bonesistools 1.2.1__tar.gz → 1.2.2__tar.gz

{bonesistools-1.2.1 → bonesistools-1.2.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: bonesistools
-Version: 1.2.1
-Summary: BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework
+Version: 1.2.2
+Summary: Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework
 Project-URL: Repository, https://github.com/bnediction/bonesistools
 Author: Théo Roncalli
 Maintainer-email: Théo Roncalli <theo.roncalli@labri.fr>
@@ -586,13 +586,13 @@ Description-Content-Type: text/markdown
 
 # BoNesisTools
 
-`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory interaction graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
+`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory influence graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
 
 The package provides:
 
 - Boolean algebra and partial Boolean abstractions
 - Boolean network manipulation and analysis
-- signed interaction and influence graph utilities
+- signed influence graph utilities
 - GRN-informed Boolean predecessor inference
 - single-cell and multimodal analysis helpers
 - biological database interfaces
@@ -631,8 +631,6 @@ Submodules:
 
 Submodules:
 
-Submodules:
-
 - Boolean algebra: `bt.bpy.ba`
   - partial Boolean abstractions and hypercube representations
   - Boolean differential and predecessor inference utilities
@@ -643,7 +641,7 @@ Submodules:
   - `.bnet` import/export
 
 - influence graph: `bt.bpy.ig`
-  - signed regulatory interaction graphs
+  - signed regulatory influence graphs
   - feedback circuit and SCC analysis
   - signed interaction scoring from bounded walks
   - graph compression and visualization utilities

{bonesistools-1.2.1 → bonesistools-1.2.2}/README.md

@@ -5,13 +5,13 @@
 
 # BoNesisTools
 
-`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory interaction graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
+`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory influence graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
 
 The package provides:
 
 - Boolean algebra and partial Boolean abstractions
 - Boolean network manipulation and analysis
-- signed interaction and influence graph utilities
+- signed influence graph utilities
 - GRN-informed Boolean predecessor inference
 - single-cell and multimodal analysis helpers
 - biological database interfaces
@@ -50,8 +50,6 @@ Submodules:
 
 Submodules:
 
-Submodules:
-
 - Boolean algebra: `bt.bpy.ba`
   - partial Boolean abstractions and hypercube representations
   - Boolean differential and predecessor inference utilities
@@ -62,7 +60,7 @@ Submodules:
   - `.bnet` import/export
 
 - influence graph: `bt.bpy.ig`
-  - signed regulatory interaction graphs
+  - signed regulatory influence graphs
   - feedback circuit and SCC analysis
   - signed interaction scoring from bounded walks
   - graph compression and visualization utilities

{bonesistools-1.2.1 → bonesistools-1.2.2}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bonesistools"
-description = "BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework"
-version = "1.2.1"
+description = "Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework"
+version = "1.2.2"
 license = {file = "LICENSE"}
 credits = ["BNeDiction", "PEPR Santé Numérique 2030"]
 authors = [

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/__init__.py

@@ -23,16 +23,18 @@ from __future__ import annotations
 import importlib as _importlib
 import sys as _sys
 import warnings as _warnings
-from types import ModuleType
-from typing import TYPE_CHECKING
+from types import ModuleType as _ModuleType
+from typing import TYPE_CHECKING as _TYPE_CHECKING
 
 from . import boolpy as bpy
 from . import databases as dbs
 from . import sctools as sct
 
-if TYPE_CHECKING:
+if _TYPE_CHECKING:
     from . import grntools as grn
 
+del annotations
+
 __credits__ = "BNeDiction; PEPR Santé Numérique 2030"
 
 __all__ = [
@@ -54,11 +56,14 @@ _sys.modules.update(
 )
 
 _sys.modules.update(
-    {f"{__name__}.bpy.{alias}": getattr(bpy, alias) for alias in ["ba", "bn", "ig"]}
+    {
+        f"{__name__}.bpy.{alias}": getattr(bpy, alias)
+        for alias in ["ba", "bn", "ig", "pl"]
+    }
 )
 
 
-def __getattr__(name: str) -> ModuleType:
+def __getattr__(name: str) -> _ModuleType:
     if name == "grn":
         message = (
             "`bt.grn` is deprecated and will be removed in a future release; "

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/__init__.py

@@ -3,8 +3,8 @@
 """
 Utilities for Boolean modelling.
 
