Directory SH/

Directory Created:
2000-11-23 11:41
Total Files:
33
Deleted Files:
8
Lines of Code:
2362

[root]/SH

Lines of Code

SH/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 189 (100.0%) 3428 (100.0%) 18.1
westram 158 (83.6%) 2893 (84.4%) 18.3
oldcode 17 (9.0%) 301 (8.8%) 17.7
richter 2 (1.1%) 115 (3.4%) 57.5
epruesse 7 (3.7%) 67 (2.0%) 9.5
aboeckma 2 (1.1%) 39 (1.1%) 19.5
meierh 1 (0.5%) 12 (0.4%) 12.0
yadhu 1 (0.5%) 1 (0.0%) 1.0
baderk 1 (0.5%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-03-26 12:00 Rev.: 17700


* add 'xed' to known editors

1 lines of code changed in 1 file:

  • SH: arb_textedit (+1 -1)
westram 2019-03-26 11:40 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 13:10 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 20:19 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 16:13 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* outdated: libxerces-c3.1 -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 12:01 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 19:22 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 18:50 Rev.: 16471


- correct indentation

16 lines of code changed in 1 file:

  • SH: arb_textedit (+16 -16)
westram 2017-10-03 18:26 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 14:40 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 16:47 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 15:53 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 12:19 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 18:12 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 12:26 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 11:17 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 13:27 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 09:13 Rev.: 13966


* added libxerces-c dependency

4 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+4 -2)
epruesse 2014-08-28 20:01 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 15:20 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 11:21 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 12:21 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 16:45 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 12:39 Rev.: 11820


- added libglib2.0-dev

2 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+2 -1)
westram 2014-03-18 21:45 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 15:43 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 12:06 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 12:44 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 16:51 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 13:52 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 16:16 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 15:49 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 15:08 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)
westram 2013-11-04 11:51 Rev.: 11064


* arb startup script
- now fails on undefined variables
- fix tests for unset variables

8 lines of code changed in 1 file:

  • SH: arb (+8 -6)
westram 2013-10-18 14:22 Rev.: 10842


* reintegrates 'help' into 'trunk':
* adds:
- log:branches/help@10647:10841
- log:branches/helptest@10704:10720

0 lines of code changed in 1 file:

  • SH: arb (-5)
westram 2013-10-01 16:29 Rev.: 10682


* always restart arb_ntree using new ARB_PID [nt_restart]
- fixes "socket ':' in use"-error when quitting merge-tool via 'Quit & start target DB'
* bug was introduced in [10083], originating somewhere around [9873]
- starting arb_ntree [nt_start] is still possible inside current ARB_PID environment
* hack to support debugging (always call arb_launcher with '--async', i.e. "do not block")

15 lines of code changed in 1 file:

  • SH: arb_launcher (+15 -4)
westram 2013-10-01 14:38 Rev.: 10681


* use script arb_launcher to launch arb processes
- inside each ARB_PID-environment
* initial call
- opens a named pipe
- starts the command passed via CLI
- listens the pipe, launching new processes
- when all launched processes terminate, the launcher terminates itself
- installs signal handlers for INT, TERM and EXIT
* INT asks whether ARB session shall be terminated
* TERM kills the ARB session (whole process tree)
* EXIT removes the named pipe
* subsequent calls just write launch-requests to the pipe
- when arb_ntree wants to restart itself, it asks arb_launcher to perform that task (synchronously!)
* doing so ensures the initial session stays open until all spawned arb-sub-sessions have terminated
* script 'arb'
- dont use exec for 'arb shell'
- dont use 'sh' use 'bash -i'
- start arb_trace and arb_trace via arb_launcher
- show arb_ntree-help above help for script 'arb'
* should fix #358

235 lines of code changed in 2 files:

  • SH: arb (+8 -6), arb_launcher (new 227)
westram 2013-09-27 19:48 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

64 lines of code changed in 3 files:

  • SH: arb (-1), arb_clean (+63 -14), arb_panic (+1 -1)
aboeckma 2013-08-14 15:28 Rev.: 10447

Added mrBayes gde menu

34 lines of code changed in 1 file:

  • SH: arb_nexus2newick.awk (new 34)
westram 2013-08-12 14:38 Rev.: 10428


* added libreadline-dev (completes r10420)

1 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+1)

(94 more)

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