[cod-tools] branch master updated (747a9d3 -> 2ba3929)
Andrius Merkys
merkys-guest at moszumanska.debian.org
Fri Oct 27 13:27:09 UTC 2017
This is an automated email from the git hooks/post-receive script.
merkys-guest pushed a change to branch master
in repository cod-tools.
from 747a9d3 Not installing STAR libraries, depending instead on non-free libstar-parser-perl.
new 9e67676 Imported Upstream version 2.1
new 9f8823d Merge tag 'upstream/2.1'
new 318dbee New upstream release.
new 2ba3929 Removing patches that were incorporated by the upstream.
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.version | 2 +-
CHANGELOG | 104 ++
Makeconf | 6 +-
Makelocal-install | 8 +-
Makelocal-manpages | 13 +-
data/AtomProperties/bin/atom_properties_merge | 2 +-
data/AtomProperties/bin/compare_properties | 2 +-
data/AtomProperties/parts/core/BlueObelisk/core | 2 +-
.../covalent_radii/Cordero2008/covalent_radii | 2 +-
.../Pyykk\303\2662009/covalent_radii" | 2 +-
.../AtomProperties/parts/valence/wikipedia/valence | 2 +-
.../parts/vdw_radii/Alvarez2012/vdw_radii | 2 +-
data/AtomProperties/parts/vdw_radii/LANL/vdw_radii | 2 +-
data/AtomProperties/sources/Alvarez2012/input.yaml | 2 +-
.../sources/BlueObelisk/atom_properties_BO | 2 +-
data/AtomProperties/sources/Cordero2008/input.yaml | 2 +-
data/AtomProperties/sources/LANL/extract_info | 2 +-
data/AtomProperties/sources/LANL/input.yaml | 2 +-
.../sources/Pyykk\303\2662009/input.yaml" | 2 +-
.../sources/wikipedia/oxidation_states | 2 +-
data/provisional-dictionaries/cif_oqmd.dic | 2 +-
data/replacement-values/replacement_values.lst | 230 +++
debian/changelog | 6 +
debian/patches/cif_split_primitive-tests.diff | 10 -
debian/patches/codcif-manpages.diff | 152 --
debian/patches/disable-test-network-access.diff | 21 -
debian/patches/executables-in-codcif.diff | 14 -
debian/patches/series | 3 -
doc/CODDictionary.xml | 2 +-
doc/IUCr/cifguide.pdf | Bin 312734 -> 0 bytes
doc/IUCr/cifguide.pdf.url | 1 +
makefiles/Makeconfig-subdirs-example | 2 +-
makefiles/Makefile-backbone | 2 +-
makefiles/Makefile-perl-multiscript-tests | 10 +-
makefiles/Makefile-run_coms | 2 +-
makefiles/Makefile-subdirs | 2 +-
makefiles/Makelocal-YAPP-module | 2 +-
makefiles/Makelocal-benchmark | 2 +-
makefiles/Makelocal-unit-test | 2 +-
scripts/cif-to-utf8 | 2 +-
scripts/cif2cod | 130 +-
scripts/cif2csv | 6 +-
scripts/cif2json | 8 +-
scripts/cif2rdf | 10 +-
scripts/cif2ref | 6 +-
scripts/cif2xyz | 6 +-
scripts/cif_CODify | 2 +-
scripts/cif_Fcalc | 6 +-
scripts/cif_adjust_journal_name_volume | 6 +-
scripts/cif_bounding_box | 6 +-
scripts/cif_cell_contents | 8 +-
scripts/cif_classify | 6 +-
scripts/cif_cod_check | 814 ++++++----
scripts/cif_cod_deposit | 2 +-
scripts/cif_cod_numbers | 6 +-
scripts/cif_correct_tags | 52 +-
scripts/cif_create_AMCSD_pressure_temp_tags | 6 +-
scripts/cif_dictionary_tags | 6 +-
scripts/cif_diff | 8 +-
scripts/cif_distances | 39 +-
scripts/cif_estimate_Z | 6 +-
scripts/cif_eval_numbers | 6 +-
scripts/cif_fillcell | 8 +-
scripts/cif_filter | 36 +-
scripts/cif_find_duplicates | 9 +-
scripts/cif_find_symmetry | 12 +-
scripts/cif_fix_values | 8 +-
scripts/cif_hkl_COD_number | 6 +-
scripts/cif_hkl_check | 6 +-
scripts/cif_mark_disorder | 8 +-
scripts/cif_merge | 18 +-
scripts/cif_molecule | 404 +----
scripts/cif_mpod_v1_to_v2 | 6 +-
scripts/cif_mpod_v1_to_v3 | 6 +-
scripts/cif_mpod_v2_to_v1 | 6 +-
scripts/cif_mpod_v3_to_v1 | 6 +-
scripts/cif_overlay | 6 +-
scripts/cif_p1 | 353 +----
scripts/cif_parse | 6 +-
scripts/cif_parse_old_star | 2 +-
scripts/cif_printout | 8 +-
scripts/cif_printout_Python | 2 +-
scripts/cif_reduce_Niggli | 6 +-
scripts/cif_reduce_cell | 6 +-
scripts/cif_reformat_AMCSD_author_names | 6 +-
scripts/cif_reformat_pubmed_author_names | 6 +-
scripts/cif_reformat_uppercase_author_names | 6 +-
scripts/cif_select | 6 +-
scripts/cif_set_value | 8 +-
scripts/cif_sort_atoms | 176 +++
scripts/cif_split | 23 +-
scripts/cif_split_primitive | 2 +-
scripts/cif_symop_apply | 6 +-
scripts/cif_tags_in_list | 6 +-
scripts/cif_tcod_tree | 41 +-
scripts/cif_validate | 156 +-
scripts/cif_values | 6 +-
scripts/cod-tools-version.in | 8 +-
scripts/cod2rdf | 6 +-
