https://github.com/zerothi/sisl

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b45ef98 fixed ubuntu runner Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2023, 20:19:37 UTC
175b9f1 prepared for 0.14.0 Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2023, 20:09:36 UTC
14a475e Merge pull request #476 from pfebrer/viz_data_sources Refactoring the viz module to a more modular design. 28 September 2023, 19:31:37 UTC
95057b4 fixed nested generated ignores Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2023, 19:13:12 UTC
bc1ea37 enh: Refactoring the viz module to a more modular design Everything is now based on functions that adhere to functional programming. We combine these functions to create workflows and then use the sisl.nodes framework to provide the update functionality. Plotting backends are now implemented each on a single `Figure` class that implements generic drawing methods, as well as subplots, animations... functionality. 28 September 2023, 14:03:52 UTC
51736b4 fixed Callable typing Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2023, 10:24:44 UTC
2cc7965 updated reqs for docs Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2023, 09:23:09 UTC
1ead994 removed print from tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2023, 09:06:08 UTC
cea8b10 added doc for env-vars, fixed units, added siesta-codata2018 - Documentation of sisl environment variables. - Added typing to sisl._environ - Fixed errors in UnitParser It should now also be much faster since the routines has been cleaned for superfluous code. - now the conversion is only getting the exact value of the requested value. This allows one to compare between different versions (previously it always converted to the default unit, which can create corner cases when comparing units between different conventions). - fixed requesting a single unit (just get the default SI value) - added test for single unit getting Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2023, 08:41:40 UTC
b02a69f updating nodes and viz docs Now using recursive Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 September 2023, 11:04:24 UTC
41c79e6 Merge pull request #616 from zerothi/dependabot/github_actions/pypa/cibuildwheel-2.16 Bump pypa/cibuildwheel from 2.15 to 2.16 25 September 2023, 18:23:42 UTC
988b865 Merge pull request #617 from zerothi/dependabot/github_actions/pypa/gh-action-pypi-publish-1.8.10 Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10 25 September 2023, 18:23:20 UTC
8d9c331 Bump pypa/cibuildwheel from 2.15 to 2.16 Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.15 to 2.16. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](https://github.com/pypa/cibuildwheel/compare/v2.15...v2.16) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 25 September 2023, 18:22:59 UTC
6d94c8f Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.6.4 to 1.8.10. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.6.4...v1.8.10) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 25 September 2023, 18:22:38 UTC
ef24018 removed dependabot checks Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 September 2023, 18:21:53 UTC
e674dfb Fixing wheel builds for easier tests Have played a lot with Mac and Windows, still with no avail. Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 September 2023, 18:16:39 UTC
dea8f6b allowed name in BandStructure, deprecated it in favor of names Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 September 2023, 09:16:41 UTC
dd7cb6f trying to fix doc builds Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 September 2023, 09:04:04 UTC
f845e95 added --remove to sgeom Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 September 2023, 07:27:40 UTC
cdcf106 adding cmake arguments Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 11:58:14 UTC
a161fb5 echo trying Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 11:45:43 UTC
65682f9 changed to single quote Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 11:37:26 UTC
edda797 trying to fix flags again Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 11:33:29 UTC
c3bd217 trying again, with explicit fc declarations Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 10:53:37 UTC
223fa62 removed 2014 from linux Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 06:08:21 UTC
1bd4a37 removed windows, and arm64 (only universal2) Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 September 2023, 05:21:09 UTC
68055a1 fixed job reference Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 20:16:35 UTC
1323960 unified wheel building Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 20:15:45 UTC
2ce228c Revert "made wheel tests be faster" This reverts commit 8a2ca6696469d3acf85bd914a93d4fd19e6cdd22. Only for the electron.py case. 18 September 2023, 20:13:56 UTC
a86e92e fixed build-wheel Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 20:11:13 UTC
6a1515e fixed windows amd64 Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 19:42:09 UTC
fe6f6ec more options for ci Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 19:40:51 UTC
cfcf317 yet another try Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 19:25:59 UTC
8a2ca66 made wheel tests be faster Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 19:08:13 UTC
c28e962 trying again with the wheels Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 13:49:17 UTC
ed465d2 Merge pull request #614 from zerothi/dependabot/github_actions/pypa/gh-action-pypi-publish-1.8.10 Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10 18 September 2023, 13:45:38 UTC
e502e86 Merge pull request #613 from zerothi/dependabot/github_actions/JamesIves/github-pages-deploy-action-4.4.3 Bump JamesIves/github-pages-deploy-action from 4.4.1 to 4.4.3 18 September 2023, 13:45:26 UTC
c9d7ea1 Merge pull request #615 from zerothi/dependabot/github_actions/actions/checkout-4 Bump actions/checkout from 3 to 4 18 September 2023, 13:44:48 UTC
270d751 Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 13:43:45 UTC
b08c1fb Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.10 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.6.4 to 1.8.10. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.6.4...v1.8.10) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 13:43:42 UTC
523003c Bump JamesIves/github-pages-deploy-action from 4.4.1 to 4.4.3 Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.4.1 to 4.4.3. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.4.1...v4.4.3) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 13:43:39 UTC
27809f7 testing new things Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 13:43:15 UTC
a3d79f0 another go Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 13:14:11 UTC
7321456 fixed wheel Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 13:11:23 UTC
905fa34 trying a new wheel Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 September 2023, 13:09:52 UTC
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
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