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Merge pull request #651 from theislab/pre-commit-ci-update-config
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[pre-commit.ci] pre-commit autoupdate
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@ArinaDanilina
ArinaDanilina authored Feb 2, 2024
2 parents ca13572 + 9cd5feb commit c9cb739
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Showing 8 changed files with 37 additions and 67 deletions.
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ repos:
additional_dependencies: [numpy>=1.25.0]
files: ^src
- repo: https://github.com/psf/black
rev: 23.12.1
rev: 24.1.1
hooks:
- id: black
additional_dependencies: [toml]
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18 changes: 6 additions & 12 deletions src/moscot/base/problems/_mixins.py
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Expand Up @@ -58,23 +58,20 @@ def _apply(
return_all: bool = False,
scale_by_marginals: bool = False,
**kwargs: Any,
) -> ApplyOutput_t[K]:
...
) -> ApplyOutput_t[K]: ...

def _interpolate_transport(
self: AnalysisMixinProtocol[K, B],
path: Sequence[tuple[K, K]],
scale_by_marginals: bool = True,
) -> LinearOperator:
...
) -> LinearOperator: ...

def _flatten(
self: AnalysisMixinProtocol[K, B],
data: dict[K, ArrayLike],
*,
key: Optional[str],
) -> ArrayLike:
...
) -> ArrayLike: ...

def push(self, *args: Any, **kwargs: Any) -> Optional[ApplyOutput_t[K]]:
"""Push distribution."""
Expand All @@ -93,8 +90,7 @@ def _cell_transition(
aggregation_mode: Literal["annotation", "cell"] = "annotation",
key_added: Optional[str] = _constants.CELL_TRANSITION,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def _cell_transition_online(
self: AnalysisMixinProtocol[K, B],
Expand All @@ -109,8 +105,7 @@ def _cell_transition_online(
other_adata: Optional[str] = None,
batch_size: Optional[int] = None,
normalize: bool = True,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def _annotation_mapping(
self: AnalysisMixinProtocol[K, B],
Expand All @@ -123,8 +118,7 @@ def _annotation_mapping(
other_adata: Optional[str] = None,
scale_by_marginals: bool = True,
cell_transition_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...


class AnalysisMixin(Generic[K, B]):
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3 changes: 1 addition & 2 deletions src/moscot/base/problems/birth_death.py
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Expand Up @@ -38,8 +38,7 @@ def score_genes_for_marginals( # noqa: D102
proliferation_key: str = "proliferation",
apoptosis_key: str = "apoptosis",
**kwargs: Any,
) -> "BirthDeathProtocol":
...
) -> "BirthDeathProtocol": ...


class BirthDeathProblemProtocol(BirthDeathProtocol, Protocol): # noqa: D101
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12 changes: 6 additions & 6 deletions src/moscot/plotting/_plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,12 +104,12 @@ def cell_transition(
row_adata=adata1,
col_adata=adata2,
transition_matrix=data["transition_matrix"],
row_annotation=data["source_groups"]
if isinstance(data["source_groups"], str)
else next(iter(data["source_groups"])),
col_annotation=data["target_groups"]
if isinstance(data["target_groups"], str)
else next(iter(data["target_groups"])),
row_annotation=(
data["source_groups"] if isinstance(data["source_groups"], str) else next(iter(data["source_groups"]))
),
col_annotation=(
data["target_groups"] if isinstance(data["target_groups"], str) else next(iter(data["target_groups"]))
),
row_annotation_label=data["source"] if row_label is None else row_label,
col_annotation_label=data["target"] if col_label is None else col_label,
cont_cmap=cmap,
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6 changes: 2 additions & 4 deletions src/moscot/problems/cross_modality/_mixins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,9 @@ class CrossModalityTranslationMixinProtocol(AnalysisMixinProtocol[K, B]):
_tgt_attr: Optional[Dict[str, Any]]
batch_key: Optional[str]

def _cell_transition(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
...
def _cell_transition(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame: ...

def _annotation_mapping(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
...
def _annotation_mapping(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame: ...


class CrossModalityTranslationMixin(AnalysisMixin[K, B]):
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3 changes: 1 addition & 2 deletions src/moscot/problems/generic/_mixins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,7 @@ def _cell_transition(
self: AnalysisMixinProtocol[K, B],
*args: Any,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...


class GenericAnalysisMixin(AnalysisMixin[K, B]):
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21 changes: 7 additions & 14 deletions src/moscot/problems/space/_mixins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,30 +46,26 @@ def _subset_spatial( # type:ignore[empty-body]
self: "SpatialAlignmentMixinProtocol[K, B]",
k: K,
spatial_key: str,
) -> ArrayLike:
...
) -> ArrayLike: ...