scripts/cod_fetch | 2 +-
scripts/cod_predeposition_check | 11 +-
scripts/codcif2sdf | 2 +-
scripts/fetch_cif_dict | 2 +-
scripts/find_numbers | 2 +-
scripts/formula_sum | 2 +-
scripts/json2cif | 8 +-
scripts/molcif2sdf | 2 +-
scripts/msg_parse | 14 +-
scripts/oqmd2cif | 2 +-
scripts/sdf_add_cod_data | 2 +-
scripts/ssg3d | 2 +-
scripts/ssg_symop_canonical | 2 +-
scripts/ssg_symop_check | 2 +-
scripts/ssg_symop_matrices | 2 +-
scripts/ssg_symop_string | 2 +-
scripts/symop_build_spacegroup | 2 +-
scripts/utf8-to-cif | 2 +-
src/components/codcif/Makefile | 2 +-
src/components/codcif/cif.c | 2 +-
src/components/codcif/cif.h | 2 +-
src/components/codcif/cif2_grammar.y | 2 +-
src/components/codcif/cif2_grammar_y.h | 2 +-
src/components/codcif/cif2_lexer.c | 6 +-
src/components/codcif/cif2_lexer.h | 2 +-
src/components/codcif/cif_compiler.c | 9 +-
src/components/codcif/cif_compiler.h | 2 +-
src/components/codcif/cif_grammar.y | 2 +-
src/components/codcif/cif_grammar_flex.c | 2 +-
src/components/codcif/cif_grammar_flex.h | 2 +-
src/components/codcif/cif_grammar_y.h | 2 +-
src/components/codcif/cif_lexer.c | 12 +-
src/components/codcif/cif_lexer.h | 2 +-
src/components/codcif/cif_options.c | 2 +-
src/components/codcif/cif_options.h | 2 +-
src/components/codcif/ciflist.c | 2 +-
src/components/codcif/ciflist.h | 2 +-
src/components/codcif/cifmessage.c | 2 +-
src/components/codcif/cifmessage.h | 2 +-
src/components/codcif/ciftable.c | 2 +-
src/components/codcif/ciftable.h | 2 +-
src/components/codcif/cifvalue.c | 2 +-
src/components/codcif/cifvalue.h | 2 +-
src/components/codcif/common.c | 2 +-
src/components/codcif/common.h | 2 +-
src/components/codcif/datablock.c | 2 +-
src/components/codcif/datablock.h | 2 +-
src/components/codcif/inputs/1004001-disorder.cif | 2 +-
.../codcif/inputs/1508696-long-text-field.cif | 2 +-
src/components/codcif/inputs/2000000.cif | 2 +-
src/components/codcif/inputs/4067640.cif | 2 +-
src/components/codcif/inputs/4318422.cif | 2 +-
src/components/codcif/inputs/4319975.cif | 2 +-
src/components/codcif/inputs/7052868.cif | 2 +-
src/components/codcif/inputs/9007991.cif | 2 +-
src/components/codcif/outputs/cifparse_019.out | 1 +
src/components/codcif/outputs/cifparse_020.out | 1 +
src/components/codcif/outputs/cifparse_053.out | 1 +
src/components/codcif/programs/cif_list_tags.c | 41 +-
src/components/codcif/programs/cifparse.c | 4 +-
src/components/codcif/programs/cifvalues.c | 4 +-
src/components/codcif/tests/cifparse_107.inp | 2 +-
src/components/codcif/tests/cifparse_108.inp | 2 +-
src/components/codcif/version.hin | 2 +-
src/components/codcif/yy.c | 2 +-
.../pycodcif/tests/outputs/cif_parser_test_071.out | 2 +
.../pycodcif/tests/outputs/cif_parser_test_107.out | 1 +
.../pycodcif/tests/scripts/cif_parser_test | 2 +-
src/database-schemas/cif2cod.sql | 2 +-
src/externals/cexceptions/Makefile | 2 +-
src/externals/cexceptions/allocx.c | 2 +-
src/externals/cexceptions/allocx.h | 2 +-
src/externals/cexceptions/cexceptions.c | 2 +-
src/externals/cexceptions/cexceptions.h | 2 +-
src/externals/cexceptions/cxprintf.c | 2 +-
src/externals/cexceptions/cxprintf.h | 2 +-
src/externals/cexceptions/stdiox.c | 2 +-
src/externals/cexceptions/stdiox.h | 2 +-
src/externals/cexceptions/stringx.c | 2 +-
src/externals/cexceptions/stringx.h | 2 +-
src/externals/cexceptions/tests/programs/fopenx.c | 2 +-
.../cexceptions/tests/programs/tcreallocx.c | 2 +-
.../cexceptions/tests/programs/tstrdupx.c | 2 +-
src/externals/getoptions/Makefile | 2 +-
src/externals/getoptions/getoptions.c | 2 +-
src/externals/getoptions/getoptions.h | 2 +-
src/externals/getoptions/tests/programs/topt.c | 2 +-
src/lib/perl5/COD/Algebra.pm | 2 +-
src/lib/perl5/COD/Algebra/JacobiEigen.pm | 2 +-
src/lib/perl5/COD/Algebra/JacobiEigenSimple.pm | 2 +-
src/lib/perl5/COD/Algebra/Vector.pm | 2 +-
src/lib/perl5/COD/AtomBricks.pm | 2 +-
src/lib/perl5/COD/AtomNeighbours.pm | 13 +-
src/lib/perl5/COD/AuthorNames.pm | 2 +-
src/lib/perl5/COD/CIF/Data.pm | 2 +-
src/lib/perl5/COD/CIF/Data/AtomList.pm | 9 +-
src/lib/perl5/COD/CIF/Data/CIF2COD.pm | 2 +-
src/lib/perl5/COD/CIF/Data/CODFlags.pm | 2 +-
