swh:1:snp:2692237457e2c940b60eeee0773122cc1b3f8ed6

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Revision Author Date Message Commit Date
2d65fc3 added pinv and pinvh to the linalg lib Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 12:55:19 UTC
0e7ad14 updated wheels for macos, trying Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 12:55:00 UTC
a912196 fixed cases where the arguments to BandStructure were wrong Now an error is raised Signed-off-by: Nick Papior <nickpapior@gmail.com> 14 September 2023, 08:58:23 UTC
99dc6c3 added now wheel for a different binutils Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 September 2023, 07:51:01 UTC
21978de fixed order negation test Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 September 2023, 07:42:20 UTC
addf8f1 added a new publication using sisl Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 September 2023, 07:34:44 UTC
1f705f5 fixed wrong mulliken calculation for polarized calculations, #611 This happened because we were forgetting to do a copy of the element matrix. This resulted in creating a view, but calculating on the same array leaving the exact calculation wrong. Essentially the old Mulliken was non-sense M[0] was M[0] + M[0] - M[1] Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 September 2023, 07:32:59 UTC
6935c06 enabled negating order arguments for fdf sile Now doing read_geometry(order='^fdf') will use the default arguments, but remove fdf from the default list (if present). This will allow one to omit specific siles, but retain compatibility with future additions of siles. Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 September 2023, 07:20:44 UTC
e75613f removed branch of reading that should not be needed (hsx) Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 September 2023, 07:09:07 UTC
5eae9dd amended units to effective_mass Signed-off-by: Nick Papior <nickpapior@gmail.com> 30 August 2023, 11:37:17 UTC
d7a2ca1 bumped rc candidate Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 August 2023, 08:06:54 UTC
fe0bdf4 fixed index checks for cylinders Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 August 2023, 08:06:09 UTC
5b4c872 fixes for arm removal (workflow) Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 09:19:08 UTC
243e362 bumped to new rc Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 09:00:35 UTC
964fc10 removing arm (for now) Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 09:00:06 UTC
8635a3b added flags to mac Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 08:38:48 UTC
9cb9593 fixed needs in upload target Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 08:21:03 UTC
22a25c3 bumped build matrix again Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 08:19:43 UTC
5d6f661 trying again Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:29:49 UTC
4539a5c new wheel matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:27:57 UTC
e960882 testing again Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:25:09 UTC
ed4ffae trying to make an rc release This is mainly for testing, but could be useful as it should be uploaded to pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:15:12 UTC
86afb76 fixed erroneous matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:14:37 UTC
def4ce4 trying to make an rc release This is mainly for testing, but could be useful as it should be uploaded to pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 August 2023, 07:12:03 UTC
e868903 simplified the matrix structure in wheels.yaml This is a maintenance workflow update. Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 August 2023, 19:55:11 UTC
7da586a Added a new shape, EllipticalCylinder This shape is a simple cylinder with elliptical base. It can be oriented in any direction. Currently there is no simple CircularCylinder which might be a handy one, this could be added later. Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 August 2023, 20:09:58 UTC
ad88dc3 removed 37 references in pyproject.toml Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 August 2023, 10:39:59 UTC
1205771 fixed #604 and #605 It was a result of a leftover check since close_sc did not return isc, and hence the check. It should now work. Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 August 2023, 19:17:33 UTC
9b1cc67 adding sub-energies to the automatic energy-min Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 July 2023, 11:02:26 UTC
aa3a012 removed custom single dispatch method Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 July 2023, 10:59:20 UTC
35ad6e2 isort fixes Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 July 2023, 09:14:00 UTC
645e3c0 removed custom single dispatch method Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 July 2023, 09:02:55 UTC
2754537 Merge pull request #421 from pfebrer/heteroribbons Function to build heteroribbons 17 July 2023, 19:15:22 UTC
e086e20 removed reference to spmatrix, now using issparse Fixes #599. Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 July 2023, 20:06:00 UTC
