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Release notes

3.4.0

Added:

  • Added set_latt_parms method into Lattice class
  • Added set_new_latt_base_vec method into Lattice class
  • Added parse_lines method in p_auto.py
  • Added parse_lines method in p_cif.py
  • Added parse_lines method in p_discus.py
  • Added parse_lines method in p_pdb.py
  • Added parse_lines method in p_pdffit.py
  • Added parse_lines method in p_rawxyz.py
  • Added parse_lines method in p_xcfg.py
  • Added parse_lines method in p_xyz.py
  • Added parse_lines method in structureparser.py
  • Added _suppress_cif_parser_output method in p_cif.py
  • Add deprecation warning for diffpy.Structure import.
  • Added diffpy.structure.Structure.add_new_atom in replace of addNewAtom
  • Added load_structure_file method in apps/anyeye.py
  • Added convert_structure_file method in apps/anyeye.py
  • Added watch_structure_file method in apps/anyeye.py
  • Added clean_up method in apps/anyeye.py
  • Added parse_formula method in apps/anyeye.py
  • Added signal_handler method in apps/anyeye.py
  • Added method load_structure in __init__.py
  • Added diffpy.structure.Structure.assign_unique_labels in replace of assignUniqueLabels
  • Support for Python 3.14
  • Added place_in_lattice method to Structure
  • Added read_structure method to Structure
  • Added write_structure method to Structure
  • Added position_formula method in GeneratorSite class
  • Added u_formula method in GeneratorSite class
  • Added eq_index method in GeneratorSite class
  • Added prune_formula_dictionary method in symmetryutilities.py
  • Added _link_atom_attribute method in diffpy.structure.utils
  • Added msd_latt method in atom.py
  • Added msd_cart method in atom.py
  • Added _get_uij method in atom.py
  • Added _set_uij method in atom.py
  • Added parse_file method in structureparser.py
  • Added parse_lines method in p_cif.py
  • Added parse_lines method in p_auto.py
  • Added parser for vesta specific files and viewer for vesta
  • Added atom_bare_symbol method in utils.py
  • Added _get_ordered_formats method in p_auto.py
  • Added _wrap_parse_method method in p_auto.py
  • Added _tr_atom_site_u_iso_or_equiv method in p_cif.py
  • Added _tr_atom_site_b_iso_or_equiv method in p_cif.py
  • Added _tr_atom_site_aniso_u_11 method in p_cif.py
  • Added _tr_atom_site_aniso_u_22 method in p_cif.py
  • Added _tr_atom_site_aniso_u_33 method in p_cif.py
  • Added _tr_atom_site_aniso_u_12 method in p_cif.py
  • Added _tr_atom_site_aniso_u_13 method in p_cif.py
  • Added _tr_atom_site_aniso_u_23 method in p_cif.py
  • Added _tr_atom_site_aniso_b_11 method in p_cif.py
  • Added _tr_atom_site_aniso_b_22 method in p_cif.py
  • Added _tr_atom_site_aniso_b_33 method in p_cif.py
  • Added _tr_atom_site_aniso_b_12 method in p_cif.py
  • Added _tr_atom_site_aniso_b_13 method in p_cif.py
  • Added _tr_atom_site_aniso_b_23 method in p_cif.py
  • Added get_symop method in parsers/p_cif.py
  • Added get_space_group method in spacegroups.py
  • Added find_space_group method in spacegroups.py