def _interpolate_scheme( # type:ignore[empty-body]
self: "SpatialAlignmentMixinProtocol[K, B]",
reference: K,
mode: Literal["warp", "affine"],
spatial_key: str,
) -> Tuple[Dict[K, ArrayLike], Optional[Dict[K, Optional[ArrayLike]]]]:
...
) -> Tuple[Dict[K, ArrayLike], Optional[Dict[K, Optional[ArrayLike]]]]: ...

def _cell_transition(
self: AnalysisMixinProtocol[K, B],
*args: Any,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def _annotation_mapping(
self: AnalysisMixinProtocol[K, B],
*args: Any,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...


class SpatialMappingMixinProtocol(AnalysisMixinProtocol[K, B]):
Expand All @@ -84,14 +80,11 @@ class SpatialMappingMixinProtocol(AnalysisMixinProtocol[K, B]):
def _filter_vars(
self: "SpatialMappingMixinProtocol[K, B]",
var_names: Optional[Sequence[str]] = None,
) -> Optional[List[str]]:
...
) -> Optional[List[str]]: ...

def _cell_transition(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
...
def _cell_transition(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame: ...

def _annotation_mapping(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
...
def _annotation_mapping(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame: ...


class SpatialAlignmentMixin(AnalysisMixin[K, B]):
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39 changes: 13 additions & 26 deletions src/moscot/problems/time/_mixins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,28 +50,23 @@ def cell_transition( # noqa: D102
batch_size: Optional[int] = None,
normalize: bool = True,
key_added: Optional[str] = _constants.CELL_TRANSITION,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def push(self, *args: Any, **kwargs: Any) -> Optional[ApplyOutput_t[K]]:
...
def push(self, *args: Any, **kwargs: Any) -> Optional[ApplyOutput_t[K]]: ...

def pull(self, *args: Any, **kwargs: Any) -> Optional[ApplyOutput_t[K]]:
...
def pull(self, *args: Any, **kwargs: Any) -> Optional[ApplyOutput_t[K]]: ...

def _cell_transition(
self: AnalysisMixinProtocol[K, B],
*args: Any,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def _annotation_mapping(
self: AnalysisMixinProtocol[K, B],
*args: Any,
**kwargs: Any,
) -> pd.DataFrame:
...
) -> pd.DataFrame: ...

def _sample_from_tmap(
self: TemporalMixinProtocol[K, B],
Expand All @@ -84,8 +79,7 @@ def _sample_from_tmap(
account_for_unbalancedness: bool = False,
interpolation_parameter: Optional[float] = None,
seed: Optional[int] = None,
) -> tuple[list[Any], list[ArrayLike]]:
...
) -> tuple[list[Any], list[ArrayLike]]: ...

def _compute_wasserstein_distance(
self: TemporalMixinProtocol[K, B],
Expand All @@ -95,8 +89,7 @@ def _compute_wasserstein_distance(
b: Optional[ArrayLike] = None,
backend: Literal["ott"] = "ott",
**kwargs: Any,
) -> float:
...
) -> float: ...

def _interpolate_gex_with_ot(
self: TemporalMixinProtocol[K, B],
Expand All @@ -109,8 +102,7 @@ def _interpolate_gex_with_ot(
account_for_unbalancedness: bool = True,
batch_size: int = 256,
seed: Optional[int] = None,
) -> ArrayLike:
...
) -> ArrayLike: ...

def _get_data(
self: TemporalMixinProtocol[K, B],
Expand All @@ -120,8 +112,7 @@ def _get_data(
posterior_marginals: bool = True,
*,
only_start: bool = False,
) -> Union[tuple[ArrayLike, AnnData], tuple[ArrayLike, ArrayLike, ArrayLike, AnnData, ArrayLike]]:
...
) -> Union[tuple[ArrayLike, AnnData], tuple[ArrayLike, ArrayLike, ArrayLike, AnnData, ArrayLike]]: ...

def _interpolate_gex_randomly(
self: TemporalMixinProtocol[K, B],
Expand All @@ -131,8 +122,7 @@ def _interpolate_gex_randomly(
interpolation_parameter: float,
growth_rates: Optional[ArrayLike] = None,
seed: Optional[int] = None,
) -> ArrayLike:
...
) -> ArrayLike: ...

def _plot_temporal(
self: TemporalMixinProtocol[K, B],
Expand All @@ -145,17 +135,14 @@ def _plot_temporal(
fill_value: float = 0.0,
save: Optional[Union[str, pathlib.Path]] = None,
**kwargs: Any,
) -> None:
...
) -> None: ...

@staticmethod
def _get_interp_param(
source: K, intermediate: K, target: K, interpolation_parameter: Optional[float] = None
) -> float:
...
) -> float: ...

def __iter__(self) -> Iterator[tuple[K, K]]:
...
def __iter__(self) -> Iterator[tuple[K, K]]: ...


class TemporalMixin(AnalysisMixin[K, B]):
Expand Down

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