******
0.15.0
******

Released 13 of August 2024.

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

A total of 4 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.

* Nick Papior
* Nils Wittemeier
* Pol Febrer
* Thomas Frederiksen

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

A total of 92 pull requests were merged for this release.

* :pull:`#393 <393>`: Linear and efficient neighbour finder
* :pull:`#496 <496>`: Calculate psi values on a sparse grid, to accelerate multiple...
* :pull:`#497 <497>`: mnt: changed spin_squared name to other name
* :pull:`#647 <647>`: Added a node to keep track of files
* :pull:`#651 <651>`: added typing hints for Lattice and LatticeChild
* :pull:`#652 <652>`: added sanitize to SparseCSR and __setitem__
* :pull:`#658 <658>`: Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11
* :pull:`#659 <659>`: Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0
* :pull:`#660 <660>`: Bump actions/setup-python from 4 to 5
* :pull:`#662 <662>`: Bump github/codeql-action from 2 to 3
* :pull:`#663 <663>`: Bump actions/upload-artifact from 3 to 4
* :pull:`#664 <664>`: Bump actions/download-artifact from 3 to 4
* :pull:`#665 <665>`: moving towards functional programming in sisl
* :pull:`#666 <666>`: Support for conditional expressions on workflows.
* :pull:`#667 <667>`: ensure that workflows have (and transmit) the right state
* :pull:`#668 <668>`: WIP: Added a matrix plot
* :pull:`#670 <670>`: Missing fdf flags error
* :pull:`#672 <672>`: first try at implementing bond-order calculations
* :pull:`#673 <673>`: removed selector from code base
* :pull:`#679 <679>`: Bump codecov/codecov-action from 3 to 4
* :pull:`#681 <681>`: Fix multisize 3D balls in plots
* :pull:`#682 <682>`: Added Jmol colors as defaults for atoms.
* :pull:`#683 <683>`: Added pre-commit config
* :pull:`#684 <684>`: Some tweaks to atom colors
* :pull:`#686 <686>`: 579 dftb hamiltonian
* :pull:`#692 <692>`: Lazy loading of the viz module
* :pull:`#693 <693>`: Fix wheels workflow
* :pull:`#695 <695>`: added typing in lots of io places, added SileSlicer
* :pull:`#696 <696>`: Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12
* :pull:`#697 <697>`: Optimize nsc after reading Hamiltonian from wann90 output
* :pull:`#702 <702>`: fixed #700 by reverting 7cf88f1a5
* :pull:`#704 <704>`: Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14
* :pull:`#706 <706>`: cleaned finder and removed pbc (getting it from Lattice)
* :pull:`#710 <710>`: removed txtSileOrca.no/info.no since it was never present
* :pull:`#711 <711>`: added warning for complex grids and isosurface
* :pull:`#714 <714>`: 675 documentation
* :pull:`#715 <715>`: Bump pypa/cibuildwheel from 2.16 to 2.17
* :pull:`#717 <717>`: Fix for reading spinful CHG/CHGCAR
* :pull:`#722 <722>`: Add `read_gtensor` and `read_hyperfine_coupling` to `txtSileORCA`
* :pull:`#723 <723>`: add test for reading Hamiltonian from wannier90 output
* :pull:`#725 <725>`: Additional energy units
* :pull:`#726 <726>`: `units` as parameter in `read_*`