-The `bpy` package provides tools for Boolean algebra, Boolean networks
-and interaction/influence graphs.
+The `bpy` package provides tools for Boolean algebra, Boolean networks,
+influence graphs and plotting.
 
 Sub-packages
 ------------
@@ -13,28 +13,34 @@ ba
 bn
     Boolean networks and logical modelling utilities.
 ig
-    Interaction and influence graph utilities.
+    Influence graph utilities.
+pl
+    Plotting utilities.
 """
 
 from __future__ import annotations
 
 import sys as _sys
 import warnings as _warnings
-from types import ModuleType
-from typing import cast
+from types import ModuleType as _ModuleType
+from typing import cast as _cast
 
 from . import boolean_algebra as ba
 from . import boolean_network as bn
-from . import interaction_graph as ig
+from . import influence_graph as ig
+from . import plotting as pl
+
+del annotations
 
 _sys.modules.update(
-    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig"]}
+    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig", "pl"]}
 )
 
-_MODULES: dict[str, ModuleType] = {
+_MODULES: dict[str, _ModuleType] = {
     "ba": ba,
     "bn": bn,
     "ig": ig,
+    "pl": pl,
 }
 
 _DEPRECATED: dict[str, tuple[str, str]] = {
@@ -49,6 +55,7 @@ __all__ = [
     "ba",
     "bn",
     "ig",
+    "pl",
 ]
 
 
@@ -61,7 +68,7 @@ def __getattr__(name: str) -> object:
             DeprecationWarning,
             stacklevel=2,
         )
-        return cast(object, getattr(_MODULES[module_alias], attr))
+        return _cast(object, getattr(_MODULES[module_alias], attr))
 
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/boolean_algebra/__init__.py

@@ -8,7 +8,7 @@ Boolean algebra, including partial Boolean values and Boolean
 differential and predecessor inference utilities.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._algebra import BooleanPredecessorInference, PartialBooleanDifferential
 from ._boolean import PartialBoolean
@@ -53,5 +53,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/boolean_algebra/_typing.py

@@ -4,23 +4,27 @@
 Typing aliases and runtime validators for Boolean algebra objects.
 """
 
-from collections.abc import Mapping as MappingABC
+from collections.abc import Mapping as _MappingABC
 from typing import (
-    Any,
-    Mapping,
-    Union,
+    Any as _Any,
+)
+from typing import (
+    Mapping as _Mapping,
+)
+from typing import (
+    Union as _Union,
 )
 
 from boolean import Expression
-from typing_extensions import TypeGuard
+from typing_extensions import TypeGuard as _TypeGuard
 
 from ._boolean import PartialBoolean
 
-BooleanRule = Union[Expression, bool, int, str]
+BooleanRule = _Union[Expression, bool, int, str]
 
-PartialBooleanLike = Union[PartialBoolean, bool, int, float, str]
-ConfigurationLike = Mapping[str, Union[PartialBoolean, bool, int]]
-HypercubeLike = Mapping[str, PartialBooleanLike]
+PartialBooleanLike = _Union[PartialBoolean, bool, int, float, str]
+ConfigurationLike = _Mapping[str, _Union[PartialBoolean, bool, int]]
+HypercubeLike = _Mapping[str, PartialBooleanLike]
 
 
 def is_boolean_expression_available() -> bool:
@@ -40,7 +44,7 @@ def is_boolean_expression_available() -> bool:
     return Expression is not type(NotImplemented)
 
 
-def is_boolean_expression_like(obj: Any) -> TypeGuard[Expression]:
+def is_boolean_expression_like(obj: _Any) -> _TypeGuard[Expression]:
     """
     Test whether an object behaves as a Boolean expression.
 
