Directory PERL2ARB/

Directory Created:
2000-11-23 11:41
Total Files:
10
Deleted Files:
12
Lines of Code:
1224

[root]/PERL2ARB

Lines of Code

PERL2ARB/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 171 (100.0%) 10715 (100.0%) 62.6
jobb 2 (1.2%) 8005 (74.7%) 4002.5
westram 148 (86.5%) 1467 (13.7%) 9.9
oldcode 13 (7.6%) 971 (9.1%) 74.6
meierh 2 (1.2%) 156 (1.5%) 78.0
richter 4 (2.3%) 115 (1.1%) 28.7
epruesse 1 (0.6%) 1 (0.0%) 1.0
baderk 1 (0.6%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-03-04 15:22 Rev.: 17634


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

11 lines of code changed in 1 file:

  • PERL2ARB: .gitignore (new 11)
westram 2017-11-28 18:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

10 lines of code changed in 2 files:

  • PERL2ARB: Makefile.main (+9 -1), perlmain_source.c (+1 -1)
westram 2017-11-06 14:54 Rev.: 16628


* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1)
westram 2017-08-09 14:59 Rev.: 16223


* reintegrates 'cover' into 'trunk'
- fixes compilation with COVERAGE
* ARB perl module failed to load (since [13739])
* linking executables broken (apparently since [14038])
* adds: log:branches/cover@16213:16222

1 lines of code changed in 1 file:

  • PERL2ARB: make_arbperl_makefile.pl (+1 -2)
westram 2017-01-16 12:17 Rev.: 15579


* reintegrates 'unittest' into 'trunk'
- activates unittests under OSX (performs #740)
* disabled a few tests + accepted a few modified results (see #741)
* {{{RegExpr}}} no longer uses exception
* fix quoting of {{{char*}}} (in reported test result)
- fixes several compiler flags unknown under OSX/clang
- fix usability of compile log (make now prints directory)
* adds: log:branches/unittest@15534:15578
* removes: [15520/branches/warnings]

3 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+3)
westram 2016-05-02 18:23 Rev.: 14799


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

2 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+2 -2)
westram 2016-05-02 10:08 Rev.: 14792


* OSX build: workaround SIP restrictions

7 lines of code changed in 1 file:

  • PERL2ARB: make_arbperl_makefile.pl (+7 -1)
westram 2016-04-29 18:02 Rev.: 14786


* reintegrates 'gde' into 'trunk'
- fixes #695
* adds: log:branches/gde@14670:14675,14682:14785

2 lines of code changed in 1 file:

  • PERL2ARB: typemap (+2)
westram 2015-04-18 12:51 Rev.: 13740


* 32bit crosscompile (on 64bit host) was broken by [13739]. fixed.

2 lines of code changed in 1 file:

  • PERL2ARB: make_arbperl_makefile.pl (+2 -1)
westram 2015-04-17 17:15 Rev.: 13739


* fix #628
- use main cflags/lflags in PERL2ARB (not cross_cflags/cross_lflags)
- use content of environment variable EXECLIBS to dynalink to asan/ubsan libs
* reactivate test of perlscripts (reverts part of [12998])
* add '-Wno-unused-parameter' for perl module (cant fix macro XS)

6 lines of code changed in 2 files:

  • PERL2ARB: Makefile.main (+4 -4), make_arbperl_makefile.pl (+2 -1)
westram 2014-10-17 16:43 Rev.: 13077


* reintegrates 'sanitize' into 'trunk'
* adds:
- log:branches/sanitize@13023:13076

6 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+6 -2)
westram 2014-09-19 14:22 Rev.: 12890


* fix #602
- added manual wrapper for GB_delete

10 lines of code changed in 1 file:

  • PERL2ARB: ARB.default.xs (+10)
westram 2014-09-19 14:22 Rev.: 12889


* ':' -> '::'

7 lines of code changed in 1 file:

  • PERL2ARB: DOC.html (+7 -7)
westram 2014-09-19 13:35 Rev.: 12888


* fix #603
- abort all TAs and close all DBs
* in arb-perl death-handler
* on exit (i.e. perl scripts will now abort unclosed TAs - not sure whether they did commit b4)

22 lines of code changed in 2 files:

  • PERL2ARB: ARB.default.xs (+6), ARB.pm (+16 -4)
westram 2014-08-29 13:35 Rev.: 12799


* describe some enhanced macro techniques:
- howto use selected alignment, tree, species, position (instead of hardcoding these values)
* added a perl-module (ali_dnapro) to support macros with custom dna and corresponding protein alignment
* some changes to global catch introduced in [12798]

3 lines of code changed in 1 file:

  • PERL2ARB: ARB.pm (+3 -2)
westram 2014-08-29 10:57 Rev.: 12798


* globally catch exceptions from macro code
- forward via arb_message
- confess to console
- example
{{{
[Action: 'perl '/home/ralf/.arb_prop/macros/_logged.amc' &']
aw_message: 'Macro execution error: bla (see console for details)'
Macro execution error: 'bla' at /home/ralf/ARB-bilbo/ARB.trunk.default/lib//ARB.pm line 32
CORE::GLOBAL::die('bla') called at /home/ralf/ARB-bilbo/ARB.trunk.default/PERL_SCRIPTS/lib/ali_dnapro.pm line 19
ali_dnapro::get_dnapro_alignments() called at /home/ralf/.arb_prop/macros/_logged.amc line 17
}}}