* :pull:`#727 <727>`: Resolve Issue #716
* :pull:`#729 <729>`: Minor ORCA/VASP documentation improvements
* :pull:`#734 <734>`: Remove deprecated `bc` argument to `Grid`
* :pull:`#736 <736>`: Some polishing of `sisl.nodes`
* :pull:`#737 <737>`: added math notation convention
* :pull:`#739 <739>`: Ensure __module__ is fine on node class creation
* :pull:`#742 <742>`: Draft: add vectorsSileSIESTA for parsing vibra output
* :pull:`#743 <743>`: Added specific functions to create animations and subplots
* :pull:`#746 <746>`: 745 rtd files
* :pull:`#749 <749>`: Ensure c-order for `Geometry` coordinates
* :pull:`#750 <750>`: `norm2` as atom-resolved quantity
* :pull:`#751 <751>`: made State.inner a very flexible matrix product
* :pull:`#752 <752>`: added hexagonal and goldene
* :pull:`#753 <753>`: removed sisl.plot from the code base
* :pull:`#754 <754>`: Reading spin densities from CHGCAR
* :pull:`#755 <755>`: Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.6.0
* :pull:`#757 <757>`: Plot update on getting attributes
* :pull:`#758 <758>`: Added declaration of some attributes in Figure
* :pull:`#759 <759>`: Removed nodes from `sisl`
* :pull:`#761 <761>`: removed 3.8 support, bumped min to 3.9
* :pull:`#762 <762>`: CI also run on minimal installation
* :pull:`#763 <763>`: changed phonon displacement shape
* :pull:`#765 <765>`: Modifying the returns of the neighbor finder
* :pull:`#767 <767>`: fixed pbc usage across sisl, fixes #764
* :pull:`#769 <769>`: Bump pypa/cibuildwheel from 2.17 to 2.18
* :pull:`#771 <771>`: Removed leftover print
* :pull:`#772 <772>`: Removed deprecated argument `diag->projection`
* :pull:`#773 <773>`: Dihedral angles
* :pull:`#774 <774>`: Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.1
* :pull:`#776 <776>`: Add support for sisl in nodify's GUI
* :pull:`#779 <779>`: fixed reading geometries from fdf + XV + STRUCT
* :pull:`#780 <780>`: Allow dash to be set in bands plots.
* :pull:`#781 <781>`: Allow tuning matplotlib subplots.
* :pull:`#784 <784>`: Legend grouping in bands plots
* :pull:`#786 <786>`: Allow custom color scales across sisl.viz
* :pull:`#787 <787>`: Clarify viz dependencies error
* :pull:`#788 <788>`: Bump pypa/cibuildwheel from 2.18 to 2.19
* :pull:`#789 <789>`: Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0
* :pull:`#790 <790>`: fixed lots of parallel calculations
* :pull:`#792 <792>`: trying to remove numpy 2 (as a temporary work-around)
* :pull:`#793 <793>`: adding test for parallel calculation
* :pull:`#796 <796>`: Clarify out of memory error on density
* :pull:`#797 <797>`: 766 shc
* :pull:`#803 <803>`: Bump JamesIves/github-pages-deploy-action from 4.6.1 to 4.6.3
* :pull:`#804 <804>`: ensured building against numpy>=2
* :pull:`#805 <805>`: Fix bug with numpy v2.0
* :pull:`#807 <807>`: Fix fatbands with negative size
* :pull:`#809 <809>`: enabled vacuum for all geometries with non-pbc directions
* :pull:`#812 <812>`: completed tests rearrangement
* :pull:`#818 <818>`: fixing many simple PEP-585 deprecations

