIDE starting with 4.7++

(reverted by [11534]; reintroduced by [11536])

27 lines of code changed in 1 file:

westram 2014-01-30 14:00 Rev.: 11529


* use GB_atclose (instead of GB_atexit) to destroy !TreeAwarRegistry
- fixes crash in branch 'gtk_only'
- allow to remove internal hack (ignore_db_callbacks)

3 lines of code changed in 2 files:

westram 2014-01-30 13:15 Rev.: 11527


* do not edit helpfile if adding to archive will fail
* remove manual aw_message indentation (auto done)

6 lines of code changed in 1 file:

westram 2014-01-30 13:07 Rev.: 11526


- typo; all in 1 line

1 lines of code changed in 1 file:

westram 2014-01-30 12:52 Rev.: 11525


* hack to allow users to edit arb helpfiles and easily send them to us

135 lines of code changed in 5 files:

westram 2014-01-29 08:56 Rev.: 11521


* reintegrates 'sai' into 'trunk'
- merges changeset [9689] (already seems to be in trunk, but mergeinfo missing)
* adds:
- log:branches/sai@9639:9685,9688:11520

1 lines of code changed in 1 file:

westram 2014-01-29 08:20 Rev.: 11518


- updated

8 lines of code changed in 1 file:

westram 2014-01-28 17:35 Rev.: 11515


- fix compilation for gcc 4.73++

1 lines of code changed in 1 file:

westram 2014-01-28 17:16 Rev.: 11513


* reintegrates 'dist' into 'trunk'
- implements #457 + #458
* adds:
- log:branches/dist@11501,11503,11506:11512

640 lines of code changed in 27 files:

westram 2014-01-28 17:13 Rev.: 11512


* merge [11502,11504,11505] from 'dist' into 'trunk'
* adds:
- log:branches/dist@11502,11504:11505

206 lines of code changed in 42 files:

westram 2014-01-23 12:29 Rev.: 11493


* fix doxygen issues for WINDOW (see [11492])

4 lines of code changed in 3 files:

westram 2014-01-23 12:28 Rev.: 11492


* fix several doxygen issues (doxygen 1.6.3)
- force macro expansion for IF_ASSERTION_USED
- fixed changed param names
- named some anonymous (nested) structs
- remove/quote several '#' (triggering unknown commands)

21 lines of code changed in 10 files:

westram 2014-01-22 10:59 Rev.: 11491


- checked cluster tool for leaks (only one non-critical leak found)

4 lines of code changed in 1 file:

westram 2014-01-20 16:08 Rev.: 11488


* reintegrates 'tree' into 'trunk'
- implements #417 (multifurcate tree)
- tree display
* adds MULTIFURC MODE
* reordered modes (synchronizes NTREE and PARSIMONY)
- branch analysis
* display number of multifurcations in 'mark long branches'
* display "in-tree-distance" and "per-species-distance"
- added function to toggle '100%' bootstraps
- document bug in GBT_remove_leafs (#452)
* adds:
- log:branches/tree@11425:11487

2196 lines of code changed in 69 files:

westram 2014-01-14 14:47 Rev.: 11472


- further hacking to allow CONSTEXPR and OVERRIDE in headers also used by PERL2ARB (see [10678])

3 lines of code changed in 2 files:

westram 2014-01-14 14:42 Rev.: 11471


- fix compiler warnings

15 lines of code changed in 6 files:

westram 2014-01-10 19:16 Rev.: 11464


- un-dummy-fied transaction (renames only)

136 lines of code changed in 60 files:

westram 2014-01-10 14:01 Rev.: 11461


* get rid of boring warnings in PROBCONS, MrBAYES and FASTTREE

13 lines of code changed in 4 files:

westram 2014-01-10 13:46 Rev.: 11460


* make usage of stabs format configurable via config.makefile

10 lines of code changed in 2 files:

westram 2014-01-09 19:06 Rev.: 11456


- gcc 4.4.7 with DEBUG also affected

2 lines of code changed in 1 file:

westram 2014-01-09 18:52 Rev.: 11455


* use is_nan etc

5 lines of code changed in 3 files:

westram 2014-01-09 18:51 Rev.: 11454


* use is_nan etc
* 'infinite' is now invalid as coordinate or angle

8 lines of code changed in 2 files:

westram 2014-01-09 18:42 Rev.: 11453


- affects only gcc 4.4.3 compiled with DEBUG

2 lines of code changed in 1 file:

westram 2014-01-09 17:40 Rev.: 11452


- gcc 4.3.3 is not affected

1 lines of code changed in 1 file:

westram 2014-01-09 17:31 Rev.: 11451


- added NAN/INF testers

68 lines of code changed in 2 files:

westram 2014-01-04 13:48 Rev.: 11423


* reintegrates 'tree' into 'trunk':
- topology ordering (beautify trees):
* new orders for radial trees
* order tree according to other tree (implements #445)
- tweaked 'Move node info' / 'Compare topology' (implements #450)
* write log entry to tree comment
* verbose output into logfile
* updated help and GUI
* adds:
- log:branches/tree@11403:11422

804 lines of code changed in 31 files:

westram 2014-01-04 13:18 Rev.: 11422


* fixed assertion failure / wrong message in NDEBUG
- when selecting a species in a folded group (with autojump activated)
- introduced in [11380]
* do not report "No species selected" during autojump

15 lines of code changed in 3 files:

December 2013 »

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