/trunk Developers: westram

Activity by Clock Time

Activity in Directories

Most Recent Commits

westram 2026-08-07 11:20 Rev.: 19983

* adds const flavors for two templates in {{{RootAsWindowCallback}}}
- this attempts to fix two remaining ambiguity errors with clang21.

25 lines of code changed in 1 file:

• SL/CB: rootAsWin.h (+25 -2)

westram 2026-08-06 20:11 Rev.: 19982

* fix {{{ParamIsMutable}}} for types passed by value (now no longer considered as mutable).

19 lines of code changed in 2 files:

• SL/CB: cb.cxx (+11 -11), cbtypes.h (+8 -7)

westram 2026-08-06 20:06 Rev.: 19981

* add tests for pointer-references and pointer-pointers.

16 lines of code changed in 1 file:

• SL/CB: cb.cxx (+16)

westram 2026-08-06 17:04 Rev.: 19980

* also remove template-backtrace-limit for clang.

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2026-08-06 16:34 Rev.: 19979

* increase macro backtrace/tracking limits for clang/gcc

11 lines of code changed in 1 file:

• Makefile (+11)

westram 2026-08-06 15:07 Rev.: 19978

* fix {{{CONST_VARIANT_REQUIRED}}}
- an extra (more) const variant of each callback builder is required for each mutable parameter (and for all combinations of such parameters).
- add template {{{ParamIsMutable}}} to detect that condition
* replaces the template {{{RequiresConstVariant}}} (this was completely broken; see test results added with r19977)

22 lines of code changed in 2 files:

• SL/CB: cb.cxx (+15 -17), cbtypes.h (+7 -8)

westram 2026-08-06 14:44 Rev.: 19977

* add static assertions for macro {{{CONST_VARIANT_REQUIRED}}} (shows misbehavior).

41 lines of code changed in 1 file:

• SL/CB: cb.cxx (+41)

westram 2026-08-03 13:14 Rev.: 19976

* update info on preprocessing.
* ignore and allow to delete *.ii (preprocessor output) and *.s (assembler output).

17 lines of code changed in 3 files:

• .gitignore (+2), Makefile (+12 -1)
• SOURCE_TOOLS: svn_apply_ignores.pl (+3)

westram 2026-07-31 16:51 Rev.: 19975

* do not create ambiguous template variants via {{{CBTYPE_FVV_BUILDER_P1}}}.

7 lines of code changed in 1 file:

• SL/CB: cbtypes.h (+7 -7)

westram 2026-07-31 15:53 Rev.: 19974

* avoid ambiguous callback template variants
- was caused by permutating constness of callback parameters
- now avoided using
* {{{std::enable_if}}} to avoid instantiation, and
* {{{RequiresConstVariant}}} to test parameter constness.
* commit is expected to fail build in callback tests
- reason: change was not applied to {{{CBTYPE_FVV_BUILDER_P1}}}
* there are several other macros which may generate ambiguous callback template variants (see comments)
* a big *thank you* goes to jan, who worked with {{{OpenCode}}} to identify the problem, and who provided me with the fundamental AI solution.

48 lines of code changed in 1 file:

• SL/CB: cbtypes.h (+48 -25)

westram 2026-07-31 15:40 Rev.: 19973

* force make to print directory.

1 lines of code changed in 1 file:

• Makefile (+1)

westram 2026-07-31 15:39 Rev.: 19972

* fix linking of unit tests for OSX.

9 lines of code changed in 1 file:

• SOURCE_TOOLS: needed_libs.pl (+9 -3)

westram 2026-07-30 16:54 Rev.: 19971

* partial merge from 'gcc' into 'trunk'
- fixes {{{make clean}}} after switching back from branch 'gcc'
- adds: [19929/branches/gcc]

7 lines of code changed in 1 file:

• GDE/SINA: Makefile (+7 -2)

westram 2026-07-03 10:31 Rev.: 19919

* force downgrade to c++14 standard for RNACMA.
* document problems with upgrading eigen + used workaround.
* add commented-out trace code to Makefile.

30 lines of code changed in 2 files:

• HEADERLIBS: README (+15)
• RNACMA: Makefile (+15 -1)

westram 2026-06-30 10:45 Rev.: 19916

* fix compile with clang 6 under linux
- parts of {{{TEST_naninf}}} also fails using clang under linux.
- parse real clang version from detailed version info
* AFAIK this effectively already happens under OSX (since change r12860).
- also set USE_OPENMP=0 for clang under linux.
- fix undefined code: variable length arrays (VLAs) cannot be initialized at declaration.
- use {{{-std=gnu++17}}} for clang.
- {{{str_iequal}}} + {{{count_spaces}}} fail to build as {{{constexpr}}} under clang.

