update changelog

Author: sbillinge

CHANGELOG.rst

@@ -4,6 +4,227 @@ Release notes
 
 .. current developments
 
+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
 =====