cellestial 0.58.1__tar.gz → 0.58.2__tar.gz

{cellestial-0.58.1 → cellestial-0.58.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellestial
-Version: 0.58.1
+Version: 0.58.2
 Summary: Interactive single-cell and spatial omics visualization library
 License-Expression: Apache-2.0
 License-File: LICENSE
@@ -46,6 +46,7 @@ Description-Content-Type: text/markdown
 [![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-ff0000)](https://opensource.org/licenses/Apache-2.0)
 [![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/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.21710312.svg)](https://doi.org/10.5281/zenodo.21710312)
 
 <img align="left" src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/cellestial.anim.svg" alt="Cellestial Logo" width="280">
 
@@ -270,6 +271,22 @@ See the [migration guide](https://cellestial.datavil.org/migrating_from_scanpy.h
 - [API reference](https://cellestial.datavil.org/API.html) — every function.
 - [Migrating from Scanpy](https://cellestial.datavil.org/migrating_from_scanpy.html).
 
+## Citation
+
+If you use Cellestial, please cite:
+
+```bibtex
+@misc{https://doi.org/10.5281/zenodo.21710312,
+  doi = {10.5281/ZENODO.21710312},
+  url = {https://zenodo.org/doi/10.5281/zenodo.21710312},
+  author = {Kosar, Zafer},
+  title = {Cellestial: A grammar of graphics for single-cell omics},
+  publisher = {Zenodo},
+  year = {2026},
+  copyright = {Apache License 2.0}
+}
+```
+
 ## License
 
 Apache 2.0. See [LICENSE](LICENSE).

{cellestial-0.58.1 → cellestial-0.58.2}/README.md

@@ -6,6 +6,7 @@
 [![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-ff0000)](https://opensource.org/licenses/Apache-2.0)
 [![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/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.21710312.svg)](https://doi.org/10.5281/zenodo.21710312)
 
 <img align="left" src="https://raw.githubusercontent.com/datavil/cellestial/master/assets/cellestial.anim.svg" alt="Cellestial Logo" width="280">
 
@@ -230,6 +231,22 @@ See the [migration guide](https://cellestial.datavil.org/migrating_from_scanpy.h
 - [API reference](https://cellestial.datavil.org/API.html) — every function.
 - [Migrating from Scanpy](https://cellestial.datavil.org/migrating_from_scanpy.html).
 
+## Citation
+
+If you use Cellestial, please cite:
+
+```bibtex
+@misc{https://doi.org/10.5281/zenodo.21710312,
+  doi = {10.5281/ZENODO.21710312},
+  url = {https://zenodo.org/doi/10.5281/zenodo.21710312},
+  author = {Kosar, Zafer},
+  title = {Cellestial: A grammar of graphics for single-cell omics},
+  publisher = {Zenodo},
+  year = {2026},
+  copyright = {Apache License 2.0}
+}
+```
+
 ## License
 
 Apache 2.0. See [LICENSE](LICENSE).

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/datasets/datasets.py

@@ -13,6 +13,7 @@ _UUID_PATTERN = re.compile(
 )
 _DOWNLOAD_TIMEOUT_SECONDS = 300
 
+
 def _resolve_cache_file(
     cache_directory: str | Path | PathLike,
     filename: str,
@@ -198,7 +199,7 @@ def from_url(
     # download cannot poison the cache.
     partial_file = cache_file.with_name(cache_file.name + ".part")
 
-    with urlopen(url, timeout = _DOWNLOAD_TIMEOUT_SECONDS) as response:
+    with urlopen(url, timeout=_DOWNLOAD_TIMEOUT_SECONDS) as response:
         total_size = int(response.headers.get("Content-Length", 0))
         progress_bar = tqdm(
             total=total_size, unit="iB", unit_scale=True, desc=f"Downloading {filename}"

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/layers/arrow.py

@@ -72,10 +72,20 @@ def _axis_arrow_layers(
     """
     arrow_kwargs = arrow_kwargs or {}
 
