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"""Generate module and stub file for arithmetic operators of various xarray classes.
For internal xarray development use only.
Usage:
python xarray/util/generate_aggregations.py
pytest --doctest-modules xarray/{core,namedarray}/_aggregations.py --accept || true
pytest --doctest-modules xarray/{core,namedarray}/_aggregations.py
This requires [pytest-accept](https://github.com/max-sixty/pytest-accept).
The second run of pytest is deliberate, since the first will return an error
while replacing the doctests.
"""
import textwrap
from dataclasses import dataclass, field
from typing import NamedTuple
MODULE_PREAMBLE = '''\
"""Mixin classes with reduction operations."""
# This file was generated using xarray.util.generate_aggregations. Do not edit manually.
from __future__ import annotations
from collections.abc import Callable, Sequence
from typing import TYPE_CHECKING, Any
from xarray.core import duck_array_ops
from xarray.core.options import OPTIONS
from xarray.core.types import Dims, Self
from xarray.core.utils import contains_only_chunked_or_numpy, module_available
if TYPE_CHECKING:
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
flox_available = module_available("flox")
'''
NAMED_ARRAY_MODULE_PREAMBLE = '''\
"""Mixin classes with reduction operations."""
# This file was generated using xarray.util.generate_aggregations. Do not edit manually.
from __future__ import annotations
from collections.abc import Callable, Sequence
from typing import Any
from xarray.core import duck_array_ops
from xarray.core.types import Dims, Self
'''
AGGREGATIONS_PREAMBLE = """
class {obj}{cls}Aggregations:
__slots__ = ()
def reduce(
self,
func: Callable[..., Any],
dim: Dims = None,
*,
axis: int | Sequence[int] | None = None,
keep_attrs: bool | None = None,
keepdims: bool = False,
**kwargs: Any,
) -> Self:
raise NotImplementedError()"""
NAMED_ARRAY_AGGREGATIONS_PREAMBLE = """
class {obj}{cls}Aggregations:
__slots__ = ()
def reduce(
self,
func: Callable[..., Any],
dim: Dims = None,
*,
axis: int | Sequence[int] | None = None,
keepdims: bool = False,
**kwargs: Any,
) -> Self:
raise NotImplementedError()"""
GROUPBY_PREAMBLE = """
class {obj}{cls}Aggregations:
_obj: {obj}
def reduce(
self,
func: Callable[..., Any],
dim: Dims = None,
*,
axis: int | Sequence[int] | None = None,
keep_attrs: bool | None = None,
keepdims: bool = False,
**kwargs: Any,
) -> {obj}:
raise NotImplementedError()
def _flox_reduce(
self,
dim: Dims,
**kwargs: Any,
) -> {obj}:
raise NotImplementedError()"""
RESAMPLE_PREAMBLE = """
class {obj}{cls}Aggregations:
_obj: {obj}
def reduce(
self,
func: Callable[..., Any],
dim: Dims = None,
*,
axis: int | Sequence[int] | None = None,
keep_attrs: bool | None = None,
keepdims: bool = False,
**kwargs: Any,
) -> {obj}:
raise NotImplementedError()
def _flox_reduce(
self,
dim: Dims,
**kwargs: Any,
) -> {obj}:
raise NotImplementedError()"""
TEMPLATE_REDUCTION_SIGNATURE = '''
def {method}(
self,
dim: Dims = None,{kw_only}{extra_kwargs}{keep_attrs}
**kwargs: Any,
) -> Self:
"""
Reduce this {obj}'s data by applying ``{method}`` along some dimension(s).
Parameters
----------'''
TEMPLATE_REDUCTION_SIGNATURE_GROUPBY = '''
def {method}(
self,
dim: Dims = None,
*,{extra_kwargs}
keep_attrs: bool | None = None,
**kwargs: Any,
) -> {obj}:
"""
Reduce this {obj}'s data by applying ``{method}`` along some dimension(s).
Parameters
----------'''
TEMPLATE_RETURNS = """
Returns
-------
reduced : {obj}
New {obj} with ``{method}`` applied to its data and the
indicated dimension(s) removed"""
TEMPLATE_SEE_ALSO = """
See Also
--------
{see_also_methods}
:ref:`{docref}`
User guide on {docref_description}."""
TEMPLATE_NOTES = """
Notes
-----
{notes}"""
_DIM_DOCSTRING = """dim : str, Iterable of Hashable, "..." or None, default: None
Name of dimension[s] along which to apply ``{method}``. For e.g. ``dim="x"``
or ``dim=["x", "y"]``. If "..." or None, will reduce over all dimensions."""