  • Added is_space_group_identifier method in spacegroups.py
  • Added _hash_symop_list method in spacegroups.py
  • Added _build_sg_lookup_table method in spacegroups.py
  • Added _get_sg_hash_lookup_table method in spacegroups.py
  • Added read_structure method into PDFFitStructure class
  • Added cell_parms method into Lattice class
  • Added _find_constraints method in SymmetryConstraints class
  • Added pos_parm_symbols method in SymmetryConstraints class
  • Added pos_parm_values method in SymmetryConstraints class
  • Added u_parm_symbols method in SymmetryConstraints class
  • Added u_parm_values method in SymmetryConstraints class
  • Added u_formulas method in SymmetryConstraints class
  • Added diffpy.structure.Structure.get_last_atom in replace of getLastAtom
  • Added get_parser method in p_auto.py
  • Added get_parser method in p_cif.py
  • Added get_parser method in p_discus.py
  • Added get_parser method in p_pdb.py
  • Added get_parser method in p_pdffit.py
  • Added get_parser method in p_rawxyz.py
  • Added get_parser method in p_xcfg.py
  • Added get_parser method in p_xyz.py
  • Added get_parser method in parsers/__init__.py
  • Added position_formulas method in SymmetryConstraints class
  • Added position_formulas_pruned method in SymmetryConstraints class
  • Added u_formulas_pruned method in SymmetryConstraints class
  • Added _parse_cif_data_source method in p_cif.py
  • Added _parse_cif_block method in p_cif.py
  • Added to_lines method in p_cif.py
  • Added to_lines method in p_pdb.py
  • Added to_lines method in p_rawxyz.py
  • Added to_lines method in p_xcfg.py
  • Added to_lines method in p_xyz.py
  • Added to_lines method in structureparser.py
  • Added _lines_iterator method in p_discus.py
  • Added to_lines method in p_discus.py
  • Added is_space_group_latt_parms method in symmetryutilities.py
  • Added is_constant_formula method in symmetryutilities.py
  • Added find_center method in expansion/shapeutils.py
  • Added make_sphere method in expansion/makeellipsoid.py
  • Added make_ellipsoid method in expansion/makeellipsoid.py
  • Added position_difference method in symmetryutilities.py
  • Added nearest_site_index method in symmetryutilities.py
  • Added _find_invariants method in symmetryutilities.py
  • Added equal_positions method in symmetryutilities.py
  • Added expand_position method in symmetryutilities.py
  • Added null_space method in symmetryutilities.py
  • Added input_formats method in parsers/__init__.py
  • Added output_formats method in parsers/__init__.py
  • Added title_lines method in p_pdb.py
  • Added cryst1_lines method in p_pdb.py
  • Added atom_lines method in p_pdb.py
  • Added convert_fp_num_to_signed_rational method in GeneratorSite class
  • Added _find_null_space method in GeneratorSite class
  • Added _find_pos_parameters method in GeneratorSite class
  • Added _find_u_space method in GeneratorSite class
  • Added _find_u_parameters method in GeneratorSite class
  • Added _find_eq_uij method in GeneratorSite class

