September 2010 Commit Log

Number of Commits:
34
Number of Active Developers:
1
westram 2010-09-28 13:23 Rev.: 6913


* suppress status update by matrix calculation with a flag. Suppress while
- calculating bootstrap trees
- marking species by distance

23 lines of code changed in 2 files:

westram 2010-09-28 13:20 Rev.: 6912


- printf -> assert

1 lines of code changed in 1 file:

westram 2010-09-22 16:17 Rev.: 6884


* updated source.lst
- merges [6883], but handles ptserver testfile different

11 lines of code changed in 1 file:

westram 2010-09-20 12:01 Rev.: 6872


- ignore error when removing timestamp

1 lines of code changed in 1 file:

westram 2010-09-18 16:39 Rev.: 6868


- updated prototypes and dependencies

719 lines of code changed in 38 files:

westram 2010-09-18 16:32 Rev.: 6867


* ARB GUI (merges [6844] [6845] [6847] [6858] [6861] from refactor)
* new central header cb.h (planned to define ALL callbacks used in ARB here later)
* refactored callback handling for some AW_root callbacks
- AW_root_callback hides function ptr + arguments
- AW_root_cblist hides lists of AW_root_callback
* DRYed AW_RCB
* reduced tight coupling between some of WINDOW/*.hxx (omg)
* removed AWUSE

1371 lines of code changed in 232 files:

westram 2010-09-18 16:20 Rev.: 6866


* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

213 lines of code changed in 67 files:

westram 2010-09-18 16:03 Rev.: 6865


* loosened dependencies between libraries (merges [6820] [6828] [6830] [6831] [6832] [6833] [6834] [6835] [6836] [6837] [6839] [6840] from refactor)
* needed_libs.pl
- fixed infinite recursion (appeared when defining cyclic lib-dependencies)
- print different error when using wrong directory
* create dependencies for AISC_MKPTPS
* iupac code
- moved interface into namespace iupac
- renamed functions
- defined iupac-groups for aminos
- added 'C' to its own group (was missing)
- added tests for nuc/amino groups data
- adapted client code
- moved iupac code to SL/PRONUC (which no longer depends on libAWT)
* redefined SERVERCNTRL/client dependencies
- SERVERCNTRL.a depends on client.a (apparently it does not matter whether PROBE_COM/client.a or NAMES_COM/client.a is used)
- all clients depend on SERVERCNTRL.a (instead of client.a)
- removed fake aisc-functions from arb_db_server (instead link client.a, as others do)
- replaced PROBE_COM/client.test by SERVERCNTRL/SERVERCNTRL.test
* removed cyclic dependency edit4->(secedit|RNA3D)->edit4
- created EDIT4 plugin interface (ED4_plugin_host)
- plugged in RNA3D and SECEDIT
* fixes:
- add menu-entries for SECEDIT and RNA3D only for RNA-alignments (like buttons)
- added help to these menu-entries

1304 lines of code changed in 71 files:

westram 2010-09-18 15:01 Rev.: 6864


* doxygen (merges [6852] [6854] [6857] from refactor)
- workaround doxygens symlink-bug
- skip .svn / removed old ARBDB dirs
- increased max. nodes per diagram and reduced max. depth to 2
- speed up dot-calls

16 lines of code changed in 2 files:

westram 2010-09-18 13:00 Rev.: 6863


* unit-test improvements (merged [6819] [6821] [6822] [6823] [6824] [6826] [6827] [6829] [6838] [6862] from refactor)
* execute SLOW tests only every XXX minutes (currently 15)
- added target 'aut' to ARB makefile to force ALL tests w/o changing test setup
* fail if a unit w/o tests gets tested
* cleanup Makefiles for unit tests
- moved code from ARB makefile downto Makefile.suite
- moved setup to Makefile.setup
- print headers for tests
* patch generation
- names of patches reflect what has been tested
- keeps at least 50 patches (even if outdated)
- moved patch handling to Makefile.suite
- avoid duplicated patches
* test code
- added test_different()
- DRYed and renamed templates
- added tests TEST_ASSERT_LOWER_EQUAL, TEST_ASSERT_LOWER and TEST_ASSERT_IN_RANGE (work with all types comparable by '<')
* library dependencies:
- dependencies on RNA3D depend on OPENGL-setting from config.makefile
- better errors when dependency is empty string (undefined envvar)
* updated SVN ignore list

572 lines of code changed in 15 files:

westram 2010-09-15 16:51 Rev.: 6843


* fixed bug introduced with [6675]
- when removing a callback from an AWAR, all callbacks installed before that callback have been deleted as well, but were left in callback list
- caused various ARB crashes (e.g. user masks)

1 lines of code changed in 1 file:

westram 2010-09-15 13:24 Rev.: 6842


* link fixture for ptpan (get_match_overlay not implemented there)

6 lines of code changed in 1 file:

westram 2010-09-15 09:54 Rev.: 6841


* added 'C' and 'X' to protein char table definition (used for folding and consensus)

