Pymatgen

* Initial implementation of MPRester2 with new API support. Basic functionality for now.

This will be the final release with the pymatgen.analysis.defects
module included in the standard pymatgen package. This release will
include the older defects code by default, but can also be replaced with
the newer defects code through installation of pymatgen-analysis-defects.

Subsequent versions of pymatgen will require
the additional installation of `pymatgen-analysis-defects <https://github.com/materialsproject/pymatgen-analysis-defects>`\_ for all defect-related
functionality via pip install pymatgen-analysis-defects.

Relevant imports will still be from the pymatgen.analysis.defects namespace but the code will now be maintained and developed in this separate repository.

There will be significant changes to the defects code to support new functionality.Existing PyCDT users should use this version of pymatgen or older. Any questions
about this change should be directed to Jimmy-Xuan Shen, jmmshn.

For more information about other pymatgen "add-on" packages, please see
`this page in our documentation <https://pymatgen.org/addons.html>`\_.

* Preparation for the removal of the defects module, PR 2582 by jmmshn

Welcome to new contributors naveensrinivasan, xivh, dgaines2, yang-ruoxi, cajfisher and mjwen!

* New: Partial periodic boundary conditions, PR 2429 by gpetretto
* New: Element.from_name(), PR 2567 by rkingsbury
* New: Materials Project input set for absorption calculations, PR 2320 by yang-ruoxi
* Enhancement: compressed LAMMPS and XYZ files in pymatgen.io.lammps, PR 2538 by ab5424
* Enhancement: remove vertical lines from VoltageProfilePlotter.get_plotly_figure(), PR 2552 by acrutt
* Enhancement: chemical potential plot background color changed, PR 2559 jmmshn
* Enhancement: ability to change voronoi_distance_cutoff in ChemEnv, PR 2568 by JaGeo
* Enhancement: Ion.oxi_state_guesses will use correct charge by default, PR 2566 by rkingsbury
* Enhancement: Remove not converged warning for VASP AIMD runs, PR 2571 by mjwen
* Fix: generation of continuous line-mode band structures, PR 2533 by munrojm
* Fix: duplicate site properties for magnetic moments hwen using `AseAtomsAdaptor`, PR 2545 by Andrew-S-Rosen
* Fix: bug in Grüneisen parameter calculation, PR 2543 by ab5424
* Fix: allow a comment on final line of KPOINTS file, PR 2549 by xivh
* Fix: for `Composition.replace` with complex mappings, PR 2555 by jacksund
* Fix: Implement equality method and fix **iter** for InputSet, PR 2575 by rkingsbury
* Fix: use negative charge convention for electron in "update_charge_from_potcar", PR 2577 by jmmshn
* Fix: ensure charge is applied to initial and final structures parsed from vasprun.xml, PR 2579 by jmmshn
* Chore: Set permissions for GitHub actions, PR 2547 by naveensrinivasan
* Chore: Included GitHub actions in the Dependabot config, PR 2548 by naveensrinivasan
* Documentation: fix typos in pymatgen.symmetry.analyzer docstrings, PR 2561 by dgaines2
* Documentation: clarification about usage of InputFile, PR 2570 by orionarcher
* Documentation: Improve messages and warnings, PR 2572 and PR 2573 by cajfisher
* Documentation: fix typo, PR 2580 by janosh

Notice: functionality from pymatgen.analysis.defects will be incorporated into a separate add-on package in the future,
see deprecation notice.

* Q-Chem updates to NBO and new geometry optimizer, PR 2521 by samblau
* Bug fix for VolumetricData, PR 2525 by jmmshn
* Bug fix for MPRester, PR 2531 by janosh

* Added option for additional criteria to be passed to MPRester.get_entries_in_chemsys (shyuep).

* Initial support for parsing ML MD runs from vasprun.xml (shyuep).