[0.15.0] - 2024-08-13
---------------------

Added
^^^^^
* conversion of list-like elements to `Lattice`
* vacuum argument for all `sisl.geom` methods that can use it
* `Geometry.find_nsc`, alternate method for calculating `nsc` with more options
* `sisl._debug_info` for more complete debug information
* `axes` argument added to `derivative` to only calculate on a subset
  of directions (can greatly improve performance for some systems)
* `operator` argument added to `derivative` to apply an operator
  to `dHk` and `dSk` matrices.
  of directions (can greatly improve performance for some systems)
* added `apply_kwargs` to methods which uses a `BrillouinZone` object.
  This enables one to leverage parallel processing for calculations.
* `SISL_PAR_CHUNKSIZE=25`, new default parameter for parallel processing.
  Can greatly improve parallel processing of BZ integrations
* added `vectorsSileSiesta` to read vibra eigenmode output
* added `dihedral` to `Geometry`, :pull:`#773 <773>`
* ability to retain sub-classes through `<class>.new` calls
* added `Listify` to ensure arguments behaves as *iterables*
* setter for `Lattice.pbc` to specify it through an array
* `Lattice.volumef` to calculate a subset volume based on axes
* added `write_grid` to Siesta binary grid files
* added the `goldene` 2D lattice, a `hexagonal` Gold 2D structure
* added the `hexagonal` 2D lattice, close-packed FCC(111) surface
* improved `atom` projections of states, :pull:`#750 <750>`
* improved typing system
* `units` to `read_*` for some `Sile`s, :pull:`#726 <726>`
* enabled reading the Hamiltonian from the Wannier90 _tb.dat file, :pull:`#727 <727>`
* "Hz", "MHz", "GHz", "THz", and "invcm" as valid energy units, :pull:`#725 <725>`
* added `read_gtensor` and `read_hyperfine_coupling` to `txtSileORCA`, :pull:`#722 <722>`
* enabled `AtomsArgument` and `OrbitalsArgument` to accept `bool` for *all* or *none*
* enabled `winSileWannier90.read_hamiltonian` to read the ``_tb.dat`` files
* `atoms` argument to `DensityMatrix.spin_align` to align a subset of atoms
  (only diagonal elements between the atoms orbitals)
* added an efficient neighbor finder, :pull:`#393 <393>`
* enabled reading DFTB+ output Hamiltonian and overlap matrices, :pull:`#579 <579>`
* `bond_order` for `DensityMatrix` objects, :pull:`#507 <507>`
* better error messages when users request quantities not calculated by Siesta/TBtrans
* functional programming of the basic sisl classes
  Now many of the `Geometry|Lattice|Grid.*` manipulation routines which
  returns new objects, are subjected to dispatch methods.
  E.g.

      sisl.tile(geometry, 2, axis=1)
      geometry.tile(2, axis=1)

  will call the same method. The first uses a dispatch method, and a `SislError`
  will be raised if the dispatch argument is not implemented.
* `SparseCSR.toarray` to comply with array handling (equivalent to `todense`)
* enabled `Grid.to|new` with the most basic stuff
  str|Path|Grid|pyamg
* `Shape.translate`, to easily translate entire shape constructs, :pull:`#655 <655>`
* Creation of chiral GNRs (`kind=chiral` in `sisl.geom.nanoribbon`/`sisl.geom.graphene_nanoribbon`
  as well as `sisl.geom.cgnr`)
* Creation of [n]-triangulenes (`sisl.geom.triangulene`)
* added `offset` argument in `Geometry.add_vacuum` to enable shifting atomic coordinates
* A new `AtomicMatrixPlot` to plot sparse matrices, :pull:`#668 <668>`

