Directory CORE/

Total Files:
48
Deleted Files:
3
Lines of Code:
9007

[root]/CORE

Lines of Code

CORE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 517 (100.0%) 10597 (100.0%) 20.4
westram 494 (95.6%) 9998 (94.3%) 20.2
epruesse 23 (4.4%) 599 (5.7%) 26.0

Most Recent Commits

westram 2019-05-10 13:57 Rev.: 17877


* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

17 lines of code changed in 5 files:

  • CORE: BufferedFileReader.h (+3 -1), arb_progress.h (+6 -6), arb_strarray.cxx (+2 -2), arb_strarray.h (+1), pos_range.h (+5)
westram 2019-05-02 15:54 Rev.: 17840


* add (n)catTrimmed to GBS_strstruct

16 lines of code changed in 1 file:

  • CORE: arb_strbuf.h (+16)
westram 2019-04-29 14:44 Rev.: 17836


* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

1 lines of code changed in 1 file:

  • CORE: arb_msg.cxx (+1)
westram 2019-04-26 16:56 Rev.: 17817


* Unit tests:
- Makefile.setup.template:
* move config sections (rarely used to bottom).
* fix trailing whitespace.
* add fun restriction vs crashtests.
* add xrefs.
* force Conf mode.
- rename 5 tests (which call crashtests) by adding suffix -> allows to filter
- count tests skipped by RESTRICT_FUN/RESTRICT_MODULE as "skipped" => list them in summary.
- ignore directory UNIT_TESTER/tests.

1 lines of code changed in 1 file:

  • CORE: arb_mem.cxx (+1 -2)
westram 2019-04-05 19:32 Rev.: 17748


* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

  • CORE: arb_diff.cxx (+1 -1)
westram 2019-04-04 16:50 Rev.: 17743


* rename diff params into fgot + fwant.
* create diff in direction "wanted->got".
* add missing defines for WARN_MISS_ARBDIFF.

1 lines of code changed in 1 file:

  • CORE: arb_diff.cxx (+1 -1)
westram 2019-04-02 17:50 Rev.: 17726


* change result type of ConfigMapping::config_string() to string.
- fix callers.

12 lines of code changed in 2 files:

  • CORE: ConfigMapping.cxx (+10 -11), ConfigMapping.h (+2 -5)
westram 2019-04-01 17:41 Rev.: 17724


* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

242 lines of code changed in 3 files:

  • CORE: ConfigMapping.cxx (+233 -2), ConfigMapping.h (+7 -50), Makefile (+2)
westram 2019-03-31 11:41 Rev.: 17711


* move {{{ConfigMapping}}} -> CORE library

212 lines of code changed in 3 files:

  • CORE: ConfigMapping.cxx (new 65), ConfigMapping.h (new 133), Makefile (+14)
westram 2019-03-25 17:01 Rev.: 17695


* dump stack-trace for assertions (failing from testcode) into compile-log
- works only if DEBUG=1, UNIT_TESTS=1 and SANITIZE=1|all

30 lines of code changed in 4 files:

  • CORE: arb_assert.h (+19), arb_core.h (+1), arb_signal.cxx (+9), arb_signal.h (+1)
westram 2018-11-21 13:05 Rev.: 17603


* do not test group- and world-settings when testing modes of files

7 lines of code changed in 1 file:

  • CORE: arb_file.cxx (+7 -4)
westram 2018-10-19 16:18 Rev.: 17491


* partial merge from 'fix' into 'trunk'
- fix OSX build (was broken by [17387]):
* uses wrapper {{{ARB_strchrnul}}} instead of directly using {{{strchrnul}}}
* OSX version uses replacement code
* adds: log:branches/fix@17486:17490

30 lines of code changed in 2 files:

  • CORE: arb_string.cxx (+19 -2), arb_string.h (+11)
westram 2018-09-20 18:43 Rev.: 17396


* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

3 lines of code changed in 3 files:

  • CORE: arb_cs.cxx (+2 -2), arb_cs.h (-1), arb_diff.cxx (+1 -1)
westram 2018-09-18 17:30 Rev.: 17378


* allow to pass zero as separator to GBT_join_strings => join w/o separator

5 lines of code changed in 1 file:

  • CORE: arb_strarray.cxx (+5 -4)
westram 2018-09-12 12:32 Rev.: 17363


* use marker from #741 (rel r17358)

2 lines of code changed in 1 file:

  • CORE: arb_cs.cxx (+2 -4)
westram 2018-09-11 12:23 Rev.: 17358


* OSX unittest "fixes":
- TEST_open_socket (disabled; this test is a PITA anyway)
- results provided by regex lib versions differs (should test sth different)

6 lines of code changed in 1 file:

  • CORE: arb_cs.cxx (+6)
westram 2018-07-23 16:52 Rev.: 17262


* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

323 lines of code changed in 4 files:

  • CORE: arb_handlers.cxx (+58 -17), arb_handlers.h (+3 -3), arb_progress.cxx (+116 -95), arb_progress.h (+146 -89)
westram 2018-07-10 16:48 Rev.: 17178


* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

1 lines of code changed in 1 file:

  • CORE: arb_strbuf.h (+1 -1)
westram 2018-07-03 17:19 Rev.: 17140


* full update from child 'fix' into 'trunk'
- fixes deadlock (for search/replace expressions containing {{{\/}}})
* adds: log:branches/fix@17124:17138

1 lines of code changed in 1 file:

  • CORE: arb_match.cxx (+1)
westram 2018-05-08 15:16 Rev.: 17002


* reintegrates 'fix' into 'trunk'
- fixes #721
* adds: log:branches/fix@16922:16938,16961:17001

1 lines of code changed in 1 file:

  • CORE: arb_string.cxx (+1)
westram 2018-05-05 14:22 Rev.: 16990


* pointer overflow reported by 8.1-sanitizer was in fact pointer arithmetic applied to NULp

1 lines of code changed in 1 file:

  • CORE: arb_string.h (+1 -1)
westram 2018-05-05 13:03 Rev.: 16989


* [16988] caused tests to fail with 7.3 sanitizer (NULp passed to memchr)
- fixes behavior of {{{ARB_strpartdup(NULp, ...)}}}: now always returns NULp

4 lines of code changed in 1 file:

  • CORE: arb_string.h (+4 -3)
westram 2018-05-05 12:16 Rev.: 16988


* gcc 8.1 sanitizer complains about a pointer overflow in ARBDB tests (in {{{ARB_strndup}}})
- document behavior of ARB_strpartdup + ARB_strndup (passes tests with gcc 7.1 sanitizer)

44 lines of code changed in 1 file:

  • CORE: arb_string.cxx (+44)
westram 2018-05-04 18:06 Rev.: 16986


* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

4 lines of code changed in 2 files:

  • CORE: arb_cs.cxx (+3 -1), arb_string.cxx (+1 -1)
westram 2018-04-30 18:27 Rev.: 16936


* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

6 lines of code changed in 1 file:

  • CORE: arb_assert.h (+6 -10)
westram 2018-02-15 12:51 Rev.: 16861


* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

107 lines of code changed in 2 files:

  • CORE: arb_diff.cxx (+104 -60), arb_diff.h (+3 -1)
westram 2017-12-08 14:30 Rev.: 16799


* reintegrates 'fix' into 'trunk'
- implements #773
- tested with asan + fixed harmless undefined behavior
* adds: log:branches/fix@16793:16798

3 lines of code changed in 1 file:

  • CORE: arb_zfile.cxx (+3)
westram 2017-12-04 12:53 Rev.: 16783


* remove unused code

0 lines of code changed in 1 file:

  • CORE: arb_mem.h (-5)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

15 lines of code changed in 5 files:

