Directory PERL2ARB/

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westram 2023-12-07 18:22 Rev.: 19493

* homebrew build looked for wrong lib-suffix. patch from jan. thx :)
* fixed a typo in {{{warn_undefined_symbols.pl}}}

4 lines of code changed in 2 files:

• PERL2ARB: Makefile.main (+3 -1), warn_undefined_symbols.pl (+1 -1)

westram 2023-09-13 17:33 Rev.: 19489

* reintegrates 'macros' into 'trunk'
* implements #856
* adds: log:branches/macros@19482:19488

17 lines of code changed in 1 file:

• PERL2ARB: ARB.pm (+17)

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

2 lines of code changed in 1 file:

• PERL2ARB: extract_perl_interface.pl (+2 -2)

westram 2022-03-19 14:06 Rev.: 18967

* correct handling of Makemaker-Makefile:
- remove workaround-hack (did accept failure + call make again)
- add lines to mark makefile recursion.
- fix reasons for hack:
* target 'Makefile' now depends on 'Makefile.PL' => 'Makefile' will no longer recreate itself and fail on first call
* avoid target '$(DOC)' triggers 'ARB.c'. Instead it depends on '$(TARGET_SO)'. Fixes random failure caused by parallel execution of both sub-targets.
- reduce risc of wrong use (by additional restrictions when conflicting targets may be called).

28 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+28 -10)

westram 2022-01-29 14:33 Rev.: 18907

* partial merge from 'stable' into 'trunk'
* adds: log:branches/stable@18903:18906

65 lines of code changed in 3 files:

• PERL2ARB: ARB.pm (+10 -2), Makefile.main (+6 -1), warn_undefined_symbols.pl (new 49)

westram 2021-10-04 16:54 Rev.: 18749

* bail out when overloaded functions are exported into perl interface.
- fails build with
{{{
Error: ambiguous function definition for 'GBT_log_to_tree_remark' (overloaded method exported to perl?)
Makefile.main:153: recipe for target 'perl-interface-function-list.txt' failed
}}}
- fixed by [18750]

1 lines of code changed in 1 file:

• PERL2ARB: extract_perl_interface.pl (+1 -1)

westram 2021-10-04 16:51 Rev.: 18748

* explicitely define function prefixes.
* link to interface generator code (and vv).
* bail out on ambiguous function suffix.

18 lines of code changed in 1 file:

• PERL2ARB: extract_perl_interface.pl (+18 -12)

westram 2021-10-02 12:13 Rev.: 18747

* gitignore file generated since [18746]

1 lines of code changed in 1 file:

• PERL2ARB: .gitignore (+1)

westram 2021-10-01 17:07 Rev.: 18746

* adds a script which generates a list of perl interface functions
- call during arb build
* update DOC.txt
- mention that list
- very basic description of interface
- describe the ancient information which already has been in this document.

783 lines of code changed in 4 files:

• PERL2ARB: DOC.html (del), DOC.txt (new 587), Makefile.main (+7 -2), extract_perl_interface.pl (new 189)

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

* eliminate trailing whitespace from Makefiles.

4 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+4 -4)

westram 2020-09-23 12:34 Rev.: 18476

* provide perl function {{{ARB::set_inGlobalEvalState}}}.
* use it to inform {{{ARB.pm}}} that {{{import_from_table.pl}}} uses eval (and does not like to get aborted).

18 lines of code changed in 1 file:

• PERL2ARB: ARB.pm (+18 -3)

westram 2020-02-26 18:46 Rev.: 18339

* full update from child 'fix' into 'trunk'
- fixes #754
* adds: log:branches/fix@18333:18338

4 lines of code changed in 1 file:

• PERL2ARB: ARB.pm (+4 -3)

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

11 lines of code changed in 1 file:

• PERL2ARB: .gitignore (new 11)

westram 2017-11-28 17:09 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 13:54 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 13:59 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 11:17 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 17:23 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 09:08 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 17:02 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 11:51 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 16:15 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 15:43 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 13:22 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 13:22 Rev.: 12889

* ':' -> '::'

7 lines of code changed in 1 file:

• PERL2ARB: DOC.html (+7 -7)

westram 2014-09-19 12:35 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 12:35 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 09:57 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 17:24 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 14:02 Rev.: 12273

- no magic exit codes

1 lines of code changed in 1 file:

• PERL2ARB: perlmain_source.c (+1 -1)

westram 2014-05-06 12:00 Rev.: 12151

pass down CXX_INCLUDES

1 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+1 -1)

westram 2014-03-31 09:17 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 15:21 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 19:52 Rev.: 11537

- removed obsolete define

1 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+1 -1)

westram 2014-01-14 14:47 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 12:48 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 16:15 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 11:04 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 20:28 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 19:11 Rev.: 11035

* untabified

9 lines of code changed in 1 file:

• PERL2ARB: ARB_ext.c (+9 -9)

(95 more)