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sfstoolbox / sfs-python

SFS Toolbox for Python
https://sfs-python.readthedocs.io
MIT License
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Replace inner1d bei einsum #163

Open fs446 opened 4 years ago

fs446 commented 4 years ago

We use from numpy.core.umath_tests import inner1d as _inner1d which is suboptimal, since its deprecated and requires non-standard library import. See also https://github.com/sfstoolbox/sfs-python/issues/77

We could use numpy's einsum do to this job instead, thus I've changed (hopefully) all occurrences of inner1d to einsum.

Besides that in the files, some PEP8 modifications were done, these suggestions came from PyCharm.

Maybe numpy's tensordot is even more performant/suitable. I don't know currently how/if these functions support parallel computation, which inner1d seemed to do and was chosen for. I will check this.

In the meantime, using einsum in this PR is definitely an improvement for the code.

mgeier commented 4 years ago

I like the PEP8 changes, except for the spaces around **.

In the meantime, using einsum in this PR is definitely an improvement for the code.

"definitely" is quite a strong word. "improvement", too.

What if it's much slower?

mgeier commented 4 years ago

I guess some instances can be replaced with the @ operator (a.k.a. __matmul__). Have you checked the performance of that?

hagenw commented 3 years ago

The test for Python 3.5 fails as the installed sphinxcontrib-bibtex package no longer supports Python 3.5:

Exception occurred:
899  File "/home/travis/virtualenv/python3.5.7/lib/python3.5/site-packages/sphinxcontrib/bibtex/roles.py", line 12, in <module>
900    import pybtex.database
901  File "/home/travis/virtualenv/python3.5.7/lib/python3.5/site-packages/pybtex/database/__init__.py", line 124
902    f"  entries={repr_entry},\n\n"
903    ^
904SyntaxError: invalid syntax

I also very much dislike Python 3.5 and would simply remove support for it.

hagenw commented 3 years ago

The other test fails as homebrew seems not to be installing pandoc

hagenw commented 3 years ago

I created a pull request where I run the tests directly on Github (and skip Python 3.5): https://github.com/sfstoolbox/sfs-python/pull/166 There the MacOS tests work as well. So it just seems to be a bug in how travis is configured.

hagenw commented 3 years ago

I rebased the master, now the tests are passing.

fs446 commented 3 years ago

I rebased and made code work for recent 0.6.1 / 0.6.2. We will need a handling once inner1d() is discontinued, so it might be a good idea to keep this einsum() handling up to date. I would vote using this some time.