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PERF: optimize DataFrame.sparse.from_spmatrix performance #32825

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Merged
merged 18 commits into from
Mar 22, 2020
Merged

PERF: optimize DataFrame.sparse.from_spmatrix performance #32825

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3ffe7f2
PERF: fix SparseArray._simple_new object initialization
jorisvandenbossche Mar 19, 2020
93bf825
Initial implementation
rth Mar 19, 2020
e21701b
Merge remote-tracking branch 'upstream/master' into opt-sparse-init
rth Mar 19, 2020
e095e7f
Improve docstring
rth Mar 19, 2020
11afe40
Add what's new
rth Mar 19, 2020
eda0732
Update doc/source/whatsnew/v1.1.0.rst
rth Mar 19, 2020
40f4cd6
Improve what's new
rth Mar 19, 2020
508fda5
Add random state
rth Mar 19, 2020
0053817
Add inline comment about sort_indices
rth Mar 19, 2020
42792a3
Use absolute import
rth Mar 19, 2020
c8f7abc
Update pandas/_libs/sparse.pyx
rth Mar 19, 2020
e541b0d
Rename variable
rth Mar 19, 2020
0a0bafc
Merge remote-tracking branch 'upstream/master' into opt-sparse-init
rth Mar 20, 2020
ce6619e
Use DataFrame._from_arrays(..., verify_integrity=False)
rth Mar 20, 2020
e063c8a
checkout upstream/master -- asv_bench/benchmarks/sparse.py
rth Mar 20, 2020
8efe3ad
Merge remote-tracking branch 'upstream/master' into opt-sparse-init
rth Mar 22, 2020
20c3685
Link to PR's by Joris in what's new
rth Mar 22, 2020
d750eb4
Use ensure_index when the columns/index is provided by the user
rth Mar 22, 2020
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Use DataFrame._from_arrays(..., verify_integrity=False)
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@rth
rth committed Mar 20, 2020
commit ce6619efd3f38f716810e2c55efa3ba284f641ea
4 changes: 3 additions & 1 deletion pandas/core/arrays/sparse/accessor.py
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Expand Up @@ -248,7 +248,9 @@ def from_spmatrix(cls, data, index=None, columns=None):
idx = IntIndex(n_rows, indices[sl], check_integrity=False)
arr = SparseArray._simple_new(array_data[sl], idx, dtype)
arrays.append(arr)
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@rth rth Mar 19, 2020

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FWIW, also tried with a generator here to avoid pre-allocating all the arrays, but it doesn't really matter. Most of the remaining run time is in DataFrame._from_arrays.
return DataFrame._from_arrays(arrays, columns=columns, index=index)
return DataFrame._from_arrays(
arrays, columns=columns, index=index, verify_integrity=False
)

def to_dense(self):
"""
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