Changed:

  • Changed private method __emptySharedStructure to __empty_shared_structure

Deprecated:

  • Deprecated setLatPar method in Lattice class for removal in version 4.0.0
  • Deprecated setLatBase method in Lattice class for removal in version 4.0.0
  • Deprecated parseLines method in p_auto.py for removal in version 4.0.0
  • Deprecated parseLines method in p_cif.py for removal in version 4.0.0
  • Deprecated parseLines method in p_discus.py for removal in version 4.0.0
  • Deprecated parseLines method in p_pdb.py for removal in version 4.0.0
  • Deprecated parseLines method in p_pdffit.py for removal in version 4.0.0
  • Deprecated parseLines method in p_rawxyz.py for removal in version 4.0.0
  • Deprecated parseLines method in p_xcfg.py for removal in version 4.0.0
  • Deprecated parseLines method in p_xyz.py for removal in version 4.0.0
  • Deprecated parseLines method in structureparser.py for removal in version 4.0.0
  • Deprecated diffpy.structure.Structure.addNewAtom method for removal in version 4.0.0
  • Deprecated loadStructureFile method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated convertStructureFile method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated watchStructureFile method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated cleanUp method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated parseFormula method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated signalHandler method in apps/anyeye.py for removal in version 4.0.0
  • Deprecated method loadStructure in __init__.py for removal in version 4.0.0
  • Deprecated diffpy.structure.Structure.assignUniqueLabels for removal in 4.0.0
  • Deprecated placeInLattice method of Structure for removal in version 4.0.0
  • Deprecated readStr method of Structure for removal in version 4.0.0
  • Deprecated writeStr method of Structure for removal in version 4.0.0
  • Deprecated positionFormula method in GeneratorSite class for removal in version 4.0.0
  • Deprecated UFormula method in GeneratorSite class for removal in version 4.0.0
  • Deprecated eqIndex method in GeneratorSite class for removal in version 4.0.0
  • Deprecated pruneFormulaDictionary method in symmetryutilities.py for removal in version 4.0.0
  • Derecated _linkAtomAttribute method in diffpy.structure.utils for removal in version 4.0.0
  • Deprecated msdLat method in atom.py for removal in version 4.0.0
  • Deprecated msdCart method in atom.py for removal in version 4.0.0
  • Deprecated parse_file method in structureparser.py for removal in version 4.0.0
  • Deprecated parse_file method in p_cif.py for removal in version 4.0.0
  • Deprecated parse_file method in p_auto.py for removal in version 4.0.0
  • Deprecated atomBareSymbol method in utils.py for removal in version 4.0.0
  • Deprecated getSymOp method in parsers/p_cif.py for removal in version 4.0.0
  • Deprecated GetSpaceGroup method in spacegroups.py for removal in version 4.0.0
  • Deprecated IsSpaceGroupIdentifier method in spacegroups.py for removal in version 4.0.0
  • Deprecated FindSpaceGroup method in spacegroups.py for removal in version 4.0.0
  • Deprecated _hashSymOpList method in spacegroups.py for removal in version 4.0.0
  • Deprecated readStr method in PDFFitStructure class for removal in version 4.0.0
  • Deprecated abcABG method in Lattice class for removal in version 4.0.0
  • Deprecated posparSymbols method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated posparValues method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated UparSymbols method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated UparValues method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated UFormulas method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated diffpy.structure.Structure.getLastAtom for removal in version 4.0.0
  • Deprecated getParser method in p_auto.py for removal in version 4.0.0
  • Deprecated getParser method in p_cif.py for removal in version 4.0.0
  • Deprecated getParser method in p_discus.py for removal in version 4.0.0
  • Deprecated getParser method in p_pdb.py for removal in version 4.0.0
  • Deprecated getParser method in p_pdffit.py for removal in version 4.0.0
  • Deprecated getParser method in p_rawxyz.py for removal in version 4.0.0
  • Deprecated getParser method in p_xcfg.py for removal in version 4.0.0
  • Deprecated getParser method in p_xyz.py for removal in version 4.0.0
  • Deprecated getParser method in parsers/__init__.py for removal in version 4.0.0
  • Deprecated positionFormulas method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated positionFormulasPruned method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated UFormulasPruned method in SymmetryConstraints class for removal in version 4.0.0
  • Deprecated toLines method in p_cif.py for removal in version 4.0.0
  • Deprecated toLines method in p_pdb.py for removal in version 4.0.0
  • Deprecated toLines method in p_rawxyz.py for removal in version 4.0.0
  • Deprecated toLines method in p_xcfg.py for removal in version 4.0.0
  • Deprecated toLines method in p_xyz.py for removal in version 4.0.0
  • Deprecated toLines method in structureparser.py for removal in version 4.0.0
  • Deprecated toLines method in p_discus.py for removal in version 4.0.0
  • Deprecated isSpaceGroupLatPar method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated isconstantFormula method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated findCenter method in expansion/shapeutils.py for removal in version 4.0.0
  • Deprecated makeSphere method in expansion/makeellipsoid.py for removal in version 4.0.0
  • Deprecated makeEllipsoid method in expansion/makeellipsoid.py for removal in version 4.0.0
  • Deprecated positionDifference method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated nearestSiteIndex method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated equalPositions method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated expandPosition method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated nullSpace method in symmetryutilities.py for removal in version 4.0.0
  • Deprecated inputFormats method in parsers/__init__.py for removal in version 4.0.0
  • Deprecated outputFormats method in parsers/__init__.py for removal in version 4.0.0
  • Deprecated titleLines method in p_pdb.py for removal in version 4.0.0
  • Deprecated crystl1Lines method in p_pdb.py for removal in version 4.0.0
  • Deprecated atomLines method in p_pdb.py for removal in version 4.0.0
  • Deprecated signedRatStr method in in GeneratorSite class for removal in version 4.0.0

Fixed:

  • Fixed load_structure with successfully loading Path object
  • Fix deprecation for open file for Python 3.14

Removed:

  • Support for Python 3.11

3.3.1

Added:

  • Spelling check via Codespell in pre-commit
  • Coverage report in each PR

Changed:

  • Use the names CODE-OF-CONDUCT.rst, docs and requirements/tests.txt according to the new group standard.