@@ -66,7 +70,7 @@ def is_boolean_expression_like(obj: Any) -> TypeGuard[Expression]:
     return is_boolean_expression_available() and isinstance(obj, Expression)
 
 
-def is_boolean_rule_like(obj: Any) -> TypeGuard[BooleanRule]:
+def is_boolean_rule_like(obj: _Any) -> _TypeGuard[BooleanRule]:
     """
     Test whether an object can be interpreted as a Boolean rule.
 
@@ -102,7 +106,7 @@ def is_boolean_rule_like(obj: Any) -> TypeGuard[BooleanRule]:
     )
 
 
-def is_partial_boolean_like(value: Any) -> TypeGuard[PartialBooleanLike]:
+def is_partial_boolean_like(value: _Any) -> _TypeGuard[PartialBooleanLike]:
     """
     Test whether an object can be coerced into a PartialBoolean.
 
@@ -134,7 +138,7 @@ def is_partial_boolean_like(value: Any) -> TypeGuard[PartialBooleanLike]:
         return False
 
 
-def is_configuration_like(obj: Any) -> TypeGuard[ConfigurationLike]:
+def is_configuration_like(obj: _Any) -> _TypeGuard[ConfigurationLike]:
     """
     Test whether an object behaves as a concrete Boolean configuration.
 
@@ -162,7 +166,7 @@ def is_configuration_like(obj: Any) -> TypeGuard[ConfigurationLike]:
         values.
     """
 
-    if not isinstance(obj, MappingABC):
+    if not isinstance(obj, _MappingABC):
         return False
 
     try:
@@ -175,7 +179,7 @@ def is_configuration_like(obj: Any) -> TypeGuard[ConfigurationLike]:
         return False
 
 
-def is_hypercube_like(obj: Any) -> TypeGuard[HypercubeLike]:
+def is_hypercube_like(obj: _Any) -> _TypeGuard[HypercubeLike]:
     """
     Test whether an object behaves as a hypercube mapping.
 
@@ -203,7 +207,7 @@ def is_hypercube_like(obj: Any) -> TypeGuard[HypercubeLike]:
         PartialBoolean-like values.
     """
 
-    if not isinstance(obj, MappingABC):
+    if not isinstance(obj, _MappingABC):
         return False
 
     try:
@@ -216,7 +220,7 @@ def is_hypercube_like(obj: Any) -> TypeGuard[HypercubeLike]:
         return False
 
 
-def _is_configuration_value_like(value: Any) -> bool:
+def _is_configuration_value_like(value: _Any) -> bool:
     if isinstance(value, PartialBoolean):
         value = value.value
 

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/boolean_network/__init__.py

@@ -7,7 +7,8 @@ The `bn` sub-package provides data structures, analyses and helper functions
 for BooleanNetworkLike objects used in logical modelling frameworks.
 """
 
-from typing import Any, List
+from typing import Any as _Any
+from typing import List as _List
 
 from . import _typing as typing
 from ._network import (
@@ -28,7 +29,7 @@ __all__ = [
 ]
 
 
-def bn_to_pydot(bn: Any, **kwargs: Any) -> Any:
+def bn_to_pydot(bn: _Any, **kwargs: _Any) -> _Any:
     """
     Deprecated. Convert a BooleanNetworkLike object into a pydot graph.
 
@@ -47,5 +48,5 @@ def bn_to_pydot(bn: Any, **kwargs: Any) -> Any:
     return BooleanNetwork(bn).to_pydot(**kwargs)
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/boolean_network/_network.py

@@ -41,7 +41,7 @@ from ..boolean_algebra import (
     is_configuration_like,
     rule_to_string,
 )
-from ..interaction_graph._influence_graph import InfluenceGraph
+from ..influence_graph._influence_graph import InfluenceGraph
 from ..plotting import (
     count_node_style,
     ratio_edge_style,

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/boolean_network/_typing.py

@@ -4,17 +4,19 @@
 Typing aliases and runtime validators for BooleanNetworkLike objects.
 """
 
-from collections.abc import Mapping as MappingABC
-from typing import Any, Mapping
+from collections.abc import Mapping as _MappingABC
+from typing import Any as _Any
+from typing import Mapping as _Mapping
 
-from typing_extensions import TypeAlias, TypeGuard
+from typing_extensions import TypeAlias as _TypeAlias
+from typing_extensions import TypeGuard as _TypeGuard
 
 from ..boolean_algebra import BooleanRule, is_boolean_rule_like
 
-BooleanNetworkLike: TypeAlias = Mapping[str, BooleanRule]
+BooleanNetworkLike: _TypeAlias = _Mapping[str, BooleanRule]
 
 
-def is_boolean_network_like(obj: Any) -> TypeGuard[BooleanNetworkLike]:
+def is_boolean_network_like(obj: _Any) -> _TypeGuard[BooleanNetworkLike]:
     """
     Test whether an object behaves as a BooleanNetworkLike mapping.
 
@@ -30,7 +32,7 @@ def is_boolean_network_like(obj: Any) -> TypeGuard[BooleanNetworkLike]:
         values.
     """
 
-    if not isinstance(obj, MappingABC):
+    if not isinstance(obj, _MappingABC):
         return False
 
     try:

{bonesistools-1.2.1/src/bonesistools/boolpy/interaction_graph → bonesistools-1.2.2/src/bonesistools/boolpy/influence_graph}/__init__.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python
 
 """
-Utilities for biological interaction graphs and regulatory domains.
+Utilities for biological influence graphs and regulatory domains.
 
 The `ig` sub-package provides parsers, analyses and graph-related
-utilities for interaction networks.
+utilities for signed regulatory networks.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._algorithms import walks_from
 from ._influence_graph import InfluenceGraph
-from ._parser import read_interaction_graph
+from ._parser import read_influence_graph
 from ._scoring import (
     InteractionScore,
     infer_signed_interactions,
@@ -20,7 +20,7 @@ from ._scoring import (
 )
 
 __all__ = [
-    "read_interaction_graph",
+    "read_influence_graph",
     "walks_from",
     "InfluenceGraph",
     "InteractionScore",
@@ -30,5 +30,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1/src/bonesistools/boolpy/interaction_graph → bonesistools-1.2.2/src/bonesistools/boolpy/influence_graph}/_parser.py

@@ -24,7 +24,7 @@ else:
     GeneSynonyms = None
 
 
-def read_interaction_graph(
+def read_influence_graph(
     infile: Union[str, Path],
     genesyn: Optional[GeneSynonyms] = None,
     input_identifier_type: InputIdentifierType = "name",
@@ -33,7 +33,7 @@ def read_interaction_graph(
     **kwargs: Any,
 ) -> nx.MultiDiGraph[Any]:
     """
-    Read an interaction graph from a tabular file.
+    Read an influence graph from a tabular file.
 
     The input file must contain at least three columns: 'source', 'target' and
     'sign'. Additional columns are kept as edge attributes.
@@ -41,7 +41,7 @@ def read_interaction_graph(
     Parameters
     ----------
     infile: str | Path
-        Path to the tabular file containing the interaction graph.
+        Path to the tabular file containing the influence graph.
     genesyn: GeneSynonyms, optional
         GeneSynonyms object used to convert graph node identifiers.
     input_identifier_type: 'name' | 'gene_id' | 'ensembl_id' | <database>
@@ -60,7 +60,7 @@ def read_interaction_graph(
     Returns
     -------
     nx.MultiDiGraph
-        Directed interaction graph.
+        Directed influence graph.
         Edges store all columns from the input file as attributes.
 
