bonesistools 1.2.3__tar.gz → 1.2.4__tar.gz

{bonesistools-1.2.3 → bonesistools-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bonesistools
-Version: 1.2.3
+Version: 1.2.4
 Summary: Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework
 Project-URL: Repository, https://github.com/bnediction/bonesistools
 Author: Théo Roncalli
@@ -627,7 +627,7 @@ Submodules:
 
 - plotting: `bt.sct.pl`
   - embedding, density, composition and graph visualizations
-  - boxplot utilities
+  - distribution utilities
 
 - datasets: `bt.sct.datasets`
   - packaged reference datasets
@@ -694,7 +694,7 @@ Submodules:
 Example:
 
 ```python
-genesyn = bt.dbs.ncbi.GeneSynonyms()
+genesyn = bt.dbs.ncbi.genesyn()
 
 grn = bt.dbs.omnipath.collectri(
     organism="mouse",

{bonesistools-1.2.3 → bonesistools-1.2.4}/README.md

@@ -49,7 +49,7 @@ Submodules:
 
 - plotting: `bt.sct.pl`
   - embedding, density, composition and graph visualizations
-  - boxplot utilities
+  - distribution utilities
 
 - datasets: `bt.sct.datasets`
   - packaged reference datasets
@@ -116,7 +116,7 @@ Submodules:
 Example:
 
 ```python
-genesyn = bt.dbs.ncbi.GeneSynonyms()
+genesyn = bt.dbs.ncbi.genesyn()
 
 grn = bt.dbs.omnipath.collectri(
     organism="mouse",

{bonesistools-1.2.3 → bonesistools-1.2.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "bonesistools"
 description = "Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework"
-version = "1.2.3"
+version = "1.2.4"
 license = {file = "LICENSE"}
 credits = ["BNeDiction", "PEPR Santé Numérique 2030"]
 authors = [

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/databases/ncbi/__init__.py

@@ -10,10 +10,11 @@ across heterogeneous biological resources.
 
 from typing import List as _List
 
-from ._genesyn import GeneSynonyms
+from ._genesyn import GeneSynonyms, genesyn
 
 __all__ = [
     "GeneSynonyms",
+    "genesyn",
 ]
 
 

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/databases/ncbi/_genesyn.py

@@ -45,6 +45,7 @@ from ._typing import (
 
 InteractionList = Sequence[Tuple[str, str, Dict[str, int]]]
 GeneInfoVersion = Union[Literal["bundled", "latest"], str, Path]
+_SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING = False
 
 ORGANISMS = Literal[
     "all archaea bacteria",
@@ -306,14 +307,14 @@ class GeneSynonyms:
     --------
     Convert a list of gene identifiers through the callable interface:
 
-    >>> genesyn = GeneSynonyms(organism="mouse")
-    >>> genesyn(["Trp53", "Myc"])
+    >>> gene_synonyms = genesyn(organism="mouse")
+    >>> gene_synonyms(["Trp53", "Myc"])
     ['Trp53', 'Myc']
 
     Convert an interaction list while preserving edge attributes:
 
     >>> interactions = [("Trp53", "Myc", {"sign": 1})]
-    >>> genesyn(interactions)
+    >>> gene_synonyms(interactions)
     [('Trp53', 'Myc', {'sign': 1})]
 
     Parameters
@@ -370,6 +371,15 @@ class GeneSynonyms:
         show_warnings: bool = False,
     ) -> None:
 
+        if not _SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING:
+            warnings.warn(
+                "`bt.dbs.ncbi.GeneSynonyms()` is deprecated as a constructor "
+                "entry point and will be removed in 2.0.0; use "
+                "`bt.dbs.ncbi.genesyn()` instead.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+
         organism = organism.lower().replace("-", " ")
 
         if organism not in get_args(ORGANISMS):
@@ -1079,12 +1089,12 @@ class GeneSynonyms:
 
         Examples
         --------
-        >>> genesyn = GeneSynonyms(organism="mouse")
-        >>> genesyn.contains("Trp53")
+        >>> gene_synonyms = genesyn(organism="mouse")
+        >>> gene_synonyms.contains("Trp53")
         [True]
-        >>> genesyn.contains("Trp53", "not-a-gene")
+        >>> gene_synonyms.contains("Trp53", "not-a-gene")
         [True, False]
-        >>> genesyn.contains("22059", identifier_type="gene_id")
+        >>> gene_synonyms.contains("22059", identifier_type="gene_id")
         [True]
 