  • CORE: BufferedFileReader.cxx (+2 -4), arb_assert.h (+7), arb_file.cxx (+2 -2), arb_match.cxx (+1 -1), arb_mem.cxx (+3 -3)
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

168 lines of code changed in 26 files:

  • CORE: BufferedFileReader.h (+5 -5), FileContent.h (+1 -1), MultiFileReader.cxx (+9 -9), MultiFileReader.h (+1 -1), arb_assert.h (+5 -5), arb_cs.cxx (+12 -12), arb_diff.cxx (+10 -10), arb_file.cxx (+16 -16), arb_handlers.cxx (+3 -3), arb_match.cxx (+16 -16), arb_mem.cxx (+4 -4), arb_misc.cxx (+7 -7), arb_msg.cxx (+15 -15), arb_msg.h (+3 -3), arb_pattern.cxx (+2 -2), arb_progress.cxx (+7 -7), arb_progress.h (+5 -5), arb_signal.cxx (+1 -1), arb_sort.cxx (+1 -1), arb_strarray.cxx (+5 -5), arb_strarray.h (+7 -7), arb_strbuf.h (+9 -9), arb_string.cxx (+7 -7), arb_string.h (+3 -3), arb_zfile.cxx (+11 -11), pos_range.cxx (+3 -3)
westram 2017-11-17 13:54 Rev.: 16668


* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

11 lines of code changed in 1 file:

  • CORE: arb_mem.cxx (+11 -5)
westram 2017-11-12 15:53 Rev.: 16649


* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

1 lines of code changed in 1 file:

  • CORE: arb_misc.cxx (+1 -1)
westram 2017-10-31 16:28 Rev.: 16595


* partial merge from 'vectorize' into 'trunk'
- reduce failures of {{{TEST_open_socket}}}
* adds: log:branches/vectorize@16586,16592:16594

68 lines of code changed in 1 file:

  • CORE: arb_cs.cxx (+68 -22)
westram 2017-10-31 14:13 Rev.: 16592


* partial merge from 'vectorize' into 'trunk'
- eliminates {{{usleep}}} (using {{{nanosleep}}} via {{{ARB_sleep}}})
* adds: log:branches/vectorize@16587:16591

8 lines of code changed in 3 files:

  • CORE: Makefile (+1), arb_cs.cxx (+6 -4), arb_handlers.cxx (+1 -1)
westram 2017-10-21 13:40 Rev.: 16564


* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

1 lines of code changed in 1 file:

  • CORE: arb_misc.cxx (+1 -1)
westram 2017-10-18 14:54 Rev.: 16552


* partial merge from 'io' into 'trunk'
- {{{GB_rename_file}}} -> {{{GB_move_file}}}
- add {{{GB_copy_file}}}
- add safe versions of both
* adds: log:branches/io@16527:16532

160 lines of code changed in 2 files:

  • CORE: arb_file.cxx (+156 -6), arb_file.h (+4 -1)
westram 2017-10-11 10:30 Rev.: 16514


* declare some classes/methods final

1 lines of code changed in 1 file:

  • CORE: arb_strarray.h (+1 -1)
westram 2017-10-08 15:54 Rev.: 16508


* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

4 lines of code changed in 1 file:

  • CORE: arb_assert.h (+4 -2)
westram 2017-09-18 19:57 Rev.: 16383


* reintegrates 'aci' into 'trunk'
- split TEST_GB_command_interpreter (too big, esp. for sanitizer)
- fix undefined behavior in {{{GBS_regreplace}}}
- reduce test DB
* adds: log:branches/aci@16376:16382

15 lines of code changed in 1 file:

  • CORE: arb_match.cxx (+15 -6)
westram 2017-09-18 15:23 Rev.: 16374


* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

31 lines of code changed in 4 files:

  • CORE: arb_match.cxx (+18 -3), arb_pattern.cxx (-1), arb_strbuf.cxx (+1 -2), arb_strbuf.h (+12)

(206 more)

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