June 2013 Commit Log

Number of Commits:
42
Number of Active Developers:
3
epruesse 2013-06-27 16:41 Rev.: 10176

Re-enable automatic setting of ARBHOME
(was disabled here
http://bugs.arb-home.de/changeset/9668/branches/gtk_only/SH/arb
not sure why tho)

1 lines of code changed in 1 file:

westram 2013-06-26 13:46 Rev.: 10175


* print full paths for some messages

4 lines of code changed in 2 files:

westram 2013-06-26 12:23 Rev.: 10174


* fix 'arb_edit4 --help'
- previously reported stupid error ("no such DB '--help'")
- failed to show that stupid error since [10083] (caused by [9876] in branch macros2)
* fixed error-display for different init-states (initial, DB loaded, AW_root created)
* show errors on stderr (when no AW_root created)
- exit early if CLI-help has been displayed
- more standard helptext

13 lines of code changed in 1 file:

westram 2013-06-26 11:16 Rev.: 10173


* fix '--help' for arb_ntree and arb_phylo (broken by [9899])

47 lines of code changed in 2 files:

westram 2013-06-20 11:39 Rev.: 10170


* needed_libs.pl
- expect envvar LINK_STATIC
* if defined 1 -> substitute .so by .a (for switch -F only)
- corrected and updated help
- now also finds dependency file for static libs in $ARBHOME/lib (e.g. lib/libARBDB.a)
* force LINK_STATIC=0 for generation of SOURCE_TOOLS/dep.*
* fix linking unit-tests of "shared" libraries (for LINK_STATIC=1)

42 lines of code changed in 3 files:

westram 2013-06-20 10:32 Rev.: 10169


- fix link error (Linux, LINK_STATIC=1)

3 lines of code changed in 1 file:

westram 2013-06-20 09:16 Rev.: 10168


- export LINK_STATIC like rest of environment

3 lines of code changed in 2 files:

aboeckma 2013-06-19 13:49 Rev.: 10166

Link dependencies now contain .a files instead of .so if static linking is enabled. This fixes the unit tests on OSX

13 lines of code changed in 3 files:

westram 2013-06-18 09:11 Rev.: 10160


* "merge" from dev [7876] [7877] (DB-callback unit-test)
- change TEST_ASSERT... -> TEST_EXPECT...
- disabled one test (tried to mark terminal db-entry, doing that fails assertion in ARBDB now)

310 lines of code changed in 1 file:

westram 2013-06-14 18:51 Rev.: 10159


* whitespace + formatting fixes of helpfiles touched by [10158]

870 lines of code changed in 32 files:

westram 2013-06-14 17:56 Rev.: 10158


* appellation
- name, shortname, ... -> (unique) species ID
- generate names -> synchronize IDs
* fixes #304
- ask to recreate ID (experts only)

143 lines of code changed in 48 files:

epruesse 2013-06-14 15:14 Rev.: 10156

re-enable unit tests for linux (typo... they were only
meant to be disabled for osx)

1 lines of code changed in 1 file:

aboeckma 2013-06-14 10:53 Rev.: 10155

A step towards working unit tests on mac os x

11 lines of code changed in 3 files:

westram 2013-06-13 19:04 Rev.: 10153


* fix AISC dependency problems
- see [9678] for an example
- added some test-targets (dependstest[1..])

28 lines of code changed in 3 files:

westram 2013-06-13 18:54 Rev.: 10152


* increase my personal unit-test timeouts

4 lines of code changed in 1 file:

westram 2013-06-13 17:49 Rev.: 10151


* no longer erase 'SOURCE_TOOLS/dep.*' on 'make clean' (resulted in missing svn-entries)

1 lines of code changed in 1 file:

westram 2013-06-13 13:31 Rev.: 10148


* makedepend changed behavior between 1.0.2 and 1.0.4
- 1.0.4 does generate impossible dependencies (see [10143] for an example)
- force correct behavior by defining SIMPLE_ARB_ASSERT on CLI (when invoking compiler and makedepend)

84 lines of code changed in 13 files:

westram 2013-06-13 10:09 Rev.: 10147


* move arb_assert.h into CORE (uses only functions from CORE, no longer from ARBDB)

363 lines of code changed in 5 files:

westram 2013-06-12 15:01 Rev.: 10141


* added ARB_in_expert_mode + ARB_in_novice_mode

10 lines of code changed in 3 files:

westram 2013-06-12 11:54 Rev.: 10137


- removes PGT (sacrificed to gtk port)

1 lines of code changed in 63 files:

westram 2013-06-12 10:50 Rev.: 10136


* ignore some subdirectories of UNIT_TESTER

5 lines of code changed in 1 file:

epruesse 2013-06-11 12:44 Rev.: 10132

osx find must have a path before the expression ("find . -...")