Fixed
^^^^^
* PEP-585 compliant
* buildable for numpy>2, :pull:`#791 <791>`
* `BrillouinZone.tocartesian()` now defaults to `k=self.k`
* reading XV/STRUCT files from fdf siles could cause problems, :pull:`#778 <778>`
* `Geometry.[ao][us]c2[su]c` methods now retains the input shapes (unless `unique=True`)
* lots of `Lattice` methods did not consistently copy over BC
* `BrillouinZone.volume` fixed to actually return BZ volume
  use `Lattice.volume` for getting the lattice volume.
* xsf files now only respect `lattice.pbc` for determining PBC, :pull:`#764 <764>`
* fixed `CHGCAR` spin-polarized density reads, :pull:`#754 <754>`
* dispatch methods now searches the mro for best matches, :pull:`#721 <721>`
* all `eps` arguments has changed to `atol`
* methods with `axis` arguments now accepts the str equivalent 0==a
* documentation links to external resources
* fixed `chgSileVASP.read_grid` for spinful calculations
* `txtSileOrca.info.no` used a wrong regex, added a test
* raises error when requesting isosurface for complex valued grids, :pull:`#709 <709>`
* some attributes associated with `Sile.info.*` will now warn instead of raising information
* reading matrices from HSX files with *weird* labels, should now work (*fingers-crossed*)
* `Atom(Z="1000")` will now correctly work, :pull:`#708 <708>`
* `AtomUnknown` now also has a default mass of 1e40
* changed `read_force_constant` to `read_hessian`, the old methods are retained with
  deprecation warnings.
* `pdosSileSiesta` plotting produced wrong spin components for NC/SOC
* `tqdm` changed API in 2019, `eta=True` in Notebooks should now work
* `SparseCSR` ufunc handling, in some corner cases could the dtype casting do things
  wrongly.
* fixed corner cases where the `SparseCSR.diags(offsets=)` would add elements
  in non-existing elements
* some cases of writing orthogonal matrices to TSHS/nc file formats :pull:`#661 <661>`
* `BDOS` from TBtrans calculations now returns the full DOS of all (Bloch-expanded)
  atoms
* `Lattice` objects now issues a warning when created with 0-length vectors
* HSX file reads should respect input geometry arguments
* enabled slicing in matrix assignments, :pull:`#650 <650>`
* changed `Shape.volume()` to `Shape.volume`
* growth direction for zigzag heteroribbons
* `BandStructure` points can now automatically add the `nsc == 1` axis as would
  be done for assigning matrix elements (it fills with 0's).

Removed
^^^^^^^
* `degenerate` argument in `velocity`/`derivative`, they do not belong there
* `xvSileSiesta.read_geometry(species_as_Z)`, deprecated in favor of `atoms=`
* `structSileSiesta.read_geometry(species_as_Z)`, deprecated in favor of `atoms=`
* `Atom.radii` is removed, `Atom.radius` is the correct invocation
* `sisl.plot` is removed (`sisl.viz` is replacing it!)
* `cell` argument for `Geometry.translate/move` (it never worked)
* removed `Selector` and `TimeSelector`, they were never used internally

Changed
^^^^^^^
* internal test structure, should improve future progress
* `Lattice.parameters` now returns a 2-tuple of ``length, angles``
* units of `conductivity` has changed to S / Ang
* `conductivity` is deprecated, use `ahc` and `shc` instead
* `berry_curvature` has completely changed, checks it API
* BZ apply methods are now by default parallel (if ``SISL_NUM_PROCS>1``)
* `hsxSileSiesta.read_hamiltonian` now implicitly shifts Fermi-level to 0 (for newer HSX versions)
* deprecated `periodic` to `axes` argument in `BrillouinZone.volume`
* changed `Eigenmode.displacement` shape, please read the documentation
* bumped minimal Python version to 3.9, :pull:`#640 <640>`
* documentation build system on RTD is updated, :pull:`#745 <745>`
* `gauge` arguments now accept 'cell' and 'orbital' in replacements for 'R' and 'r', respectively
* `siesta.*.read_basis` now defaults to read an `Atoms` object with all atoms
* `atoms.specie` changed to `atoms.species`, generally species is the singular form
* `in_place` arguments changed to `inplace`
* renamed `stdoutSileVASP` to `outcarSileVASP`, :pull:`#719 <719>`
* deprecated scale_atoms in favor of scale_basis in `Geometry.scale`
* changed default number of eigenvalues calculated in sparse `eigsh`, from 10 to 1
* `stdoutSileSiesta.read_*` now defaults to read the *next* entry, and not the last
* `stdoutSileSiesta.read_*` changed MD output functionality, see :pull:`#586 <586>` for details
* `AtomNeighbours` changed name to `AtomNeighbor` to follow :pull:`#393 <393>`
* changed method name `spin_squared` to `spin_contamination`
* removed `Lattice.translate|move`, they did not make sense, and so their
  usage should be deferred to `Lattice.add` instead.
* `vacuum` is now an optional parameter for all ribbon structures
* enabled `array_fill_repeat` with custom axis, to tile along specific
  dimensions
* Importing `sisl.viz` explicitly is no longer needed, as it will be lazily
  loaded whenever it is required.