_DIM_DOCSTRING_GROUPBY = """dim : str, Iterable of Hashable, "..." or None, default: None
Name of dimension[s] along which to apply ``{method}``. For e.g. ``dim="x"``
or ``dim=["x", "y"]``. If None, will reduce over the {cls} dimensions.
If "...", will reduce over all dimensions."""
_SKIPNA_DOCSTRING = """skipna : bool or None, optional
If True, skip missing values (as marked by NaN). By default, only
skips missing values for float dtypes; other dtypes either do not
have a sentinel missing value (int) or ``skipna=True`` has not been
implemented (object, datetime64 or timedelta64)."""
_MINCOUNT_DOCSTRING = """min_count : int or None, optional
The required number of valid values to perform the operation. If
fewer than min_count non-NA values are present the result will be
NA. Only used if skipna is set to True or defaults to True for the
array's dtype. Changed in version 0.17.0: if specified on an integer
array and skipna=True, the result will be a float array."""
_DDOF_DOCSTRING = """ddof : int, default: 0
“Delta Degrees of Freedom”: the divisor used in the calculation is ``N - ddof``,
where ``N`` represents the number of elements."""
_KEEP_ATTRS_DOCSTRING = """keep_attrs : bool or None, optional
If True, ``attrs`` will be copied from the original
object to the new one. If False, the new object will be
returned without attributes."""
_KWARGS_DOCSTRING = """**kwargs : Any
Additional keyword arguments passed on to the appropriate array
function for calculating ``{method}`` on this object's data.
These could include dask-specific kwargs like ``split_every``."""
_NUMERIC_ONLY_NOTES = "Non-numeric variables will be removed prior to reducing."
_FLOX_NOTES_TEMPLATE = """Use the ``flox`` package to significantly speed up {kind} computations,
especially with dask arrays. Xarray will use flox by default if installed.
Pass flox-specific keyword arguments in ``**kwargs``.
See the `flox documentation <https://flox.readthedocs.io>`_ for more."""
_FLOX_GROUPBY_NOTES = _FLOX_NOTES_TEMPLATE.format(kind="groupby")
_FLOX_RESAMPLE_NOTES = _FLOX_NOTES_TEMPLATE.format(kind="resampling")
_CUM_NOTES = """Note that the methods on the ``cumulative`` method are more performant (with numbagg installed)
and better supported. ``cumsum`` and ``cumprod`` may be deprecated
in the future."""
class ExtraKwarg(NamedTuple):
docs: str
kwarg: str
call: str
example: str
skipna = ExtraKwarg(
docs=_SKIPNA_DOCSTRING,
kwarg="skipna: bool | None = None,",
call="skipna=skipna,",
example="""\n
Use ``skipna`` to control whether NaNs are ignored.
>>> {calculation}(skipna=False)""",
)
min_count = ExtraKwarg(
docs=_MINCOUNT_DOCSTRING,
kwarg="min_count: int | None = None,",
call="min_count=min_count,",
example="""\n
Specify ``min_count`` for finer control over when NaNs are ignored.
>>> {calculation}(skipna=True, min_count=2)""",
)
ddof = ExtraKwarg(
docs=_DDOF_DOCSTRING,
kwarg="ddof: int = 0,",
call="ddof=ddof,",
example="""\n
Specify ``ddof=1`` for an unbiased estimate.
>>> {calculation}(skipna=True, ddof=1)""",
)
@dataclass
class DataStructure:
name: str
create_example: str
example_var_name: str
numeric_only: bool = False
see_also_modules: tuple[str, ...] = tuple
class Method:
def __init__(
self,
name,
bool_reduce=False,
extra_kwargs=tuple(),
numeric_only=False,
see_also_modules=("numpy", "dask.array"),
see_also_methods=(),
min_flox_version=None,
additional_notes="",
):
self.name = name
self.extra_kwargs = extra_kwargs
self.numeric_only = numeric_only
self.see_also_modules = see_also_modules
self.see_also_methods = see_also_methods
self.min_flox_version = min_flox_version
self.additional_notes = additional_notes
if bool_reduce:
self.array_method = f"array_{name}"
self.np_example_array = (
"""np.array([True, True, True, True, True, False], dtype=bool)"""
)
else:
self.array_method = name
self.np_example_array = """np.array([1, 2, 3, 0, 2, np.nan])"""
@dataclass
class AggregationGenerator:
_dim_docstring = _DIM_DOCSTRING
_template_signature = TEMPLATE_REDUCTION_SIGNATURE
cls: str
datastructure: DataStructure
methods: tuple[Method, ...]