     Raises
@@ -86,17 +86,17 @@ def read_interaction_graph(
     if not infile.is_file():
         raise FileNotFoundError(f"file not found: {infile}")
 
-    interaction_graph = pd.read_csv(infile, sep=sep, **kwargs)
+    influence_graph = pd.read_csv(infile, sep=sep, **kwargs)
 
     required_columns = {"source", "target", "sign"}
-    missing_columns = required_columns - set(interaction_graph.columns)
+    missing_columns = required_columns - set(influence_graph.columns)
 
     if missing_columns:
         raise ValueError(f"invalid file: missing columns {sorted(missing_columns)}")
 
-    interaction_graph["sign"] = interaction_graph["sign"].astype(float)
+    influence_graph["sign"] = influence_graph["sign"].astype(float)
 
-    invalid_signs = set(interaction_graph["sign"].dropna().unique()) - {-1.0, 1.0}
+    invalid_signs = set(influence_graph["sign"].dropna().unique()) - {-1.0, 1.0}
 
     if invalid_signs:
         raise ValueError(
@@ -104,7 +104,7 @@ def read_interaction_graph(
         )
 
     grn = nx.from_pandas_edgelist(
-        df=interaction_graph,
+        df=influence_graph,
         source="source",
         target="target",
         edge_attr=True,

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/boolpy/plotting/__init__.py

@@ -8,7 +8,7 @@ helpers for objects related to logical modelling, including Boolean
 networks, influence graphs and ensemble representations.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._styles import (
     count_node_style,
@@ -23,5 +23,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/databases/__init__.py

@@ -14,7 +14,7 @@ omnipath
     Access to regulatory and interaction prior knowledge databases.
 """
 
-from typing import List
+from typing import List as _List
 
 from . import ncbi, omnipath
 
@@ -24,5 +24,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/databases/ncbi/__init__.py

@@ -8,22 +8,20 @@ standardising gene identifiers and handling ambiguous nomenclature
 across heterogeneous biological resources.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._genesyn import (
     GeneSynonyms,
     InputIdentifierType,
     OutputIdentifierType,
-    support_legacy_gene_synonyms_args,
 )
 
 __all__ = [
     "InputIdentifierType",
     "OutputIdentifierType",
     "GeneSynonyms",
-    "support_legacy_gene_synonyms_args",
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/databases/omnipath/__init__.py

@@ -8,7 +8,7 @@ constructing biological interaction priors and regulatory domains
 from OmniPath-related resources such as CollecTRI and DoRothEA.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._collectri import load_collectri_grn
 from ._dorothea import load_dorothea_grn
@@ -19,5 +19,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/grntools/__init__.py

@@ -3,19 +3,19 @@
 """
 Deprecated GRN namespace.
 
-This module re-exports interaction-graph utilities for backward
+This module re-exports influence-graph utilities for backward
 compatibility. Prefer `bonesistools.bpy.ig` for new code.
 """
 
-from typing import List
+from typing import List as _List
 
-from ..boolpy.interaction_graph import (
+from ..boolpy.influence_graph import (
     InfluenceGraph,
     InteractionScore,
     infer_signed_interactions,
     infer_signed_interactions_from_walks,
     interaction_scores_from_walks,
-    read_interaction_graph,
+    read_influence_graph,
     walks_from,
 )
 
@@ -25,10 +25,10 @@ __all__ = [
     "infer_signed_interactions",
     "infer_signed_interactions_from_walks",
     "interaction_scores_from_walks",
-    "read_interaction_graph",
+    "read_influence_graph",
     "walks_from",
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/__init__.py

@@ -20,7 +20,7 @@ datasets
 """
 
 import sys as _sys
-from typing import List
+from typing import List as _List
 
 from . import _typing as typing
 from . import datasets
@@ -44,5 +44,5 @@ _sys.modules.update(
 )
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/datasets/__init__.py

@@ -9,23 +9,25 @@ tests and tutorials.
 
 from __future__ import annotations
 
-import sys
-from typing import List
+import sys as _sys
+from typing import List as _List
 
-if sys.version_info >= (3, 9):
-    from importlib.resources import files
+if _sys.version_info >= (3, 9):
+    from importlib.resources import files as _files
 else:
-    from importlib_resources import files
+    from importlib_resources import files as _files
 
-import anndata as ad
-from anndata import AnnData
+import anndata as _ad
+from anndata import AnnData as _AnnData
+
+del annotations
 
 __all__ = [
     "nestorowa",
 ]
 
 
-def nestorowa() -> AnnData:
+def nestorowa() -> _AnnData:
     """
     Load the Nestorowa et al. hematopoietic stem and progenitor cell dataset.
     The dataset is a lightweight version intended for examples, testing and tutorials.
@@ -45,10 +47,10 @@ def nestorowa() -> AnnData:
         Blood 128(8): e20-e31
     """
 
-    path = files(__package__) / "nestorowa_hvg.h5ad"
+    path = _files(__package__) / "nestorowa_hvg.h5ad"
 
-    return ad.read_h5ad(str(path))
+    return _ad.read_h5ad(str(path))
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/plotting/__init__.py

@@ -7,7 +7,7 @@ The `pl` namespace provides embedding, density, boxplot and graph plotting
 helpers, along with colour palettes and Matplotlib styling utilities.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._boxplot import boxplot
 from ._colors import (
@@ -46,5 +46,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

bonesistools-1.2.2/src/bonesistools/sctools/plotting/_typing.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+
+from typing import Tuple as _Tuple
+
+RGB = _Tuple[int, int, int]

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/preprocessing/__init__.py

@@ -9,7 +9,8 @@ related AnnData objects.
 """
 
 import warnings as _warnings
-from typing import Any, List
+from typing import Any as _Any
+from typing import List as _List
 
 from ..tools import regress_out as _regress_out
 from ._genename import (
@@ -42,7 +43,7 @@ __all__ = [
 ]
 
 
-def regress_out(*args: Any, **kwargs: Any) -> Any:
+def regress_out(*args: _Any, **kwargs: _Any) -> _Any:
     """
     Deprecated. Regress out unwanted sources of variation.
 
@@ -59,5 +60,5 @@ def regress_out(*args: Any, **kwargs: Any) -> Any:
     return _regress_out(*args, **kwargs)
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/preprocessing/_genename.py

@@ -13,8 +13,8 @@ from ...databases.ncbi import (
     GeneSynonyms,
     InputIdentifierType,
     OutputIdentifierType,
-    support_legacy_gene_synonyms_args,
 )
+from ...databases.ncbi._genesyn import support_legacy_gene_synonyms_args
 from .._typing import (
     Axis,
     ScData,

{bonesistools-1.2.1 → bonesistools-1.2.2}/src/bonesistools/sctools/tools/__init__.py

@@ -8,7 +8,7 @@ distance calculations, marker statistics, lightweight export functions and
 feature classification utilities.
 """
 
-from typing import List
+from typing import List as _List
 
 from ._classification import mitochondrial_genes, ribosomal_genes
 from ._conversion import anndata_to_dataframe
@@ -58,5 +58,5 @@ __all__ = [
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

bonesistools-1.2.1/tests/bpy/test_interaction_graph_parser.py → bonesistools-1.2.2/tests/bpy/test_influence_graph_parser.py

@@ -6,10 +6,10 @@ import networkx as nx
 import pytest
 
 import bonesistools as bt
-from bonesistools.boolpy.interaction_graph import _parser
+from bonesistools.boolpy.influence_graph import _parser
 
 
-def test_read_interaction_graph_keeps_edge_attributes(tmp_path):
+def test_read_influence_graph_keeps_edge_attributes(tmp_path):
     infile = tmp_path / "graph.csv"
     infile.write_text(
         "source,target,sign,confidence\n"
@@ -18,7 +18,7 @@ def test_read_interaction_graph_keeps_edge_attributes(tmp_path):
         "C,A,,unknown\n",
     )
 
-    graph = bt.bpy.ig.read_interaction_graph(infile)
+    graph = bt.bpy.ig.read_influence_graph(infile)
 
     assert isinstance(graph, nx.MultiDiGraph)
     assert set(graph.nodes) == {"A", "B", "C"}
@@ -28,45 +28,45 @@ def test_read_interaction_graph_keeps_edge_attributes(tmp_path):
     assert math.isnan(graph["C"]["A"][0]["sign"])
 