19 lines of code changed in 1 file:

  • PERL2ARB: ARB.pm (+19)
westram 2014-05-28 18:24 Rev.: 12308


- fix !MacPorts compilation (in PERL2ARB)
- exports CC CXX from arb Makefile and from PERL2ARB/Makefile.main (avoiding fallback to sth present in environment)

9 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+9 -8)
westram 2014-05-17 15:02 Rev.: 12273


- no magic exit codes

1 lines of code changed in 1 file:

  • PERL2ARB: perlmain_source.c (+1 -1)
westram 2014-05-06 13:00 Rev.: 12151


pass down CXX_INCLUDES

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2014-03-31 10:17 Rev.: 11914


- fixes compilation error on OSX (with perl 5.16)
thx to matt

11 lines of code changed in 1 file:

  • PERL2ARB: ARB.default.xs (+11)
westram 2014-03-18 16:21 Rev.: 11805


* export 'LINUX' and 'REDHAT' to submakefiles
* use ifeq instead of ifdef (completes [11804])

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2014-01-30 20:52 Rev.: 11537


- removed obsolete define

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2014-01-14 15:47 Rev.: 11472


- further hacking to allow CONSTEXPR and OVERRIDE in headers also used by PERL2ARB (see [10678])

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2013-12-26 13:48 Rev.: 11401


* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

2 lines of code changed in 2 files:

  • PERL2ARB: ARB_ext.c (+1 -1), Makefile.main (+1 -1)
westram 2013-12-12 17:15 Rev.: 11338


* suppress "invalid suffix on literal" warnings (cause is in perl-headers)

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2013-11-03 12:04 Rev.: 11053


- predefine and use common GB_CB_TYPE combinations

2 lines of code changed in 1 file:

  • PERL2ARB: ARB_ext.c (+2 -2)
westram 2013-11-02 21:28 Rev.: 11048


* use typed DB callbacks (rest)

7 lines of code changed in 1 file:

  • PERL2ARB: ARB_ext.c (+7 -12)
westram 2013-11-02 20:11 Rev.: 11035


* untabified

9 lines of code changed in 1 file:

  • PERL2ARB: ARB_ext.c (+9 -9)
westram 2013-11-01 15:50 Rev.: 11023


* publish DB callback interface separately from rest of DB interface

1 lines of code changed in 1 file:

  • PERL2ARB: ARB_ext.c (+1)
westram 2013-10-31 16:40 Rev.: 11002


* 'class { public' -> struct

1 lines of code changed in 1 file:

  • PERL2ARB: ARB_ext.c (+1 -2)
westram 2013-10-31 14:37 Rev.: 10993


* added detection for gcc vs clang
- separated allowed version for both compilers
- renamed a bunch of gcc-specific make variables
- dumps compiler version output (-dumpversion and --version) to compile log in case of failure

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)
westram 2013-10-30 16:26 Rev.: 10973


* merge makefile-generation scripts (creating perl-makefile no longer differed between OSX and LINUX)

56 lines of code changed in 5 files:

  • PERL2ARB: DARWIN.PL (del), LINUX.PL (del), Makefile.main (+6 -4), arb_common.pm (del), make_arbperl_makefile.pl (new 50)
westram 2013-10-30 15:58 Rev.: 10971


* use compiler settings from ARB-Makefile (A_CXX)

4 lines of code changed in 2 files:

  • PERL2ARB: DARWIN.PL (+2 -2), LINUX.PL (+2 -2)
westram 2013-09-27 15:55 Rev.: 10678


* hack to allow combination of gcc 4.7.3 and perl 5.10.1
- failed compilation due to an incompatibility in XS_VERSION_BOOTCHECK (see also [10566])
- simply removes '-std=gnu++11' for the above combination

15 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+15 -1)
westram 2013-09-27 12:25 Rev.: 10675


- dump used perl version to build log

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1)
westram 2013-09-10 11:32 Rev.: 10568


- fix warnings in PERL2ARB (most by removing option '-Weffc++')

8 lines of code changed in 2 files:

  • PERL2ARB: ARB_ext.c (+1 -1), Makefile.main (+7 -3)
westram 2013-09-09 18:08 Rev.: 10566


* pass down $(cppflags) (esp. '-std=gnu++11')
* PERL2ARB/Makefile now depends on ARB main Makefile (has to change if settings change there)

amendment:
* breaks compilation with gcc 4.7.3 and perl 5.10.1 (XS_VERSION_BOOTCHECK does not compile
{{{
ARB.c:10863:5: error: unable to find string literal operator 'operator"" SVf'
}}}
). On ubuntu 13.04 (where 4.7.3 is the system compiler) it works.

2 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+2 -1)
westram 2013-03-27 17:15 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.

2 lines of code changed in 1 file:

  • PERL2ARB: DARWIN.PL (+2 -2)
westram 2013-03-23 12:52 Rev.: 9724


* fixed 2 broken code links

2 lines of code changed in 2 files:

  • PERL2ARB: ARB.default.xs (+1 -1), typemap (+1 -1)
westram 2013-02-13 13:23 Rev.: 9574


- show from where dependencies are updated

1 lines of code changed in 1 file:

  • PERL2ARB: Makefile.main (+1 -1)

(83 more)

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