Directory GDEHELP/

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westram 2022-08-12 17:40 Rev.: 19234

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19228:19233

6 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+6 -2)

westram 2022-08-11 18:12 Rev.: 19227

* {{{|&}}} is a bash 4 feature
- OSX still uses bash 3.2\\=> fall-back to {{{2>&1 |}}}.

1 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+1 -1)

westram 2022-05-20 14:34 Rev.: 19047

* partial merge from 'sina' into 'trunk'
- fixes for ubuntu 10.04
* adds: log:branches/sina@19044:19045

1 lines of code changed in 1 file:

• GDEHELP: Makefile (+1 -1)

westram 2022-02-09 12:46 Rev.: 18931

* define unique IDs for jobs running via GDE:
- provide in menu-code via {{{$AGDE_JOBID}}}.
- use as window-logname => allows to relate separate parts of jobs in arb log.

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -1)

westram 2022-02-09 12:41 Rev.: 18930

* tee output from commands running in console windows into log.
* cat log to standard arb console after window is closed.

5 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+5 -2)

westram 2021-12-17 15:34 Rev.: 18864

* remove 'Start a slave ARB on a foreign host' (obsolete).

0 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (-5)

westram 2021-12-17 15:32 Rev.: 18863

* document 'Import fields from calc-sheet'.
* link to 'Export fields (to calc-sheet using NDS)'.
* add another pointer, where to add helpfiles for GDE menus.

3 lines of code changed in 1 file:

• GDEHELP: Makefile.helpfiles (+3 -1)

westram 2021-11-14 12:18 Rev.: 18842

* allow conditional build of OPENMP version of {{{FastTree}}}
- tweak preprocessor: allow to {{{#define}}} via CLI.
- globally define whether OPENMP shall be used
* export to submakefiles.
* disable under OSX
- capability to build OPENMP binary depends on compiler
- LLVM/Clang 3.7 required
- forward {{{USE_OPENMP}}} into preprocessor.
- in fasttree.menu: when not defined {{{USE_OPENMP}}} -> skip MP option from GUI + hardcode binary.
- conditionally build OPENMP binary depending on {{{USE_OPENMP}}}.

14 lines of code changed in 2 files:

• GDEHELP: Makefile (+9 -1), pp.pl (+5)

westram 2021-11-07 19:53 Rev.: 18837

* add {{{FastTree}}} for protein.
- mention STYPE in tree comment.
* customize {{{FastTree}}}:
- allow to configure rate categories.
- NJ
* also provide -slow mode.
* provide weighted NJ
- allow to configure bootstraps.
* rename controlling define

5 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+5 -1)

westram 2021-11-07 19:39 Rev.: 18836

* define items for "RAxML 7" using #defines
- fixes bogus warning about missing itemhelp for "RAxML 7 (DNA)" [18831]
- show sequence type in tree comments (uses NUC/PRO)
- use nucleotide/protein in menu entries (resets properties *sic*)
* rename controlling define

3 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+3 -2)

westram 2021-11-07 19:33 Rev.: 18835

* define items for "PHYML-20130708" using #defines
- fixes bogus warning about missing itemhelp for "PHYML-20130708 (DNA)" [18831]
- use nucleotide/protein in menu entries (resets properties *sic*)
- change STYPE stored in tree comment to NUC/PRO
* rename controlling define

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -2)

westram 2021-11-07 19:25 Rev.: 18832

* improve documentation of generated help.

7 lines of code changed in 1 file:

• GDEHELP: Makefile.helpfiles (+7)

westram 2021-11-07 19:22 Rev.: 18831

* improve GDE-menu robustness
- warn if 'item' lacks an 'itemhelp' entry.
- fail if 'itemhelp' lacks .hlp name.
- bail out if 'item' contains duplicated 'itemhelp' or 'itemmeta' (menu parser)
* currently results in the following warnings:
{{{
MENUS/import.menu:15: Warning: item 'Import fields from calc-sheet' lacks an 'itemhelp' entry!
MENUS/align.menu:1: Warning: item 'ProbCons' lacks an 'itemhelp' entry!
MENUS/align.menu:50: Warning: item 'Muscle' lacks an 'itemhelp' entry!
MENUS/phyml_20130708.menu:24: Warning: item 'PHYML-20130708 (DNA)' lacks an 'itemhelp' entry!
MENUS/raxml.menu:18: Warning: item 'RAxML 7 (DNA)' lacks an 'itemhelp' entry!
MENUS/start_arb.menu:1: Warning: item 'Start a slave ARB on a foreign host ...' lacks an 'itemhelp' entry!
}}}

Edit: fixed by [18863:18865]

62 lines of code changed in 2 files:

• GDEHELP: Makefile (+6 -1), warn_missing_itemhelp.pl (new 56)

westram 2021-11-07 19:13 Rev.: 18829

* correctly skip handling of preprocessor directives when in inactive branch.

13 lines of code changed in 1 file:

• GDEHELP: pp.pl (+13 -6)

westram 2021-11-04 15:08 Rev.: 18823

* split menufile for treepuzzle, mrbayes and fasttree.
* add separators for readability.

