August 2025 Commit Log

Number of Commits:

9

Number of Active Developers:

1

westram 2025-08-13 09:25 #9 Rev.: 19532

* reintegrates 'help' into 'trunk'
- tweak arb documentation:
* automatically link
- ticket references to arb bug tracker (only affects html version).
- found URLs.
* page titles
- warn about long titles.
- introduce {{{SUBTITLE}}}s (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
* cleanup header sections in all helpfiles.
* fix and/or update several help files.
* document syntax of help sources.
* build issues:
- when xml validation fails, next build no longer uses invalid xml => keeps failing.
- remove output files on error (including files below {{{ARBHOME/lib}}}).
- pipe output through logs to ensure proper wrapping in {{{Entering/Leaving}}} lines.
- moves {{{Tree admin}}} + {{{NDS}}} menu entries to top of menu
* adds: log:branches/help@18783:19531

3271 lines of code changed in 689 files:

• arb_CHANGES.txt (+6 -2)
• GDEHELP/HELP_WRITTEN: MrBayes.help (+1 -1), ProbCons.help (+1 -1), fasttree.help (+1 -1), muscle.help (+1 -1), raxml8.help (+2 -2)
• HELP_SOURCE: Makefile (+14 -8), arb_help.dtd (+3 -2), arb_help2xml.cxx (+203 -35), generate_index.pl (+42 -18), help.readme (+49), to_help.xsl (+51 -18), to_html.xsl (+20 -6)
• HELP_SOURCE/genhelp: Makefile (+4 -4), postprocess_genhelp.pl (+41 -8), standard.header (+4 -4)
• HELP_SOURCE/source: FAQS.hlp (new), FORM.hlp (+5 -5), Protection.hlp (new), aaali.hlp (new), accessibility_sai.hlp (+5 -5), aci.hlp (new), acisrt.hlp (+7 -8), ad_align.hlp (new), ad_extended.hlp (+8 -8), advice.hlp (new), alignment.hlp (+9 -9), ap_stack.hlp (+8 -8), arb.hlp (+18 -18), arb_commands.hlp (new), arb_db.hlp (new), arb_edit4.hlp (new), arb_envar.hlp (+7 -7), arb_export.hlp (new), arb_export_nds.hlp (+8 -8), arb_gde.hlp (new), arb_import.hlp (+13 -13), arb_intro.hlp (new), arb_merge.hlp (+10 -10), arb_merge_into.hlp (+7 -7), arb_merge_outof.hlp (+9 -9), arb_merge_workflow.hlp (new), arb_ntree.hlp (+73 -44), arb_pars.hlp (new), arb_pars_init.hlp (+8 -8), arb_secedit.hlp (+10 -10), asciiprint.hlp (new), awt_csp.hlp (new), bonds.hlp (new), bootstrap.hlp (new), branch_analysis.hlp (new), bugtracker.hlp (new 30), checkfield.hlp (new), chimera_check.hlp (+7 -7), cluster_group.hlp (+8 -8), color.hlp (new), color_loadsave.hlp (new), color_props.hlp (+7 -7), color_props_groups.hlp (new), color_ranges.hlp (+7 -7), colorize.hlp (+10 -10), compare_taxonomy.hlp (+7 -7), compare_topo.hlp (new), concatenate.hlp (+6 -7), consense_algo.hlp (+4 -4), consense_tree.hlp (new), consensus.hlp (+10 -10), consensus_def.hlp (+4 -4), console.hlp (+5 -5), copyNpaste.hlp (+8 -8), count_chars.hlp (new), csp_2_gnuplot.hlp (new), del_list.hlp (+11 -11), di_clusters.hlp (new), displayField.hlp (+6 -6), dist.hlp (+18 -18), dssp_ift.hlp (new), e4.hlp (new), e4_background_priority.hlp (new), e4_block.hlp (new), e4_consensus.hlp (+7 -7), e4_defaults.hlp (new), e4_get_species.hlp (+7 -7), e4_mode.hlp (+5 -5), e4_modsai.hlp (+9 -9), e4_options.hlp (+9 -9), e4_replace.hlp (new), e4_search.hlp (new), ecoliref.hlp (+5 -5), ed4_flags.hlp (+6 -6), ed4_nds.hlp (+6 -6), exec_bug.hlp (new), experiment_info.hlp (+7 -7), experiment_search.hlp (+7 -7), export_format.hlp (new), export_test.hlp (+5 -5), extended.hlp (new), faligner.hlp (+12 -12), field_sel_new.hlp (+8 -8), field_shader.hlp (+4 -4), gde_flat_ift.hlp (new), gde_menus.hlp (+1 -1), gen_create.hlp (+9 -9), gen_disp_style.hlp (+7 -7), gen_jump.hlp (+8 -8), gen_mode.hlp (new), gen_new_view.hlp (+5 -5), gen_options.hlp (+7 -7), gene_extract.hlp (new), gene_hide.hlp (new), gene_info.hlp (+6 -6), gene_map.hlp (+8 -8), gene_mark.hlp (new), gene_mode.hlp (+8 -8), gene_search.hlp (+16 -16), gene_species.hlp (new), gene_species_field_transfer.hlp (new), gene_species_mark.hlp (+8 -8), genes.hlp (new), glossary.hlp (+13 -13), group_by_field.hlp (new), group_rename.hlp (+7 -7), group_search.hlp (new), group_trees.hlp (new), helix.hlp (+11 -11), helixsym.hlp (+10 -10), help.hlp (new), import_test.hlp (new), importift.hlp (+8 -8), input_mask.hlp (new), input_mask_format.hlp (new), input_mask_new.hlp (new), insdel.hlp (new), insdel_sai.hlp (+7 -7), islandhopping.hlp (new), iupac-codes.hlp (+7 -7), keeled_groups.hlp (+4 -4), kernlin.hlp (new), macro.hlp (+7 -7), man_arb_edit4.hlp (new), manage_test.hlp (new), manual.hlp (new), mark.hlp (new), mark_duplicates.hlp (new), mark_genes.hlp (new), mark_list.hlp (new), markbyref.hlp (+5 -5), matrix_settings.hlp (new), max_freq.hlp (+10 -8), merge_species.hlp (+7 -7), mergetaggedfield.hlp (new), mg_alignment.hlp (new), mg_extendeds.hlp (new), mg_names.hlp (+4 -4), mg_preserve.hlp (new), mg_species.hlp (+4 -4), mg_species_configs.hlp (+8 -8), mg_trees.hlp (new), mg_xfer_field_of_listed.hlp (+4 -4), mg_xfer_field_of_sel.hlp (+7 -7), missbase.hlp (new), mod_field_list.hlp (+10 -10), mode.hlp (+21 -21), mode_group.hlp (new), mode_info.hlp (new), mode_kernlin.hlp (new), mode_length.hlp (new), mode_lzoom.hlp (new), mode_mark.hlp (new), mode_move.hlp (new), mode_nni.hlp (new), mode_optimize.hlp (new), mode_pzoom.hlp (+8 -8), mode_rotate.hlp (new), mode_select.hlp (+9 -9), mode_setroot.hlp (new), mode_spread.hlp (+8 -8), mode_swap.hlp (new), mode_width.hlp (new), mode_www.hlp (new), move_groups.hlp (new), mp_params.hlp (new), multifurcate.hlp (+5 -5), multiprobe.hlp (new), multiproberesults.hlp (new), namesadmin.hlp (new), ne_align_seq.hlp (+9 -9), nekey_map.hlp (new), newwindow.hlp (new), next_neighbours.hlp (+9 -9), next_neighbours_common.hlp (+13 -13), next_neighbours_listed.hlp (new), nni.hlp (+14 -14), no_tree.hlp (new), nt_align_select.hlp (new), nt_keys.hlp (+7 -7), nt_tree_marker_settings.hlp (+5 -5), nt_tree_select.hlp (+14 -20), nt_tree_settings.hlp (+7 -7), nt_tree_settings_bootstrap.hlp (new), nt_tree_settings_expert.hlp (new), optimize.hlp (+5 -5), organism_mark.hlp (+8 -8), organisms.hlp (+10 -10), pa_add.hlp (+7 -7), pa_bootstrap.hlp (+3 -3), pa_branchlengths.hlp (new), pa_globopti.hlp (new), pa_kernlin.hlp (new), pa_locopti.hlp (new), pa_mixtree.hlp (+7 -7), pa_optimizer.hlp (new), pa_partial.hlp (+9 -9), pa_quick.hlp (+9 -9), pa_reset.hlp (+8 -8), pa_value.hlp (new), pars.hlp (new), partial_sequences.hlp (+7 -7), pd_match_iupac.hlp (+8 -8), pd_spec_param.hlp (new), pfold.hlp (new), pfold_props.hlp (+8 -8), pfold_sai.hlp (new), ph_export_markerline.hlp (new), phylo.hlp (new), pm_spec_param.hlp (+7 -7), pos_var_pars.hlp (new), primer.hlp (new), primer_new.hlp (+6 -6), primer_result.hlp (+7 -7), probe_param.hlp (+9 -9), probeadmin.hlp (new), probedesign.hlp (+9 -9), probedesignresult.hlp (new), probematch.hlp (+5 -5), probespec.hlp (new), prop_configs.hlp (+8 -8), prop_configs_edit.hlp (new), props_frame.hlp (new), props_nds.hlp (+11 -11), props_www.hlp (new), proteinViewer.hlp (new), pt_server.hlp (+4 -4), questions.hlp (new), quit.hlp (+7 -7), realign_dna.hlp (new), reg.hlp (+11 -11), rename.hlp (new), rerepair.hlp (+7 -7), reset_win_layout.hlp (new), resortbyother.hlp (new), resorttree.hlp (new), rna3d_changeMolecule.hlp (new), rna3d_dispBases.hlp (new), rna3d_dispHelices.hlp (+10 -10), rna3d_dispMolecule.hlp (new), rna3d_general.hlp (+12 -10), rna3d_mapSeqData.hlp (+13 -13), rst_log_zoom.hlp (+8 -8), rst_phys_zoom.hlp (+8 -8), saiProbe.hlp (new), saicalc.hlp (new), save.hlp (+4 -4), save_matrix.hlp (+5 -5), savedef.hlp (+7 -7), scandb.hlp (new), search_duplicates.hlp (+7 -7), search_equal_fields.hlp (new), searching.hlp (+8 -8), sec_bonddef.hlp (+5 -5), sec_display.hlp (new), sec_imexport.hlp (new), sec_keys.hlp (new), sec_main.hlp (+10 -10), sec_mode.hlp (new), sec_props.hlp (new), secedit_imexport.hlp (new), security.hlp (new), sel_box.hlp (new), sel_fil.hlp (new), selected.hlp (new), selected_gene.hlp (new), seq_quality.hlp (+7 -7), sequence_colors.hlp (new), set_color_of_listed.hlp (new), set_protection.hlp (+8 -8), sina_main.hlp (+6 -7), sp_IDs.hlp (new), sp_del_mrkd.hlp (new), sp_info.hlp (+4 -4), sp_info_locked.hlp (new), sp_mark.hlp (+8 -8), sp_search.hlp (+15 -15), sp_sort_fld.hlp (new), sp_sort_phyl.hlp (+8 -8), sp_sp_2_ext.hlp (+8 -8), spa_copy.hlp (+4 -4), spa_create.hlp (new), spa_delete.hlp (+9 -9), spa_rename.hlp (+4 -4), spaf_convert.hlp (+7 -7), spaf_create.hlp (new), spaf_delete.hlp (+8 -8), spaf_reorder.hlp (new), species.hlp (new), species_configs.hlp (+8 -8), species_configs_highlight.hlp (+7 -7), species_configs_saveload.hlp (+7 -7), species_join.hlp (new), srt.hlp (+5 -5), st_ml.hlp (new), submission.hlp (+5 -5), sync_colors.hlp (+7 -7), syncroots.hlp (+5 -5), syncscroll.hlp (+5 -5), tags.hlp (new), tbl_boot2len.hlp (+7 -7), tbl_justify.hlp (new), tbl_reset.hlp (new), tbl_scale.hlp (new), ted_boot.hlp (+5 -5), tkeep_mrkd.hlp (+7 -7), toggle_secinfo.hlp (new), topology_shader.hlp (+5 -5), tr_export.hlp (+6 -6), tr_import.hlp (new), tr_jump.hlp (new), tr_type_dendro.hlp (new 34), tr_type_irs.hlp (+16 -16), tr_type_list.hlp (del), tr_type_nds.hlp (+16 -16), tr_type_radial.hlp (+16 -21), track_ali_changes.hlp (+7 -7), trans_anal.hlp (new), transl_table.hlp (+4 -4), translate_dna_2_pro.hlp (new), tree2file.hlp (+7 -7), tree2prt.hlp (+6 -6), tree_group.hlp (+5 -5), tree_pseudo.hlp (+7 -7), tree_shading.hlp (new), treeadm.hlp (+7 -7), trees.hlp (new), trm_boot.hlp (new), trm_del.hlp (+6 -6), trm_mrkd.hlp (+7 -7), undo.hlp (new), unittest.hlp (new), universal_ift.hlp (+5 -5), unmark_list.hlp (new), user_matrix.hlp (new), version.hlp (+5 -5), viewdiff.hlp (+8 -8), visualizeSAI.hlp (+7 -7), vn_delete.hlp (new), vn_import.hlp (new), vn_search.hlp (new), vn_suggest.hlp (new), write_field_list.hlp (+5 -5), xferset.hlp (+5 -5), xterm.hlp (new)
• HELP_SOURCE/source/prompt: format_alignments.hlp (new)
• NTREE: NT_extern.cxx (+5 -10)
• PARSIMONY: PARS_main.cxx (+1 -1)
• SOURCE_TOOLS: check_resources.pl (+1)
• UNIT_TESTER/run/help: unittest.xml (+1 -1)
• XML: xml.cxx (+2 -1)
• lib/pictures: help.fig (+14 -15)
• util: arb_fig (+1 -1)