src/lib/perl5/COD/CIF/Data/CODNumbers.pm | 2 +-
.../perl5/COD/CIF/Data/CODPredepositionCheck.pm | 114 +-
src/lib/perl5/COD/CIF/Data/CellContents.pm | 25 +-
src/lib/perl5/COD/CIF/Data/Classifier.pm | 157 +-
src/lib/perl5/COD/CIF/Data/Diff.pm | 2 +-
src/lib/perl5/COD/CIF/Data/EstimateZ.pm | 2 +-
.../perl5/COD/CIF/Data/ExcludeFromStatistics.pm | 2 +-
src/lib/perl5/COD/CIF/Data/SymmetryGenerator.pm | 405 ++++-
src/lib/perl5/COD/CIF/JSON.pm | 2 +-
src/lib/perl5/COD/CIF/Parser.pm | 8 +-
.../Bison/tests/outputs/cif_parser_test_071.out | 2 +
.../Bison/tests/outputs/cif_parser_test_107.out | 1 +
.../CIF/Parser/Bison/tests/scripts/cif_parser_test | 6 +-
.../tests/shtests/multiline_text_field_001.sh | 2 +-
.../Parser/Bison/tests/shtests/precisions_001.sh | 2 +-
.../CIF/Parser/Bison/tests/shtests/unicode_001.sh | 2 +-
src/lib/perl5/COD/CIF/Parser/Yapp/Yapp.yp | 15 +-
.../inputs/cif2-unicode-deeply-nested-numeric.cif | 2 +-
.../tests/inputs/cif2-unicode-deeply-nested.cif | 2 +-
.../Yapp/tests/inputs/cif2-unicode-multiblock.cif | 2 +-
.../Yapp/tests/inputs/cif2-unicode-save-frames.inp | 2 +-
.../Yapp/tests/inputs/cif2-unicode-simple.inp | 2 +-
.../tests/inputs/complex_structure_precisions.cif | 2 +-
.../Yapp/tests/inputs/loops_with_precisions.cif | 2 +-
.../tests/inputs/nested_structure_precisions.cif | 2 +-
.../tests/inputs/save_frame_with_precisions.cif | 2 +-
.../CIF/Parser/Yapp/tests/scripts/cif_parser_test | 6 +-
.../COD/CIF/Parser/Yapp/tests/shtests/empty_01.sh | 2 +-
.../COD/CIF/Parser/Yapp/tests/shtests/empty_02.sh | 2 +-
.../Parser/Yapp/tests/shtests/err_no_data_01.sh | 2 +-
.../Parser/Yapp/tests/shtests/err_no_data_02.sh | 2 +-
.../Parser/Yapp/tests/shtests/err_no_data_03.sh | 2 +-
.../Parser/Yapp/tests/shtests/error_messages.sh | 6 +-
.../Parser/Yapp/tests/shtests/file_not_defined.sh | 2 +-
.../Yapp/tests/shtests/float_mis-increase_lexer.sh | 2 +-
.../CIF/Parser/Yapp/tests/shtests/global_errors.sh | 2 +-
.../CIF/Parser/Yapp/tests/shtests/local_tags.sh | 2 +-
.../COD/CIF/Parser/Yapp/tests/shtests/loop_001.sh | 2 +-
.../Parser/Yapp/tests/shtests/loop_misparsing.sh | 2 +-
.../tests/shtests/missing_closing_dq_string.sh | 2 +-
.../tests/shtests/missing_closing_sq_string.sh | 2 +-
.../CIF/Parser/Yapp/tests/shtests/save_block.sh | 2 +-
.../COD/CIF/Parser/Yapp/tests/shtests/simple.sh | 2 +-
.../tests/shtests/standard_uncertainty_handling.sh | 2 +-
.../Parser/Yapp/tests/shtests/text_field_001.sh | 2 +-
.../Parser/Yapp/tests/shtests/unquoted_string.sh | 2 +-
.../tests/shtests/unquoted_string_with_brackets.sh | 2 +-
.../tests/shtests/unquoted_string_wo_brackets.sh | 2 +-
src/lib/perl5/COD/CIF/Tags/AMCSD.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/COD.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/CanonicalNames.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/DFT.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/DictTags.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/Excluded.pm | 2 +-
src/lib/perl5/COD/CIF/Tags/Manage.pm | 37 +-
src/lib/perl5/COD/CIF/Tags/Print.pm | 47 +-
src/lib/perl5/COD/CIF/Tags/TCOD.pm | 2 +-
src/lib/perl5/COD/CIF/Unicode2CIF.pm | 2 +-
src/lib/perl5/COD/Cell.pm | 2 +-
src/lib/perl5/COD/Cell/Conventional/deWG91.pm | 2 +-
src/lib/perl5/COD/Cell/Delaunay/Delaunay.pm | 2 +-
src/lib/perl5/COD/Cell/Niggli/KG76.pm | 2 +-
src/lib/perl5/COD/CromerMann.pm | 2 +-
src/lib/perl5/COD/ErrorHandler.pm | 10 +-
src/lib/perl5/COD/Escape.pm | 2 +-
src/lib/perl5/COD/Formulae/Parser/AdHoc/AdHoc.yp | 2 +-
.../Parser/AdHoc/tests/scripts/formula_parser_test | 2 +-
src/lib/perl5/COD/Formulae/Parser/IUCr/IUCr.yp | 2 +-
.../Parser/IUCr/tests/scripts/formula_parser_test | 2 +-
src/lib/perl5/COD/Formulae/Print.pm | 2 +-
src/lib/perl5/COD/Fractional.pm | 2 +-
src/lib/perl5/COD/MorganFingerprints.pm | 2 +-
src/lib/perl5/COD/Overlays/Kabsch.pm | 2 +-
src/lib/perl5/COD/Overlays/Kearsley.pm | 2 +-
src/lib/perl5/COD/Overlays/Theobald.pm | 2 +-
src/lib/perl5/COD/Precision.pm | 2 +-
src/lib/perl5/COD/RDF.pm | 2 +-
src/lib/perl5/COD/SOptions.pm | 2 +-
src/lib/perl5/COD/SUsage.pm | 2 +-
