* also disable tree-loop-vectorize for gcc 6.3.0 (see #700)
* added error for future gcc versions
23 lines of code changed in 1 file:
* reintegrates 'warnings' into 'trunk'
- fixes compiler warnings (gcc 5.x)
* adds: log:branches/warnings@15468,15471,15473,15477,15481:15483
36 lines of code changed in 6 files:
* partial merge from 'warnings' into 'trunk'
- no spam from GDE (filter compiler warnings, do not request vectorizer info)
- remove leftover occurrences of {{{grep -P}}} (harmless for OSX; only used for targets 'tags' and 'ut')
* adds: log:branches/warnings@15469:15470,15472,15474:15475,15479:15480
22 lines of code changed in 6 files:
* partial merge from 'warnings' into 'trunk'
- fixes for {{{arb_raxml8.sh}}}
* OSX compatibility (grep/sed)
* {{{LD_LIBRARY_PATH}}}
* adds: log:branches/warnings@15476,15478
10 lines of code changed in 1 file:
* reintegrates 'pars' into 'trunk'
- performs #643
* adds: log:branches/pars@15428:15450,15452:15458
580 lines of code changed in 25 files:
* adds gcc 6.3.0
1 lines of code changed in 1 file:
* merge [15451] from 'pars' into 'trunk'
- Note: this change fixes the double evaluation problem, but introduces new problems (see #737)
40 lines of code changed in 2 files:
* reintegrates 'sanitize' into 'trunk'
* adds: log:branches/sanitize@15434:15446
63 lines of code changed in 2 files:
* [15429] broke compilation w/o unit-tests. fixed.
1 lines of code changed in 1 file:
* fix unit-tests for stabs-format
29 lines of code changed in 8 files:
* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424
693 lines of code changed in 16 files:
* 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}}}
50 lines of code changed in 2 files:
* partial merge from 'mladd' into 'trunk'
- GDE fixes
* adds: log:branches/mladd@15395,15397
31 lines of code changed in 4 files:
* reintegrates 'mladd' into 'trunk'
- adds help for RAxML8 integration (#623)
- remove default "non-random seed"
- fixes warnings about unrecommended use (messages where truncated; GTRGAMMA warning never showed up; GTRCAT warning always popped up)
- fixes CPU cores detection (broken by [14939])
* adds: log:branches/mladd@15377:15391
159 lines of code changed in 3 files: