Pymatgen

1. **PR 3680** - Add support for `vaspout.h5`, improvements to POTCAR handling by esoteric-ephemera
- Added support for parsing `vaspout.h5` and improvements in POTCAR handling.
- Major additions include methods for processing `vaspout.h5` and ensuring compatibility with existing VASP I/O infrastructure.

2. **PR 4319** - Update `abitimer` in `io.abinit` by gpetretto
- Fixes parsing issues for newer versions of Abinit.
- Updates compatibility with `pandas > 2` and includes test files for validation.

3. **PR 4315** - Patch to allow `pyzeo` integration by daniel-sintef
- Provides a patch to swap out `zeo++` with `pyzeo`, which is a more actively maintained version.

4. **PR 4281** - Add method to get the Pearson symbol to `SpaceGroupAnalyzer` by CompRhys
- Introduced a new method to retrieve the Pearson Symbol in `SpaceGroupAnalyzer`.

6. **PR 4295** - Pass `kwargs` to `IStructure.to` method in JSON format by DanielYang59
- Provides finer control over `json.dumps` behavior during format conversion.

7. **PR 4306** - `IStructure.to` defaults to JSON when `filename` is unspecified by DanielYang59
- Adjusts default file output behavior to JSON.

8. **PR 4297** - Bugfix for `Structure/ase.Atoms` interconversion by wolearyc
- Ensures deep copying to avoid shared memory issues between `Atoms.info` and `Structure.properties`.

9. **PR 4304** - `MagneticStructureEnumerator`: Expose `max_orderings` argument by mkhorton
- Makes `max_orderings` configurable via keyword argument.

10. **PR 4299** - Update inequality in `get_linear_interpolated_value` by kavanase
- Fixes interpolation logic to handle edge cases more robustly.

1. **PR 4288**: `Dos.get_cbm_vbm` updates by kavanase
- Improvements for determining VBM/CBM eigenvalues from a DOS object to match expected values for `emmet-core` tests.

2. **PR 4278**: [Breaking] Fix valence electron configuration parsing by DanielYang59
- Addresses valence electron configuration parsing issue in `PotcarSingle.electron_configuration`, resolving 4269.

3. **PR 4275**: Fix default `transformation_kwargs` in `MagneticStructureEnumerator` by DanielYang59
- Corrects default `transformation_kwargs` to close 4184, with additional comment and type cleanup.

4. **PR 4274**: Move `occ_tol` to init in `OrderDisorderedStructureTransformation` by Tinaatucsd
- Resolved incompatibility with `StandardTransmuter` by moving `occ_tol` to class initialization.

5. **PR 4276**: Fix timeout in `EnumlibAdaptor` by DanielYang59
- Adjusts timeout handling to fix 4185 with associated unit test corrections.

6. **PR 4280**: Pre-commit autoupdate by pre-commit-ci[bot]
- Updates multiple pre-commit configurations, including ruff-pre-commit and markdownlint-cli.

7. **PR 4290**: Migrate type annotation tweaks from 4100 by DanielYang59
- Integrates type annotation improvements to aid review, addressing 4286.

8. **PR 4291**: Remove deprecated memory units from `core` by DanielYang59
- Eliminates outdated memory units in `core` for clarity.

9. **PR 4292**: Fix for `plotly` `PDPlotter`/`ChemicalPotentialDiagram.get_plot()` by kavanase
- Resolves deprecated `titlefont` issue in plotly v6, updating dependency requirements.

10. **PR 4283**: `Composition` support formula strings with curly brackets by janosh
- Expands formula parsing to include curly brackets, with added tests for verification.

11. **PR 4279**: Fix P1 SymmOp string for `CifParser.get_symops` by DanielYang59
- Corrects SymmOp string to close 4230, supplemented by a unit test.

12. **PR 4265**: Clarify return type for `core.Composition.reduced_composition` by DanielYang59
- Refines return types and cleans up types in `core.Composition`.

13. **PR 4268**: Add `Structure.get_symmetry_dataset` method by janosh
- Introduces convenience method for `moyopy` symmetry analysis with a new optional dependency set.

14. **PR 4271**: Add missing parenthesis to `BoltztrapAnalyzer.get_extreme.is_isotropic` by DanielYang59
- Minor syntax fix and cleanup for the method, resolving 4165.

15. **PR 4270**: Add `seed: int = 0` parameter to `Structure.perturb()` by janosh

16. New NEBSet and CINEBSet for NEB calculations. These replace the old MITNEBSet. shyuep

1. **PR 4159 by DanielYang59**
- Avoid using full equality `==` to compare float values to address issue 4158.
- Recommend using `assert_allclose` over `assert_array_equal` for float arrays due to numerical imprecision.
- Implement a ~3x speedup tweak to the `_proj` implementation.
- Partially replace sequence of float comparison using `==` for list/tuple/dict as referenced [here](https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/core/test_bonds.py#L56).
- Introduce other type and comment tweaks.