src/lib/perl5/COD/Serialise.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Builder.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Cosets.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Lookup.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Lookup/CCP4.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Lookup/COD.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Names.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Symop/Algebra.pm | 2 +-
src/lib/perl5/COD/Spacegroups/Symop/Parse.pm | 19 +-
src/lib/perl5/COD/Spacegroups/Symop/SSGParse.pm | 2 +-
src/lib/perl5/COD/ToolsVersion.pmin | 2 +-
src/lib/perl5/COD/UserMessage.pm | 24 +-
tests/cases/cif2cod_047.opt | 1 +
tests/cases/cif_cod_check_112.inp | 1 +
...cif_cod_check_051.opt => cif_cod_check_112.opt} | 0
tests/cases/cif_cod_check_112.tst | 2 +
tests/cases/cif_cod_check_113.inp | 1 +
tests/cases/cif_cod_check_113.tst | 3 +
tests/cases/cif_filter_043.opt | 2 +-
tests/cases/cif_filter_045.opt | 2 +-
tests/cases/cif_filter_046.opt | 2 +-
.../cases/{cif2csv_001.inp => cif_filter_181.inp} | 0
tests/cases/cif_filter_181.opt | 1 +
tests/cases/cif_merge_007.opt | 1 +
.../{cif2cod_001.inp => cif_sort_atoms_001.inp} | 0
.../{cif2cod_001.inp => cif_sort_atoms_002.inp} | 0
tests/cases/cif_sort_atoms_002.opt | 1 +
.../{cif2cod_001.inp => cif_sort_atoms_003.inp} | 0
tests/cases/cif_sort_atoms_003.opt | 1 +
.../cases/{cif_split_001.inp => cif_split_004.inp} | 0
tests/cases/cif_split_004.opt | 1 +
...cif_tcod_tree_003.inp => cif_tcod_tree_004.inp} | 0
tests/cases/cif_tcod_tree_004.opt | 1 +
.../cases/cif_validate_039.inp | 0
tests/cases/cif_validate_039.opt | 1 +
...ers_002.chk => cod_predeposition_check_033.chk} | 0
tests/inputs/10000001.cif | 2 +-
tests/inputs/1000002-test-hall.cif | 2 +-
tests/inputs/1000002-test-hm.cif | 2 +-
tests/inputs/1000002-test-hm2.cif | 2 +-
tests/inputs/1000002-test-symop.cif | 2 +-
tests/inputs/1000023.cif | 2 +-
tests/inputs/1000026-MgB2.cif | 2 +-
tests/inputs/1000035.cif | 2 +-
tests/inputs/1000039.cif | 2 +-
tests/inputs/1000054.cif | 2 +-
tests/inputs/1000055-unrecognised-spacegroup.cif | 2 +-
tests/inputs/1000125-cell-diff.cif | 2 +-
tests/inputs/1000451.cif | 2 +-
tests/inputs/1001012-no-cell.cif | 2 +-
tests/inputs/1001627-spacegroup-A-1.cif | 2 +-
tests/inputs/1004001-disorder.cif | 2 +-
tests/inputs/1004001.cif | 2 +-
tests/inputs/1004008-90-dot.cif | 2 +-
tests/inputs/1008449.cif | 2 +-
tests/inputs/1010050-zero-sigmas.cif | 2 +-
tests/inputs/1010800-no-spcgrp-info.cif | 2 +-
tests/inputs/1011060-graphite-atom-label.cif | 2 +-
tests/inputs/1011060-graphite-atom-type-symbol.cif | 2 +-
tests/inputs/1011060-graphite-err.cif | 2 +-
tests/inputs/1011060-graphite.cif | 2 +-
.../inputs/1100107-spacegroup-with-underscore.cif | 2 +-
tests/inputs/1100709-uqstring-brackets.cif | 2 +-
tests/inputs/1100910-simple-fractions.cif | 2 +-
.../inputs/1100914-incorrect-weighting-scheme.cif | 2 +-
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tests/inputs/2004198-no-cell-angles.cif | 2 +-
tests/inputs/2004325-cell-questionmark.cif | 2 +-
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tests/inputs/2009397-syntax-error.cif | 2 +-
tests/inputs/2009397.cif | 2 +-
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tests/inputs/2010442-Uiso-value-bug.cif | 2 +-
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tests/inputs/2011406-xy-simple-fract.cif | 2 +-
tests/inputs/2014244.cif | 2 +-
tests/inputs/2015717-long-title.cif | 2 +-
tests/inputs/2016470-long-title.cif | 2 +-
tests/inputs/2019572.cif | 2 +-
tests/inputs/2100348-benzene-dist-test.cif | 2 +-
tests/inputs/2100428-superspacegroup.cif | 2 +-
tests/inputs/2100438-cell-vol.cif | 2 +-
tests/inputs/2100831-incomplete-unit-cell-info.cif | 2 +-
tests/inputs/2101499-diamond.cif | 2 +-
tests/inputs/2101923-value-with-precision.cif | 2 +-
tests/inputs/2103187-misaligned-loop.cif | 2 +-
tests/inputs/2103514-with-P-and-T.cif | 2 +-
tests/inputs/2103654-head.cif | 2 +-
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tests/inputs/2104634-new-symop-tags-no-SG.cif | 2 +-
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tests/inputs/2105936-strange-centering.cif | 2 +-
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tests/inputs/2202108.cif | 2 +-
