smiles-scripts (unreleased)

  * Added:
    - cml-to-smi:
      - warning about unsupported wedge/hatch stereochemistry.
    - sdf-to-smi:
      - command line option to turn off charge adjustment after type-8
        bond conversion.
      - handling of attached hydrogen atoms.
      - handling of radicals.
      - the '--remove-alkali-bonds' command line option.
      - the '--remove-excess-stereochemistry' command line option.
      - the '--no-estimate-attached-hydrogens' command line option.
      - removal of superfluous cis/trans settings.
      - marking of square planar stereochemistry.
      - marking of trigonal bipyramidal stereochemistry.
      - handling of chiral molecules in non-Sohncke space groups.
    - smi_canonicalise:
      - the '--ignore-class' command line option.
      - the '--canonicalise-nitro-groups' command line option.
      - the '--canonicalise-haloanions' command line option (on by
        default).
    - smi_isomorphism:
      - the '--print-side-of-superfluous-moieties' command line option.
    - the 'cdksdf2inchi' program.
    - the 'smi_check' program.
    - the 'smi_check_racemate' program.
    - the 'smi_chemical_formula' program.
    - the SmilesScripts::Isomorphism module.
    - the SmilesScripts::OPSIN module.
    - dependency installers for Ubuntu 22.04, Ubuntu 24.04, Debian 11 and
      Debian 12.
  * Changed:
    - switched to Chemistry::OpenSMILES v0.11.6: Perl modules
      Chemistry::OpenSMILES::Aromaticity and Chemistry::OpenSMILES::Stereo
      have been moved to Chemistry::OpenSMILES in v0.8.2, thus they are
      removed from the project.
    - cml-to-smi:
      - disable network access by default.
    - sdf-to-smi:
      - preserving original valences for atoms participating in type-8
        bonds;
      - converting [C-]#[O+] to [C]#[O].
    - smi_canonicalise:
      - using canonical atom order during kekulisation.
    - smi_isomorphism:
      - doubling nauty worksize.
    - switched to a more conservative method of passing cis/trans settings
      to SMILES writer, resulting in a smaller amount of warnings.
  * Fixed:
    - cml-to-smi:
      - incorrect attached hydrogen estimation for atoms with nonstandard
        valency.
    - sdf-to-smi:
      - handling of unusual valences.
      - accidental removal of ring closing bonds in aromatic rings.
    - smi_isomorphism:
      - restoring compatibility with Graph v0.9722 and earlier.
  * Removed:
    - dependency installer for LinuxMint 19.3.

smiles-scripts (0.2.0)

  * Added:
    - the 'cml-to-smi' script.
    - the 'completalowz' script.
    - the 'sdf-to-smi' script.
    - the 'smi_canonicalise' script.
    - the 'smi_parse' script.
    - fixalot:
      - handling of a couple more compounds.
  * Changed:
    - fixalot:
      - handling more compounds.
    - fixhighz:
      - improving the user interface.
  * Fixed:
    - dependencies of Java classes.
    - cdkcif2xyz:
      - set a fixed locale to avoid unexpected number formatting
        under different system locales.
    - cdkdepict:
      - fixed a typo in the help message.

smiles-scripts (0.1.0)

  * Initial release.