-    x_min = frame[x].min()
-    x_max = frame[x].max()
-    y_min = frame[y].min()
-    y_max = frame[y].max()
+    bounds = frame.select(
+        pl.col(x).min().alias("x_min"),
+        pl.col(x).max().alias("x_max"),
+        pl.col(y).min().alias("y_min"),
+        pl.col(y).max().alias("y_max"),
+    ).row(0, named=True)
+    if any(value is None for value in bounds.values()):
+        msg = "Arrow axes require at least one valid coordinate pair."
+        raise ValueError(msg)
+
+    x_min = bounds["x_min"]
+    x_max = bounds["x_max"]
+    y_min = bounds["y_min"]
+    y_max = bounds["y_max"]
 
     # find total difference between the max and min for both axis
     x_diff = x_max - x_min

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/layers/ondata_legend.py

@@ -6,7 +6,7 @@ import polars as pl
 from lets_plot import aes, geom_label, geom_label_repel, geom_text, geom_text_repel, theme
 
 from cellestial.layers._deferred import DeferredLayer
-from cellestial.util import get_mapping, retrieve
+from cellestial.util import _drop_nonfinite_rows, get_mapping, retrieve
 from cellestial.util.errors import MissingAestheticError
 
 if TYPE_CHECKING:
@@ -22,7 +22,7 @@ def _compute_label_positions(
     group_by: str,
 ) -> DataFrame:
     """Aggregate per-group median coordinates for `geom_text` placement."""
-    frame = frame.filter(pl.col(group_by).is_not_null())
+    frame = _drop_nonfinite_rows(frame, [x, y]).filter(pl.col(group_by).is_not_null())
     return frame.group_by(group_by).agg(
         pl.col(x).median(),
         pl.col(y).median(),

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/layers/outline.py

@@ -8,7 +8,7 @@ from lets_plot import aes, geom_path
 from scipy.stats import gaussian_kde
 
 from cellestial.layers._deferred import DeferredLayer
-from cellestial.util import get_mapping
+from cellestial.util import _drop_nonfinite_rows, get_mapping
 from cellestial.util.errors import MissingAestheticError
 
 if TYPE_CHECKING:
@@ -50,7 +50,8 @@ def _get_density_boundaries(
     boundaries = []
     for group in groups:
         group_label = "+".join(group) if len(group) > 1 else group[0]
-        points = frame.filter(pl.col(group_by).is_in(group)).select([x, y]).to_numpy()
+        group_frame = frame.filter(pl.col(group_by).is_in(group))
+        points = _drop_nonfinite_rows(group_frame, [x, y]).select([x, y]).to_numpy()
         if len(points) < 5:
             continue
 

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/layers/stream.py

@@ -12,7 +12,7 @@ from lets_plot import (
 )
 
 from cellestial.layers._deferred import DeferredLayer
-from cellestial.util import get_mapping, retrieve
+from cellestial.util import _drop_nonfinite_rows, get_mapping, retrieve
 from cellestial.util.errors import MissingAestheticError
 
 if TYPE_CHECKING:
@@ -227,6 +227,8 @@ def stream(
             msg = "`scvelo` must be installed to use the stream layer."
             raise ImportError(msg) from err
 
+        frame = _drop_nonfinite_rows(frame, [x, y, x_velocity, y_velocity])
+
         # extract coordinates and velocities as numpy arrays
         dimensions = frame.select(pl.col(x), pl.col(y)).to_numpy()
         velocities = frame.select(pl.col(x_velocity), pl.col(y_velocity)).to_numpy()

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/common/xyplot.py

@@ -17,6 +17,7 @@ from cellestial.themes import _THEME_SCATTER
 from cellestial.util import (
     _collect_aes_columns,
     _determine_axis,
+    _drop_nonfinite_rows,
     _resolve_tooltips,
     _select_variable_keys,
     _validate_tooltips,
@@ -221,6 +222,7 @@ def xyplot(
             include_dimensions=include_dimensions,
             metadata_columns=metadata_columns,
         )
+    frame = _drop_nonfinite_rows(frame, [x, y])
     _validate_tooltips(tooltips, frame)
 
