Added:

• Added Structure.get_lattice_vectors() method to return the lattice vectors.
• Added Structure.get_lattice_vector_angles() method to return the angles between the lattice vectors.
• Added Structure.get_isotropic_displacement_parameters() method to return the isotropic displacement parameters.
• Added Structure.get_anisotropic_displacement_parameters() method to return the anisotropic displacement parameters.
• Added Structure.get_occupancies() method to return the occupancies of the sites.
• Added Structure.get_cartesian_coordinates() method to return the Cartesian coordinates of the sites.
• Added Structure.get_fractional_coordinates() method to return the fractional coordinates of the sites.
• Added Structure.get_chemical_symbols() method to return the chemical symbols of the sites.

What's Changed

• chore: fix CI badge in README.rst by @stevenhua0320 in #195
• feat: Add functions for getting information from Structure by @cadenmyers13 in #187
• chore: update pre-commit by @danielsirakov in #199
• chore: Fix internal deprecated function usage by @cadenmyers13 in #202

New Contributors

• @danielsirakov made their first contribution in #199

Full Changelog: 3.4.0...3.5.0-rc.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 ve...

What's Changed

• chore: deprecated addNewAtom by @stevenhua0320 in #157
• chore: deprecate getLastAtom and add a test by @stevenhua0320 in #159
• chore: deprecate read/writeStr, placeInLattice method by @stevenhua0320 in #161
• chore: deprecate private function in utils by @stevenhua0320 in #162
• chore: deprecate setLatPar and setLatBase method by @stevenhua0320 in #163
• chore: deprecate abcABG and readStr method by @stevenhua0320 in #164
• chore: deprecate methods in symmetryutilities.py by @stevenhua0320 in #165
• chore:deprecate methods in symmetryutilities.py and add test for methods by @stevenhua0320 in #166
• chore: deprecate method in symmetryutilities by @stevenhua0320 in #167
• chore: deprecate method in GeneratorSite class by @stevenhua0320 in #168
• chore: deprecate methods in GeneratorSite class by @stevenhua0320 in #169
• chore: deprecate SymmetryConstraints class method by @stevenhua0320 in #170
• chore: deprecate symmetryutilities method by @stevenhua0320 in #171
• chore: deprecate utils method and private methods in parsers by @stevenhua0320 in #172
• chore: deprecate parseLines method in all parsers by @stevenhua0320 in #173
• chore: deprecate parseFile method by @stevenhua0320 in #174
• chore: deprecate toLines method across of parsers by @stevenhua0320 in #175
• chore: deprecate getParser method across all parsers format. by @stevenhua0320 in #176
• chore: derepcate P_pdb method by @stevenhua0320 in #177
• chore: deprecate expansion functional utilities method. by @stevenhua0320 in #178
• chore: deprecate apps method by @stevenhua0320 in #179
• chore: deprecate spacegroup method by @stevenhua0320 in #180
• chore: deprecate Atom class method by @stevenhua0320 in #181
• chore: change utility script to snake_case method. by @stevenhua0320 in #182
• fix: fix load_structure method with loading Path object. by @stevenhua0320 in #185
• chore: add readme.md for devutils files by @stevenhua0320 in #184
• feat: add vesta viewer by @stevenhua0320 in #188
• chore: add assignUniqueLabels deprecation message by @stevenhua0320 in #190
• V3.4.0 by @sbillinge in #189
• license by @sbillinge in #193
• fix: fix documentation rendered properly by @stevenhua0320 in #192

Full Changelog: 3.4.0-rc.0...3.4.0-rc.1

What's Changed

• deprecate: Add deprecation warning for diffpy.Structure by @cadenmyers13 in #149
• skpkg: redo scikit-package with latest version with minimal fix by @stevenhua0320 in #152
• fix: fix deprecation warning by @stevenhua0320 in #153
• chore: deprecate assignUniqueLabels by @stevenhua0320 in #158

New Contributors

• @cadenmyers13 made their first contribution in #149

Full Changelog: 3.3.1...3.4.0-rc.0

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.

What's Changed

• style: use docs and requirements/tests.txt according to the new group standard by @ycexiao in #143
• fix: let tests compatible to newer versions of pycifrw by @ycexiao in #146

New Contributors

• @ycexiao made their first contribution in #143

Full Changelog: 3.3.1-rc.0...3.3.1-rc.1

What's Changed

• Recut - codecov in PR, Codespell, release checklist by @bobleesj in #120
• Add conda-forge release checklist to GitHub Issue template by @bobleesj in #121
• chored: fixed filenames by @TingwenZhang in #128
• skpkg: apply black line-length 115 to all files in the project directory by @kwagoner94 in #132
• Level 5 by @TingwenZhang in #138
• skpkg: new files by @TingwenZhang in #139
• Migration by @sbillinge in #140

New Contributors

• @TingwenZhang made their first contribution in #128
• @kwagoner94 made their first contribution in #132

Full Changelog: 3.3.0...3.3.1-rc.0

Added:

• Support for Python 3.13

Removed:

• Support for Python 3.10

What's Changed

• Support Python 3.13, drop 3.10 by @Tieqiong in #116

Full Changelog: 3.2.3...3.3.0rc0