From 0ac59625060ca6411e6602059369eade1eba2bd4 Mon Sep 17 00:00:00 2001 From: Nick Papior Date: Tue, 13 Aug 2024 10:30:23 +0200 Subject: [PATCH] preparing 0.15.0 release Signed-off-by: Nick Papior --- CHANGELOG.md | 6 +- CITATION.cff | 6 +- docs/changelog/index.rst | 1 + docs/changelog/v0.15.0.rst | 259 +++++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- 5 files changed, 269 insertions(+), 5 deletions(-) create mode 100644 docs/changelog/v0.15.0.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index de8e48c36..ebbe8b4ba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 we hit release version 1.0.0. -## [0.15.0] - YYYY-MM-DD +## [0.15.1] - YYYY-MM-DD + + + +## [0.15.0] - 2024-08-13 ### Added - conversion of list-like elements to `Lattice` diff --git a/CITATION.cff b/CITATION.cff index aab8960b7..aa52f3803 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,6 +1,6 @@ -version: 0.15.0rc8 -commit: "v0.15.0rc8" -date-released: "2024-02-04" +version: 0.15.0 +commit: "v0.15.0" +date-released: "2024-08-13" cff-version: 1.2.0 message: "Please cite sisl in any paper to acknowledge and support development." type: software diff --git a/docs/changelog/index.rst b/docs/changelog/index.rst index 400265eb9..050bc65c7 100644 --- a/docs/changelog/index.rst +++ b/docs/changelog/index.rst @@ -30,6 +30,7 @@ Changelogs .. toctree:: :maxdepth: 1 + v0.15.0 v0.14.3 v0.14.2 v0.14.0 diff --git a/docs/changelog/v0.15.0.rst b/docs/changelog/v0.15.0.rst new file mode 100644 index 000000000..a377cc77b --- /dev/null +++ b/docs/changelog/v0.15.0.rst @@ -0,0 +1,259 @@ +****** +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 `.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. diff --git a/pyproject.toml b/pyproject.toml index acf946043..398dbfb68 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ [tool.setuptools_scm] write_to = "src/sisl/_version.py" version_file = "src/sisl/_version.py" -fallback_version = "0.15.0rc8" +fallback_version = "0.15.0" # First we define the build-system which we will probably alter the most [build-system]