         Parameters
@@ -1136,10 +1146,10 @@ class GeneSynonyms:
 
         Examples
         --------
-        >>> genesyn = GeneSynonyms(organism="mouse")
-        >>> genesyn.find("Trp53", "not-a-gene", "Myc")
+        >>> gene_synonyms = genesyn(organism="mouse")
+        >>> gene_synonyms.find("Trp53", "not-a-gene", "Myc")
         ['Trp53', 'Myc']
-        >>> genesyn.find("22059", "bad-id", identifier_type="gene_id")
+        >>> gene_synonyms.find("22059", "bad-id", identifier_type="gene_id")
         ['22059']
 
         Parameters
@@ -1522,7 +1532,7 @@ class GeneSynonyms:
         awk_script = (
             'BEGIN {OFS="\\t"; print "gene_id", "official_name", "ncbi_name", '
             '"synonyms", "dbXrefs", "gene_type"} '
-            'NR>1 {print $2, $11, $3, $5, $6, $10}'
+            "NR>1 {print $2, $11, $3, $5, $6, $10}"
         )
         if str(outfile).endswith(".gz"):
             cmd = (
@@ -1810,3 +1820,41 @@ class GeneSynonyms:
             path.unlink()
         except FileNotFoundError:
             pass
+
+
+def genesyn(
+    organism: str = "mouse",
+    version: GeneInfoVersion = "bundled",
+    show_warnings: bool = False,
+) -> GeneSynonyms:
+    """
+    Create a GeneSynonyms converter.
+
+    Parameters
+    ----------
+    organism: str (default: "mouse")
+        Common name of the organism of interest.
+    version: "bundled", "latest", str path or Path (default: "bundled")
+        NCBI gene_info version to load.
+    show_warnings: bool (default: False)
+        If True, warn when a requested gene identifier has no correspondence.
+
+    Returns
+    -------
+    GeneSynonyms
+        Converter for gene identifier resolution, conversion and
+        standardisation.
+    """
+
+    global _SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING
+
+    previous = _SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING
+    _SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING = True
+    try:
+        return GeneSynonyms(
+            organism=organism,
+            version=version,
+            show_warnings=show_warnings,
+        )
+    finally:
+        _SUPPRESS_GENE_SYNONYMS_CONSTRUCTOR_WARNING = previous

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/sctools/plotting/__init__.py

@@ -3,14 +3,14 @@
 """
 Plotting utilities for single-cell annotated data.
 
-The `pl` namespace provides embedding, density, composition, boxplot and graph
-plotting helpers, along with colour palettes and Matplotlib styling utilities.
+The `pl` namespace provides embedding, density, composition, distribution and
+graph plotting helpers, along with colour palettes and Matplotlib styling
+utilities.
 """
 
 from typing import List as _List
 
 from ._barplot import composition
-from ._boxplot import boxplot
 from ._colors import (
     COLORS,
     LIGHT_COLORS,
@@ -23,18 +23,21 @@ from ._colors import (
     rgb2hex,
 )
 from ._density import cdf, density, ecdf_plot, kde_plot
+from ._distribution import boxplot, distribution
 from ._figure import set_default_axis, set_default_params
-from ._graph import add_graph, draw_paga, paga, trajectory
+from ._graph import add_graph, draw_paga, graph_overlay, paga, trajectory
 from ._scatterplot import embedding, embedding_plot
 
 __all__ = [
     "embedding",
     "embedding_plot",
+    "distribution",
     "boxplot",
     "composition",
     "density",
     "cdf",
     "trajectory",
+    "graph_overlay",
     "add_graph",
     "paga",
     "draw_paga",

bonesistools-1.2.3/src/bonesistools/sctools/plotting/_boxplot.py → bonesistools-1.2.4/src/bonesistools/sctools/plotting/_distribution.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import warnings
 from collections.abc import Mapping as MappingABC
 from pathlib import Path
 from typing import (
@@ -151,7 +152,7 @@ def __add_points(
 
 
 @anndata_or_mudata_checker
-def boxplot(
+def distribution(
     scdata: ScData,  # type: ignore
     obs: str,
     groupby: Optional[str] = None,
@@ -179,7 +180,7 @@ def boxplot(
     **kwargs: Any,
 ) -> Optional[Tuple[Figure, Axes, BoxplotReturn]]:
     """
-    Draw a boxplot for an observation-level variable.
+    Draw a distribution plot for an observation-level variable.
 
