pytest --store-durations --durations-path tests/files/.pytest-split-durations

* add new PMG_VASP_PSP_SUB_DIRS SETTING used in from_symbol_and_functional to allow customizing currently hard-coded subfolder structure of PMG_VASP_PSP_DIR

* fix TestMatPESStaticSet.test_default and TestLobsterSet.test_potcar

* add TestPotcarSingle.test_from_symbol_and_functional_raises

* uncomment and fix test_default_functional

* del outdated test.yml comment

thanks @DanielYang59

* try fix test_from_symbol_and_functional_raises on windows

* put `is_symmetric/polar` next to `property`

* BREAKING: reverse `get_slab` shift direction

* clarify `shift` for single atom

* use `isclose` to determine overlap atoms

* correct tolerance unit

* Revert "put `is_symmetric/polar` next to `property`"

This reverts commit 65e3ec86a19903272e24b7036924d70403bcd5ed.

* reapply docstring changes

* use `isclose` to check close

* fix typo in tag

* remove debug tag

* pre-commit auto-fixes

* make `center_slab` very simple

* Failed: make center_slab and get_slab_regions methods for `Slab`

* revert deprecation of `center_slab` function

* revert "overlap position check with isclose"

* revert deprecation of center_slab and get_slab_regions

* revert changes for `center_slab` function

* recover docstring

* rename slab to struct (type is Structure)

* revert adding minus sign

* fix slab type

* keep shift def consistent (need clarify)

* unify usage of shift outside Slab

* fix unit test

* add missing minus sign for single atom shift

* [need confirm] fix test for coh-interface

* add TODO tag

* clarify shift definition

* revert ALL change related to the direction of shift

* rename arg shift to termination

* tweak comments

* clarify `shift` attrib in `Slab`

* clarify magic number

* simplify doc

* reuse `center_slab` func

* remove unneeded TODO tag

* revert shift to termination rename

* remove finished TODO tag

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* add CI run on macos-latest, python=3.12 with resolution: lowest and extras: '' to test pymatgen without any optional deps installed

* restore quotes around py version

* fix error: Failed to parse: `.[ci,]`
  Caused by: Couldn't parse requirement at position 5
  Caused by: Expected an alphanumeric character starting the extra name, found ']'
.[ci,]

* change uv resolution to lowest-direct on macos

* skip pwmat input tests that require seekpath if optional seekpath is not installed

* Trajectory class: raise ImportError with ASE installation instructions when reading .traj files

* fix TestTrajectory.test_from_file() when ase not installed, test expected error message

* Fix outdated NO_ASE_ERR attribute access in test_ase.py

* simplify ComputedEntry.__eq__

f-strings, better var names, fix ruff RUF002

* fix filter condition and to list

* update unit test for err msg

* increase monty version

* Revert "increase monty version"

This reverts commit e281fdfdcb047a2cb0703be6b3235aaad760875b.

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* fix typing_extensions ImportError

https://github.com/materialsproject/pymatgen/pull/3752#issuecomment-2142954988

* bump min ase to 3.23.0

* test both lowest-direct and highest uv package resolutions in CI

* establish some loose lower bounds on all deps

needed for deps install with --resolution=lowest-direct to work

* netcdf4>=1.6

* pin chgnet==0.3.6

* try chgnet==0.3.5

* bump pre-commit hooks

* imperative doc strings

* doc str white space

* test_string->test_str

* ruff auto fixes

* matgl>=1.1.1 numba>=0.55

* try fix netcdf4 install

* h5py>=3.9.0

* monty>=2024.5.24

fixes TypeError: deprecated() got an unexpected keyword argument 'deadline'

* revert TestWavecar to again inherit from PymatgenTest

* h5py>=3.11.0

* phonopy>=2.23

* scipy>=1.13.0

* matplotlib>=3.8

* requests>=2.32

* don't run oldest/newest supported python twice on linux AND windows

* fix bad refactor in get_atom_map

fixes KeyError: 'Co' ipot = self.pot_dict[el.symbol]

* remove a lot of ignore tags

* first go: quick look and comment/type tweaks

* remove ALL type: ignore[reportPossiblyUnboundVariable]

* a quick look

* tweak module docstring

* fix/supress PossiblyUnboundVariable

* pre-commit fix

* revert changes from other branch

* [Need Discussion] set IVDW default to 0

* suppress None error for ElementTree searches

* replace dict update with |=

* fix typo in update -> |=, and mypy fixes

* fix another typo in update -> |=

* add DEBUG tag and mypy fixes

* remove DEBUG tag

* more mypy fixes

* more mypy fixes

* mypy fixes

* finish mypy errors

[Deprecation] Replace `Element` property `is_rare_earth_metal` with `is_rare_earth` to include Y and Sc  (#3817)