westram 2025-08-07 17:50 #8 Rev.: 19517

* fix typo.

1 lines of code changed in 1 file:

• HELP_SOURCE/source: macro.hlp (+1 -1)

westram 2025-08-07 17:30 #7 Rev.: 19516

* document automation using macros.

20 lines of code changed in 2 files:

• HELP_SOURCE/source: arb_envar.hlp (+3 -3), macro.hlp (+17 -4)

westram 2025-08-07 17:27 #6 Rev.: 19515

* allow to reduce the time-to-wait on error, by defining {{{ARB_SCRIPTED_SECS_WAIT_ON_ERROR}}}.

16 lines of code changed in 3 files:

• HELP_SOURCE/source: arb_envar.hlp (new)
• SH: arb_launcher (+9 -4)

westram 2025-08-07 17:24 #5 Rev.: 19514

* do not ask (if sure to quit) while quitting from macro.

34 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+34 -32)

westram 2025-08-02 14:00 #4 Rev.: 19513

* fix part of #867:
- allow detection of macro running.
- {{{NT_exit()}}} waits for macro to terminate (up to 100 seconds).

82 lines of code changed in 6 files:

• NTREE: Makefile (+1), NT_extern.cxx (+59 -2)
• SL/MACROS: macro_gui.cxx (+9), macros.hxx (+1), trackers.cxx (+10 -2), trackers.hxx (+2)

westram 2025-08-01 15:29 #3 Rev.: 19512

* fix wrong group counts (slighly too many for some DBs).

1 lines of code changed in 1 file:

• PERL_SCRIPTS/DB: databaseReport.pl (+1 -1)

westram 2025-08-01 15:02 #2 Rev.: 19511

* DRYed code to read entries
* simplified nested sort conditions

53 lines of code changed in 1 file:

• PERL_SCRIPTS/DB: databaseReport.pl (+53 -56)

westram 2025-08-01 11:09 #1 Rev.: 19510

* fix int overflow while calculating steps for parsimony quick add (#807)
- thx to jan for providing a log for huge insertions

1 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+1 -1)

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