tests/inputs/2203315.cif | 2 +-
tests/inputs/2204100.cif | 2 +-
tests/inputs/2205051_cif_molecule.cif | 2 +-
tests/inputs/2205053-molecule.cif | 2 +-
tests/inputs/2208311-zero-occupancies.cif | 2 +-
tests/inputs/2208504.cif | 2 +-
tests/inputs/2209560-cell-vol.cif | 2 +-
tests/inputs/2217081-cell-vol.cif | 2 +-
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tests/inputs/2219444.cif | 2 +-
tests/inputs/2222274.cif | 2 +-
tests/inputs/2224635.cif | 2 +-
tests/inputs/2224874.cif | 2 +-
tests/inputs/2228759-multiple-diacritics.cif | 2 +-
tests/inputs/2231955.cif | 2 +-
tests/inputs/2238212-only-doi.cif | 2 +-
tests/inputs/2238212.cif | 2 +-
tests/inputs/2300214-new-sg-name-H-M.cif | 2 +-
tests/inputs/2300214-new-sg-name-Hall.cif | 2 +-
tests/inputs/4000911-high-precision-cell.cif | 2 +-
tests/inputs/4001780.cif | 2 +-
tests/inputs/4021421-non-dict-tags-in-loop.cif | 2 +-
tests/inputs/4024741.cif | 2 +-
tests/inputs/4024913-with-new-symop-tags.cif | 2 +-
tests/inputs/4063196-short-H-M.cif | 2 +-
tests/inputs/4063260-wrong-formula-sum.cif | 2 +-
tests/inputs/4101385.cif | 2 +-
tests/inputs/4101585-truncated-page-last.cif | 2 +-
tests/inputs/4105625.cif | 2 +-
tests/inputs/4300013.cif | 2 +-
tests/inputs/4300015.cif | 2 +-
tests/inputs/4300056.cif | 2 +-
tests/inputs/4300081.cif | 2 +-
tests/inputs/4301885-I12slash1-spacegroup.cif | 2 +-
tests/inputs/4302333-Ortho-and-missing-braces.cif | 2 +-
tests/inputs/4302587-symetry.cif | 2 +-
tests/inputs/4303187-double-underscore.cif | 2 +-
tests/inputs/4303187-multiple-underscores.cif | 2 +-
tests/inputs/4308312-audit-dict-name.cif | 2 +-
tests/inputs/4310545-temperature-tag.cif | 2 +-
tests/inputs/4320780-negative-value.cif | 2 +-
tests/inputs/4334605.cif | 2 +-
tests/inputs/4503694.cif | 2 +-
tests/inputs/5000332.cif | 2 +-
tests/inputs/6000001-without-cordinates.cif | 2 +-
tests/inputs/7000165-disorder.cif | 2 +-
tests/inputs/7004184-decomp-celsius.cif | 2 +-
tests/inputs/7011014-occupancy-is-a-dot.cif | 2 +-
tests/inputs/7050234-non-ascii-text-field.cif | 2 +-
.../inputs/7052819-thermal-hist-with-newlines.cif | 2 +-
tests/inputs/7101147.cif | 2 +-
tests/inputs/7101937-degrees-celsius.cif | 2 +-
tests/inputs/7105218-complex-author-name.cif | 2 +-
.../7105250-oriental-name-capitalisation.cif | 2 +-
tests/inputs/7105573-no-Z.cif | 2 +-
tests/inputs/7106028-temerature-not-important.cif | 2 +-
tests/inputs/7200679-spacegroup-P4.cif | 2 +-
tests/inputs/7201670-limits-with-precision.cif | 2 +-
tests/inputs/8000003.cif | 2 +-
tests/inputs/8000008-mixed-case-tags.cif | 2 +-
tests/inputs/8100877-bump.cif | 2 +-
tests/inputs/8102326.cif | 2 +-
tests/inputs/9000020.cif | 2 +-
tests/inputs/9000133-annealed.cif | 2 +-
tests/inputs/9000579-annealing.cif | 2 +-
tests/inputs/9001201-then-quenched.cif | 2 +-
tests/inputs/9001205-then-quenched.cif | 2 +-
tests/inputs/9001907-broken-unit-cell.cif | 2 +-
tests/inputs/9001922-long-formula.cif | 2 +-
tests/inputs/9003333-nonquenchable.cif | 2 +-
tests/inputs/9003354.cif | 2 +-
tests/inputs/9003733-Annealed.cif | 2 +-
tests/inputs/9003869-long-title.cif | 2 +-
tests/inputs/9005205-Quenched.cif | 2 +-
tests/inputs/9005728.cif | 2 +-
tests/inputs/9007346-Annealing.cif | 2 +-
tests/inputs/9007872-one-funny-word-title.cif | 2 +-
tests/inputs/9007874-strange-H-names-no-types.cif | 2 +-
tests/inputs/9007874-strange-H-names.cif | 2 +-
tests/inputs/9008098.cif | 2 +-
tests/inputs/9008564-diamond.cif | 2 +-
tests/inputs/9010219-synthesized.cif | 2 +-
tests/inputs/9010340-with-P-value.cif | 2 +-
tests/inputs/9010753-C-D-bond.cif | 99 +-
tests/inputs/9011575-diamond.cif | 2 +-
tests/inputs/9012705.cif | 2 +-
tests/inputs/9012939-with-T-in-deg-C.cif | 2 +-
tests/inputs/9013186-pressure-hist.cif | 2 +-
tests/inputs/9013187-pressure-hist.cif | 2 +-
tests/inputs/9013191-pressure-hist.cif | 2 +-
tests/inputs/9013273-Pressure.cif | 2 +-
.../cifs-with-errors/2009397-syntax-error.cif | 2 +-
tests/inputs/cifs-with-errors/2009397.cif | 2 +-
tests/inputs/close-cells/cod/9006017.cif | 2 +-
tests/inputs/close-cells/cod/9006022.cif | 2 +-
tests/inputs/close-cells/cod/9006038.cif | 2 +-
