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ENH: Add lazy copy to concat and round #50501

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20 changes: 18 additions & 2 deletions pandas/core/internals/concat.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,12 @@
import itertools
from typing import (
TYPE_CHECKING,
List,
Optional,
Sequence,
cast,
)
import weakref

import numpy as np

Expand Down Expand Up @@ -61,7 +64,10 @@
ensure_block_shape,
new_block_2d,
)
from pandas.core.internals.managers import BlockManager
from pandas.core.internals.managers import (
BlockManager,
using_copy_on_write,
)

if TYPE_CHECKING:
from pandas import Index
Expand Down Expand Up @@ -267,6 +273,8 @@ def _concat_managers_axis0(

offset = 0
blocks = []
refs = []
parent = None
for i, mgr in enumerate(mgrs):
# If we already reindexed, then we definitely don't need another copy
made_copy = had_reindexers[i]
Expand All @@ -283,8 +291,16 @@ def _concat_managers_axis0(
nb._mgr_locs = nb._mgr_locs.add(offset)
blocks.append(nb)

if not made_copy and not copy and using_copy_on_write():
refs.extend([weakref.ref(blk) for blk in mgr.blocks])
parent = mgr
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We are obviously overwriting parent here when we have more than one object, is this a problem?

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Ah, yes, I suppose that is a problem. parent is just used to keep a reference but is not otherwise used, so it doesn't really matter what object it is. So I think we can also make it a list of parent objects in this case.

(will try to make a test that fails because of this; generally it is for chained operations, which you might have less often with concat)

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A "chained" concat (not very normal usage .., but still should work correctly ;)):

In [9]: pd.options.mode.copy_on_write = True

In [36]: res = pd.concat([pd.concat([df1, df2], axis=1), df3], axis=1)

In [37]: df1 = pd.DataFrame({'a': [1, 2, 3], 'b': [0.1, 0.2, 0.3]})

In [38]: df2 = pd.DataFrame({'c': [4, 5, 6]})

In [39]: df3 = pd.DataFrame({'d': [4, 5, 6]})

In [40]: res = pd.concat([pd.concat([df1, df2], axis=1), df3], axis=1)

In [41]: df1._mgr._has_no_reference(0)
Out[41]: True

In [42]: df1.iloc[0, 0] = 100

In [43]: res
Out[43]: 
     a    b  c  d
0  100  0.1  4  4
1    2  0.2  5  5
2    3  0.3  6  6

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Yep, definitely agree. I'll keep track of a list of parent objects then. Series does not work correctly either, but this should be straightforward to fix I think


offset += len(mgr.items)
return BlockManager(tuple(blocks), axes)

result = BlockManager(tuple(blocks), axes)
result.parent = parent
result.refs = cast(Optional[List[Optional[weakref.ref]]], refs) if refs else None
return result


def _maybe_reindex_columns_na_proxy(
Expand Down
25 changes: 22 additions & 3 deletions pandas/core/reshape/concat.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@

import numpy as np

from pandas._config import get_option
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Suggested change
from pandas._config import get_option
from pandas._config import get_option, using_copy_on_write

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Ah this is annoying, I thought that ci should fail, but makes sense that the import continues to work through there...


from pandas._typing import (
Axis,
AxisInt,
Expand Down Expand Up @@ -47,6 +49,8 @@
get_unanimous_names,
)
from pandas.core.internals import concatenate_managers
from pandas.core.internals.construction import dict_to_mgr
from pandas.core.internals.managers import using_copy_on_write
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Suggested change
from pandas.core.internals.managers import using_copy_on_write


if TYPE_CHECKING:
from pandas import (
Expand Down Expand Up @@ -155,7 +159,7 @@ def concat(
names=None,
verify_integrity: bool = False,
sort: bool = False,
copy: bool = True,
copy: bool | None = None,
) -> DataFrame | Series:
"""
Concatenate pandas objects along a particular axis.
Expand Down Expand Up @@ -363,6 +367,12 @@ def concat(
0 1 2
1 3 4
"""
if copy is None:
if using_copy_on_write():
copy = False
else:
copy = True

