From 851d78c55d40d1f7aa1f5d8320aae1d3364064b8 Mon Sep 17 00:00:00 2001 From: Nick Papior Date: Wed, 18 Jan 2023 11:43:32 +0100 Subject: [PATCH] rel: updating to next release --- CHANGELOG.md | 5 +- CITATION.cff | 2 +- docs/changelog/index.rst | 1 + docs/changelog/v0.13.0.rst | 109 +++++++++++++++++++++++++++++++++++++ 4 files changed, 115 insertions(+), 2 deletions(-) create mode 100644 docs/changelog/v0.13.0.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index c5d93f6ec..bab8e6cb6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) once we hit release version 1.0.0. -## [0.13.0] - YYYY-MM-DD +## [X.Y.Z] - YYYY-MM-DD + + +## [0.13.0] - 2023-1-18 ### Added - `Geometry.apply` apply functions to slices of data depending on the geometry diff --git a/CITATION.cff b/CITATION.cff index c8dfba271..c9301b1c1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,7 +7,7 @@ authors: orcid: "https://orcid.org/0000-0003-3038-1855" alias: zerothi title: sisl -version: 0.13.0rc5 +version: 0.13.0 identifiers: - description: "Collection DOI for all sisl versions (preferred to use)" type: doi diff --git a/docs/changelog/index.rst b/docs/changelog/index.rst index cfbafa1db..bb8f5d018 100644 --- a/docs/changelog/index.rst +++ b/docs/changelog/index.rst @@ -27,6 +27,7 @@ between versions. .. toctree:: :maxdepth: 1 + v0.13.0 v0.12.2 v0.12.1 v0.12.0 diff --git a/docs/changelog/v0.13.0.rst b/docs/changelog/v0.13.0.rst new file mode 100644 index 000000000..745c127af --- /dev/null +++ b/docs/changelog/v0.13.0.rst @@ -0,0 +1,109 @@ +****** +0.13.0 +****** + +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.