docref: str
docref_description: str
example_call_preamble: str
definition_preamble: str
has_keep_attrs: bool = True
notes: str = ""
preamble: str = field(init=False)
def __post_init__(self):
self.preamble = self.definition_preamble.format(
obj=self.datastructure.name, cls=self.cls
)
def generate_methods(self):
yield [self.preamble]
for method in self.methods:
yield self.generate_method(method)
def generate_method(self, method: Method):
has_kw_only = method.extra_kwargs or self.has_keep_attrs
template_kwargs = dict(
obj=self.datastructure.name,
method=method.name,
keep_attrs=(
"\n keep_attrs: bool | None = None,"
if self.has_keep_attrs
else ""
),
kw_only="\n *," if has_kw_only else "",
)
if method.extra_kwargs:
extra_kwargs = "\n " + "\n ".join(
[kwarg.kwarg for kwarg in method.extra_kwargs if kwarg.kwarg]
)
else:
extra_kwargs = ""
yield self._template_signature.format(
**template_kwargs,
extra_kwargs=extra_kwargs,
)
for text in [
self._dim_docstring.format(method=method.name, cls=self.cls),
*(kwarg.docs for kwarg in method.extra_kwargs if kwarg.docs),
_KEEP_ATTRS_DOCSTRING if self.has_keep_attrs else None,
_KWARGS_DOCSTRING.format(method=method.name),
]:
if text:
yield textwrap.indent(text, 8 * " ")
yield TEMPLATE_RETURNS.format(**template_kwargs)
# we want Dataset.count to refer to DataArray.count
# but we also want DatasetGroupBy.count to refer to Dataset.count
# The generic aggregations have self.cls == ''
others = (
self.datastructure.see_also_modules
if self.cls == ""
else (self.datastructure.name,)
)
see_also_methods_from_modules = (
" " * 8 + f"{mod}.{method.name}"
for mod in (method.see_also_modules + others)
)
see_also_methods_from_methods = (
" " * 8 + f"{self.datastructure.name}.{method}"
for method in method.see_also_methods
)
see_also_methods = "\n".join(
[*see_also_methods_from_modules, *see_also_methods_from_methods]
)
# Fixes broken links mentioned in #8055
yield TEMPLATE_SEE_ALSO.format(
**template_kwargs,
docref=self.docref,
docref_description=self.docref_description,
see_also_methods=see_also_methods,
)
notes = self.notes
if method.numeric_only:
if notes != "":
notes += "\n\n"
notes += _NUMERIC_ONLY_NOTES
if method.additional_notes:
if notes != "":
notes += "\n\n"
notes += method.additional_notes
if notes != "":
yield TEMPLATE_NOTES.format(notes=textwrap.indent(notes, 8 * " "))
yield textwrap.indent(self.generate_example(method=method), "")
yield ' """'
yield self.generate_code(method, self.has_keep_attrs)
def generate_example(self, method):
created = self.datastructure.create_example.format(
example_array=method.np_example_array
)
calculation = f"{self.datastructure.example_var_name}{self.example_call_preamble}.{method.name}"
if method.extra_kwargs:
extra_examples = "".join(
kwarg.example for kwarg in method.extra_kwargs if kwarg.example
).format(calculation=calculation, method=method.name)
else:
extra_examples = ""
return f"""
Examples
--------{created}
>>> {self.datastructure.example_var_name}
>>> {calculation}(){extra_examples}"""
class GroupByAggregationGenerator(AggregationGenerator):
_dim_docstring = _DIM_DOCSTRING_GROUPBY
_template_signature = TEMPLATE_REDUCTION_SIGNATURE_GROUPBY
def generate_code(self, method, has_keep_attrs):
extra_kwargs = [kwarg.call for kwarg in method.extra_kwargs if kwarg.call]
if self.datastructure.numeric_only:
extra_kwargs.append(f"numeric_only={method.numeric_only},")
# median isn't enabled yet, because it would break if a single group was present in multiple
# chunks. The non-flox code path will just rechunk every group to a single chunk and execute the median
method_is_not_flox_supported = method.name in ("median", "cumsum", "cumprod")