40 lines of code changed in 5 files:

• Makefile (+4 -8)
• CONVERTALN: global.h (+2 -2)
• CORE: arb_diff.cxx (+3 -3)
• SL/TREE_READ: TreeRead.cxx (+6 -3)
• SOURCE_TOOLS: arb_compiler_version.pl (+25 -4)

westram 2026-06-30 10:22 Rev.: 19915

* stuff leaks in {{{TEST_SLOW_treeIO_stable}}} + {{{setBranchName_acceptingBootstrap}}}
- DRY code in latter

10 lines of code changed in 2 files:

• SL/TREE_READ: TreeRead.cxx (+6 -13)
• TOOLS: arb_consensus_tree.cxx (+4 -1)

westram 2026-06-30 10:13 Rev.: 19914

* partial merge from 'gcc' into 'trunk'
* adds: [19738/branches/gcc]

21 lines of code changed in 3 files:

• Makefile (+18 -9)
• PROBE: PT_new_design.cxx (+1 -1)
• TEMPLATES: cxxforward.h (+2 -2)

westram 2026-06-26 15:01 Rev.: 19910

* reintegrates 'tree' into 'trunk'
- fixes #787
- implements #668 + #845
- contains several changes related to #774
* adds:
- log:branches/revert@18784:18786
- log:branches/tree@18706:18758,18787:19813,19816:19909
- log:branches/update@19813:19814

7050 lines of code changed in 236 files:

• arb_CHANGES.txt (+4)
• ARBDB: TreeNode.cxx (+176 -26), TreeNode.h (+87 -20), ad_prot.h (+1), ad_t_prot.h (+4 -1), adlang1.cxx (+1 -1), adseqcompr.cxx (+2 -2), adstring.cxx (+5), adtree.cxx (+140 -52), arbdb.cxx (+1 -1), arbdbt.h (+1)
• CONSENSUS_TREE: Makefile (+2)
• CORE: arb_strbuf.h (+5)
• DIST: DI_clusters.cxx (+1 -1)
• HELP_SOURCE/source: nt_tree_settings_bootstrap.hlp (+1), tbl_boot2len.hlp (+10 -4), tr_export.hlp (+16 -3), tr_import.hlp (+14 -4)
• NTREE: Makefile (+5), NT_extern.cxx (+6 -5), NT_sort.cxx (+1 -1), NT_tree_cmp.cxx (+3 -3), ad_trees.cxx (+101 -26)
• PARSIMONY: PARS_dtree.cxx (+25 -25)
• PERL2ARB: typemap (+5 -1)
• SEQ_QUALITY: SQ_main.cxx (+1 -1)
• SL/AP_TREE: AP_Tree.cxx (+4 -2)
• SL/ARB_TREE: ARB_Tree.cxx (+2 -2), ARB_Tree.hxx (+3 -2)
• SL/NEIGHBOURJOIN: NJ.cxx (+1 -1)
• SL/PVP: pvp.cxx (+1 -1)
• SL/SPECSEL: selection_admin.cxx (+1 -1)
• SL/TREEDISP: TreeCallbacks.cxx (+30 -8), TreeDisplay.cxx (+46 -12), TreeDisplay.hxx (+1 -1)
• SL/TREE_READ: LabelTranslator.cxx (new 144), LabelTranslator.h (new 74), Makefile (+36), TreeRead.cxx (+558 -95), TreeRead.h (+5 -2), TreeTools.cxx (+12 -9)
• SL/TREE_WRITE: TreeWrite.cxx (+86 -25), TreeWrite.h (+11 -1)
• SOURCE_TOOLS: generate_all_links.sh (+2)
• STAT: ST_ml.cxx (+2 -2)
• TEMPLATES: ErrorOrType.h (+1), arb_unordered_set.h (new 33)
• TOOLS: Makefile (+12), arb_calc_pvp.cxx (+1 -1), arb_consensus_tree.cxx (+68 -14), arb_export_newick.cxx (+44 -15), arb_read_tree.cxx (+7 -7), arb_test.cxx (+11 -5)
• UNIT_TESTER: Makefile.setup.template (+3 -2), reporter.pl (+1 -1)
• UNIT_TESTER/run: group_xfer_21.log.expected (+1 -1)
• UNIT_TESTER/run/consense/1: consense1_expected.tree (+44 -44), consense1_single_expected.tree (+44 -44)
• UNIT_TESTER/run/consense/2: consense2_expected.tree (+116 -116)
• UNIT_TESTER/run/consense/3: consense3_expected.tree (+243 -243)
• UNIT_TESTER/run/consense/4: disjunct_merged_expected.tree (+30 -30), overlap_merged_expected.tree (+30 -30), overlap_mini_merged_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/5: help_merged_expected.tree (+12 -12)
• UNIT_TESTER/run/consense/6: overlap_twothirds_merged_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/7: overlap_mostly_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/8: overlap2_mostly_expected.tree (new)
• UNIT_TESTER/run/pars: nucl-add-NNI.tree.expected (+28 -28), nucl-add-quick.tree.expected (+28 -28), nucl-addPart-CloButyP.tree.expected (new), nucl-addPart-CorGlutP-CloButyP.tree.expected (new), nucl-addPart-CorGlutP.tree.expected (+29 -29), nucl-addPart-bug609.tree.expected (+34 -34), nucl-addPartialAsFull-CorGlutP.tree.expected (+30 -30), nucl-calclength.tree.expected (+28 -28), nucl-initial.tree.expected (+27 -27), nucl-opti-NNI.tree.expected (+28 -28), nucl-opti-all-NNI.tree.expected (+28 -28), nucl-opti-global.tree.expected (+28 -28), nucl-opti-marked-global.tree.expected (+28 -28), nucl-opti-visible-global.tree.expected (+28 -28), nucl-readdall-NNI.tree.expected (+28 -28), nucl-readdall-quick.tree.expected (+28 -28), nucl-removed.tree.expected (+15 -15), prot-add-NNI.tree.expected (+20 -20), prot-add-quick.tree.expected (+20 -20), prot-addPart-MucRaceP-StrCoelP.tree.expected (+24 -24), prot-addPart-MucRaceP.tree.expected (new), prot-addPart-StrCoelP.tree.expected (new), prot-addPart-bug609.tree.expected (+26 -26), prot-addPartialAsFull-MucRaceP.tree.expected (+22 -22), prot-calclength.tree.expected (+14 -14), prot-initial.tree.expected (+20 -20), prot-mixed.tree.expected (+14 -14), prot-opti-NNI.tree.expected (+17 -17), prot-opti-all-NNI.tree.expected (+19 -19), prot-opti-global.tree.expected (+19 -19), prot-opti-marked-global.tree.expected (+20 -20), prot-removed.tree.expected (new)