tests/inputs/close-cells/cod/9006039.cif | 2 +-
tests/inputs/close-cells/cod/9006040.cif | 2 +-
tests/inputs/close-cells/cod/9006041.cif | 2 +-
tests/inputs/cod-different-contents/1011335.cif | 2 +-
tests/inputs/cod-different-contents/9011403.cif | 2 +-
tests/inputs/cod-similar-angles/9001833.cif | 2 +-
tests/inputs/cod-similar-angles/9001838.cif | 2 +-
.../cod-with-errors/2009397-syntax-error.cif | 2 +-
tests/inputs/cod-with-errors/2009397.cif | 2 +-
tests/inputs/cod1/9002543.cif | 2 +-
tests/inputs/cod1/9002544.cif | 2 +-
tests/inputs/cod1/9002545.cif | 2 +-
tests/inputs/cod1/9002546.cif | 2 +-
tests/inputs/cod1/9002547.cif | 2 +-
tests/inputs/cod1/9002548.cif | 2 +-
tests/inputs/cod1/9002549.cif | 2 +-
tests/inputs/cod1/9002550.cif | 2 +-
tests/inputs/cod1/9002551.cif | 2 +-
tests/inputs/cod2/9002543.cif | 2 +-
tests/inputs/cod2/9002544.cif | 2 +-
tests/inputs/cod2/9002545.cif | 2 +-
tests/inputs/cod2/9002546.cif | 2 +-
tests/inputs/cod2/9002547.cif | 2 +-
tests/inputs/cod2/9002548.cif | 2 +-
tests/inputs/cod2/9002549.cif | 2 +-
tests/inputs/cod2/9002550.cif | 2 +-
tests/inputs/cod2/9002551.cif | 2 +-
tests/inputs/malformed_symop_new_sym_tag.cif | 12 +
tests/inputs/merge_7b.cif | 5 +
tests/inputs/new_symop_tag.cif | 12 +
tests/inputs/sample-history/cod/9005952.cif | 2 +-
tests/inputs/sample-history/cod/9005953.cif | 2 +-
tests/inputs/sample-history/cod/9005954.cif | 2 +-
tests/inputs/unparsable-formulae1/1100062.cif | 2 +-
tests/inputs/unparsable-formulae1/1100811.cif | 2 +-
tests/inputs/unparsable-formulae1/2010785.cif | 2 +-
tests/inputs/unparsable-formulae2/1100062.cif | 2 +-
tests/inputs/unparsable-formulae2/1100811.cif | 2 +-
tests/inputs/unparsable-formulae2/2010785.cif | 2 +-
tests/outputs/cif2cod_047.out | 1 +
tests/outputs/cif_classify_002.out | 2 +-
tests/outputs/cif_cod_check_008.out | 3 +-
tests/outputs/cif_cod_check_009.out | 3 +-
tests/outputs/cif_cod_check_010.out | 3 +-
tests/outputs/cif_cod_check_012.out | 5 +-
tests/outputs/cif_cod_check_013.out | 5 +-
tests/outputs/cif_cod_check_015.out | 3 +-
tests/outputs/cif_cod_check_018.out | 4 +-
tests/outputs/cif_cod_check_019.out | 1 +
tests/outputs/cif_cod_check_020.out | 4 +-
tests/outputs/cif_cod_check_023.out | 2 +-
tests/outputs/cif_cod_check_025.out | 3 +-
tests/outputs/cif_cod_check_026.out | 3 +-
tests/outputs/cif_cod_check_050.out | 3 +-
tests/outputs/cif_cod_check_051.out | 4 +-
tests/outputs/cif_cod_check_056.out | 3 +-
tests/outputs/cif_cod_check_063.out | 3 +-
tests/outputs/cif_cod_check_072.out | 3 +-
tests/outputs/cif_cod_check_082.out | 3 +-
tests/outputs/cif_cod_check_083.out | 3 +-
tests/outputs/cif_cod_check_084.out | 3 +-
tests/outputs/cif_cod_check_085.out | 3 +-
tests/outputs/cif_cod_check_086.out | 3 +-
tests/outputs/cif_cod_check_087.out | 3 +-
tests/outputs/cif_cod_check_088.out | 3 +-
tests/outputs/cif_cod_check_089.out | 12 +-
tests/outputs/cif_cod_check_090.out | 8 +-
tests/outputs/cif_cod_check_091.out | 8 +-
tests/outputs/cif_cod_check_092.out | 8 +-
tests/outputs/cif_cod_check_093.out | 8 +-
tests/outputs/cif_cod_check_094.out | 8 +-
tests/outputs/cif_cod_check_095.out | 6 +-
tests/outputs/cif_cod_check_096.out | 8 +-
tests/outputs/cif_cod_check_097.out | 6 +-
tests/outputs/cif_cod_check_098.out | 7 +-
tests/outputs/cif_cod_check_099.out | 1 +
tests/outputs/cif_cod_check_102.out | 3 +-
tests/outputs/cif_cod_check_103.out | 8 +-
tests/outputs/cif_cod_check_104.out | 6 +-
tests/outputs/cif_cod_check_105.out | 3 +-
tests/outputs/cif_cod_check_108.out | 2 +-
tests/outputs/cif_cod_check_109.out | 4 +-
tests/outputs/cif_cod_check_110.out | 10 +-
tests/outputs/cif_cod_check_112.out | 2 +
tests/outputs/cif_cod_check_113.out | 3 +
tests/outputs/cif_correct_tags_005.out | 2 +
tests/outputs/cif_distances_024.out | 3 +-
tests/outputs/cif_filter_136.out | 2 +
tests/outputs/cif_filter_137.out | 2 +
tests/outputs/cif_filter_181.out | 69 +
tests/outputs/cif_find_symmetry_001.out | 24 +-
tests/outputs/cif_find_symmetry_002.out | 12 +-
tests/outputs/cif_find_symmetry_003.out | 96 +-
tests/outputs/cif_find_symmetry_004.out | 6 +-
tests/outputs/cif_find_symmetry_008.out | 20 +-
