From 52ca2d8be359dba74cbe25d119befc10d09e9fda Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Mar 2026 18:04:46 +0000
Subject: [PATCH 1/4] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.4.4 → v2.4.6](https://github.com/biomejs/pre-commit/compare/v2.4.4...v2.4.6)
- [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.4...v0.15.5)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3944a93..fc122a6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.4
+    rev: v2.4.6
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
@@ -16,7 +16,7 @@ repos:
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.5
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

From e594d43293551d9c8dab8cdcdefbf11b28419a54 Mon Sep 17 00:00:00 2001
From: Phil Schaf <flying-sheep@web.de>
Date: Tue, 10 Mar 2026 13:01:52 +0100
Subject: [PATCH 2/4] hm

---
 pyproject.toml               |  8 +--
 src/anndata_plot/__init__.py | 15 +-----
 src/anndata_plot/pl/utils.py | 94 ------------------------------------
 tests/test_basic.py          |  8 +--
 4 files changed, 6 insertions(+), 119 deletions(-)
 delete mode 100644 src/anndata_plot/pl/utils.py

diff --git a/pyproject.toml b/pyproject.toml
index bb9eefa..e4b0c44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ maintainers = [
 authors = [
   { name = "Tim Treis" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.10",
@@ -25,7 +25,7 @@ classifiers = [
 ]
 dependencies = [
   "anndata",
-  "holoviews",
+  "hv-anndata",
   # for debug logging (referenced from the issue template)
   "session-info2",
 ]
@@ -69,9 +69,9 @@ envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.hatch-test.features = [ "dev", "test" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
-  { deps = [ "stable" ], python = [ "3.10", "3.13" ] },
+  { deps = [ "stable" ], python = [ "3.14", "3.12" ] },
   # Test the newest supported Python version also with pre-release deps
-  { deps = [ "pre" ], python = [ "3.13" ] },
+  { deps = [ "pre" ], python = [ "3.14" ] },
 ]
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
diff --git a/src/anndata_plot/__init__.py b/src/anndata_plot/__init__.py
index 5e3d9ab..199a50d 100644
--- a/src/anndata_plot/__init__.py
+++ b/src/anndata_plot/__init__.py
@@ -1,16 +1,3 @@
-from importlib.metadata import version
-
-import holoviews as hv
-
 from . import pl, pp, tl
-from .pl.utils import AnnDataInterface
-
-__all__ = ["pl"]
-
-__version__ = version("anndata-plot")
-
-# register the AnnDataInterface with holoviews
-if AnnDataInterface.datatype not in hv.core.data.datatypes:
-    hv.core.data.datatypes.append(AnnDataInterface.datatype)
 