eefa952 added CompositeGeometrySection to docs Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 July 2023, 20:01:00 UTC
1915527 renamed section class names Now they are exposed Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 July 2023, 19:01:12 UTC
22c51e1 rebase isort fixes Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 July 2023, 19:01:12 UTC
628cee4 fixed tests and docs Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 July 2023, 19:01:12 UTC
076e18d fixed tests after rebasing Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 July 2023, 19:01:12 UTC
331d3e4 bug: corrected some bugs on valid shifts 15 July 2023, 19:01:12 UTC
201c953 bug: less buggy way of shifting the cell 15 July 2023, 19:01:12 UTC
0dafb02 new paradigm 15 July 2023, 19:01:12 UTC
579de54 ensured workflows has correct requirements This ensures the installation also installs netCDF4 Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 July 2023, 19:00:56 UTC
8d725ed removed debug statements Signed-off-by: Nick Papior <nickpapior@gmail.com> 14 July 2023, 04:44:22 UTC
01e705d ensured that wavefunctions do not translate coordinates Now if a translation would have shifted the atoms, an information notice will be shown. Users should in this case try and shift everything into the primary unit cell which should disable the warning and ensure proper function. Ideally this should be solved otherwise, and will probably be solved later, but for now this seems like the most appropriate thing to do. Fixes #592. Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 July 2023, 20:46:26 UTC
8d2a675 removed unneeded functions Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 July 2023, 13:44:22 UTC
d10f112 added vacuum addition to the orthogonal direction of planes This could be used in wavefunction/densities to reduce the search space for very hexagonal cells. Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 July 2023, 13:40:10 UTC
708e494 Merge pull request #598 from pfebrer/sparse_fixes maint: Adapt to breaking changes in scipy.sparse.isspmatrix 13 July 2023, 12:28:11 UTC
3b6a434 maint: Adapt to breaking changes in scipy.sparse.isspmatrix This used to return True with sparse arrays as well, but now it only returns True for sparse matrices. To keep the old behavior, we use `scipy.sparse.issparse` instead. 13 July 2023, 11:09:40 UTC
1ef16ed fixed lattice handling in Grid Previously one could tile non-commensurate grids. A commensurate grid has a lattice and a geometry that are integer repetitions of the original geometry. This is now checked before one can tile the grid. The Grid.__str__ has been updated to highlight this configuration where the commensurability is shown (instead of lattice). However, when they are not commensurate, the full lattice + full geometry is shown. Removed some set_lattice when calling this on LatticeChild. It had the side-effect of setting the lattice for some hamiltonians etc when calling wavefunction. Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 July 2023, 08:10:07 UTC
3a9a946 removed APPLICATION from isort, not needed Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 20:23:38 UTC
72a78ee Merge branch 'isort-2' 10 July 2023, 20:18:41 UTC
8f7c0bb isort amendment for PR Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 20:18:35 UTC
56f10c0 isort is now fully functional The recommended way to produce PR's is also to run isort at the top-directory. Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 20:16:52 UTC
4cad90b changed fallback version shouldn't be needed Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 19:42:52 UTC
1f1f0ef typing for nodes Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 19:34:47 UTC
a6ba1f8 removed unused assignments Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 13:49:43 UTC
3ce018d deleted netCDF4 from requirements.txt Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 10:11:01 UTC
0298005 changed casing of code-of-conduct Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 09:34:55 UTC
2af10b6 moved error raising into the respective codes This makes security detection better. Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 08:47:22 UTC
761f808 added code-of-conduct.md Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 08:43:06 UTC
8f45d78 Merge pull request #596 from zerothi/595-netcdf4-removall netCDF4 is now an optional dependency 10 July 2023, 08:27:11 UTC
e0e9be4 netCDF4 is now an optional dependency An import error will be raised with explanation on how to mitigate the problem. Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 July 2023, 08:10:36 UTC
fc1da2c copied netCDF4 to the optional dependencies Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 July 2023, 12:58:32 UTC
e9f8818 added importorskips for netCDF4 module missing Still now sisl depends on netCDF4, while it actually doesn't. Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 July 2023, 12:46:54 UTC
300592e small clean-up fo the documentation process Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 July 2023, 10:17:56 UTC