op = _Concatenator(
objs,
axis=axis,
Expand Down Expand Up @@ -584,7 +594,16 @@ def get_result(self):
cons = sample._constructor_expanddim

index, columns = self.new_axes
df = cons(data, index=index, copy=self.copy)
mgr = dict_to_mgr(
data,
index,
None,
copy=self.copy,
typ=get_option("mode.data_manager"),
)
if using_copy_on_write() and not self.copy:
mgr = mgr.copy(deep=False)
df = cons(mgr, copy=False)
df.columns = columns
return df.__finalize__(self, method="concat")

Expand All @@ -611,7 +630,7 @@ def get_result(self):
new_data = concatenate_managers(
mgrs_indexers, self.new_axes, concat_axis=self.bm_axis, copy=self.copy
)
if not self.copy:
if not self.copy and not using_copy_on_write():
new_data._consolidate_inplace()

cons = sample._constructor
Expand Down
83 changes: 83 additions & 0 deletions pandas/tests/copy_view/test_functions.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,83 @@
import numpy as np

from pandas import (
DataFrame,
Series,
concat,
)
import pandas._testing as tm
from pandas.tests.copy_view.util import get_array


def test_concat_frames(using_copy_on_write):
df = DataFrame({"b": ["a"] * 3})
df2 = DataFrame({"a": ["a"] * 3})
df_orig = df.copy()
result = concat([df, df2], axis=1)

if using_copy_on_write:
assert np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert np.shares_memory(get_array(result, "a"), get_array(df2, "a"))
else:
assert not np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert not np.shares_memory(get_array(result, "a"), get_array(df2, "a"))

result.iloc[0, 0] = "d"
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert np.shares_memory(get_array(result, "a"), get_array(df2, "a"))

result.iloc[0, 1] = "d"
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "a"), get_array(df2, "a"))
tm.assert_frame_equal(df, df_orig)


def test_concat_frames_updating_input(using_copy_on_write):
df = DataFrame({"b": ["a"] * 3})
df2 = DataFrame({"a": ["a"] * 3})
result = concat([df, df2], axis=1)

if using_copy_on_write:
assert np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert np.shares_memory(get_array(result, "a"), get_array(df2, "a"))
else:
assert not np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert not np.shares_memory(get_array(result, "a"), get_array(df2, "a"))

expected = result.copy()
df.iloc[0, 0] = "d"
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "b"), get_array(df, "b"))
assert np.shares_memory(get_array(result, "a"), get_array(df2, "a"))

df2.iloc[0, 0] = "d"
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "a"), get_array(df2, "a"))
tm.assert_frame_equal(result, expected)


def test_concat_series(using_copy_on_write):
ser = Series([1, 2], name="a")
ser2 = Series([3, 4], name="b")
ser_orig = ser.copy()
ser2_orig = ser2.copy()
result = concat([ser, ser2], axis=1)

if using_copy_on_write:
assert np.shares_memory(get_array(result, "a"), ser.values)
assert np.shares_memory(get_array(result, "b"), ser2.values)
else:
assert not np.shares_memory(get_array(result, "a"), ser.values)
assert not np.shares_memory(get_array(result, "b"), ser2.values)

result.iloc[0, 0] = 100
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "a"), ser.values)
assert np.shares_memory(get_array(result, "b"), ser2.values)

result.iloc[0, 1] = 1000
if using_copy_on_write:
assert not np.shares_memory(get_array(result, "b"), ser2.values)
tm.assert_series_equal(ser, ser_orig)
tm.assert_series_equal(ser2, ser2_orig)
17 changes: 17 additions & 0 deletions pandas/tests/copy_view/test_methods.py
Original file line number Diff line number Diff line change
Expand Up @@ -575,6 +575,23 @@ def test_sort_index(using_copy_on_write):
tm.assert_series_equal(ser, ser_orig)


