8000 PERF: optimize DataFrame.sparse.from_spmatrix performance by rth · Pull Request #32825 · pandas-dev/pandas · GitHub
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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 absolute import
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@rth
rth committed Mar 19, 2020
commit 42792a396dc51b5cfd1a75c30207ccd150e20341
4 changes: 2 additions & 2 deletions pandas/core/arrays/sparse/accessor.py
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Expand Up @@ -227,8 +227,8 @@ def from_spmatrix(cls, data, index=None, columns=None):
1 0.0 1.0 0.0
2 0.0 0.0 1.0
"""
from pandas import DataFrame, SparseDtype
from . import IntIndex, SparseArray
from pandas import DataFrame
from pandas._libs.sparse import IntIndex

data = data.tocsc()
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Could be tocsc(copy=False) for newer scipy versions, but the gain in performance is minimal anyway with respect to the total runtime.

index, columns = cls._prep_index(data, index, columns)
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@jorisvandenbossche jorisvandenbossche Mar 22, 2020 •
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I think the problem is that this _pre_index doesn't actually return Index objects when columns or index is not None (and passing actual Index objects is required when doing verify_integrity=False)

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OK, I see. Thanks for confirming that passing duplicate columns names in an Index object is expected to work in _from_arrays. Will look into it. Thanks Joris!

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@jorisvandenbossche jorisvandenbossche Mar 22, 2020 •
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That seems to be it, as doing pd.DataFrame.sparse.from_spmatrix(mat, columns=pd.Index(['a', 'a'])) instead of pd.DataFrame.sparse.from_spmatrix(mat, columns=['a', 'a']) works.

You can add in here a ensure_index call on both index and columns. (from pandas.core.indexes.api import ensure_index)

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