     # BUILD: the scatterplot

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/core/dimensional.py

@@ -24,6 +24,7 @@ from cellestial.themes import _THEME_DIMENSION
 from cellestial.util import (
     _collect_aes_columns,
     _color_gradient,
+    _drop_nonfinite_rows,
     _reject_sequence_key,
     _require_feature_key,
     _resolve_embedding_key,
@@ -282,6 +283,7 @@ def dimensional(
             include_dimensions=max(xy),
             metadata_columns=metadata_columns,
         )
+    frame = _drop_nonfinite_rows(frame, [x, y])
     _validate_tooltips(tooltips, frame)
 
     # HANDLE: groups filter (categorical-only)

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/core/utilities.py

@@ -25,6 +25,7 @@ from cellestial.themes import _THEME_DIST
 from cellestial.util import (
     _collect_aes_columns,
     _determine_axis,
+    _drop_nonfinite_rows,
     _resolve_tooltips,
     _validate_tooltips,
     _warn,
@@ -178,7 +179,7 @@ def _distribution(
     frame = frame.unpivot(
         on=keys, index=index, value_name=value_column, variable_name=variable_column
     )
-    frame = frame.drop_nulls(subset=[value_column])
+    frame = _drop_nonfinite_rows(frame, [value_column])
     if threshold is not None:
         frame = frame.filter(pl.col(value_column) >= threshold)
     if group_by is None:

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/differential/utilities.py

@@ -134,6 +134,13 @@ def _build_volcano_frame(
     else:
         raise _unsupported_data_type(data, AnnData)
 
+    frame = frame.filter(
+        pl.col(logfoldchange_column).is_not_null()
+        & pl.col(logfoldchange_column).is_finite()
+        & pl.col(pvalue_column).is_not_null()
+        & pl.col(pvalue_column).is_finite()
+    )
+
     # CRITICAL PARTS: Dataframe Operations
     # 1. -log10(pvalue) transform
     frame = frame.with_columns(
@@ -299,6 +306,7 @@ def _build_markers_frame(
         # Round scores to keep the embedded JSON compact when the frame is
         # serialized into the plot output.
         frame = frame.with_columns(pl.col(score_column).round(4))
+        frame = frame.filter(pl.col(score_column).is_not_null() & pl.col(score_column).is_finite())
 
         return frame, list(selected), str(stored_group_by)
 

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/differential/volcano.py

@@ -248,10 +248,6 @@ def volcano(
         .otherwise(cap)
         .alias(neg_log_pvalue_column)
     )
-    # logFC infinities mean the gene is expressed in only one group; fold change
-    # is undefined, drop those rows.
-    frame = frame.filter(pl.col(logfoldchange_column).is_finite())
-
     # SUBSAMPLE: cap non-significant points to keep the embedded data small.
     # The non-significant cloud overplots itself heavily, so dropping most of
     # it has no visible effect but shrinks the rendered plot's on-disk size.

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/heatmap/dotplot.py

@@ -315,6 +315,7 @@ def dotplot(
         variable_name=variable_column,
         value_name=value_name,
     )
+    frame = frame.filter(pl.col(value_name).is_not_null() & pl.col(value_name).is_finite())
     # 2. Aggregate and compute stats
     frame = frame.group_by([group_by, variable_column]).agg(
         [

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/heatmap/heatmap.py

@@ -372,7 +372,9 @@ def heatmap(
         value_name=value_column,
     )
     if aggregate:
-        frame = frame.group_by(group_by, variable_column).agg(pl.col(value_column).mean())
+        frame = frame.group_by(group_by, variable_column).agg(
+            pl.col(value_column).filter(pl.col(value_column).is_finite()).mean()
+        )
     frame = frame.drop_nulls()
 
     # HANDLE: standard scaling

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/heatmap/stacked_violin.py

@@ -29,6 +29,7 @@ from cellestial.single.heatmap.utilities import (
 )
 from cellestial.themes import _THEME_DOTPLOT
 from cellestial.util import (
+    _drop_nonfinite_rows,
     _fill_gradient,
     _get_dendrogram,
     _get_dendrogram_path_frame,
@@ -332,7 +333,7 @@ def stacked_violin(
         variable_name=variable_column,
         value_name=value_column,
     )
-    frame = frame.drop_nulls(subset=[value_column])
+    frame = _drop_nonfinite_rows(frame, [value_column])
     # 2. Apply threshold filter
     if threshold is not None:
         frame = frame.filter(pl.col(value_column) >= threshold)

