Directory SH/

Directory Created:
2000-11-23 10:41
Total Files:
33
Deleted Files:
9
Lines of Code:
2380

[root]/SH

Lines of Code

SH/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 198 (100.0%) 3521 (100.0%) 17.7
westram 167 (84.3%) 2986 (84.8%) 17.8
oldcode 17 (8.6%) 301 (8.5%) 17.7
richter 2 (1.0%) 115 (3.3%) 57.5
epruesse 7 (3.5%) 67 (1.9%) 9.5
aboeckma 2 (1.0%) 39 (1.1%) 19.5
meierh 1 (0.5%) 12 (0.3%) 12.0
yadhu 1 (0.5%) 1 (0.0%) 1.0
baderk 1 (0.5%) 0 (0.0%) 0.0

Most Recent Commits

westram 2021-08-13 10:27 Rev.: 18664


* again install libxerces-c3.2 (tested with ubuntu 20.04)
- reverts [18102]

1 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+1 -2)
westram 2021-05-08 14:53 Rev.: 18648


* updated for ubuntu 20.04 (removed unknown package).

5 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+5 -2)
westram 2020-04-22 14:36 Rev.: 18439


* improve error exit from script (kill self).
* protect functions vs. wrong use (check param 3 of addpath; deny param 3 for append and prepend).
* quote several expressions (to allow installation paths containing spaces)
- arb is NOT intended to be installed into such paths! see also next commit.

41 lines of code changed in 1 file:

  • SH: arb (+41 -30)
westram 2020-03-07 16:47 Rev.: 18373


* reintegrates 'opengl' into 'trunk'
- fixes OPENGL build (using packages from distribution)
- fix several broken .png (1x crash, 16x warnings)
* adds: log:branches/opengl@18367:18372

5 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+5 -34)
westram 2020-02-26 18:46 Rev.: 18339


* full update from child 'fix' into 'trunk'
- fixes #754
* adds: log:branches/fix@18333:18338

36 lines of code changed in 2 files:

  • SH: README (+1), arb_macro_compatibility.sh (new 35)
westram 2020-02-26 18:36 Rev.: 18337


* partial merge from 'fix' into 'trunk'
- fix some warnings
- remove obsolete script
* adds: log:branches/fix@18331:18332

3 lines of code changed in 2 files:

  • SH: README (+3 -4), arb_ludwig (del)
westram 2019-09-18 16:12 Rev.: 18102


* remove libxerces-c3.2 dependency (invalid for 14.04)

2 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+2 -1)
westram 2019-03-26 11:00 Rev.: 17700


* add 'xed' to known editors

1 lines of code changed in 1 file:

  • SH: arb_textedit (+1 -1)
westram 2019-03-26 10:40 Rev.: 17699


* arb_textedit:
- if launching editor reports error => report error (to GUI) and mention {{{ARB_TEXTEDIT}}}
- log definition of ARB_TEXTEDIT to console

8 lines of code changed in 1 file:

  • SH: arb_textedit (+8 -3)
westram 2019-03-06 12:10 Rev.: 17645


update doxygen docs:

- updated obsolete setting using "doxygen -u".
- use Helvetica font for dot-gfx generated by doxygen.
- activates conf-mode in emacs.

1 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+1 -1)
westram 2018-11-25 19:19 Rev.: 17618


* full update from child 'fix' into 'trunk'
- fixes undefined variables in makefiles
- fixes perl tests
* adds: log:branches/fix@17599:17617

1 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+1 -1)
westram 2018-11-08 15:13 Rev.: 17601


* arb_installubuntu4arb.sh
- now works on Linux Mint 19
- should also work on ubuntu 18.04 (untested)
- dependencies for arb
* missing: libxm4 (run) + libboost-random-dev (build)
* outdated: libxerces-c3.1 -> libxerces-c3.2 (run)

7 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+7 -4)
westram 2018-11-08 11:01 Rev.: 17600


* split parameter into two parameters ('what' + 'openGL')
- rest should behave like before

82 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+82 -67)
westram 2017-11-28 18:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

