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Merged
jkanche merged 1 commit into from
Jan 3, 2026
Merged

Classes extend BiocObject from biocutils. #47

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2 changes: 1 addition & 1 deletion .github/workflows/run-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
test:
strategy:
matrix:
python: ["3.9", "3.10", "3.11", "3.12", "3.13"]
python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
platform:
- ubuntu-latest
- macos-latest
Expand Down
6 changes: 6 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## Version 0.6.0

- Class extends `BiocObject` from biocutils.
- Github actions run from 3.10-3.14.
- `validate` renamed to `_validate` for consistency.

## Version 0.5.0 - 0.5.2

- chore: Remove Python 3.8 (EOL)
Expand Down
101 changes: 26 additions & 75 deletions src/multiassayexperiment/MultiAssayExperiment.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from __future__ import annotations

from collections import OrderedDict, namedtuple
from typing import Any, Dict, List, Optional, Sequence, Union
from warnings import warn
Expand All @@ -15,7 +17,7 @@

def _sanitize_frame(frame):
if se._frameutils.is_pandas(frame):
frame = biocframe.from_pandas(frame)
frame = biocframe.BiocFrame.from_pandas(frame)

return frame

Expand Down Expand Up @@ -121,7 +123,7 @@ def _create_smap_from_experiments(experiments):
return col_data, sample_map


class MultiAssayExperiment:
class MultiAssayExperiment(ut.BiocObject):
"""Container class for representing and managing multi-omics genomic experiments.

Checkout the
Expand All @@ -132,10 +134,10 @@ class MultiAssayExperiment:
def __init__(
self,
experiments: Dict[str, Any],
column_data: biocframe.BiocFrame = None,
sample_map: biocframe.BiocFrame = None,
metadata: Optional[dict] = None,
validate: bool = True,
column_data: Optional[biocframe.BiocFrame] = None,
sample_map: Optional[biocframe.BiocFrame] = None,
metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
_validate: bool = True,
) -> None:
"""Initialize an instance of ``MultiAssayExperiment``.

Expand Down Expand Up @@ -194,11 +196,12 @@ def __init__(
metadata:
Additional study-level metadata. Defaults to None.

validate:
_validate:
Internal use only.
"""
super().__init__(metadata=metadata, _validate=_validate)

self._experiments = experiments if experiments is not None else {}
self._metadata = metadata if metadata is not None else {}

if sample_map is not None and column_data is not None:
self._sample_map = _sanitize_frame(sample_map)
Expand All @@ -211,17 +214,11 @@ def __init__(
"Either 'sample_map' or 'column_data' is `None`. Either both should be provided or set both to `None`."
)

if validate:
if _validate:
_validate_experiments(self._experiments)
_validate_column_data(self._column_data)
_validate_sample_map(self._sample_map, self._column_data, self._experiments)

def _define_output(self, in_place: bool = False) -> "MultiAssayExperiment":
if in_place is True:
return self
else:
return self.__copy__()

#########################
######>> Copying <<######
#########################
Expand All @@ -244,6 +241,7 @@ def __deepcopy__(self, memo=None, _nil=[]):
column_data=_column_data_copy,
sample_map=_sample_map_copy,
metadata=_metadata_copy,
_validate=False,
)

def __copy__(self):
Expand All @@ -257,6 +255,7 @@ def __copy__(self):
column_data=self._column_data,
sample_map=self._sample_map,
metadata=self._metadata,
_validate=False,
)

def copy(self):
Expand Down Expand Up @@ -321,7 +320,7 @@ def get_experiments(self) -> Dict[str, Any]:

return self._experiments

def set_experiments(self, experiments: Dict[str, Any], in_place: bool = False) -> "MultiAssayExperiment":
def set_experiments(self, experiments: Dict[str, Any], in_place: bool = False) -> MultiAssayExperiment:
"""Set new experiments.

Args:
Expand Down Expand Up @@ -387,7 +386,7 @@ def get_experiment_names(self) -> List[str]:
"""
return list(self._experiments.keys())

def set_experiment_names(self, names: List[str], in_place: bool = False) -> "MultiAssayExperiment":
def set_experiment_names(self, names: List[str], in_place: bool = False) -> MultiAssayExperiment:
"""Replace :py:attr:`~experiments`'s names.

Args:
Expand Down Expand Up @@ -513,7 +512,7 @@ def get_sample_map(self) -> biocframe.BiocFrame:
"""
return self._sample_map

def set_sample_map(self, sample_map: biocframe.BiocFrame, in_place: bool = False) -> "MultiAssayExperiment":
def set_sample_map(self, sample_map: biocframe.BiocFrame, in_place: bool = False) -> MultiAssayExperiment:
"""Set new sample mapping.

Args:
Expand Down Expand Up @@ -563,7 +562,7 @@ def get_column_data(self) -> biocframe.BiocFrame:
"""
return self._column_data

def set_column_data(self, column_data: biocframe.BiocFrame, in_place: bool = False) -> "MultiAssayExperiment":
def set_column_data(self, column_data: biocframe.BiocFrame, in_place: bool = False) -> MultiAssayExperiment:
"""Set new sample metadata.