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/quick/highest.py

@@ -12,6 +12,7 @@ from lets_plot import (
 
 from cellestial.frames import _highest_expressed_genes_frame
 from cellestial.themes import _THEME_HIGHEST
+from cellestial.util import _drop_nonfinite_rows
 from cellestial.util.errors import _unsupported_data_type
 
 if TYPE_CHECKING:
@@ -134,8 +135,8 @@ def highest_expressed_genes(
         descending=True,
     )
 
-    # FILTER: drop nulls and apply threshold if provided
-    frame = frame.drop_nulls()
+    # FILTER: keep finite values and apply threshold if provided
+    frame = _drop_nonfinite_rows(frame, [value_column])
     frame = frame.filter(
         pl.col(value_column) >= threshold if threshold is not None else True,
     )

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/single/quick/ridge.py

@@ -18,6 +18,7 @@ from cellestial.frames import build_frame
 from cellestial.util import (
     _collect_aes_columns,
     _determine_axis,
+    _drop_nonfinite_rows,
     _reject_sequence_key,
     _resolve_tooltips,
     _validate_tooltips,
@@ -201,8 +202,8 @@ def ridge(
             metadata_columns=metadata_columns,
         )
 
-    # FILTER: drop nulls and apply threshold
-    frame = frame.drop_nulls(subset=[key])
+    # FILTER: keep finite values and apply threshold
+    frame = _drop_nonfinite_rows(frame, [key]).filter(pl.col(group_by).is_not_null())
     frame = frame.filter(
         pl.col(key) >= threshold if threshold is not None else True,
     )

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/spatial/spatial.py

@@ -25,6 +25,7 @@ from cellestial.themes import _THEME_SPATIAL
 from cellestial.util import (
     _collect_aes_columns,
     _color_gradient,
+    _drop_nonfinite_rows,
     _fill_gradient,
     _reject_sequence_key,
     _resolve_tooltips,
@@ -358,6 +359,17 @@ def spatial(
             pl.Series("spatial_y", spot_coordinates[:, 1]),
         )
 
+    if is_polygon:
+        finite_vertex = pl.all_horizontal(
+            pl.col("polygon_x").is_not_null(),
+            pl.col("polygon_x").is_finite(),
+            pl.col("polygon_y").is_not_null(),
+            pl.col("polygon_y").is_finite(),
+        )
+        frame = frame.filter(finite_vertex.all().over("instance_id"))
+    else:
+        frame = _drop_nonfinite_rows(frame, ["spatial_x", "spatial_y"])
+
     _validate_tooltips(tooltips, frame)
 
     # HANDLE: groups filter (categorical-only)

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/util/__init__.py

@@ -9,6 +9,7 @@ from cellestial.util.utilities import (
     _collect_aes_columns,
     _color_gradient,
     _determine_axis,
+    _drop_nonfinite_rows,
     _fill_gradient,
     _is_observation_key,
     _is_variable_key,
@@ -30,6 +31,7 @@ __all__ = [
     "_collect_aes_columns",
     "_color_gradient",
     "_determine_axis",
+    "_drop_nonfinite_rows",
     "_fill_gradient",
     "_get_dendrogram",
     "_get_dendrogram_path_frame",

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/util/operations.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, cast
 
 from lets_plot import gggrid
 from lets_plot.plot.core import PlotSpec
@@ -30,32 +30,39 @@ def _normalize_widths(
         msg = f"`widths` must be a flat or nested sequence, but received {type(widths)}"
         raise TypeError(msg)
 