tests/outputs/cif_find_symmetry_010.out | 6 +-
tests/outputs/cif_find_symmetry_011.out | 36 +-
tests/outputs/cif_find_symmetry_012.out | 24 +-
tests/outputs/cif_find_symmetry_013.out | 12 +-
tests/outputs/cif_fix_values_051.out | 2 +
tests/outputs/cif_merge_007.out | 17 +
tests/outputs/cif_molecule_003.out | 2 +
tests/outputs/cif_molecule_004.out | 12 +-
tests/outputs/cif_molecule_005.out | 12 +-
tests/outputs/cif_molecule_007.out | 12 +-
tests/outputs/cif_molecule_008.out | 46 +-
tests/outputs/cif_molecule_009.out | 4 +-
tests/outputs/cif_molecule_016.out | 4 +-
tests/outputs/cif_molecule_020.out | 2 +
tests/outputs/cif_molecule_023.out | 2 +
tests/outputs/cif_molecule_024.out | 51 +-
tests/outputs/cif_molecule_026.out | 46 +-
tests/outputs/cif_molecule_028.out | 8 +-
tests/outputs/cif_molecule_029.out | 2 +
tests/outputs/cif_molecule_030.out | 8 +
tests/outputs/cif_molecule_031.out | 8 +
tests/outputs/cif_molecule_032.out | 8 +
tests/outputs/cif_molecule_035.out | 2 +
tests/outputs/cif_molecule_036.out | 2 +
tests/outputs/cif_molecule_047.out | 2 +
tests/outputs/cif_molecule_048.out | 2 +
tests/outputs/cif_molecule_056.out | 2 +
tests/outputs/cif_molecule_059.out | 2 +
tests/outputs/cif_molecule_080.out | 6 +
tests/outputs/cif_molecule_085.out | 2 +
tests/outputs/cif_molecule_086.out | 2 +
tests/outputs/cif_molecule_092.out | 2 +
tests/outputs/cif_p1_001.out | 30 +-
tests/outputs/cif_p1_004.out | 2 +
tests/outputs/cif_p1_005.out | 2 +
tests/outputs/cif_p1_006.out | 2 +
tests/outputs/cif_p1_007.out | 2 +
tests/outputs/cif_p1_008.out | 56 +-
tests/outputs/cif_sort_atoms_001.out | 421 +++++
tests/outputs/cif_sort_atoms_002.out | 421 +++++
tests/outputs/cif_sort_atoms_003.out | 421 +++++
tests/outputs/cif_split_004.out | 1671 ++++++++++++++++++++
tests/outputs/cif_tcod_tree_004.out | 69 +
tests/outputs/cif_validate_003.out | 8 +-
tests/outputs/cif_validate_004.out | 8 +-
tests/outputs/cif_validate_005.out | 8 +-
tests/outputs/cif_validate_007.out | 2 +-
tests/outputs/cif_validate_008.out | 2 +-
tests/outputs/cif_validate_015.out | 8 +-
tests/outputs/cif_validate_016.out | 8 +-
tests/outputs/cif_validate_018.out | 8 +-
tests/outputs/cif_validate_020.out | 2 +-
tests/outputs/cif_validate_021.out | 2 +-
tests/outputs/cif_validate_022.out | 2 +-
tests/outputs/cif_validate_024.out | 8 +-
tests/outputs/cif_validate_025.out | 8 +-
tests/outputs/cif_validate_026.out | 8 +-
tests/outputs/cif_validate_027.out | 4 +-
tests/outputs/cif_validate_029.out | 2 +-
tests/outputs/cif_validate_030.out | 6 +-
tests/outputs/cif_validate_031.out | 6 +-
tests/outputs/cif_validate_032.out | 6 +-
tests/outputs/cif_validate_039.out | 4 +
tests/outputs/cod_predeposition_check_004.out | 2 +-
tests/outputs/cod_predeposition_check_009.out | 6 +-
tests/outputs/cod_predeposition_check_010.out | 6 +-
tests/outputs/cod_predeposition_check_011.out | 6 +-
tests/outputs/cod_predeposition_check_012.out | 6 +-
tests/outputs/cod_predeposition_check_016.out | 2 +-
tests/outputs/cod_predeposition_check_018.out | 7 +-
tests/outputs/cod_predeposition_check_019.out | 2 +-
tests/outputs/cod_predeposition_check_020.out | 200 +--
tests/outputs/cod_predeposition_check_021.out | 3 +-
tests/outputs/cod_predeposition_check_023.out | 5 +-
tests/outputs/cod_predeposition_check_024.out | 2 +-
tests/outputs/cod_predeposition_check_028.out | 2 +-
tests/outputs/cod_predeposition_check_029.out | 2 +-
tests/outputs/cod_predeposition_check_030.out | 2 +-
tests/shoutputs/check_option_descriptions.out | 2 +-
tests/shoutputs/cif_print_loop_001.out | 9 +
tests/shoutputs/cif_print_loop_002.out | 16 +
tests/shoutputs/cif_split_002.out | 6 +
tests/shoutputs/cif_tcod_tree_007.out | 109 ++
tests/shoutputs/neighbour_list_from_mol_002.out | 181 +++
tests/shtests/check_spacegroups_001.sh | 2 +-
tests/shtests/check_spacegroups_002.sh | 2 +-
tests/shtests/cif_disorder_groups_001.sh | 2 +-
tests/shtests/cif_disorder_groups_002.sh | 2 +-
tests/shtests/cif_disorder_groups_003.sh | 2 +-
tests/shtests/cif_disorder_groups_004.sh | 2 +-
tests/shtests/cif_disorder_groups_005.sh | 2 +-
tests/shtests/cif_disorder_groups_006.sh | 2 +-
tests/shtests/cif_disorder_groups_007.sh | 2 +-