4 lines of code changed in 1 file:

  • SH: dszmconnect.pl (+4 -3)
westram 2017-10-03 17:50 Rev.: 16471


- correct indentation

16 lines of code changed in 1 file:

  • SH: arb_textedit (+16 -16)
westram 2017-10-03 17:26 Rev.: 16469


* reintegrates 'textedit' into 'trunk'
- fixes #586
* editor now always started asynchronously
* uses inotify to track file changes
- ~~also use inotify to track directory updates (in order to update file selections when needed)~~\\(./) by [16515] ff.; merged by [16551]
* adds: log:branches/textedit@16448:16468

65 lines of code changed in 1 file:

  • SH: arb_textedit (+65 -28)
westram 2017-09-19 13:40 Rev.: 16391


* full update from child 'aci' into 'trunk'
- allow to view console from inside ARB
- slightly tweaked ACI trace
* adds: log:branches/aci@16386:16390

52 lines of code changed in 3 files:

  • SH: arb_launcher (+2), arb_show_log.pl (new 49), arb_wait (+1 -1)
westram 2016-05-02 15:47 Rev.: 14798


* fix Ubuntu 16.04 build
- add gcc 5.3.1
* fix isnan/isinf use (only in testcode)
- fix libdepends in install-scripts and -READMEs

12 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+12 -9)
westram 2016-04-26 14:53 Rev.: 14770


* increase default size for xterms started from arb

2 lines of code changed in 2 files:

  • SH: arb (+1 -1), arb_textedit (+1 -1)
westram 2015-11-20 11:19 Rev.: 14509


* fix for #492
- call pt- and name-servers as daemons, i.e.
* do not forward any kill signals
* remove them from the joblist
* redirect their output into a logfile
- this is only done if arb is called from launcher
* trigger is envar {{{ARB_SERVER_LOG}}} (contains the name of the logfile used for daemon output)
* logfile gets tailed to console; tail is killed when launcher terminates => doesnt block

24 lines of code changed in 1 file:

  • SH: arb_launcher (+24 -2)
westram 2015-11-18 17:12 Rev.: 14501


* use argument quoting for
- NDS export (target file, print header and postscript output file)
- calling external editor (e.g. "edit macro file")
- calling macros (tested from GUI and CLI with {{{1'2"3.amc}}})
- canvas -> xfig/printer/postscript
- calling editor with user defined configuration name
- merge from/to arb database
- when passing DB name to ptserver
- to pass search expression to grep (while searching helpfiles)

2 lines of code changed in 1 file:

  • SH: arb_textedit (+2 -2)
westram 2015-11-12 11:26 Rev.: 14493


* arb_launcher
- added some debug messages; show debug messages
- wait for subshells in {{{listen_pipe_unlogged}}}
- call {{{arb_clean session}}} as soon as launcher thinks no arb process is running (basically fixes #492)

13 lines of code changed in 1 file:

  • SH: arb_launcher (+13 -2)
westram 2015-11-12 10:17 Rev.: 14492


* arb_clean
- renamed action 'targets' -> 'show_all'
- added new action 'show_session'
- both 'show_...'-actions use 'ps' to create process listing (instead of just dumping PIDs)

38 lines of code changed in 1 file:

  • SH: arb_clean (+38 -12)
westram 2015-10-10 12:27 Rev.: 14409


* fix links to ~~dev.mikro.biologie.tu-muenchen.de/debian~~

1 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+1 -1)
westram 2015-07-04 08:13 Rev.: 13966


* added libxerces-c dependency

4 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+4 -2)
epruesse 2014-08-28 19:01 Rev.: 12794

SECURITY: arb_launcher sockets and socketdir must have mode 0700 and 0600

4 lines of code changed in 1 file:

  • SH: arb_launcher (+4 -3)
epruesse 2014-08-06 14:20 Rev.: 12687

merge log:branches/stable@12685 to trunk

3 lines of code changed in 1 file:

