backport of #837, #838, #834 plus distutils fix #835
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joostvanzwieten
approved these changes
Oct 20, 2023
The function sphinx.util.status_iterator was deprecated in favour of sphinx.util.display.status_iterator. This patch changes the generate_api function sphinx_mods.py accordingly.
This patch updates the URL to the Intel OneAPI documentation to its new location.
MKL version 2024.0.0 that appeared on PyPi on Nov 14, 2023, triggers an as yet unexplained WinError exception on Windows. This patch limits the dependency to the most recent version before it, which is 2023.2.1 released Oct 19, 2023, until these problems are resolved.
The implementations of the degree one std and the bubble bases for the `SimplexTopology` incorrectly assume that the `simplices` array contains vertex in `range(nverts)` without holes, and use this array as is as dofs, thereby introducing zeros in the basis for every dof in `set(range(simplices.max() + 1)) - set(simplices.flat)`. The boundary of a `SimplexTopology`, however, simply returns a subset of the volume `simplices` array, without renumbering. This bug was introduced by 7e29a28, which removes `_renumber` as preprocessor for the `simplices` parameter of the `SimplexTopology` constructor. To fix this problem this patch adds a `contiguous_simplices` property and uses thses as dofs. The alternative, requiring constructing a `SimplexTopology` with contiguous `simplices`, was rejected because this puts a computational burden on every boundary of a `SimplexTopology`, even if we don't create a basis.
This patch adds the `connectivity` attribute to `EmptyTopology` for completeness.
This patch implements the `boundary` and `interfaces` attributes for the `EmptyTopology`, which is needed by a subsequent patch fixing empty boundaries of a `SimplexTopology`.
The constructor of `SimplexTopology` trips over
assert numpy.greater(self.simplices[:, 1:], self.simplices[:, :-1]).all()
if there are no simplices. This is triggered when taking the boundary of
a fully periodic mesh.
This patch fixes the problem by returning an `EmptyTopology` when the
boundary is empty. In addition this patch adds a slightly improved error
message when trying to create an empty `SimplexTopology.
This patch changed the implementation of _takeslice such that it wraps evaluable.Range directly rather than a lambda function, which caused the resulting array to not be picklable. A unit test is added to safeguard against similar mistakes in future.
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gertjanvanzwieten
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This patch removes the version check from __init__.py, which broke in Python 3.12 with the removal of distutils after being deprecated since Python 3.10. No replacement test is introduced as dependency checks should be the responsibility of pip.
gertjanvanzwieten
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joostvanzwieten
approved these changes
Nov 29, 2023
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