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Improve behaviour of DataTree accessor (#32)
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* better default for datatree group handling

* add test for datatree accessor group behaviour

* lint
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OriolAbril authored Oct 25, 2024
1 parent d622d99 commit feb3084
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Showing 8 changed files with 80 additions and 13 deletions.
4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
rev: v5.0.0
hooks:
- id: check-added-large-files
- id: check-toml
Expand All @@ -11,7 +11,7 @@ repos:
- id: trailing-whitespace

- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.4.9
rev: v0.6.9
hooks:
- id: ruff
args: [ --fix, --exit-non-zero-on-fix ]
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26 changes: 20 additions & 6 deletions src/arviz_stats/accessors.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""ArviZ stats accessors."""

import warnings
from collections.abc import Hashable

import numpy as np
import xarray as xr
Expand Down Expand Up @@ -214,27 +215,40 @@ def _process_input(self, group, method, allow_non_matching=True):
)
return self._obj
raise ValueError(
f"Group {group} not available in DataTree. Present groups are {self._obj.children}"
f"Group {group} not available in DataTree. Present groups are {self._obj.children} "
f"and the DataTree itself is named {self._obs.name}"
)

def _apply(self, fun_name, group, **kwargs):
allow_non_matching = False
if isinstance(group, str):
hashable_group = False
if isinstance(group, Hashable):
group = [group]
allow_non_matching = True
return DataTree.from_dict(
hashable_group = True
out_dt = DataTree.from_dict(
{
group_i: xr.Dataset(
{
var_name: get_function(fun_name)(da, **update_kwargs_with_dims(da, kwargs))
for var_name, da in self._process_input(
group_i, fun_name, allow_non_matching=allow_non_matching
# if group is a single str/hashable that doesn't match the group
# name, still allow it and apply the function to the top level of
# the provided datatree
group_i,
fun_name,
allow_non_matching=hashable_group,
).items()
}
)
for group_i in group
}
)
if hashable_group:
# if group was a string/hashable, return a datatree with a single node
# (from the provided group) as the root of the DataTree
return out_dt[group[0]]
# if group was a sequence, return a DataTree with multiple groups in the 1st level,
# as many groups as requested
return out_dt

def filter_vars(self, group="posterior", var_names=None, filter_vars=None):
"""Access and filter variables of the provided group."""
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1 change: 1 addition & 0 deletions tests/base/test_diagnostics.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import pandas as pd
import pytest
from arviz_base import load_arviz_data, xarray_var_iter

from arviz_stats.base import array_stats

# For tests only, recommended value should be closer to 1.01-1.05
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5 changes: 3 additions & 2 deletions tests/base/test_stats_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,12 @@
# pylint: disable=no-member,unnecessary-lambda-assignment
import numpy as np
import pytest
from arviz_stats.base.stats_utils import logsumexp as _logsumexp
from arviz_stats.base.stats_utils import make_ufunc, not_valid
from numpy.testing import assert_array_almost_equal
from scipy.special import logsumexp

from arviz_stats.base.stats_utils import logsumexp as _logsumexp
from arviz_stats.base.stats_utils import make_ufunc, not_valid


@pytest.mark.parametrize("ary_dtype", [np.float64, np.float32, np.int32, np.int64])
@pytest.mark.parametrize("axis", [None, 0, 1, (-2, -1)])
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48 changes: 48 additions & 0 deletions tests/test_accessors.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
# pylint: disable=redefined-outer-name
"""Test accessors.
Accessor methods are very short, with the bulk of the computation/processing
handled by private methods. Testing this shared infrastructural methods
is the main goal of this module even if it does so via specific "regular" methods.
"""

import numpy as np
import pytest
from arviz_base import from_dict
from datatree import DataTree


@pytest.fixture(scope="module")
def idata():
return from_dict(
{
"posterior": {
"a": np.random.normal(size=(4, 100)),
"b": np.random.normal(size=(4, 100, 3)),
},
"posterior_predictive": {
"y": np.random.normal(size=(4, 100, 7)),
},
}
)


def test_accessors_available(idata):
assert hasattr(idata, "azstats")
assert hasattr(idata.posterior.ds, "azstats")
assert hasattr(idata.posterior["a"], "azstats")


def test_datatree_single_group(idata):
out = idata.azstats.ess(group="posterior")
assert isinstance(out, DataTree)
assert not out.children
assert out.name == "posterior"


def test_datatree_multiple_groups(idata):
out = idata.azstats.ess(group=["posterior", "posterior_predictive"])
assert isinstance(out, DataTree)
assert len(out.children) == 2
assert "posterior" in out.children
assert "posterior_predictive" in out.children
3 changes: 2 additions & 1 deletion tests/test_psense.py
Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
import os

from arviz_base import convert_to_datatree
from arviz_stats import psense, psense_summary
from numpy import isclose
from numpy.testing import assert_almost_equal

from arviz_stats import psense, psense_summary

file_path = os.path.join(os.path.dirname(__file__), "univariate_normal.nc")
uni_dt = convert_to_datatree(file_path)

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1 change: 1 addition & 0 deletions tests/test_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import numpy as np
import pytest
from arviz_base import from_dict, rcParams

from arviz_stats.base.dataarray import dataarray_stats
from arviz_stats.utils import ELPDData, get_function, get_log_likelihood

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5 changes: 3 additions & 2 deletions tox.ini
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,10 @@ isolated_build_env = build

[gh-actions]
python =
3.10: check, py310
3.10: py310
3.11: py311
3.12: py312
3.12: py312, check
3.13: py313

[testenv]
basepython =
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