cellestial 0.49.2__tar.gz → 0.49.3__tar.gz

{cellestial-0.49.2 → cellestial-0.49.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellestial
-Version: 0.49.2
+Version: 0.49.3
 Summary: Interactive single-cell and spatial omics visualization library
 License-Expression: Apache-2.0
 License-File: LICENSE
@@ -44,12 +44,10 @@ Description-Content-Type: text/markdown
 [![Powered by Polars](https://img.shields.io/badge/Powered%20by-Polars-377eb8?logo=polars&logoColor=white)](https://www.pola.rs/)
 [![Graphics: Lets-Plot](https://img.shields.io/badge/Graphics-Lets--Plot-FF00CC?logo=jetbrains&logoColor=white)](https://lets-plot.org/)
 
-<img align="right" src="assets/cellestial.svg" alt="Cellestial Logo" width="300">
+<img align="left" src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/cellestial.svg" alt="Cellestial Logo" width="280">
 
 The __Grammar of Graphics__ for single-cell omics.
 
-## Introduction
-
 __Cellestial__ is an interactive and a highly customizable _Single-Cell_ & _Spatial_ omics data visualization library. Built on top [Lets-Plot](https://lets-plot.org/), it offers a ggplot-like layered and modular approach offering __high customizability__ and __publication-ready figures__.
 
 Cellestial is highly integrated with scverse's [AnnData](https://github.com/scverse/anndata) with room for integration with any upcoming single-cell omics data type in the Python single-cell omics ecosystem.
@@ -90,7 +88,7 @@ cl.umap(
 ```
 
 <p align="center">
-  <img src="assets/first-umap.svg" alt="UMAP coloured by cell type" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/first-umap.svg" alt="UMAP coloured by cell type" width="600">
 </p>
 
 ## Examples
@@ -120,7 +118,7 @@ gggrid(
 </details>
 
 <p align="center">
-  <img src="assets/spatial-categorical.svg" alt="Spatial categorical overlay" width="800">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/spatial-categorical.svg" alt="Spatial categorical overlay" width="800">
 </p>
 
 ### Dimensionality reduction with layers
@@ -157,7 +155,7 @@ gggrid([outlined, streamed])
 </details>
 
 <p align="center">
-  <img src="assets/dimensionality-layers.svg" alt="UMAP with cluster outlines and velocity stream" width="800">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/dimensionality-layers.svg" alt="UMAP with cluster outlines and velocity stream" width="800">
 </p>
 
 ### Marker genes
@@ -194,7 +192,7 @@ cl.heatmap(
 </details>
 
 <p align="center">
-  <img src="assets/heatmap.svg" alt="Marker gene heatmap" width="700">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/heatmap.svg" alt="Marker gene heatmap" width="700">
 </p>
 
 ### Statistical comparisons
@@ -226,7 +224,7 @@ cl.boxplot(
 </details>
 
 <p align="center">
-  <img src="assets/boxplot-bracket.svg" alt="Boxplot with significance brackets" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/boxplot-bracket.svg" alt="Boxplot with significance brackets" width="600">
 </p>
 
 ### Ridge plots
@@ -248,7 +246,7 @@ cl.ridge(
 </details>
 
 <p align="center">
-  <img src="assets/ridge.svg" alt="Ridge plot of B2M expression" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/ridge.svg" alt="Ridge plot of B2M expression" width="600">
 </p>
 
 ## Migrating from Scanpy

{cellestial-0.49.2 → cellestial-0.49.3}/README.md

@@ -7,12 +7,10 @@
 [![Powered by Polars](https://img.shields.io/badge/Powered%20by-Polars-377eb8?logo=polars&logoColor=white)](https://www.pola.rs/)
 [![Graphics: Lets-Plot](https://img.shields.io/badge/Graphics-Lets--Plot-FF00CC?logo=jetbrains&logoColor=white)](https://lets-plot.org/)
 
-<img align="right" src="assets/cellestial.svg" alt="Cellestial Logo" width="300">
+<img align="left" src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/cellestial.svg" alt="Cellestial Logo" width="280">
 
 The __Grammar of Graphics__ for single-cell omics.
 
-## Introduction
-
 __Cellestial__ is an interactive and a highly customizable _Single-Cell_ & _Spatial_ omics data visualization library. Built on top [Lets-Plot](https://lets-plot.org/), it offers a ggplot-like layered and modular approach offering __high customizability__ and __publication-ready figures__.
 
 Cellestial is highly integrated with scverse's [AnnData](https://github.com/scverse/anndata) with room for integration with any upcoming single-cell omics data type in the Python single-cell omics ecosystem.
@@ -53,7 +51,7 @@ cl.umap(
 ```
 
 <p align="center">
-  <img src="assets/first-umap.svg" alt="UMAP coloured by cell type" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/first-umap.svg" alt="UMAP coloured by cell type" width="600">
 </p>
 
 ## Examples
@@ -83,7 +81,7 @@ gggrid(
 </details>
 
 <p align="center">
-  <img src="assets/spatial-categorical.svg" alt="Spatial categorical overlay" width="800">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/spatial-categorical.svg" alt="Spatial categorical overlay" width="800">
 </p>
 