-hv.core.Interface.register(AnnDataInterface)
+__all__ = ["pl", "pp", "tl"]
diff --git a/src/anndata_plot/pl/utils.py b/src/anndata_plot/pl/utils.py
deleted file mode 100644
index a8b05d8..0000000
--- a/src/anndata_plot/pl/utils.py
+++ /dev/null
@@ -1,94 +0,0 @@
-from dataclasses import dataclass
-from enum import Enum, auto
-from typing import cast, overload
-
-import anndata as ad
-import holoviews as hv
-import numpy as np
-
-
-class Raise(Enum):
-    """Marker sentry for raising an exception."""
-
-    Sentry = auto()
-
-
-@dataclass
-class AnnDataProxy:
-    """Proxy for anndata, used to get arrays with a mapping-like interface."""
-
-    # from: https://gist.github.com/flying-sheep/3ff54234019cc7c84e84cbbe649209c5
-
-    adata: ad.AnnData
-
-    @overload
-    def get(self, k: str, /, default: None = None) -> np.ndarray | None: ...
-    @overload
-    def get(self, k: str, /, default: np.ndarray | Raise) -> np.ndarray: ...
-
-    def get(self, k: str, /, default: np.ndarray | Raise | None = None) -> np.ndarray | None:
-        """Get an array from an AnnData object."""
-        k_orig = k
-        if "." not in k:
-            if default is not Raise.Sentry and k not in self.adata.var_names:
-                return default
-            return self.adata[:, k].X.flatten()
-        attr_name, k = k.split(".", 1)
-        attr = getattr(self.adata, attr_name)
-        if "." not in k:
-            if default is not Raise.Sentry and k not in attr:
-                return default
-            return attr[k]
-        k, i = k.split(".", 1)
-        arr = attr[k]
-        if "." not in i:
-            if default is not Raise.Sentry and not (0 <= int(i) < arr.shape[1]):
-                return default
-            return arr[:, int(i)]
-        raise KeyError(k_orig)
-
-    def __contains__(self, k: str) -> bool:
-        return self.get(k) is not None
-
-    def __getitem__(self, k: str) -> object:
-        return self.get(k, Raise.Sentry)
-
-    def __len__(self) -> int:
-        return len(self.adata)
-
-
-class AnnDataInterface(hv.core.Interface):
-    """Interface for AnnData objects."""
-
-    types = (ad.AnnData,)
-    datatype = "anndata"
-
-    @classmethod
-    def init(
-        cls, eltype, data: ad.AnnData | AnnDataProxy, kdims: list[str] | None, vdims: list[str] | None
-    ) -> tuple[AnnDataProxy, dict, dict]:
-        """Initialize the interface and return dataset and dimensions."""
-        proxy = AnnDataProxy(data) if isinstance(data, ad.AnnData) else data
-        return proxy, {"kdims": kdims, "vdims": vdims}, {}
-
-    @classmethod
-    def values(
-        cls,
-        data: hv.Dataset,
-        dim: hv.Dimension | str,
-        expanded=True,
-        flat=True,
-        compute=True,
-        keep_index=False,
-    ) -> np.ndarray:
-        """Get the values of a dimension."""
-        dim = data.get_dimension(dim)
-        proxy = cast(AnnDataProxy, data.data)
-        return proxy[dim.name]
-
-    @classmethod
-    def dimension_type(cls, data: hv.Dataset, dim: hv.Dimension | str) -> np.dtype:
-        """Get the dtype of a dimension."""
-        dim = data.get_dimension(dim)
-        proxy = cast(AnnDataProxy, data.data)
-        return proxy[dim.name].dtype
diff --git a/tests/test_basic.py b/tests/test_basic.py
index 19d6058..92eb3ad 100644
--- a/tests/test_basic.py
+++ b/tests/test_basic.py
@@ -1,12 +1,6 @@
 import pytest
 
-import anndata_plot
-
-
-def test_package_has_version():
-    assert anndata_plot.__version__ is not None
-
 
 @pytest.mark.skip(reason="This decorator should be removed when test passes.")
-def test_example():
+def test_example() -> None:
     assert 1 == 0  # This test is designed to fail.

From b42839b36ecfe4d4c9148afdb1b61bbb34238076 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Mar 2026 12:02:39 +0000
Subject: [PATCH 3/4] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e4b0c44..c674976 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,8 +17,6 @@ authors = [
 requires-python = ">=3.12"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",

From c198c2f449ed11973a5528e57a0a5024710895dd Mon Sep 17 00:00:00 2001
From: Phil Schaf <flying-sheep@web.de>
Date: Tue, 10 Mar 2026 13:08:30 +0100
Subject: [PATCH 4/4] actually import it

---
 tests/test_basic.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/test_basic.py b/tests/test_basic.py
index 92eb3ad..05eda61 100644
--- a/tests/test_basic.py
+++ b/tests/test_basic.py
@@ -1,5 +1,11 @@
 import pytest
 
+import anndata_plot
+
+
+def test_all() -> None:
+    assert set(dir(anndata_plot)) > {"pl", "pp", "tl"}
+
 
 @pytest.mark.skip(reason="This decorator should be removed when test passes.")
 def test_example() -> None: