[cod-tools] branch master updated (b8bc747 -> 485f2d4)

Andrius Merkys merkys-guest at moszumanska.debian.org
Fri Dec 15 11:48:18 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  b8bc747   Requalifying dependency on non-free libstar-parser-perl as 'Suggests' in order not to hard-depend on non-free.
       new  06b6f21   Revert "Requalifying dependency on non-free libstar-parser-perl as 'Suggests' in"
       new  8436aa1   Revert "Updating source in debian/copyright."
       new  1295150   Revert "Changing svnversion in codcif-svnversion.diff patch."
       new  2803b4b   Revert "Explicitly distributing the right manpages between cod-tools and codcif packages."
       new  7689c25   Revert "Removing patches that were incorporated by the upstream."
       new  3f2036e   Revert "New upstream release."
       new  f916d0a   Revert "Merge tag 'upstream/2.1'"
       new  da826d9   Revert "Not installing STAR libraries, depending instead on non-free libstar-parser-perl."
       new  7976097   Revert "Adding missed debian/copyright entry for CIFTEST_2.1."
       new  485f2d4   Revert "Adding missed debian/copyright entry for spglib."

The 10 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/cod-tools.install                           |    1 +
 debian/cod-tools.manpages                          |   53 +-
 debian/codcif.manpages                             |    4 +-
 debian/control                                     |    1 -
 debian/copyright                                   |   58 +-
 debian/patches/cif_split_primitive-tests.diff      |   10 +
 debian/patches/codcif-manpages.diff                |  152 ++
 debian/patches/codcif-svnversion.diff              |    2 +-
 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 0 -> 312734 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 -
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 tests/inputs/1004001-disorder.cif                  |    2 +-
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 tests/inputs/1010050-zero-sigmas.cif               |    2 +-
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 .../inputs/1100107-spacegroup-with-underscore.cif  |    2 +-
 tests/inputs/1100709-uqstring-brackets.cif         |    2 +-
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 .../inputs/1100914-incorrect-weighting-scheme.cif  |    2 +-
 tests/inputs/1502949.cif                           |    2 +-
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 tests/inputs/2000000_e_temperature.cif             |    2 +-
 tests/inputs/20000097.cif                          |    2 +-
 tests/inputs/2000056.cif                           |    2 +-
 tests/inputs/2000080-molecule.cif                  |    2 +-
 tests/inputs/2000135.cif                           |    2 +-
 tests/inputs/2000318-r91933.cif                    |    2 +-
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 tests/inputs/2000373-modified-merge-limits.cif     |    2 +-
 tests/inputs/2000488-reset-limits.cif              |    2 +-
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 delete mode 120000 tests/cases/cif_validate_039.inp
 delete mode 100644 tests/cases/cif_validate_039.opt
 delete mode 120000 tests/cases/cod_predeposition_check_033.chk
 delete mode 100644 tests/inputs/malformed_symop_new_sym_tag.cif
 delete mode 100644 tests/inputs/merge_7b.cif
 delete mode 100644 tests/inputs/new_symop_tag.cif
 delete mode 100644 tests/outputs/cif2cod_047.out
 delete mode 100644 tests/outputs/cif_cod_check_112.out
 delete mode 100644 tests/outputs/cif_cod_check_113.out
 delete mode 100644 tests/outputs/cif_filter_181.out
 delete mode 100644 tests/outputs/cif_merge_007.out
 delete mode 100644 tests/outputs/cif_sort_atoms_001.out
 delete mode 100644 tests/outputs/cif_sort_atoms_002.out
 delete mode 100644 tests/outputs/cif_sort_atoms_003.out
 delete mode 100644 tests/outputs/cif_split_004.out
 delete mode 100644 tests/outputs/cif_tcod_tree_004.out
 delete mode 100644 tests/outputs/cif_validate_039.out
 delete mode 100644 tests/shoutputs/cif_print_loop_001.out
 delete mode 100644 tests/shoutputs/cif_print_loop_002.out
 delete mode 100644 tests/shoutputs/cif_tcod_tree_007.out
 delete mode 100644 tests/shoutputs/neighbour_list_from_mol_002.out
 delete mode 100755 tests/shtests/cif_print_loop_001.sh
 delete mode 100755 tests/shtests/cif_print_loop_002.sh
 delete mode 100755 tests/shtests/cif_tcod_tree_007.sh
 delete mode 100755 tests/shtests/neighbour_list_from_mol_002.chk
 delete mode 100755 tests/shtests/neighbour_list_from_mol_002.sh

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