     Parameters
     ----------
@@ -498,3 +499,16 @@ def boxplot(
         return None
     else:
         return fig, ax, bps
+
+
+def boxplot(*args: Any, **kwargs: Any) -> Optional[Tuple[Figure, Axes, BoxplotReturn]]:
+    """
+    Deprecated alias for `distribution`.
+    """
+
+    warnings.warn(
+        "`bt.sct.pl.boxplot` is deprecated; use " "`bt.sct.pl.distribution` instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return distribution(*args, **kwargs)

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/sctools/plotting/_graph.py

@@ -28,13 +28,13 @@ from matplotlib.lines import Line2D
 from mpl_toolkits.mplot3d import art3d
 
 from .._typing import ScData, anndata_checker, anndata_or_mudata_checker
-from ..tools import get_paga_graph
+from ..tools import extract_paga_graph
 from ._colors import black
 from ._scatterplot import Colors, embedding
 
 
 @anndata_or_mudata_checker
-def add_graph(
+def graph_overlay(
     scdata: ScData,  # type: ignore
     graph_key: str = "epg",
     ax: Optional[Axes] = None,
@@ -271,7 +271,7 @@ def trajectory(
     )
     fig, drawn_ax = cast(Tuple[Figure, Axes], result)
 
-    add_graph(
+    graph_overlay(
         scdata,
         graph_key=graph_key,
         ax=drawn_ax,
@@ -350,7 +350,7 @@ def paga(
     if ax is None:
         ax = plt.gca()
 
-    paga_graph = get_paga_graph(
+    paga_graph = extract_paga_graph(
         adata=adata, obs=obs, use_rep=use_rep, edges=edges, threshold=threshold
     )
     barycenters = {
@@ -385,6 +385,20 @@ def paga(
     return ax
 
 
+def add_graph(*args: Any, **kwargs: Any) -> Axes:
+    """
+    Deprecated alias for `graph_overlay`.
+    """
+
+    warnings.warn(
+        "`bt.sct.pl.add_graph` is deprecated; use "
+        "`bt.sct.pl.graph_overlay` instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return graph_overlay(*args, **kwargs)
+
+
 def draw_paga(*args: Any, **kwargs: Any) -> Union[Axes, None]:
     """
     Deprecated alias for `paga()`.

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/sctools/plotting/_scatterplot.py

@@ -650,11 +650,11 @@ def embedding(
         )
 
     if draw_deprecated_graph or draw_deprecated_graph_labels:
-        from ._graph import add_graph
+        from ._graph import graph_overlay
 
         _kwargs = {"linewidth": 2.5, "zorder": 10}
         _kwargs.update({} if "graph" not in kwargs else kwargs["graph"])
-        add_graph(
+        graph_overlay(
             scdata,
             ax=ax,
             n_components=component_number,

{bonesistools-1.2.3 → bonesistools-1.2.4}/src/bonesistools/sctools/preprocessing/__init__.py

@@ -13,21 +13,26 @@ from typing import Any as _Any
 from typing import List as _List
 
 from ..tools import regress_out as _regress_out
+from ._duplicates import (
+    merge_duplicate_vars,
+    var_names_merge_duplicates,
+)
 from ._genename import (
     convert_gene_identifiers,
     standardize_gene_identifiers,
-    var_names_merge_duplicates,
 )
 from ._simple import (
     filter_obs,
     filter_var,
-    merge,
     sort_anndata,
 )
 from ._transfer import (
+    merge,
     transfer_layer,
     transfer_obs_its,
     transfer_obs_sti,
+    transfer_obs_to_integrated,
+    transfer_obs_to_specific,
 )
 
 __all__ = [
@@ -36,10 +41,13 @@ __all__ = [
     "merge",
     "sort_anndata",
     "transfer_layer",
+    "transfer_obs_to_integrated",
+    "transfer_obs_to_specific",
     "transfer_obs_sti",
     "transfer_obs_its",
     "convert_gene_identifiers",
     "standardize_gene_identifiers",
+    "merge_duplicate_vars",
     "var_names_merge_duplicates",
     "regress_out",
 ]