pypi biotite 0.8.0
Biotite 0.8.0

latest releases: 0.40.0, 0.39.0, 0.38.0...
5 years ago

Changelog

Additions

  • Added support for Python 3.7
  • Discontinued support for Python 3.4 and 3.5
  • Added type hints for public API via stub files (PEP 484)
  • Revamped documentation
    • New sidebar
    • New main page
    • Summaries in API documentation
    • New layout of class attributes in API documentation
    • Function signatues of C-extension functions are shown
    • Documentation of decorated functions are correctly shown
    • Cross references in tutorial
    • Tutorial output is dynamically generated using sphinx-gallery
  • Specified version number for dependencies
  • Created environment.yaml for convenient creation of a development
    environment in conda
  • Improvements to structure.CellList
    • Improved perfromance
    • get_atoms() and get_atoms_in_cells() can be used in a vectorized
      manner (replacing efficient mode)
    • get_atoms() and get_atoms_in_cells() have optional as_mask parameter
    • Added create_adjacency_matrix() method
  • Added hydrogen bond detection (structure.hbond())
  • Missing element names in structure.io.pdb.PDBFile are automatically
    inferred (Gromacs support)
  • Added support for Gromacs' .gro file format (structure.io.gro).
  • Color schemes can bes loaded from custom files
  • File objects can read/write from/to a file object
  • Temporary files automastically generate a file name
  • STDOUT adn STDERR are accessible from application.Application runs

Changes

  • Changes in Enum types
    • sequence.Location.Strand is an Enum
    • sequence.Location.Defect is a Flag
    • structure.BondType is an Enum
    • application.AppState is a Flag
  • Usage of f-strings for exception messages (and some other places)
  • res_id is read from auth_seq_id instead of label_seq_id in mmCIF files

Fixes

  • Fixed custom color schemes in
    sequence.graphics.AlignmentSimilarityVisualizer
  • All integral types can be used as indices, instead of only int
  • Installing Biotite from a .whl no longer requires Cython to be installed

Don't miss a new biotite release

NewReleases is sending notifications on new releases.