September 2013 Commit Log

Number of Commits:
52
Number of Active Developers:
2
westram 2013-09-27 18:48 Rev.: 10680


* rewrote arb_clean
- make it more difficult to kill numerous random processes if you have enough old arb_pids in /tmp
- behave proper when there are no arb_pids at all

65 lines of code changed in 4 files:

westram 2013-09-27 14:55 Rev.: 10678


* hack to allow combination of gcc 4.7.3 and perl 5.10.1
- failed compilation due to an incompatibility in XS_VERSION_BOOTCHECK (see also [10566])
- simply removes '-std=gnu++11' for the above combination

16 lines of code changed in 2 files:

westram 2013-09-27 12:17 Rev.: 10677


* fix [10676]
- pid-files are NOT REMOVED when unit-tests succeed
- always remove them (silently)

4 lines of code changed in 1 file:

westram 2013-09-27 12:05 Rev.: 10676


* repair [10672]
- failed when no unittest-pid-files were found
- only attempted to delete pid-files when tests succeeded (in that case they are normally removed)
- added target 'cleanup_faked_arbpids_and_fail' and call it when tests or test-cleanup fails
* ls affected files to buildlog

8 lines of code changed in 1 file:

westram 2013-09-27 11:25 Rev.: 10675


- dump used perl version to build log

1 lines of code changed in 1 file:

westram 2013-09-27 10:34 Rev.: 10674


- revert [10673] - arb has to like gcc 4.7.3 (u1304 system compiler)

3 lines of code changed in 2 files:

westram 2013-09-26 19:55 Rev.: 10673


- ~~disallow gcc 4.7.3 (too broken)~~

(reverted by [10674])

5 lines of code changed in 2 files:

westram 2013-09-26 18:51 Rev.: 10672


- remove /tmp/arb_pids...-files generated by running unit tests (/tmp is full of them)

1 lines of code changed in 1 file:

westram 2013-09-24 14:05 Rev.: 10646


- remove write permission for generated help-files

50 lines of code changed in 4 files:

westram 2013-09-24 13:13 Rev.: 10645


- missing depends for [10629]

5 lines of code changed in 1 file:

epruesse 2013-09-24 12:45 Rev.: 10644

show file name in main window title (fixes #279)

14 lines of code changed in 1 file:

epruesse 2013-09-24 12:20 Rev.: 10643

fix NULL ptr in nt_start_2nd if current file name does not contain slash

3 lines of code changed in 1 file:

epruesse 2013-09-24 12:19 Rev.: 10642

fix GB_find_latest_file showing non-files (directories etc)
- should symlinks be allowed?

3 lines of code changed in 1 file:

epruesse 2013-09-22 18:50 Rev.: 10629

add expert/novice support to GDE -- all items novice for now
expert/novice mode is now configured in GDE menu files for each menu, menuitem
and argument individually. default is AWM_ALL. use "menumask: expert",
"menuitemmask: expert" or "argmask: expert" to limit access to any field.

29 lines of code changed in 3 files:

epruesse 2013-09-20 17:32 Rev.: 10621

limit NGS field length range to 0 - 1,000,000 (fixes #331)
(1mio should suffice even for sequence exports, theoretical
max is probably MAX_INT)

1 lines of code changed in 1 file:

westram 2013-09-20 16:24 Rev.: 10618


* remove some (previously) generated patch-files, if WC unmodified
* ignore two patch-names (using them in emacs)

1 lines of code changed in 1 file:

westram 2013-09-18 15:57 Rev.: 10610


* cleanup: elim DUMP_DATA code (rewrite if needed)

0 lines of code changed in 1 file:

westram 2013-09-18 15:45 Rev.: 10609


* another (more sucessful) attempt to track origin linenumber info

83 lines of code changed in 1 file:

westram 2013-09-18 13:21 Rev.: 10608


* minor (renames,..)