def test_round(using_copy_on_write):
df = DataFrame({"a": [1, 2], "b": "c"})
df2 = df.round()
df_orig = df.copy()

if using_copy_on_write:
assert np.shares_memory(get_array(df2, "b"), get_array(df, "b"))
assert np.shares_memory(get_array(df2, "a"), get_array(df, "a"))
else:
assert not np.shares_memory(get_array(df2, "b"), get_array(df, "b"))

df2.iloc[0, 1] = "d"
if using_copy_on_write:
assert not np.shares_memory(get_array(df2, "b"), get_array(df, "b"))
tm.assert_frame_equal(df, df_orig)


def test_reorder_levels(using_copy_on_write):
index = MultiIndex.from_tuples(
[(1, 1), (1, 2), (2, 1), (2, 2)], names=["one", "two"]
Expand Down
2 changes: 2 additions & 0 deletions pandas/tests/io/pytables/test_store.py
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
timedelta_range,
)
import pandas._testing as tm
from pandas.core.internals.managers import using_copy_on_write
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Suggested change
from pandas.core.internals.managers import using_copy_on_write
from pandas._config import using_copy_on_write

from pandas.tests.io.pytables.common import (
_maybe_remove,
ensure_clean_store,
Expand Down Expand Up @@ -1007,6 +1008,7 @@ def test_to_hdf_with_object_column_names(tmp_path, setup_path):
assert len(result)


@pytest.mark.skipif(using_copy_on_write(), reason="strides buggy with cow")
def test_hdfstore_strides(setup_path):
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Is this caused by the concat changes?

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Yeah strides changed from 8 to 16, this is really weird

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@jorisvandenbossche jorisvandenbossche Jan 16, 2023

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Looking into this a little bit, I think the issue is that in

pandas/pandas/io/pytables.py

Lines 3207 to 3212 in a0071f9

if len(dfs) > 0:
out = concat(dfs, axis=1)
out = out.reindex(columns=items, copy=False)
return out
return DataFrame(columns=axes[0], index=axes[1])

where we are creating the DataFrame, with the changes in this PR that concat won't copy if CoW is enabled. But it seems that the data from the HDF store always come back as F contiguous, while in pandas we want it as C contiguous for optimal performance.
Maybe we should just add a copy=True in the concat call in the mentioned snippet. That's already the default for non-CoW so won't change anything, and for CoW enabled also ensures we get the desired memory layout (at the expense of an extra copy while reading in, but to fix that, that can be a follow-up optimization investigating why the HDF store always returns F contiguous arrays)

Also commented about that on the related issue (that triggered adding this test): #22073

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Yeah this seems to fix it

# GH22073
df = DataFrame({"a": [1, 2, 3, 4], "b": [5, 6, 7, 8]})
Expand Down
4 changes: 2 additions & 2 deletions pandas/tests/reshape/concat/test_concat.py
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ def test_append_concat(self):
assert isinstance(result.index, PeriodIndex)
assert result.index[0] == s1.index[0]

def test_concat_copy(self, using_array_manager):
def test_concat_copy(self, using_array_manager, using_copy_on_write):
df = DataFrame(np.random.randn(4, 3))
df2 = DataFrame(np.random.randint(0, 10, size=4).reshape(4, 1))
df3 = DataFrame({5: "foo"}, index=range(4))
Expand Down Expand Up @@ -82,7 +82,7 @@ def test_concat_copy(self, using_array_manager):
result = concat([df, df2, df3, df4], axis=1, copy=False)
for arr in result._mgr.arrays:
if arr.dtype.kind == "f":
if using_array_manager:
if using_array_manager or using_copy_on_write:
# this is a view on some array in either df or df4
assert any(
np.shares_memory(arr, other)
Expand Down