 ### Dimensionality reduction with layers
@@ -120,7 +118,7 @@ gggrid([outlined, streamed])
 </details>
 
 <p align="center">
-  <img src="assets/dimensionality-layers.svg" alt="UMAP with cluster outlines and velocity stream" width="800">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/dimensionality-layers.svg" alt="UMAP with cluster outlines and velocity stream" width="800">
 </p>
 
 ### Marker genes
@@ -157,7 +155,7 @@ cl.heatmap(
 </details>
 
 <p align="center">
-  <img src="assets/heatmap.svg" alt="Marker gene heatmap" width="700">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/heatmap.svg" alt="Marker gene heatmap" width="700">
 </p>
 
 ### Statistical comparisons
@@ -189,7 +187,7 @@ cl.boxplot(
 </details>
 
 <p align="center">
-  <img src="assets/boxplot-bracket.svg" alt="Boxplot with significance brackets" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/boxplot-bracket.svg" alt="Boxplot with significance brackets" width="600">
 </p>
 
 ### Ridge plots
@@ -211,7 +209,7 @@ cl.ridge(
 </details>
 
 <p align="center">
-  <img src="assets/ridge.svg" alt="Ridge plot of B2M expression" width="600">
+  <img src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/ridge.svg" alt="Ridge plot of B2M expression" width="600">
 </p>
 
 ## Migrating from Scanpy

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/layers/arrow.py

@@ -95,9 +95,7 @@ def _axis_arrow_layers(
     tip_y = (yend - y0) * _TIP_FRACTION
 
     # semi-square L (stopping short of both tips), drawn as one connected path
-    path_frame = pl.DataFrame(
-        {"x": [xend - tip_x, x0, x0], "y": [y0, y0, yend - tip_y]}
-    )
+    path_frame = pl.DataFrame({"x": [xend - tip_x, x0, x0], "y": [y0, y0, yend - tip_y]})
 
     layers = geom_path(
         data=path_frame,

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/single/core/subdimensionals.py

@@ -14,6 +14,7 @@ if TYPE_CHECKING:
     from anndata import AnnData
     from lets_plot.plot.subplots import SupPlotsSpec
 
+
 def dimensionals(
     data: AnnData,
     keys: Sequence[str],
@@ -281,6 +282,7 @@ def dimensionals(
 
     return scttrs
 
+
 def umaps(
     data: AnnData,
     keys: Sequence[str],
@@ -543,6 +545,7 @@ def umaps(
 
     return scttrs
 
+
 def tsnes(
     data: AnnData,
     keys: Sequence[str],
@@ -803,6 +806,7 @@ def tsnes(
 
     return scttrs
 
+
 def pcas(
     data: AnnData,
     keys: Sequence[str],
@@ -1064,6 +1068,7 @@ def pcas(
 
     return scttrs
 
+
 def expressions(
     data: AnnData,
     keys: Sequence[str],

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/single/core/utilities.py

@@ -34,7 +34,6 @@ if TYPE_CHECKING:
     from lets_plot.plot.core import PlotSpec
 
 
-
 def _distribution(
     data: AnnData,
     key: str | Sequence[str],
@@ -218,4 +217,3 @@ def _distribution(
         dst += ggtb(size_zoomin=-1)
 
     return dst
-

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/single/differential/utilities.py

@@ -166,7 +166,6 @@ def _build_volcano_frame(
     return frame
 
 
-
 def _build_markers_frame(
     data: AnnData,
     *,
@@ -306,4 +305,3 @@ def _build_markers_frame(
 
     msg = f"Unsupported data type: `{type(data)}`"
     raise UnsupportedDataTypeError(msg)
-

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/spatial/utilities.py

@@ -358,10 +358,7 @@ def _spatial_components(
         scale_factor = scale_factors.get(scalef_key)
         if scale_factor is None:
             if image:
-                _warn(
-                    f"Scale factor `{scalef_key}` missing; "
-                    "spots may not align with the image."
-                )
+                _warn(f"Scale factor `{scalef_key}` missing; spots may not align with the image.")
             scale_factor = 1.0
         spot_coordinates = data.obsm[spatial_key] * scale_factor
 
@@ -376,4 +373,3 @@ def _spatial_components(
 
     msg = f"Unsupported data type: `{type(data)}`"
     raise UnsupportedDataTypeError(msg)
-

{cellestial-0.49.2 → cellestial-0.49.3}/cellestial/util/utilities.py

@@ -287,6 +287,7 @@ def _fill_gradient(
             midpoint=mid_value,
         )
 
+
 # cache to avoid recomputing for every plot in a grid...
 @lru_cache(maxsize=32)
 def _grid_places(total: int, ncol: int | None) -> tuple[frozenset[int], frozenset[int]]:
@@ -588,8 +589,7 @@ def _resolve_embedding_key(
             return key.upper()
 
     prefix_matches = [
-        key for key in candidates
-        if any(key.upper().startswith(t) for t in search_targets)
+        key for key in candidates if any(key.upper().startswith(t) for t in search_targets)
     ]
     if not prefix_matches:
         msg = (

{cellestial-0.49.2 → cellestial-0.49.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cellestial"
-version = "0.49.2"
+version = "0.49.3"
 description = "Interactive single-cell and spatial omics visualization library"
 authors = [
     { name = "Zaf4", email = "zafermolbio@gmail.com" },