* make Sc and Y rare earth ele

* update docstring

* log breaking change

* revert removal of blank line

* update grace period

* add is_rare_earth and deprecate the old

* update `monty` to use `deadline`

* update monty to latest

---------

Signed-off-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

Improve unphysical (greater than 1) occupancy handling in `CifParser` and add missing site label `if not check_occu` (#3819)

* fix tol def and add error msg

* no verify

* allow any occupancy when not check_occu

* remove unnecessary warning

* simplify warning message

* add one more unit test

* fix var name in comment

* revise docstring

* fix missing label when `check_occu`

* update unit test

* revert accidental change during merge

* revert change to `occupancy_tolerance`

* fix comment and revert a unnecessary deletion

* filter valid occupancy

* revert docstring change

* use isclose over == for position check

* fix some types

* update unit test for `test_get_slabs`

* revert change to unit test

* add `ztol` argument

* rectify docstring

updated-dependencies:
- dependency-name: requests
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

electronic_structure. #3849, #3850

* Replace deprecated 'delim_whitespace=True` with `sep="\s+"`

* pre-commit auto-fixes

* sio->str_io

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* remove a lot of ignore tags

* first go: quick look and comment/type tweaks

* remove ALL type: ignore[reportPossiblyUnboundVariable]

* a quick look

* tweak module docstring

* fix/supress PossiblyUnboundVariable

* pre-commit fix

* add debug tag

* fix some mypy errors

* fix some mypy errors

* suppress errors in `__setitem__`

* fix typos

* fix union

* revert change to md

* tweaks

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* updates for consistency with atomate2 updates

* lint

* further patch for atomate2 support, make sure tests are respected or updated

* linting

* merge DictSet into VaspInputSet, deprecate DictSet as an alias of VaspInputSet to avoid breakage

* test_dict_set_alias subclass and deprecation message

* Change deprecation warning to be on init of DictSet

* remove deprecated decorator, only works for functions, error msg less clear when wrapped on init

* move remaining VaspInputGenerator features to PMG

* pre-commit auto-fixes

* added tests

* add incar, kpoints, poscar, potcar attr to io.vasp.inputs.VaspInput + tests

* linted

* Bump rexml from 3.2.5 to 3.2.8 in /docs (#3836)

Bumps [rexml](https://github.com/ruby/rexml) from 3.2.5 to 3.2.8.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](https://g...

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.16.2 to 1.16.5.
- [Release notes](https://github.com/sparklemotion/nokogiri/releases)
- [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md)
- [Commits](https://github.com/sparklemotion/nokogiri/compare/v1.16.2...v1.16.5

)

---
updated-dependencies:
- dependency-name: nokogiri
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

Bumps [rexml](https://github.com/ruby/rexml) from 3.2.5 to 3.2.8.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](https://github.com/ruby/rexml/compare/v3.2.5...v3.2.8

)

---
updated-dependencies:
- dependency-name: rexml
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* relocate dunder methods to top for core.trajectory

fix `core.operations`

add types for site, mypy errors to fix

remove no_type_check decorator

move dunder methods to the top

fix mypy errors

remove debug tag

improve `spectrum`

finish `core.tensors`

finish `xcfunc`

fix hash of `SymmOp`

finish `core.trajectory`

Add types for `core.molecular_orbitals/operations/sites/spectrum/tensor/xcfunc`  (#3829)

* fix `core.molecular_orbitals`

* fix `core.operations`

* add types for site, mypy errors to fix

* remove no_type_check decorator

* move dunder methods to the top

* fix mypy errors

* remove debug tag

* improve `spectrum`

* finish `core.tensors`

* finish `xcfunc`

* fix hash of `SymmOp`

* add a missing type

* Revert "fix hash of `SymmOp`"

This reverts commit bf2a953acfdd3f48a4c379b7030b3c897e43c8bf.

* fix some types in operations

* "TEST": remove one unused var, relocate another

* final tweak types

* avoid hard-code class name

* format tweaks

* type tweak

* fix unit test

* replace all `[0:x]` with `[:x]`

Guard `TYPE_CHECKING` only imports (#3827)

* flake8 --select=TYP001

* fix type import

* format docstring to google style

* fix more unguarded typecheck imports

* format more docs to Google format

* trigger CI (better var names)

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

move structures out of util dir (#3831)

Add matgenb in the aux link section. Because apparently it is not
"discoverable". Fixes #3811.

More updates.

Move AIMS notebooks to matgenb.

Add README in examples folder that point to proper resources.