3 lines of code changed in 1 file:

westram 2010-09-09 21:49 Rev.: 6817


- depends for [6816]

410 lines of code changed in 61 files:

westram 2010-09-09 21:40 Rev.: 6816


* unit-test improvements (merged [6757] [6758] [6759] [6760] [6761] [6762] [6764] [6791] [6795] [6798] [6799] [6800] [6801] [6802] [6809] [6810])
* moved file compare to test_unit.h
* fake report for skipped tests
* added templates for char compare
* perform minihexdump
* flush output
* added
- {{{TEST_ASSERT_FILES_EQUAL__BROKEN}}}
- {{{TEST_ASSERT_ZERO_OR_SHOW_ERRNO}}}
* create a fake.patch if there are no changes
* all code affecting assertions in UNIT_TESTS-mode went to test_global.h
- overwrites arb_assert()
* undefine UNIT_TESTS for GDE submakefiles (foreign code there)
* arb_test::FlushedOutput::errorf raises assertion itself
* test against I/O errors
* moved test code
- into class StaticCode: class w/o functionality, only holds global static code.
- assertfailmsg -> GlobalTestData
* refactored message printing
* unit-tester switches to run directory itself
- eliminates path hack for valgrind
* control leak-check by variable
* added global test-environment (does nothing yet)

497 lines of code changed in 12 files:

westram 2010-09-09 19:29 Rev.: 6815


* compile ISLAND_HOPPING as C++ (merges [6794])

1699 lines of code changed in 11 files:

westram 2010-09-09 19:25 Rev.: 6814


* depends updated for [6812] + [6813]

509 lines of code changed in 59 files:

westram 2010-09-09 19:23 Rev.: 6813


* merged from refactor [6796] [6804] [6806] [6808]
* added header for planned library ARB_CORE
* renamed inline.h into arb_str.h
* header for global general purpose defines/inlines (arb_defs.h)
- use ARRAY_ELEMS where applicable
* removed duplicate of ARB_strscmp (GBS_strscmp). No longer needed cause ARBDB is now C++

156 lines of code changed in 36 files:

westram 2010-09-09 18:58 Rev.: 6812


* merged r6753, r6788 + r6789 from refactor:
- multiple attributes get promoted to headers
- make depends scans {{{__cplusplus}}} sections

373 lines of code changed in 8 files:

westram 2010-09-09 12:03 Rev.: 6811


* report more information about broken configurations
* GBT_commit_rename_session did NEVER report error (since [2])
- added {{{__ATTR__USERESULT}}}
* forward error in AWTC_pars_names (and abort complete rename)
* this fixes the bug with noticable broken configs after merge/rename
- cause of bug: the config parser used inside ABRDB is much more picky than the one used in NTREE (needs to be DRYed)
- no idea when this bug was introduced (maybe by introduction of GBT_config_parser in [3824]) and why it popped up now

26 lines of code changed in 4 files:

westram 2010-09-05 16:49 Rev.: 6775


- updated ubuntu package info/script

25 lines of code changed in 2 files:

westram 2010-09-05 16:35 Rev.: 6774


- merged changelog from stable (all changes are already in trunk)

25 lines of code changed in 1 file:

westram 2010-09-05 12:10 Rev.: 6771


- renamed release building targets

5 lines of code changed in 1 file:

westram 2010-09-04 20:55 Rev.: 6770


- sabcmd -> xsltproc

1 lines of code changed in 1 file:

westram 2010-09-04 20:22 Rev.: 6768


- shut up :)

2 lines of code changed in 1 file:

westram 2010-09-04 20:19 Rev.: 6767


- finally removed sablotron

19 lines of code changed in 1 file:

westram 2010-09-04 19:48 Rev.: 6766


- generate help with sabcmd AND xsltproc and compare results

16 lines of code changed in 1 file:

westram 2010-09-04 19:47 Rev.: 6765


- do not indent html
- changed header of one SECTION

4 lines of code changed in 2 files:

westram 2010-09-03 19:17 Rev.: 6750


- sync with refactor branch (branching sux)

303 lines of code changed in 22 files:

westram 2010-09-03 16:12 Rev.: 6748


- do not complain if log directory does not exist yet

5 lines of code changed in 1 file:

westram 2010-09-03 14:48 Rev.: 6745


* when one unittest fails to compile or crashes, overall target fails

12 lines of code changed in 2 files:

westram 2010-09-03 14:45 Rev.: 6744


* reduced code bloat from unit tests

(partly reverted by [6747] in branch; which was AFAIK not merged back to trunk)

87 lines of code changed in 1 file:

westram 2010-09-03 12:55 Rev.: 6743


* count warnings raised by unittests (e.g. broken, missing test, ..)
* log unittests to UNIT_TESTER/logs
* create final report summarizing all executed unittests
- report generates global exitcode (single unittests always succeed)
* SLOW unittests may be skipped by flag in Makefile.test

268 lines of code changed in 8 files:

westram 2010-09-02 13:38 Rev.: 6742


- fixed some comment references

2 lines of code changed in 2 files:

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