• UNIT_TESTER/run/trees: acc.tree (new 32), acc_name_fullname-nondup.tree (new 24), acc_name_fullname.tree (new 46), bg_exp_p_Bs100GrpLen_1.tree (new 50), bg_exp_p_Bs100GrpLen_2.tree (new 50), bg_exp_p_Bs100Grp_1.tree (new 50), bg_exp_p_Bs100Grp_2.tree (new 50), bg_exp_p_Bs100Len_0.tree (new 50), bg_exp_p_Bs100Len_1.tree (new 50), bg_exp_p_Bs100Len_2.tree (new 50), bg_exp_p_Bs100_0.tree (new 50), bg_exp_p_Bs100_1.tree (new 50), bg_exp_p_Bs100_2.tree (new 50), bg_exp_p_BsGrpLen_0.tree (del), bg_exp_p_BsGrpLen_1.tree (new), bg_exp_p_BsGrpLen_2.tree (new), bg_exp_p_BsGrp_0.tree (del), bg_exp_p_BsGrp_1.tree (+4 -4), bg_exp_p_BsGrp_2.tree (+4 -4), bg_exp_p_BsLen_0.tree (+32 -32), bg_exp_p_BsLen_1.tree (new 50), bg_exp_p_BsLen_2.tree (new 50), bg_exp_p_Bs_0.tree (new), bg_exp_p_Bs_1.tree (new 50), bg_exp_p_Bs_2.tree (new 50), bg_exp_p_CusGrpLen_1.tree (new 50), bg_exp_p_CusGrpLen_2.tree (new 50), bg_exp_p_CusGrp_1.tree (new 50), bg_exp_p_CusGrp_2.tree (new 50), bg_exp_p_CusLen_1.tree (new 50), bg_exp_p_CusLen_2.tree (new 50), bg_exp_p_Cus_1.tree (new 50), bg_exp_p_Cus_2.tree (new 50), bg_exp_p_GrpLen_0.tree (+31 -31), bg_exp_p_Grp_0.tree (new), bg_exp_p_Len_0.tree (+31 -31), bg_exp_p_Rem100GrpLen_1.tree (new 50), bg_exp_p_Rem100GrpLen_2.tree (new 50), bg_exp_p_Rem100Grp_1.tree (new 50), bg_exp_p_Rem100Grp_2.tree (new 50), bg_exp_p_Rem100Len_1.tree (new 50), bg_exp_p_Rem100Len_2.tree (new 50), bg_exp_p_Rem100_1.tree (new 50), bg_exp_p_Rem100_2.tree (new 50), bg_exp_p_RemGrpLen_1.tree (new 50), bg_exp_p_RemGrpLen_2.tree (new 50), bg_exp_p_RemGrp_1.tree (new 50), bg_exp_p_RemGrp_2.tree (new 50), bg_exp_p_RemLen_1.tree (new 50), bg_exp_p_RemLen_2.tree (new 50), bg_exp_p_Rem_1.tree (new 50), bg_exp_p_Rem_2.tree (new 50), bg_exp_s_Bs100GrpLen_1.tree (new 35), bg_exp_s_Bs100GrpLen_2.tree (new 35), bg_exp_s_Bs100Grp_1.tree (new 35), bg_exp_s_Bs100Grp_2.tree (new 35), bg_exp_s_Bs100Len_0.tree (new 35), bg_exp_s_Bs100Len_1.tree (new 35), bg_exp_s_Bs100Len_2.tree (new 35), bg_exp_s_Bs100_0.tree (new 35), bg_exp_s_Bs100_1.tree (new 35), bg_exp_s_Bs100_2.tree (new 35), bg_exp_s_BsGrpLen_0.tree (del), bg_exp_s_BsGrpLen_1.tree (new), bg_exp_s_BsGrpLen_2.tree (+32 -32), bg_exp_s_BsGrp_0.tree (del), bg_exp_s_BsGrp_1.tree (new), bg_exp_s_BsGrp_2.tree (new), bg_exp_s_BsLen_0.tree (+32 -32), bg_exp_s_BsLen_1.tree (new 35), bg_exp_s_BsLen_2.tree (new 35), bg_exp_s_Bs_0.tree (+4 -4), bg_exp_s_Bs_1.tree (new 35), bg_exp_s_Bs_2.tree (new 35), bg_exp_s_CusGrpLen_1.tree (new 35), bg_exp_s_CusGrpLen_2.tree (new 35), bg_exp_s_CusGrp_1.tree (new 35), bg_exp_s_CusGrp_2.tree (new 35), bg_exp_s_CusLen_1.tree (new 35), bg_exp_s_CusLen_2.tree (new 35), bg_exp_s_Cus_1.tree (new 35), bg_exp_s_Cus_2.tree (new 35), bg_exp_s_GrpLen_0.tree (new), bg_exp_s_Grp_0.tree (+2 -2), bg_exp_s_Len_0.tree (new), bg_exp_s_Rem100GrpLen_1.tree (new 35), bg_exp_s_Rem100GrpLen_2.tree (new 35), bg_exp_s_Rem100Grp_1.tree (new 35), bg_exp_s_Rem100Grp_2.tree (new 35), bg_exp_s_Rem100Len_1.tree (new 35), bg_exp_s_Rem100Len_2.tree (new 35), bg_exp_s_Rem100_1.tree (new 35), bg_exp_s_Rem100_2.tree (new 35), bg_exp_s_RemGrpLen_1.tree (new 35), bg_exp_s_RemGrpLen_2.tree (new 35), bg_exp_s_RemGrp_1.tree (new 35), bg_exp_s_RemGrp_2.tree (new 35), bg_exp_s_RemLen_1.tree (new 35), bg_exp_s_RemLen_2.tree (new 35), bg_exp_s_Rem_1.tree (new 35), bg_exp_s_Rem_2.tree (new 35), bootstrap_groups.arb (new), full_name-unique.tree (new 22), full_name.tree (new 32)

westram 2026-05-21 16:02 Rev.: 19811

* updated PHYLIP urls
* store {{{Interpretation of "Newick's 8:45" Tree Format Standard}}}

210 lines of code changed in 6 files:

• GDE/PHYLIP/doc: draw.html (+2 -2), main.html (+10 -10)
• GDE/TREEPUZZLE/doc: manual.html (+1 -1)
• HELP_SOURCE/source: tr_import.hlp (+1 -1)
• SOURCE_TOOLS/docs: newick_845_doc.html (new 191), newick_doc.html (+5)

westram 2026-05-18 15:28 Rev.: 19808

* update changes.

1 lines of code changed in 1 file:

• arb_CHANGES.txt (+1)

(9026 more)