kwant merge requestshttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests2024-01-09T20:07:17Zhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/370Dependency fixes2024-01-09T20:07:17ZAnton AkhmerovDependency fixesList of changes:
- Update all dependencies in line with the "Debian stable/Ubuntu LTS from 6 months ago".
- Remove legacy code that was there fore backwards compatibility
- Fix *a lot* of deprecation warnings due to changes in python/sc...List of changes:
- Update all dependencies in line with the "Debian stable/Ubuntu LTS from 6 months ago".
- Remove legacy code that was there fore backwards compatibility
- Fix *a lot* of deprecation warnings due to changes in python/scipy/numpy/mpl
- Update all links to use https, resolve several permanent redirects, update or remove a few broken links
- Remove unmaintained macports/homebrew installation instructions
~~Still TODO: squash/regroup commits.~~
Closes #386Kwant 1.5Christoph GrothChristoph Grothhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/389Clean up linear algebra (related to modes)2024-01-07T11:14:47ZAnton AkhmerovClean up linear algebra (related to modes)I initially planned to implement a computation of modes with the sparse unit cell here. This, however, prompted code review and subsequent cleanup.
In summary, this MR:
- Eliminates our custom wrappers for LAPACK lu and gen_eig. The fo...I initially planned to implement a computation of modes with the sparse unit cell here. This, however, prompted code review and subsequent cleanup.
In summary, this MR:
- Eliminates our custom wrappers for LAPACK lu and gen_eig. The former I reimplemented using scipy.linalg.lapack, and the latter wasn't used anywhere.
- Shortens linalg tests by using pytest parameterization.
- Uses `a @ b` instead of `np.dot(a, b)` or `a.dot(b)`. This helps both readability and customization, because `@` is properly dispatched by sparse matrices (unlike `.dot`).
- Requires that `setup_linsys` takes square matrices as input. For some time already, we only passed square matrices to it, see [this comment](https://gitlab.kwant-project.org/kwant/kwant/-/blob/master/kwant/physics/leads.py#L1044-1048).Anton AkhmerovAnton Akhmerovhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/356use tinyarrays for Site tags in tests, rather than tuples2020-05-12T15:28:07ZJoseph Westonuse tinyarrays for Site tags in tests, rather than tuplesTinyarrays used to have identical hashes to tuples, but this
was not part of the official interface. While the core of
Kwant did not depend on this implementation detail, the
tests did.
Closes #359.Tinyarrays used to have identical hashes to tuples, but this
was not part of the official interface. While the core of
Kwant did not depend on this implementation detail, the
tests did.
Closes #359.Christoph GrothChristoph Grothhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/354use correct (sequential) Mumps libraries in testing image2020-03-27T22:55:52ZJoseph Westonuse correct (sequential) Mumps libraries in testing imageConda forge recently updated their Mumps packaging so that the
sequential version of Mumps is in a separate package,
[mumps-seq](https://anaconda.org/conda-forge/mumps-seq),
as are the include files
[mumps-include](https://anaconda.org/c...Conda forge recently updated their Mumps packaging so that the
sequential version of Mumps is in a separate package,
[mumps-seq](https://anaconda.org/conda-forge/mumps-seq),
as are the include files
[mumps-include](https://anaconda.org/conda-forge/mumps-include).
Related to #358 (but does not fix it)https://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/359fix docstring for kwant.system.System.site_ranges2020-03-27T22:30:08ZJoseph Westonfix docstring for kwant.system.System.site_rangeshttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/324provide "shape" and "format" to empty Qsymm models as required by 1.22019-10-23T14:38:34ZJoseph Westonprovide "shape" and "format" to empty Qsymm models as required by 1.2Not providing these is now deprecated.
Close #325.Not providing these is now deprecated.
Close #325.Kwant 1.5https://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/270maint: clear up a bunch of warnings in tests2019-01-04T14:51:33ZAnton Akhmerovmaint: clear up a bunch of warnings in testsThis silences a deprecation warning on scipy < 1.2 and numpy > 1.15.This silences a deprecation warning on scipy < 1.2 and numpy > 1.15.Kwant 1.4https://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/222fix docstrings in plotter2018-08-02T16:11:27ZJoseph Westonfix docstrings in plotterPreviously parts of the docstrings for 'density' and 'current'
had been switched.Previously parts of the docstrings for 'density' and 'current'
had been switched.Christoph GrothChristoph Grothhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/204fix problem in discretizer that occur when onsite is set to "int(1)"2018-02-16T17:25:05ZRafal Skolasinskifix problem in discretizer that occur when onsite is set to "int(1)"Thanks to @torosdahl for reporting.
```
Running "kwant.continuum.discretize('k_x**2 + 1')" was resulting
in an "AssertionError". This happend because "1 * expr = expr"
in SymPy and therefore a wrong argument has been passed to
"...Thanks to @torosdahl for reporting.
```
Running "kwant.continuum.discretize('k_x**2 + 1')" was resulting
in an "AssertionError". This happend because "1 * expr = expr"
in SymPy and therefore a wrong argument has been passed to
"_read_offset" function.
```https://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/12Add piwik code2015-12-15T10:46:27ZAnton AkhmerovAdd piwik codeNow building for the website can be done using
`make html SPHINXOPTS="-A website_deploy=True"`
I decided to not set `release = version` because it was hard to do through CLI, and because it doesn't hurt if the patch version shows u...Now building for the website can be done using
`make html SPHINXOPTS="-A website_deploy=True"`
I decided to not set `release = version` because it was hard to do through CLI, and because it doesn't hurt if the patch version shows up in the descriptions.
With this we should be able to also setup docs auto-deploy to the website.Christoph GrothChristoph Grothhttps://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/4migrate TODO to the issue tracker2015-11-11T06:51:37ZAnton Akhmerovmigrate TODO to the issue trackerMake line comments to discuss separate TODO list items. Optimally we should merge this when all the items have comments.Make line comments to discuss separate TODO list items. Optimally we should merge this when all the items have comments.