Fixed:

  • Let diffpy.structure pass the tests with pycifrw installed from PyPI.

3.3.0

Added:

  • Support for Python 3.13

Deprecated:

  • Support for Python 3.10

3.2.3

Added:

  • Use GitHub Actions to build, release, upload to PyPI
  • Added issue template for PyPI/GitHub release
  • Include GitHub Issues templates for bug report and feature request

Fixed:

  • Add getting started section and re-arrange install success check instructions
  • Added terminal script for transtru app in pyproject.toml
  • Changed requires-python to align with classifiers

3.2.2

Added:

  • Unit test for version.py
  • support for numpy >=2.0

Fixed:

  • tests folder at the root of the repo
  • Add pip dependencies under pip.txt and conda dependencies under conda.txt
  • element/label itemsize to 5 in _linkAtomAttribute to support numpy >=2.0
  • Recookiecut package to the group standard

3.2.1

3.2.0

Changed:

  • Removed support for Python 2
  • This version only supporting Python 3.10, 3.11, 3.12
  • All docstrings style updated to numpydoc

Deprecated:

  • Deprecated the diffpy.structure.applications module. Use diffpy.structure.apps instead

Removed:

  • Removed all six compatibility code

Fixed:

  • Repo structure modified to the new diffpy standard

Version 3.1.0 - 2022-12-04

Added

  • Compatibility with Python 3.10, 3.9, 3.8

Changed

Deprecated

Removed

  • Remove the support for Python 3.5, 3.6.

Fixed

Version 3.0.2 - 2022-10-12

Added

  • A string representation of SpaceGroup with key information.

Changed

  • Bumped minimum PyCifRW version to 4.4.3.

Deprecated

Removed

Fixed

  • Handling of paths on Windows when using the P_cif parser.

Version 3.0.1 - 2019-06-27

Added

  • Function FindSpaceGroup for space group lookup from its list of symmetry operations.

Changed

  • Reuse existing SpaceGroup instance when loading a CIF file.
  • Improve check of SpaceGroup identifiers in GetSpaceGroup.
  • When loading CIF file, preset Atom.anisotropy according to symmetry constraints at each site. Adhere to specific ADP type when specified in the CIF.

Removed

  • Unused attribute SpaceGroup.alt_name.

Fixed

  • Fix inconsistent (Atom, Structure) pickle. Preserve Atom ownership in a Structure after pickling and unpickling.
  • Spuriously linked array-view values after stru.xyz = 0.
  • Preserve scalar value type when setting stru.occupancy = value.
  • Process unknown CIF occupancy "?" as an occupancy of 1.
  • Incorrect SymOp list for spacegroup "B11m" (number 1008).

Version 3.0.0 - 2019-03-11

Notable differences from version 1.3.5.

Added

  • Compatibility with Python 3.7, 3.6, 3.5 in addition to 2.7.
  • Aliases for 17 non-standard space group names from cctbx.
  • Support for intersphinx links to Python and NumPy documentation.
  • Dependency and use of the six PY2/PY3 compatibility package.
  • Documentation hosting at readthedocs.org.

Changed

  • Rename the package and all its module names to lowercase.
  • Use UTF-8 encoding when writing structure files.
  • Refactor parsing of XCFG format. Avoid use of generated code.
  • Refactor all starred imports to explicit so they can be checked.
  • Adopt napoleon style for docstrings.
  • Update docstrings for Atom, Lattice, SymOp, SpaceGroup.
  • Switch to platform-independent "noarch" Anaconda package.

Deprecated

  • Old camel case module names such as diffpy.Structure.
  • Variable __gitsha__ in the version module which was renamed to __git_commit__.

Removed

  • Unused exception IsotropyError.
  • Unused class BRAtomsStructure and associated parser.

Fixed

  • Loading of empty CIF files with no specified sites.
  • Parsing of CIFs with ? value for unknown displacement parameters.
  • Symmetry constraint equations for ADPs so they avoid self-reference.
  • Use StructureFormatError exception for CIF with unknown space group.
  • Open files within the with context so they get closed when done.
  • Invalid escape sequences in string values.