Args:
Expand Down Expand Up @@ -603,54 +602,6 @@ def column_data(self, column_data: biocframe.BiocFrame):
)
self.set_column_data(column_data, in_place=True)

###########################
######>> metadata <<#######
###########################

def get_metadata(self) -> dict:
"""
Returns:
Dictionary of metadata for this object.
"""
return self._metadata

def set_metadata(self, metadata: dict, in_place: bool = False) -> "MultiAssayExperiment":
"""Set additional metadata.

Args:
metadata:
New metadata for this object.

in_place:
Whether to modify the ``MultiAssayExperiment`` in place.

Returns:
A modified ``MultiAssayExperiment`` object, either as a copy of the original
or as a reference to the (in-place-modified) original.
"""
if not isinstance(metadata, dict):
raise TypeError(f"`metadata` must be a dictionary, provided {type(metadata)}.")
output = self._define_output(in_place)
output._metadata = metadata
return output

@property
def metadata(self) -> dict:
"""Alias for :py:attr:`~get_metadata`."""
return self.get_metadata()

@metadata.setter
def metadata(self, metadata: dict):
"""Alias for :py:attr:`~set_metadata` with ``in_place = True``.

As this mutates the original object, a warning is raised.
"""
warn(
"Setting property 'metadata' is an in-place operation, use 'set_metadata' instead",
UserWarning,
)
self.set_metadata(metadata, in_place=True)

#########################
######>> subset <<#######
#########################
Expand Down Expand Up @@ -812,7 +763,7 @@ def _generic_slice(

return SlicerResult(_new_experiments, _new_sample_map, _new_column_data)

def subset_by_experiments(self, experiments: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment":
def subset_by_experiments(self, experiments: Union[str, int, bool, Sequence]) -> MultiAssayExperiment:
"""Subset by experiment(s).

Args:
Expand All @@ -831,7 +782,7 @@ def subset_by_experiments(self, experiments: Union[str, int, bool, Sequence]) ->
sresult = self._generic_slice(experiments=experiments)
return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)

def subset_by_row(self, rows: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment":
def subset_by_row(self, rows: Union[str, int, bool, Sequence]) -> MultiAssayExperiment:
"""Subset by rows.

Args:
Expand All @@ -848,7 +799,7 @@ def subset_by_row(self, rows: Union[str, int, bool, Sequence]) -> "MultiAssayExp
sresult = self._generic_slice(rows=rows)
return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)

def subset_by_column(self, columns: Union[str, int, bool, Sequence]) -> "MultiAssayExperiment":
def subset_by_column(self, columns: Union[str, int, bool, Sequence]) -> MultiAssayExperiment:
"""Subset by column.

Args:
Expand All @@ -865,7 +816,7 @@ def subset_by_column(self, columns: Union[str, int, bool, Sequence]) -> "MultiAs
sresult = self._generic_slice(columns=columns)
return MultiAssayExperiment(sresult.experiments, sresult.column_data, sresult.sample_map, self.metadata)

def __getitem__(self, args: tuple) -> "MultiAssayExperiment":
def __getitem__(self, args: tuple) -> MultiAssayExperiment:
"""Subset a `MultiAssayExperiment`.

Args:
Expand Down Expand Up @@ -988,7 +939,7 @@ def find_common_row_names(self) -> List[str]:

return _common

def intersect_rows(self) -> "MultiAssayExperiment":
def intersect_rows(self) -> MultiAssayExperiment:
"""Finds common row names across all experiments and filters the MAE to these rows.

Returns:
Expand Down Expand Up @@ -1060,7 +1011,7 @@ def add_experiment(
sample_map: biocframe.BiocFrame,
column_data: Optional[biocframe.BiocFrame] = None,
in_place: bool = False,
) -> "MultiAssayExperiment":
) -> MultiAssayExperiment:
"""Add a new experiment to `MultiAssayExperiment`.

``sample_map`` must be provided to map the columns from this experiment to
Expand Down Expand Up @@ -1155,7 +1106,7 @@ def to_mudata(self):
return MuData(exptsList)

@classmethod
def from_mudata(cls, input: "mudata.MuData") -> "MultiAssayExperiment":
def from_mudata(cls, input: "mudata.MuData") -> MultiAssayExperiment:
"""Create a ``MultiAssayExperiment`` object from :py:class:`~mudata.MuData`.

The import naively creates sample mapping, each ``experiment`` is considered to be a `sample`.
Expand Down Expand Up @@ -1215,7 +1166,7 @@ def from_mudata(cls, input: "mudata.MuData") -> "MultiAssayExperiment":
)

@classmethod
def from_anndata(cls, input: "anndata.AnnData", name: str = "unknown") -> "MultiAssayExperiment":
def from_anndata(cls, input: "anndata.AnnData", name: str = "unknown") -> MultiAssayExperiment:
"""Create a ``MultiAssayExperiment`` from :py:class:`~anndata.AnnData`.

Since :py:class:`~anndata.AnnData` does not contain sample information,
Expand Down
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