18 lines of code changed in 1 file:

westram 2013-09-18 11:47 Rev.: 10607


* cleaned up handling of warnings
- prefix "Warning: " during output (so errors and warnings can share more code)
- remove preadd_warning (unused)
* fixed lineNrs stores in !ParagraphTree
- they were completely wrong, always pointing to start of top-level section
* test another helpfile

25 lines of code changed in 1 file:

westram 2013-09-18 10:56 Rev.: 10606


* ParagraphTree::format_enums()
- renamed locals
- made !ParagraphTree* const where possible

35 lines of code changed in 1 file:

westram 2013-09-17 17:16 Rev.: 10602


- fix warnings

3 lines of code changed in 2 files:

westram 2013-09-17 17:10 Rev.: 10601


* added missing check for todos (completing [10594])
* renamed one flavor of check_duplicates -> check_specific_duplicates
- removed unused parameter
* rethrow !LineAttachedMessage (fixes error suppressed by [10585])
* avoid warning about location for duplicated inlined link (these are silently accepted since [7767], but the warning was still raised if defined as subtarget, due to an merge error in [7815])

18 lines of code changed in 1 file:

westram 2013-09-17 15:53 Rev.: 10600


* help files triggered by GDE menus
- only helpfiles referenced in first found .menu were expected/generated (found menu was align.menu). broken by [8806]
- added missing generation of phylip.help from phylip.html
- reactivates the following files
{{{
agde_DNAml_rates.hlp
agde_dnaml.hlp
agde_dnaml_sub_AxML_doc.hlp
agde_dnaml_sub_fastDNAml_doc.hlp
agde_dnapars.hlp
agde_lsadt.hlp
agde_phylip.hlp
agde_phylip_distance.hlp
agde_phylip_distance_sub_dnadist_doc.hlp
agde_phylip_distance_sub_fitch_doc.hlp
agde_phylip_distance_sub_kitsch_doc.hlp
agde_phylip_distance_sub_neighbor_doc.hlp
agde_phylip_distance_sub_protdist_doc.hlp
agde_phylip_sub_dnadist_doc.hlp
agde_phylip_sub_fitch_doc.hlp
agde_phylip_sub_kitsch_doc.hlp
agde_phylip_sub_neighbor_doc.hlp
agde_phylip_sub_protdist_doc.hlp
agde_phyml.hlp
agde_proml.hlp
agde_protpars.hlp
agde_readseq.hlp
agde_readseq_sub_Formats.hlp
agde_readseq_sub_Readme.hlp
agde_readseq_sub_Readseq_help.hlp
agde_treepuzzle.hlp
}}}

11 lines of code changed in 2 files:

westram 2013-09-17 15:07 Rev.: 10599


* include unistd.h (ubuntu 13.04 failed to build)

1 lines of code changed in 1 file:

westram 2013-09-17 15:04 Rev.: 10598


* now really only interpret as list if '-' or '*' is followed by '''exactly one''' whitespace
* fixed copyright (formatting issues)

33 lines of code changed in 2 files:

westram 2013-09-17 14:55 Rev.: 10597


* only interpret as list if '-' or '*' is followed by '''exactly one''' whitespace
* fixed affected helpsources

103 lines of code changed in 3 files:

westram 2013-09-17 14:07 Rev.: 10596


* fixed layout (of resulting html output)

42 lines of code changed in 3 files:

westram 2013-09-17 14:07 Rev.: 10595


* only interpret as list if '-' or '*' is followed by whitespace

1 lines of code changed in 1 file:

westram 2013-09-17 13:43 Rev.: 10594


* help unittest
- at start: change to directory HELP_SOURCE
- also perform output (unchecked; just to /dev/null)
* recognize TODOs in comments
* allow '*' as list indicator
* checked and corrected affected help files