2. **PR 4190 by benrich37**
- **Feature 0:** Hierarchical structure using class objects to represent data within a JDFTx out file.
- Main hierarchy classes:
- `JDFTXOutputs`
- `JDFTXOutputs.outfile`
- `JDFTXOutfile`
- `JDFTXOutfile.slices[i]`
- `JDFTXOutfileSlice`, etc.
- **Feature 1:** `outputs.py` module with `JDFTXOutfile` for representing a JDFTx out file.
- **Feature 2:** `jdftxoutfileslice.py` module with `JDFTXOutfileSlice` for file slices of a single JDFTx call.
- **Feature 3:** `joutstructures.py` with `JOutStructures` for representing structures from an out file slice.
- **Feature 4:** `joutstructure.py` with `JOutStructure` for each single structure within an out file.
- **Feature 5:** `jelstep.py` with `JElStep` and `JElSteps` for SCF steps and convergences.
- **Feature 6:** `jminsettings.py` with `JMinSettings` for minimization settings representations.

3. **PR 4189 by benrich37**
- **Feature 1:** `inputs.py` module containing `JDFTXInfile` for Pythonic representation of JDFTx calculation inputs.
- **Feature 2:** `generic_tags.py` module with "Tag" objects (`AbstractTag` and its inheritors) for JDFTx input structure representation.
- **Feature 3:** `jdftxinfile_master_format.py` for creating proper "Tag" objects for inputs.
- **Feature 4:** `jdftxinfile_ref_options.py` for holding lists of acceptable strings for input tags.

1. **PR 4255 by peikai**: This PR resolves an inconsistency in the `run_type` for entries in a mixing scheme. The entry type was changed to 'r2SCAN', but the `MaterialsProjectDFTMixingScheme()` expected 'R2SCAN', causing errors and ignored entries in GGA(+U)/R2SCAN mixing scheme corrections.

2. **PR 4160 by DanielYang59**: Enhancements and clarifications were made to the `io.vasp.outputs.Outcar` docstring/comment. This includes more specific type annotations for parsers and updating the default value in `getattr` to `False` for condition checks.

3. **PR 4257 by njzjz**: This PR covers the intention to build Linux arm64 wheels, referencing the availability of free hosted runners for public repositories. However, specific features and fixes were not detailed.

4. **PR 4240 by kavanase**: A minor fix in `FermiDos` improves the robustness of the `get_doping` method, addressing issues with handling rare cases with minimal energy increments between VBM and CBM indices.

5. **PR 4254 by tpurcell90**: Adjustments regarding the use of libxc with FHI-aims to automatically add an override warning call, ensuring the process behaves as expected.

6. **PR 4256 by kavanase**: Addresses a behavior issue with `Composition` for mixed species and element compositions, providing a fix that ensures compositions are interpreted correctly, avoiding incorrect results in representations and calculations.

7. **PR 4253 by esoteric-ephemera**: This PR introduces the ability to convert between ASE and pymatgen trajectories, maintaining additional data such as energies, forces, and stresses, thus improving integration between the two programs and addressing related issues.

These updates range from bug fixes and enhancements to new features aimed at improving the functionality and reliability of the codebase.

- Iterating Element no longer contains isotopes (D and T). (DanielYang59)
- Remove is_rare_earth_metal from ElementBase (jdewasseigeosium)
- Fix DOS parsing for SOC calculations (kavanase)
- Added Pure Random Algo to OrderDisorderedStructureTransformation (jmmshn)
- Fix ion formula check in ion_or_solid_comp_object of analysis.pourbaix_diagram (DanielYang59)
- AseAtomsAdaptor: Support arbitrary selective dynamics constraints (yantar92)
- Explicit UTF-8 encoding for zopen and open. (DanielYang59)

- CP2K fixes (janosh)
- Fix borg.hive.SimpleVaspToComputedEntryDrone.assimilate ValueError when core file missing (DanielYang59)
- Revert breaking analysis.local_env default_op_params/cn_opt_params rename (DanielYang59)
- Added new Flag for AutoOxiStateDecorationTransformation (jmmshn)
- Fixed execution of packmol in relative path. (davidwaroquiers)
- Improve element mismatch handling with POTCAR for Poscar.from_file/str (DanielYang59)
- Preprocess Structure Reduction Before Bulk Match (lan496)
- Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop (DanielYang59)