16 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+16 -1)

westram 2021-09-15 12:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

2 lines of code changed in 1 file:

• GDEHELP: Makefile (+2 -2)

westram 2019-03-04 14:22 Rev.: 17634

* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

3 lines of code changed in 1 file:

• GDEHELP: .gitignore (new 3)

westram 2017-08-23 12:42 Rev.: 16237

* fix spelling for 'occurrence'

1 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+1 -1)

westram 2016-12-13 11:33 Rev.: 15411

* fix warnings caused by converted documentation
- conversion of html docs
* remove lynx-"<HR/>"-output (arb-help-converter tries to add that to paragraphs)
* add empty line after "generated from" message
- manual reflow of one problematic section in {{{READSEQ/Formats}}}

8 lines of code changed in 1 file:

• GDEHELP: Makefile.helpfiles (+8 -4)

westram 2016-05-02 17:23 Rev.: 14799

* make 4.1 spams the compile log with
{{{
recipe for target 'xxx' failed
}}}
* replaces {{{-oktofail}}} by {{{oktofail || true}}}

5 lines of code changed in 2 files:

• GDEHELP: Makefile (+1 -1), Makefile.helpfiles (+4 -4)

epruesse 2015-05-01 23:41 Rev.: 13797

fix spelling of likelihood

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -2)

westram 2015-03-24 13:22 Rev.: 13598

* rename menu 'User' -> 'Network'
* reuse menu 'User' to place custom entries into 'ARB/Tools' menu

7 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+7 -2)

westram 2014-03-24 17:57 Rev.: 11874

* reintegrates 'customize' into 'trunk'
- implements #484
- clean up worst things in GDE to allow use of custom menu-files
* adds:
- log:branches/customize@11828:11840,11844:11873

15 lines of code changed in 3 files:

• GDEHELP: ARB_GDEmenus.source (+3 -3), Makefile (+11 -12), pp.pl (+1 -1)

westram 2014-03-18 20:45 Rev.: 11815

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

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -4)

westram 2014-02-15 15:51 Rev.: 11626

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

24 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+24 -4)

westram 2013-10-18 13:22 Rev.: 10842

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

17 lines of code changed in 4 files:

• GDEHELP: GDE2.2_manual_postscript (del), GDE2.2_manual_text (del), Makefile.helpfiles (+16 -7), genhelptree.sh (+1 -1)

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

- remove write permission for generated help-files

32 lines of code changed in 3 files:

• GDEHELP: Makefile.helpfiles (+27 -16), genhelp.sh (+2), genhelptree.sh (+3)

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:

• GDEHELP: Makefile (+2 -2), Makefile.helpfiles (+9 -4)

westram 2013-08-28 16:23 Rev.: 10513

* DRYed PHYML interface (Amino vs DNA)

4 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+4)

westram 2013-08-28 16:19 Rev.: 10512

* helper target to ease refactoring ARB_GDEmenus

20 lines of code changed in 1 file:

• GDEHELP: Makefile (+20 -1)

westram 2013-08-28 15:38 Rev.: 10510

* split menu-sources for both versions of phyml

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2)

westram 2013-08-28 15:29 Rev.: 10509

* remove trailing '3' in fastdnaml.menu (was ignored by arb_read_tree)
* split menu-sources for phylip_ml and phyml

1 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+1)

westram 2013-03-27 16:15 Rev.: 9750

- applied (not merged!) [9668] from gtk_only.
- merge did not work w/o conflicts since the patch mixes gtk-specific changes with general changes (better would have been applied to some non-gtk-branch and then merged into gtk-branch)
- merging and resolving conflicts now would skip unmergeable parts. when gtk is merged someday, these parts would get lost.

17 lines of code changed in 4 files:

• GDEHELP: Makefile (+4 -2), Makefile.helpfiles (+4 -4), genhelp.sh (+2 -1), genhelptree.sh (+7 -6)

westram 2012-11-15 16:12 Rev.: 9170

merge from stable_5.0 [9163] [9164] [9166]

8 lines of code changed in 1 file:

• GDEHELP: Makefile (+8 -2)

westram 2012-09-10 12:44 Rev.: 8875

- removed gotos

33 lines of code changed in 1 file:

• GDEHELP: pp.pl (+33 -25)

westram 2012-06-13 19:58 Rev.: 8808

* cleanup generated menu

3 lines of code changed in 1 file:

• GDEHELP: Makefile (+3 -2)

westram 2012-06-13 19:54 Rev.: 8807

* no longer use C-preprocessor

4 lines of code changed in 1 file:

• GDEHELP: Makefile (+4 -18)

westram 2012-06-13 19:44 Rev.: 8806

* cooked my own preprocessor for ARB_GDEmenus generation
* intermediate checkin:
- uses two methods to generate ARB_GDEmenus
- compares results and fails on difference. Branch from here, if own pp needs changes

388 lines of code changed in 3 files:

• GDEHELP: Makefile (+28 -11), cleanmenu.pl (new 21), pp.pl (new 339)

westram 2012-04-25 06:53 Rev.: 8660

* workaround quoting error in ARB_GDEmenus (clang)

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -1)

westram 2012-04-21 14:07 Rev.: 8644

* removed commented code

0 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (-2)

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