91 lines of code changed in 10 files:

westram 2013-09-17 13:40 Rev.: 10593


- recommend trusting your users

2 lines of code changed in 1 file:

westram 2013-09-17 13:29 Rev.: 10589


* no longer use AW_window_message
- will be eliminated in gtk branch
- (Note: behavior changed when clicking X in merge-error-message; dont care)

3 lines of code changed in 1 file:

westram 2013-09-17 11:21 Rev.: 10585


* define magic number
* always wrap exceptions into !LineAttachedMessage
* unknown input file -> error (instead of failing assertion)
* wrap most testcode into expectation function
- added a failing help-compilation

87 lines of code changed in 1 file:

westram 2013-09-13 13:00 Rev.: 10582


- ACI: calling 'command(...)' failed when no item is passed in

1 lines of code changed in 1 file:

westram 2013-09-13 08:53 Rev.: 10579


- renamed icon

34 lines of code changed in 3 files:

westram 2013-09-13 08:43 Rev.: 10578


- mark test as slow

1 lines of code changed in 1 file:

westram 2013-09-12 17:02 Rev.: 10577


- added a bunch of small arb tools into dependency decls

61 lines of code changed in 14 files:

westram 2013-09-11 12:54 Rev.: 10573


* do not create tags for HEADERLIBS, GDE and generated code (reduces size to ~60%)

6 lines of code changed in 1 file:

westram 2013-09-10 10:32 Rev.: 10568


- fix warnings in PERL2ARB (most by removing option '-Weffc++')

8 lines of code changed in 2 files:

westram 2013-09-09 17:08 Rev.: 10566


* pass down $(cppflags) (esp. '-std=gnu++11')
* PERL2ARB/Makefile now depends on ARB main Makefile (has to change if settings change there)

amendment:
* breaks compilation with gcc 4.7.3 and perl 5.10.1 (XS_VERSION_BOOTCHECK does not compile
{{{
ARB.c:10863:5: error: unable to find string literal operator 'operator"" SVf'
}}}
). On ubuntu 13.04 (where 4.7.3 is the system compiler) it works.

3 lines of code changed in 2 files:

westram 2013-09-09 16:33 Rev.: 10565


* make ARB compilation fail if gcc 4.8++ is used, but language is not C++11

6 lines of code changed in 1 file:

westram 2013-09-09 15:58 Rev.: 10564


- fix gcc.4.8++ compilation for RNACMA (clash with boost namespace)

5 lines of code changed in 1 file:

westram 2013-09-09 15:36 Rev.: 10563


- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

247 lines of code changed in 55 files:

westram 2013-09-09 13:07 Rev.: 10560


- fix compile error

1 lines of code changed in 1 file:

westram 2013-09-09 12:41 Rev.: 10559


* added unit test for rename-session
- does not use nameserver (just tests renaming of species and correction of names in trees and configs)

1451 lines of code changed in 3 files:

westram 2013-09-09 12:23 Rev.: 10558


- added species configurations to test DB

23 lines of code changed in 3 files:

westram 2013-09-09 11:55 Rev.: 10557


- rename

20 lines of code changed in 9 files:

westram 2013-09-04 15:51 Rev.: 10542


merge from log:branches/tree@10535:10541
* added rotate subtrees (right-click in SWAP-mode)
* removed some unused code

130 lines of code changed in 8 files:

westram 2013-09-04 11:55 Rev.: 10533


* create MODE infoline in ARB_SECEDIT and ARB_GENE_MAP using macros
* unique description for zoom mode

34 lines of code changed in 6 files:

westram 2013-09-04 11:18 Rev.: 10532


* create MODE infoline (shown at bottom of top area in ARB_NT) using macros
- ensures proper spacing + improves readability

60 lines of code changed in 4 files:

westram 2013-09-04 09:58 Rev.: 10530


* UTF8 -> ASCII

9 lines of code changed in 8 files:

westram 2013-09-02 18:54 Rev.: 10525


* display of zombies was broken by [10494]. fixed.

7 lines of code changed in 2 files:

August 2013 »

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