  • SH: arb_panic (+3 -1)
westram 2014-05-23 10:21 Rev.: 12288


* list shared library dependencies (instead of listing glib); implements #547
* eval collect-CMD (instead of executing it in a subshell; allows to call local commands)
* shortened tags

35 lines of code changed in 1 file:

  • SH: arb_launcher (+35 -12)
westram 2014-05-22 11:21 Rev.: 12282


* launcher also waits for keypress when arb terminates abnormmally (i.e. with error)

25 lines of code changed in 1 file:

  • SH: arb_launcher (+25 -12)
westram 2014-05-17 15:45 Rev.: 12276


* added a bunch of arguments to CLI that allow to test various ways to terminate
* exit from signal handler with exitcode>=128
* arb_launcher knows about 3 types of exitcodes:
- 0 = success
- 1 = failure (no crash); no longer tell arb did crash in this case, fixing #538
- else = crash

7 lines of code changed in 1 file:

  • SH: arb_launcher (+7 -8)
westram 2014-03-19 11:39 Rev.: 11820


- added libglib2.0-dev

2 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+2 -1)
westram 2014-03-18 20:45 Rev.: 11815


* reintegrates 'deb' into 'trunk'
- fixes #215
- performs #489
* adds:
- log:branches/deb@11801:11814

25 lines of code changed in 4 files:

  • SH: arb_clean (+2 -2), arb_fastdnaml (+4 -2), arb_panic (+6 -5), dszmconnect.pl (+13 -7)
westram 2014-03-11 14:43 Rev.: 11773


* work around situations where ARB_PROP is undefined (can't create session log -> skip it; fixes #482)
* avoid warning ("rm: cannot remove `/home/ralf/.arb_prop/logs/20140311_143417.16245/crashed': No such file or directory")

55 lines of code changed in 1 file:

  • SH: arb_launcher (+55 -47)
westram 2014-03-08 11:06 Rev.: 11754


* reintegrates 'bugrep' into 'trunk'
- implements #391
* adds:
- log:branches/bugrep@11744:11753

142 lines of code changed in 2 files:

  • SH: arb_launcher (+131 -22), arb_trace (+11 -20)
westram 2014-02-21 11:44 Rev.: 11649


- fix test for "no tree selected" in arb_raxml
- passing an empty tree to RAxML caused it to run forever under some circumstances
- added comments at "no tree selected"-tests

1 lines of code changed in 1 file:

  • SH: arb_raxml (+1 -1)
westram 2014-02-15 15:51 Rev.: 11626


* reintegrates 'fix' into 'trunk'
- implements: #158
- fixes: #386, #463, #459
* adds:
- log:branches/fix@11579:11625

57 lines of code changed in 6 files:

  • SH: arb_dnapars (+5 -3), arb_fastdnaml (+1), arb_phyml (+2 -1), arb_proml (+5 -3), arb_protpars (+4 -2), arb_raxml (+40 -16)
westram 2014-01-30 12:52 Rev.: 11525


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

70 lines of code changed in 1 file:

  • SH: arb_help_useredit.sh (new 70)
westram 2013-11-04 15:16 Rev.: 11070


* tested 'arb' script with EMPTY environment. sets defaults for
- $HOME ('~'; seems to work; might be problematic, but i have no better idea how to get a default)
- $DISPLAY (':0')

10 lines of code changed in 1 file:

  • SH: arb (+10)
westram 2013-11-04 14:49 Rev.: 11069


* '~/.arb_prop' replaced by environmentvariable ARB_PROP
- define/accept $ARB_PROP in 'arb' script
- replaced all hardcoded occurrences
- corrected several help files
* fixed two conditions in 'arb'-script (broken by [11064])

@elmar '-u' = fail early = good idea :)

11 lines of code changed in 1 file:

  • SH: arb (+11 -7)
epruesse 2013-11-04 14:08 Rev.: 11068

fix ARB not launching if ARBHOME unset or if no parameter supplied
was broken by r11064 -- is "-u" really a good idea?

2 lines of code changed in 1 file:

  • SH: arb (+2 -2)

(101 more)

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