if method_is_not_flox_supported:
indent = 12
else:
indent = 16
if extra_kwargs:
extra_kwargs = textwrap.indent("\n" + "\n".join(extra_kwargs), indent * " ")
else:
extra_kwargs = ""
if method_is_not_flox_supported:
return f"""\
return self.reduce(
duck_array_ops.{method.array_method},
dim=dim,{extra_kwargs}
keep_attrs=keep_attrs,
**kwargs,
)"""
min_version_check = f"""
and module_available("flox", minversion="{method.min_flox_version}")"""
return (
"""\
if (
flox_available
and OPTIONS["use_flox"]"""
+ (min_version_check if method.min_flox_version is not None else "")
+ f"""
and contains_only_chunked_or_numpy(self._obj)
):
return self._flox_reduce(
func="{method.name}",
dim=dim,{extra_kwargs}
# fill_value=fill_value,
keep_attrs=keep_attrs,
**kwargs,
)
else:
return self.reduce(
duck_array_ops.{method.array_method},
dim=dim,{extra_kwargs}
keep_attrs=keep_attrs,
**kwargs,
)"""
)
class GenericAggregationGenerator(AggregationGenerator):
def generate_code(self, method, has_keep_attrs):
extra_kwargs = [kwarg.call for kwarg in method.extra_kwargs if kwarg.call]
if self.datastructure.numeric_only:
extra_kwargs.append(f"numeric_only={method.numeric_only},")
if extra_kwargs:
extra_kwargs = textwrap.indent("\n" + "\n".join(extra_kwargs), 12 * " ")
else:
extra_kwargs = ""
keep_attrs = (
"\n" + 12 * " " + "keep_attrs=keep_attrs," if has_keep_attrs else ""
)
return f"""\
return self.reduce(
duck_array_ops.{method.array_method},
dim=dim,{extra_kwargs}{keep_attrs}
**kwargs,
)"""
AGGREGATION_METHODS = (
# Reductions:
Method("count", see_also_modules=("pandas.DataFrame", "dask.dataframe.DataFrame")),
Method("all", bool_reduce=True),
Method("any", bool_reduce=True),
Method("max", extra_kwargs=(skipna,)),
Method("min", extra_kwargs=(skipna,)),
Method("mean", extra_kwargs=(skipna,), numeric_only=True),
Method("prod", extra_kwargs=(skipna, min_count), numeric_only=True),
Method("sum", extra_kwargs=(skipna, min_count), numeric_only=True),
Method("std", extra_kwargs=(skipna, ddof), numeric_only=True),
Method("var", extra_kwargs=(skipna, ddof), numeric_only=True),
Method(
"median", extra_kwargs=(skipna,), numeric_only=True, min_flox_version="0.9.2"
),
# Cumulatives:
Method(
"cumsum",
extra_kwargs=(skipna,),
numeric_only=True,
see_also_methods=("cumulative",),
additional_notes=_CUM_NOTES,
),
Method(
"cumprod",
extra_kwargs=(skipna,),
numeric_only=True,
see_also_methods=("cumulative",),
additional_notes=_CUM_NOTES,
),
)
DATATREE_OBJECT = DataStructure(
name="DataTree",
create_example="""
>>> dt = xr.DataTree(
... xr.Dataset(
... data_vars=dict(foo=("time", {example_array})),
... coords=dict(
... time=("time", pd.date_range("2001-01-01", freq="ME", periods=6)),
... labels=("time", np.array(["a", "b", "c", "c", "b", "a"])),
... ),
... ),
... )""",
example_var_name="dt",
numeric_only=True,
see_also_modules=("Dataset", "DataArray"),
)
DATASET_OBJECT = DataStructure(
name="Dataset",
create_example="""
>>> da = xr.DataArray(
... {example_array},
... dims="time",
... coords=dict(
... time=("time", pd.date_range("2001-01-01", freq="ME", periods=6)),
... labels=("time", np.array(["a", "b", "c", "c", "b", "a"])),
... ),
... )
>>> ds = xr.Dataset(dict(da=da))""",
example_var_name="ds",
numeric_only=True,
see_also_modules=("DataArray",),
)
DATAARRAY_OBJECT = DataStructure(
name="DataArray",
create_example="""
>>> da = xr.DataArray(
... {example_array},
... dims="time",
... coords=dict(
... time=("time", pd.date_range("2001-01-01", freq="ME", periods=6)),
... labels=("time", np.array(["a", "b", "c", "c", "b", "a"])),