tests/shtests/cif_print_loop_001.sh | 42 +
tests/shtests/cif_print_loop_002.sh | 48 +
tests/shtests/cif_split_primitive_001.sh | 2 +-
tests/shtests/cif_split_primitive_002.sh | 2 +-
tests/shtests/cif_split_primitive_003.sh | 2 +-
tests/shtests/cif_split_primitive_004.sh | 2 +-
tests/shtests/cif_split_primitive_005.sh | 2 +-
tests/shtests/cif_split_primitive_006.sh | 2 +-
tests/shtests/cif_split_primitive_007.sh | 2 +-
tests/shtests/cif_split_primitive_008.sh | 2 +-
tests/shtests/cif_split_primitive_009.sh | 2 +-
tests/shtests/cif_split_primitive_010.sh | 2 +-
tests/shtests/cif_tcod_tree_007.sh | 30 +
...mol_001.chk => neighbour_list_from_mol_002.chk} | 0
tests/shtests/neighbour_list_from_mol_002.sh | 21 +
tests/shtests/symop_algebra_001.sh | 2 +-
tests/shtests/symop_algebra_002.sh | 2 +-
tests/shtests/symop_algebra_003.sh | 2 +-
tests/shtests/symop_algebra_004.sh | 2 +-
tools/check_option_descriptions | 2 +-
tools/check_symop_canonicality | 2 +-
tools/duplicate_space_groups | 2 +-
tools/help2man | 40 +-
tools/mkperldepend | 2 +-
720 files changed, 6936 insertions(+), 2975 deletions(-)
create mode 100644 data/replacement-values/replacement_values.lst
delete mode 100644 debian/patches/codcif-manpages.diff
delete mode 100644 debian/patches/disable-test-network-access.diff
delete mode 100644 debian/patches/executables-in-codcif.diff
delete mode 100644 doc/IUCr/cifguide.pdf
create mode 100644 doc/IUCr/cifguide.pdf.url
create mode 100755 scripts/cif_sort_atoms
create mode 100644 tests/cases/cif2cod_047.opt
create mode 120000 tests/cases/cif_cod_check_112.inp
copy tests/cases/{cif_cod_check_051.opt => cif_cod_check_112.opt} (100%)
create mode 100644 tests/cases/cif_cod_check_112.tst
create mode 120000 tests/cases/cif_cod_check_113.inp
create mode 100644 tests/cases/cif_cod_check_113.tst
copy tests/cases/{cif2csv_001.inp => cif_filter_181.inp} (100%)
create mode 100644 tests/cases/cif_filter_181.opt
create mode 100644 tests/cases/cif_merge_007.opt
copy tests/cases/{cif2cod_001.inp => cif_sort_atoms_001.inp} (100%)
copy tests/cases/{cif2cod_001.inp => cif_sort_atoms_002.inp} (100%)
create mode 100644 tests/cases/cif_sort_atoms_002.opt
copy tests/cases/{cif2cod_001.inp => cif_sort_atoms_003.inp} (100%)
create mode 100644 tests/cases/cif_sort_atoms_003.opt
copy tests/cases/{cif_split_001.inp => cif_split_004.inp} (100%)
create mode 100644 tests/cases/cif_split_004.opt
copy tests/cases/{cif_tcod_tree_003.inp => cif_tcod_tree_004.inp} (100%)
create mode 100644 tests/cases/cif_tcod_tree_004.opt
copy src/components/codcif/tests/cifparse_041.inp => tests/cases/cif_validate_039.inp (100%)
create mode 100644 tests/cases/cif_validate_039.opt
copy tests/cases/{cif_cod_numbers_002.chk => cod_predeposition_check_033.chk} (100%)
create mode 100644 tests/inputs/malformed_symop_new_sym_tag.cif
create mode 100644 tests/inputs/merge_7b.cif
create mode 100644 tests/inputs/new_symop_tag.cif
create mode 100644 tests/outputs/cif2cod_047.out
create mode 100644 tests/outputs/cif_cod_check_112.out
create mode 100644 tests/outputs/cif_cod_check_113.out
create mode 100644 tests/outputs/cif_filter_181.out
create mode 100644 tests/outputs/cif_merge_007.out
create mode 100644 tests/outputs/cif_sort_atoms_001.out
create mode 100644 tests/outputs/cif_sort_atoms_002.out
create mode 100644 tests/outputs/cif_sort_atoms_003.out
create mode 100644 tests/outputs/cif_split_004.out
create mode 100644 tests/outputs/cif_tcod_tree_004.out
create mode 100644 tests/outputs/cif_validate_039.out
create mode 100644 tests/shoutputs/cif_print_loop_001.out
create mode 100644 tests/shoutputs/cif_print_loop_002.out
create mode 100644 tests/shoutputs/cif_tcod_tree_007.out
create mode 100644 tests/shoutputs/neighbour_list_from_mol_002.out
create mode 100755 tests/shtests/cif_print_loop_001.sh
create mode 100755 tests/shtests/cif_print_loop_002.sh
create mode 100755 tests/shtests/cif_tcod_tree_007.sh
copy tests/shtests/{neighbour_list_from_mol_001.chk => neighbour_list_from_mol_002.chk} (100%)
create mode 100755 tests/shtests/neighbour_list_from_mol_002.sh
--
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