 
-def test_read_interaction_graph_supports_custom_separator(tmp_path):
+def test_read_influence_graph_supports_custom_separator(tmp_path):
     infile = tmp_path / "graph.tsv"
     infile.write_text(
         "source\ttarget\tsign\n" "A\tB\t1\n",
     )
 
-    graph = bt.bpy.ig.read_interaction_graph(infile, sep="\t")
+    graph = bt.bpy.ig.read_influence_graph(infile, sep="\t")
 
     assert list(graph.edges(data=True)) == [("A", "B", {"sign": 1.0})]
 
 
-def test_read_interaction_graph_validates_file_columns_and_signs(tmp_path):
+def test_read_influence_graph_validates_file_columns_and_signs(tmp_path):
     missing = tmp_path / "missing.csv"
 
     with pytest.raises(FileNotFoundError):
-        bt.bpy.ig.read_interaction_graph(missing)
+        bt.bpy.ig.read_influence_graph(missing)
 
     missing_column = tmp_path / "missing_column.csv"
     missing_column.write_text("source,target\nA,B\n")
 
     with pytest.raises(ValueError, match="missing columns"):
-        bt.bpy.ig.read_interaction_graph(missing_column)
+        bt.bpy.ig.read_influence_graph(missing_column)
 
     invalid_sign = tmp_path / "invalid_sign.csv"
     invalid_sign.write_text("source,target,sign\nA,B,0\n")
 
     with pytest.raises(ValueError, match="unsupported sign values"):
-        bt.bpy.ig.read_interaction_graph(invalid_sign)
+        bt.bpy.ig.read_influence_graph(invalid_sign)
 
 
-def test_read_interaction_graph_rejects_invalid_genesyn(tmp_path):
+def test_read_influence_graph_rejects_invalid_genesyn(tmp_path):
     infile = tmp_path / "graph.csv"
     infile.write_text("source,target,sign\nA,B,1\n")
 
     with pytest.raises(TypeError, match="unsupported argument type for 'genesyn'"):
-        bt.bpy.ig.read_interaction_graph(infile, genesyn=object())
+        bt.bpy.ig.read_influence_graph(infile, genesyn=object())
 
 
-def test_read_interaction_graph_applies_genesyn(monkeypatch, tmp_path):
+def test_read_influence_graph_applies_genesyn(monkeypatch, tmp_path):
     class FakeGeneSynonyms:
         def __init__(self):
             self.calls = []
@@ -80,7 +80,7 @@ def test_read_interaction_graph_applies_genesyn(monkeypatch, tmp_path):
 
     monkeypatch.setattr(_parser, "GeneSynonyms", FakeGeneSynonyms)
 
-    graph = bt.bpy.ig.read_interaction_graph(
+    graph = bt.bpy.ig.read_influence_graph(
         infile,
         genesyn=genesyn,
         input_identifier_type="gene_id",

bonesistools-1.2.1/tests/bpy/test_interaction_graph_scoring.py → bonesistools-1.2.2/tests/bpy/test_influence_graph_scoring.py

@@ -4,10 +4,10 @@ import networkx as nx
 import pytest
 
 import bonesistools as bt
-from bonesistools.boolpy.interaction_graph import _scoring
+from bonesistools.boolpy.influence_graph import _scoring
 
 
-def test_interaction_graph_scoring_is_exported_from_public_namespace():
+def test_influence_graph_scoring_is_exported_from_public_namespace():
     score = bt.bpy.ig.InteractionScore(score=0.0, total_weight=0.0, path_number=0)
 
     assert score.normalized_score == 0.0

bonesistools-1.2.1/src/bonesistools/sctools/plotting/_typing.py

@@ -1,5 +0,0 @@
-#!/usr/bin/env python
-
-from typing import Tuple
-
-RGB = Tuple[int, int, int]