Improve type annotations and comments for `io.cif` (#3820)

* remove duplicate warning

* type and docstring tweaks

* add some types for io.cif

* add comments and types

* temp save of some formatting

* revert functional change

* revert unrelated changes

* fix unit test

* remove update that does nothing

* relocate `sub_space_group` and `space_groups` to their usage

* add more types

* pre-commit auto-fixes

* breaking: make parse_magmom/oxi_stats private

* remove merge header

* fix unit test

* add more types

* fix mypy errors

* add a few spaces

* remove if name ==main

* simplify "check to see if" in comments

* final tweaks

* revise docstring

* replace deprecated abc.abstractproperty

* add missing doc strings and standardize existing

* breaking: fix typo in method name orthongonalize_structure

* revert accidental change in test_composition.py

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* remove accidental change

* fix mypy errors

* fix mypy error

* add some for core.units

* rename `ArrayWithFloatWithUnit` to `ArrayWithUnit` in comment

* fix mypy errors

* tweak docstring for units

* nest internal funcs for units

* simplify module docstring

* revert to accessing private attrib

* fix unit test and revert support for `Unit`

* use `str` over `Unit`

* support unit as both str and Unit

* tweak docstring example

* improve IndexError messages

* test_index_error

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* remove duplicate warning

* type and docstring tweaks

* add some types for io.cif

* add comments and types

* temp save of some formatting

* revert functional change

* revert unrelated changes

* fix unit test

* remove update that does nothing

* relocate `sub_space_group` and `space_groups` to their usage

* add more types

* pre-commit auto-fixes

* breaking: make parse_magmom/oxi_stats private

* remove merge header

* fix unit test

* add more types

* fix mypy errors

* add a few spaces

* remove if name ==main

* simplify "check to see if" in comments

* final tweaks

* revise docstring

* replace deprecated abc.abstractproperty

* add missing doc strings and standardize existing

* breaking: fix typo in method name orthongonalize_structure

* revert accidental change in test_composition.py

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

"discoverable". Fixes #3811.

* flake8 --select=TYP001

* fix type import

* format docstring to google style

* fix more unguarded typecheck imports

* format more docs to Google format

* trigger CI (better var names)

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* fix `core.molecular_orbitals`

* fix `core.operations`

* add types for site, mypy errors to fix

* remove no_type_check decorator

* move dunder methods to the top

* fix mypy errors

* remove debug tag

* improve `spectrum`

* finish `core.tensors`

* finish `xcfunc`

* fix hash of `SymmOp`

* add a missing type

* Revert "fix hash of `SymmOp`"

This reverts commit bf2a953acfdd3f48a4c379b7030b3c897e43c8bf.

* fix some types in operations

* "TEST": remove one unused var, relocate another

* final tweak types

* avoid hard-code class name

* format tweaks

* type tweak

* fix unit test

* replace all `[0:x]` with `[:x]`

* Modify code compatible for latest version PWmat

* pre-commit auto-fixes

* Add test for keyword  keyword

* pre-commit auto-fixes

* refactor tests to use pytest parametrization

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

Add types for `core.periodic_table/bonds/composition/ion/lattice/libxcfunc`, new type `MillerIndex` and fix Lattice hash (#3814)

* tweak type and docstring

* move dunder methods to the top

* add more types and tweaks

* relocate more dunder methods to top

* more types and format tweaks

* fix type error

* add types for composition

* help fix https://github.com/materialsproject/pymatgen/pull/3792#discussion_r1584003750

* reverse compare order for readability

* Revert "reverse compare order for readability"

This reverts commit 05ea23a35ffaf03dc70e9dcbdbf302ac69765603.

* Revert "help fix https://github.com/materialsproject/pymatgen/pull/3792#discussion_r1584003750"

This reverts commit cae7aed4464f4f54c1b2f76d4f12c7a07a49d04e.

* add types for `core.bonds`

* finish `core.ion`

* add some types

* revert changes on core.interface

* add types for `libxfunc`

* remove unnecessary `libxc_version`

* recover header

* finish `Lattice`

* fix unit test

* Reve...

* remove COM812

* remove ISC001

* fix `RUF012`

* enable `C408`

* enable `PLC1901`

* enable `PYI024` to fix partially

* revert change for abiobjects

* finish `PYI024`

* remove `PERF203` no change to code

* Revert "enable `C408`"

This reverts commit 38a5aa7c800e7d048922d4d80271dcbe28f7c761.

* address https://github.com/materialsproject/pymatgen/pull/3813#issuecomment-2098194729



---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* Add a `from_ase_atoms()` to `Structure`

* pre-commit auto-fixes

* tweak doc str, add more tests, fix possibly unbound vars in test_structure.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>