zerothi/sisl: v0.13.0

Released 18 of January 2023.

Contributors
============

A total of 5 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* A.H. Kole
* Nick Papior
* Nils Wittemeier +
* Pol Febrer
* Thomas Frederiksen

Pull requests merged
====================

A total of 18 pull requests were merged for this release.

* #487: Fix issue 486 - in correct sign of the y component of the spin...
* #489: bug: fixed #488 with the cell order
* #494: enh: enabling reading of file-handles and StringIO
* #498: 495 deprecation
* #499: Easy construction of hydrogenic orbitals
* #500: Reading output from ORCA
* #503: Plotly is incompatible with ipywidgets 8.x
* #504: Allow reading forces from transiesta in output file
* #508: New keywords in `step_to()`
* #510: Add CodeQL workflow for GitHub code scanning
* #511: Possible bug: within_inf with periodic=False returns sc atoms...
* #514: Surface slab geometries: clarify `vacuum=None` as a possibility...
* #515: doc: fixed indices in sums
* #516: mnt: changed index ordering of spin-charge quantities
* #519: Fix reading of basis
* #520: ORCA API
* #521: Minor fixes for IO-API
* #526: bug: reading the EDM from fdf did not read geometry automatically

### Added
- `Geometry.apply` apply functions to slices of data depending on the geometry
- enabled Gaussian and Slater type orbitals, #463
  Please give feedback!
- deltancSileTBtrans.merge allowing easy merging of several delta
  siles, #513
- implemented reading of output files from ORCA, #500
- HydrogenicOrbital is added for simple handling of 1-valence electron
  orbitals, #499
- Bohr radius to constants
- enabled ASCII siles to read from file-handles and buffers, #484
- enabled unit specification for lengths in cube-files
- added `kwargs` passed to eigenstate functions in `berry_phase`
  and `conductivity`
- ensured that non-orthogonal `transform` will copy over overlap matrix
  in case the matrix is only touching the non-overlap elements
- enabled dictionary entries for the `Atoms` initialization
  in place of `atoms` argument. Both in the list-like entry, or
  as the only argument.

### Fixed
- rare compiler bug, #512
- `within_inf` with periodic arguments, #511
- reading TranSiesta data from outSileSiesta
- regression from 80f27b05, reading version 0 HSX content, #492
- delta-files (netCDF) would always have diagonal components,
  this has now been removed since it only needs the elements with
  values
- Siesta sparse matrices could in some cases set wrong diagonal
  components
- too large energies in Siesta files could result in crash, #482
- orbital quantum numbers from HSX file was wrong in v1, #462
- corrected sign for spin-Y direction, `PDOS`, `spin_moment`, #486
- RealSpaceSI for right semi-infinite directions, #475
- tbtrans files now have a separate entry in the documentation

### Changed
- removed all deprecated routines, #495
- oplist now can do in-place operations on generators
- significant performance improvement for COOP calculations,
  thanks to Susanne Leitherer for discovering the issue
- changed argument order of ElectronState.COP
- index ordering of spin and coordinate quantities are now changed to
  have these as the first indices. This ensures consistency across
  return types and allows easier handling.
  Note that non-polarized PDOS calculations now has an extra dimension
  for coherence with non-colinear spin.  (see #501)
- ensured all units are now CODATA-2018 values
- `cell_length` changed to `cell2length` with new axes argument
- enabled orbitals up to the h-shell, #491
- swapped order of `honeycomb` (`graphene` derivatives)
  lattice vectors, to ensure the vectors are following right-hand-rule, #488
- changed DIIS solver to assume the matrix is symmetric (it is)
- tbtncSileTBtrans and its derivates has changed, drastically.
  This will accommodate changes related to #477 and #478.
  Now `*_transmission` refers to energy resolved transmissions
  and `*_current` reflects bias-window integrated quantities.
  The defaults and argument order has changed drastically, so
  users should adapt their scripts depending on `sisl` version.
  A check can be made, `if sisl.__version_tuple__[:3] >= (0, 13, 0):`
- To streamline argument order the `*_ACO[OH]P` routines have changed
  `elec` and `E` argument order. This makes them compatible with
  `orbital_transmission` etc.