2 lines of code changed in 1 file:

epruesse 2013-06-11 12:22 Rev.: 10131

put jenkins build script into svn for tracking

68 lines of code changed in 1 file:

epruesse 2013-06-07 18:04 Rev.: 10130

more class/struct ambiguity removed (2nd try)

16 lines of code changed in 5 files:

epruesse 2013-06-07 17:59 Rev.: 10129

revert r10128 (contained accidental delete of gb_data.h range):-/

210 lines of code changed in 5 files:

epruesse 2013-06-07 17:54 Rev.: 10128

~~more class/struct ambiguity removed (using struct for now, doesn't really matter)~~

(reverted by [10129])

16 lines of code changed in 5 files:

epruesse 2013-06-07 16:04 Rev.: 10127

forward decl and decl have to match struct/class (lots of warnings on OSX)

2 lines of code changed in 1 file:

epruesse 2013-06-07 15:45 Rev.: 10126

fix another define check

1 lines of code changed in 1 file:

epruesse 2013-06-07 15:43 Rev.: 10125

on osx, there is no _STDLIB_H -- it's called _STDLIB_H_

4 lines of code changed in 1 file:

westram 2013-06-06 11:05 Rev.: 10122


* send errors in config manager via aw_message (fixes #297)

1 lines of code changed in 1 file:

westram 2013-06-06 10:04 Rev.: 10121


* fixes #295
- when first key is pseudo-key
* do never display key-value (instead show hit description - as done in 'by hit'-sort-order)
* temporarily skip key-dependent sort-orders (drawback: sort-order may change by changing 1st search key)
- no longer automatically switch to 'by hit'-sort-order when performing search for pseudo-keys

58 lines of code changed in 1 file:

westram 2013-06-05 14:37 Rev.: 10120


* removed outdated code that attempted to send email
- replaced 'Registration' by '!MailingList'
- '!MailingList' and '!BugReport' link to trac-wiki instead
- obsoletes #291 and #292

12 lines of code changed in 4 files:

epruesse 2013-06-05 13:21 Rev.: 10119

don't exclude hidden files from arb.tgz (import filters)

1 lines of code changed in 1 file:

westram 2013-06-04 19:08 Rev.: 10117


* fix include-chaos in NTREE
- all headers named
* .h (some had .hxx)
* as .cxx file
- removed obsolete header (NT_dbrepair.hxx, nt_join.hxx)
* removed some more definitions of nt_assert

626 lines of code changed in 47 files:

westram 2013-06-04 17:29 Rev.: 10116


- removed obsolete include-hack

0 lines of code changed in 2 files:

westram 2013-06-04 16:50 Rev.: 10115


* no longer popdown tree-select window when clicking admin button

7 lines of code changed in 4 files:

westram 2013-06-04 16:18 Rev.: 10114


* NTREE
- renamed local prototypes header (nt_internal.h -> nt_local_proto.h)
- moved ntree.hxx to nt_local.h (none of the decls there is used globally, unlinked from INCLUDE)
* include local prototypes
* defines (nt_assert, removed unused, some moved into NT_extern.cxx)

249 lines of code changed in 31 files:

westram 2013-06-04 14:20 Rev.: 10113


* changed dynamic value-initializations into default-initializations
- i believe/know they were used with ignorance of [http://stackoverflow.com/questions/620137/do-the-parentheses-after-the-type-name-make-a-difference-with-new?answertab=active#tab-top ctor-behavior].

45 lines of code changed in 31 files:

westram 2013-06-04 13:24 Rev.: 10112


* trees shown in two NTREE windows were not BOTH selectable (since [10019])
- NT_create_select_tree_window now creates exactly one window for each tree-awar

22 lines of code changed in 3 files:

epruesse 2013-06-03 15:27 Rev.: 10111

backport [10108] to trunk (stack corruption caused by passing int* to aisc_get)

1 lines of code changed in 1 file:

westram 2013-06-02 13:57 Rev.: 10106


* fix a bunch of compiler warnings
- several NDEBUG warnings (variables only used in DEBUG mode)
- wrong use of string literals as char*
- enum type mismatches (AW_VARIABLE_TYPE vs GB_TYPES)

32 lines of code changed in 11 files:

westram 2013-06-02 13:13 Rev.: 10105


- tested and enabled gcc 4.8.0 and 4.8.1

1 lines of code changed in 1 file:

May 2013 »

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