8f0c55a Merge pull request #594 from juijan/missing_import_siesta_grid Fix missing import in siesta_grid. 07 July 2023, 09:47:47 UTC
ed0a6aa Fix missing import in siesta_grid. This import is needed when the `read_grid` routine receives an array of floats for the kwarg `spin`. 07 July 2023, 09:40:27 UTC
10d1da3 Merge pull request #585 from pfebrer/583-t2uc-matrix `translate2uc` for sparse matrices with associated geometries. 06 July 2023, 16:10:13 UTC
98af2b8 trying to hide the __doc__ to the __call__ method as well this is for silebinder stuff Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 13:59:56 UTC
7e8006f fixed SileBinder for documentation problems Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 11:34:41 UTC
d3fe31f updated docs to reflect removed objects Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 11:17:49 UTC
cd99581 added tab for config-settings flag for cmake defines Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 11:06:21 UTC
9862512 added test for sparseorbital Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 10:59:09 UTC
b107ebc minor fixes here and there Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 July 2023, 10:21:41 UTC
cb7e3cb performance improvement for Sparse*.nonzero, also changed interface Now uses pure array functions, should be much faster! Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 July 2023, 13:43:20 UTC
08f50fe bumped to 0.14.0 Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 July 2023, 12:56:04 UTC
e641677 bug fixed numpy>=1.25 handling of stack stack and friends now forces tuple/list, no generators Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 June 2023, 06:47:03 UTC
1a06052 fixed bug with __slots__ behaviour A missing _D was present in the SparseCSR. Weirdly enough it was never caught, but has been present, basically for ever. Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 June 2023, 06:33:31 UTC
2971430 Merge pull request #589 from zerothi/del-collection removed Collection + GeometryCollection 21 June 2023, 06:01:30 UTC
ead65f7 removed Collection + GeometryCollection Basically reverted #546 Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 June 2023, 06:00:05 UTC
9852fbf VASP forces from OUTCAR (#573) added read_trajectory for VASP OUTCAR This will now use the SileBinder approach --------- Co-authored-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 19:31:28 UTC
853a9b7 amended changelog for txt orca sile Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 19:27:24 UTC
2f840ce updated orca/txt to use SileBinder Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 19:22:36 UTC
0e04bf0 added tests 20 June 2023, 19:21:51 UTC
3068d32 fix annotations 20 June 2023, 15:14:37 UTC
3782251 enabled deleting an argument Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 12:26:54 UTC
974026e add atoms and axes arguments 20 June 2023, 11:26:22 UTC
dcbd9a6 moved functionality to _SparseGeometry so that it works for SparseAtom 20 June 2023, 11:17:55 UTC
4d4219a removed geometry_coords argument 20 June 2023, 11:17:55 UTC
29bd643 enh: first sketch of translate2uc for matrices 20 June 2023, 11:17:55 UTC
0b17eec Merge pull request #586 from zerothi/584-sile-slicer Slicing IO read_ routines 20 June 2023, 08:12:23 UTC
34a265e removed parameters from xyz Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
6eb605c converted orca.stdout to use SileBinder This makes the read-functionalities more useable to retain other parts of the information. All tests are functional again. Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
0552845 added last/next in the slicer Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
1a56852 added default slice to the patched documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
3665e05 added negative test and reversing elements Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
5203e9d removed try..except if the file reads raises something, then announce Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:12:06 UTC
e00a557 preliminary test-bed for slicing io stuff Fixed documentation issues and enabled this. Storing sliced objects will also work. Currently nested slicing is not possible. enabled nested with of a sile and changed to SileBinder The sile_read_multiple has been deleted, now the way to do it is SileBinder. This is more versatile and allows better handling. It also patches the documentation. This changes the behaviour of all files using this. By default a read_* with the SileBinder will only read the next entry, however to read multiple one should use read_*[...] for slicing the data. The bound method will try and be smart about only reading the needed elements, there is a bit of overhead, but largely it should be fast. All tests are functional again. Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 June 2023, 08:11:22 UTC
a8665e9 enabled True for translate2uc for all axes Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 June 2023, 06:51:07 UTC
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