November 2021 Commit Log

Number of Commits:
21
Number of Active Developers:
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}}}.

47 lines of code changed in 6 files:

westram 2021-11-12 13:47 Rev.: 18841


* add progress to {{{neighbourjoining()}}}-phase (this may be really long running)
- add one extra progress to {{{di_calculate_tree_cb()}}} encapsulating matrix-calculation + {{{neighbourjoining()}}}-phase.
- progress inside {{{di_calculate_matrix()}}} now counts 2 steps: loading data + matrix-calculation.

30 lines of code changed in 3 files:

westram 2021-11-10 14:46 Rev.: 18840


* also build OPENMP version of {{{FastTree}}}
- add selector for single/multi processor version to GUI.
- store used version in tree comment.
- svn/git-ignore MP binary

18 lines of code changed in 3 files:

westram 2021-11-10 14:36 Rev.: 18839


* upgrade {{{FastTree}}} to version 2.1.11
- cleanup: define flags and use make variables.
- specify fasttree version in help.
- update changelog.

281 lines of code changed in 4 files:

westram 2021-11-10 14:32 Rev.: 18838


* minor fixes to fasttree GUI:
- only use single line in description (otherwise parts are not visible).
- fix duplicated itemmeta.

2 lines of code changed in 1 file:

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

70 lines of code changed in 3 files:

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

18 lines of code changed in 2 files:

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

19 lines of code changed in 2 files:

westram 2021-11-07 19:29 Rev.: 18834


* use real LINK.

1 lines of code changed in 1 file:

westram 2021-11-07 19:27 Rev.: 18833


* fix whitespace in HELP_WRITTEN.

46 lines of code changed in 5 files:

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


* improve documentation of generated help.

9 lines of code changed in 3 files:

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]

64 lines of code changed in 3 files:

westram 2021-11-07 19:17 Rev.: 18830


* whitespace + typo.

4 lines of code changed in 3 files:

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:

westram 2021-11-07 19:08 Rev.: 18828


* prepare for Cxx17 builds.

20 lines of code changed in 1 file:

westram 2021-11-05 14:15 Rev.: 18827


* cleanup merge selectors.

20 lines of code changed in 2 files:

westram 2021-11-05 11:35 Rev.: 18826


* add SAI selectors for both databases
- fixes crash when opening SAI transfer

64 lines of code changed in 1 file:

westram 2021-11-05 11:33 Rev.: 18825


* merging via FTS into new database did not copy alignment information. fixed.

2 lines of code changed in 1 file:

westram 2021-11-04 15:54 Rev.: 18824


* add help for fasttree (copied start of text from homepage and link there).

25 lines of code changed in 2 files:

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


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

177 lines of code changed in 4 files:

westram 2021-11-04 15:02 Rev.: 18822


* do not generate a local binary.
* instead directly build installed binary in $ARBHOME/bin.

5 lines of code changed in 1 file:

October 2021 »

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