... ),
... )""",
example_var_name="da",
numeric_only=False,
see_also_modules=("Dataset",),
)
DATATREE_GENERATOR = GenericAggregationGenerator(
cls="",
datastructure=DATATREE_OBJECT,
methods=AGGREGATION_METHODS,
docref="agg",
docref_description="reduction or aggregation operations",
example_call_preamble="",
definition_preamble=AGGREGATIONS_PREAMBLE,
)
DATASET_GENERATOR = GenericAggregationGenerator(
cls="",
datastructure=DATASET_OBJECT,
methods=AGGREGATION_METHODS,
docref="agg",
docref_description="reduction or aggregation operations",
example_call_preamble="",
definition_preamble=AGGREGATIONS_PREAMBLE,
)
DATAARRAY_GENERATOR = GenericAggregationGenerator(
cls="",
datastructure=DATAARRAY_OBJECT,
methods=AGGREGATION_METHODS,
docref="agg",
docref_description="reduction or aggregation operations",
example_call_preamble="",
definition_preamble=AGGREGATIONS_PREAMBLE,
)
DATAARRAY_GROUPBY_GENERATOR = GroupByAggregationGenerator(
cls="GroupBy",
datastructure=DATAARRAY_OBJECT,
methods=AGGREGATION_METHODS,
docref="groupby",
docref_description="groupby operations",
example_call_preamble='.groupby("labels")',
definition_preamble=GROUPBY_PREAMBLE,
notes=_FLOX_GROUPBY_NOTES,
)
DATAARRAY_RESAMPLE_GENERATOR = GroupByAggregationGenerator(
cls="Resample",
datastructure=DATAARRAY_OBJECT,
methods=AGGREGATION_METHODS,
docref="resampling",
docref_description="resampling operations",
example_call_preamble='.resample(time="3ME")',
definition_preamble=RESAMPLE_PREAMBLE,
notes=_FLOX_RESAMPLE_NOTES,
)
DATASET_GROUPBY_GENERATOR = GroupByAggregationGenerator(
cls="GroupBy",
datastructure=DATASET_OBJECT,
methods=AGGREGATION_METHODS,
docref="groupby",
docref_description="groupby operations",
example_call_preamble='.groupby("labels")',
definition_preamble=GROUPBY_PREAMBLE,
notes=_FLOX_GROUPBY_NOTES,
)
DATASET_RESAMPLE_GENERATOR = GroupByAggregationGenerator(
cls="Resample",
datastructure=DATASET_OBJECT,
methods=AGGREGATION_METHODS,
docref="resampling",
docref_description="resampling operations",
example_call_preamble='.resample(time="3ME")',
definition_preamble=RESAMPLE_PREAMBLE,
notes=_FLOX_RESAMPLE_NOTES,
)
NAMED_ARRAY_OBJECT = DataStructure(
name="NamedArray",
create_example="""
>>> from xarray.namedarray.core import NamedArray
>>> na = NamedArray(
... "x", {example_array}
... )""",
example_var_name="na",
numeric_only=False,
see_also_modules=("Dataset", "DataArray"),
)
NAMED_ARRAY_GENERATOR = GenericAggregationGenerator(
cls="",
datastructure=NAMED_ARRAY_OBJECT,
methods=AGGREGATION_METHODS,
docref="agg",
docref_description="reduction or aggregation operations",
example_call_preamble="",
definition_preamble=NAMED_ARRAY_AGGREGATIONS_PREAMBLE,
has_keep_attrs=False,
)
def write_methods(filepath, generators, preamble):
with open(filepath, mode="w", encoding="utf-8") as f:
f.write(preamble)
for gen in generators:
for lines in gen.generate_methods():
f.writelines(line + "\n" for line in lines)
if __name__ == "__main__":
import os
from pathlib import Path
p = Path(os.getcwd())
write_methods(
filepath=p.parent / "xarray" / "xarray" / "core" / "_aggregations.py",
generators=[
DATATREE_GENERATOR,
DATASET_GENERATOR,
DATAARRAY_GENERATOR,
DATASET_GROUPBY_GENERATOR,
DATASET_RESAMPLE_GENERATOR,
DATAARRAY_GROUPBY_GENERATOR,
DATAARRAY_RESAMPLE_GENERATOR,
],
preamble=MODULE_PREAMBLE,
)
write_methods(
filepath=p.parent / "xarray" / "xarray" / "namedarray" / "_aggregations.py",
generators=[NAMED_ARRAY_GENERATOR],
preamble=NAMED_ARRAY_MODULE_PREAMBLE,
)
# filepath = p.parent / "core" / "_aggregations.py" # Run from script location
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