-    is_nested = any(isinstance(row_widths, (list, tuple)) for row_widths in widths)
-    if is_nested:
-        if not all(isinstance(row_widths, (list, tuple)) for row_widths in widths):
-            msg = "`widths` mixes numbers and sub-lists; use a fully nested list, one per row."
+    nested_flags = [
+        isinstance(row_widths, Sequence) and not isinstance(row_widths, (str, bytes))
+        for row_widths in widths
+    ]
+    if any(nested_flags):
+        if not all(nested_flags):
+            msg = "`widths` mixes numbers and sequences; use one sequence per row."
             raise ValueError(msg)
-        if len(widths) != len(plots):
-            msg = f"nested `widths` has {len(widths)} rows but `plots` has {len(plots)} rows."
+        nested_widths = cast("Sequence[Sequence[float]]", widths)
+        if len(nested_widths) != len(plots):
+            msg = (
+                f"nested `widths` has {len(nested_widths)} rows but `plots` has {len(plots)} rows."
+            )
             raise ValueError(msg)
-        for index, (row, row_widths) in enumerate(zip(plots, widths, strict=True)):
+        for index, (row, row_widths) in enumerate(zip(plots, nested_widths, strict=True)):
             if len(row_widths) != len(row):
                 msg = (
                     f"`widths[{index}]` has {len(row_widths)} values "
                     f"but row {index} has {len(row)} plots."
                 )
                 raise ValueError(msg)
-        return [list(row_widths) for row_widths in widths]
+        return [list(row_widths) for row_widths in nested_widths]
 
     # flat widths: broadcast to every row, valid only when all rows share that length.
-    uneven = [index for index, row in enumerate(plots) if len(row) != len(widths)]
+    flat_widths = cast("Sequence[float]", widths)
+    uneven = [index for index, row in enumerate(plots) if len(row) != len(flat_widths)]
     if uneven:
         msg = (
-            f"flat `widths` of length {len(widths)} cannot broadcast to rows {uneven} "
+            f"flat `widths` of length {len(flat_widths)} cannot broadcast to rows {uneven} "
             "with differing plot counts; pass a nested `widths` instead."
         )
         raise ValueError(msg)
-    return [list(widths) for _ in plots]
+    return [list(flat_widths) for _ in plots]
 
 
 def layout(

{cellestial-0.58.1 → cellestial-0.58.2}/cellestial/util/utilities.py

@@ -65,6 +65,22 @@ def _warn(message: str) -> None:
         warnings.formatwarning = original_format
 
 
+def _drop_nonfinite_rows(frame: pl.DataFrame, columns: Sequence[str]) -> pl.DataFrame:
+    """Keep rows whose selected numeric columns are present and finite."""
+    numeric_columns = [
+        column
+        for column in dict.fromkeys(columns)
+        if column in frame.columns and frame.schema[column].is_numeric()
+    ]
+    if not numeric_columns:
+        return frame
+    return frame.filter(
+        pl.all_horizontal(
+            pl.col(column).is_not_null() & pl.col(column).is_finite() for column in numeric_columns
+        )
+    )
+
+
 def _build_tooltips(
     *,
     tooltips: list[str] | str,

{cellestial-0.58.1 → cellestial-0.58.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cellestial"
-version = "0.58.1"
+version = "0.58.2"
 description = "Interactive single-cell and spatial omics visualization library"
 authors = [
     { name = "Zaf4", email = "zafermolbio@gmail.com" },
@@ -71,6 +71,8 @@ tqdm = "^4.67.3"
 pytest = "^9.0.3"
 pytest-cov = "^7.1.0"
 nbstripout = "^0.9.1"
+pytest-xdist = "^3.8.0"
+pytest-playwright = "^0.8.0"
 
 [tool.poetry.group.docs.dependencies]
 sphinx = ">=8.0.0"
@@ -84,7 +86,10 @@ squidpy = "^1.8.1"
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-addopts = "--cov=cellestial --cov-report=xml:tests/coverage.xml --cov-report=term-missing"
+addopts = "-n 4 --dist=loadscope -m 'not browser' --cov=cellestial --cov-report=xml:tests/coverage.xml --cov-report=term-missing"
+markers = [
+    "browser: exercises Lets-Plot in a real browser",
+]
 
 [tool.coverage.run]
 data_file = "tests/.coverage"