Read Matrix Market with fast_matrix_market
#391
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CC , @alugowski
@alugowski, when writing Matrix Market files, do you recommend passing scipy CSR or CSC matrices instead of COO? I'm curious whether |
| if _output_type(A) is _Vector: | ||
| indices, values = A.to_coo(sort=False) | ||
| s = COO(indices, values, shape=A.shape) |
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btw @SultanOrazbayev I just special-cased Vector in to_pydata_sparse, b/c previously it was creating a (1, n)-shaped sparse array from a Vector instead of a (n,)-shaped array.
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Oops, sorry about that!
But run `autoflake`, `isort`, `pyupgrade`, and `black` first (for now).
SultanOrazbayev
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Looks great, @eriknw !
| try: | ||
| from fast_matrix_market import mmwrite # noqa: F811 | ||
| except ImportError: # pragma: no cover (import) | ||
| if engine != "auto": | ||
| raise ImportError( | ||
| "fast_matrix_market is required to write Matrix Market files " | ||
| f'using the "{engine}" engine' |
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Not sure to what extent DRY principle is useful here, but perhaps there is scope for generalising this check for suitable import as some utility function (as a separate PR).
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I'm open to such a PR :)
You may notice that my style sometimes doesn't adhere to DRY for small, straightforward (to me) things, but I suspect there are cases where things could be improved.
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Thanks for reviewing @SultanOrazbayev! I just finished the final TODO for this PR--I added documentation to |
Closes #384.
This uses
fast_matrix_market(which looks pretty fast) by default if available, but will fall back toscipyif necessary.scipyis still necessary to be installed even if using "fast_matrix_market" engine.There were three small issues I encountered that I plan to raise upstream, but I was able to work around them.
TODO:
fast-matrix-marketto get better performance: https://python-graphblas.readthedocs.io/en/latest/user_guide/io.htmlfrom_dense/to_dense