Merge pull request #16 from HiDiHlabs/dev

Update zarr from dev

.github/workflows/cibuildwheel.yml

@@ -24,7 +24,7 @@ jobs:
       - name: set up python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - uses: actions-rust-lang/setup-rust-toolchain@v1
 

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
   skip: [fmt, cargo-check]
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         exclude_types: ["jupyter"]
@@ -18,7 +18,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch=main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.9
+    rev: v0.7.0
     hooks:
       - id: ruff
         args: [--fix]
@@ -27,11 +27,11 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.10.0
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         additional_dependencies:
@@ -49,10 +49,10 @@ repos:
         additional_dependencies:
           - tomli
   - repo: https://github.com/google/yamlfmt
-    rev: v0.12.1
+    rev: v0.13.0
     hooks:
       - id: yamlfmt
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
       - id: mdformat

.readthedocs.yaml

@@ -2,7 +2,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
     rust: "1.78"
 sphinx:
   configuration: docs/source/conf.py

Cargo.toml

@@ -10,17 +10,17 @@ crate-type = ["cdylib"]
 
 [dependencies]
 bincode       = { version = "1.3" }
-indexmap      = { version = "2.1.0", features = ["rayon"] }
+indexmap      = { version = ">= 2.1, < 2.6", features = ["rayon"] }
 itertools     = { version = "0.12.1" }
 ndarray       = { version = "0.15.6", features = ["rayon"] }
 ndarray-stats = { version = "0.5.1" }
 num           = { version = "0.4.1" }
-numpy         = { version = "0.21.0" }
+numpy         = { version = "0.21" }
 polars        = { version = "0.41", features = ["partition_by", "dtype-categorical"] }
 polars-arrow  = { version = "0.41" }
-pyo3          = { version = "0.21.0", features = ["extension-module"] }
-pyo3-polars   = { version = "0.15.0" }
-rayon         = { version = "1.8.0" }
+pyo3          = { version = "0.21", features = ["extension-module"] }
+pyo3-polars   = { version = "0.15" }
+rayon         = { version = "1.8" }
 serde_json    = { version = "1" }
-sprs          = { version = "0.11.1", features = ["serde"] }
+sprs          = { version = "= 0.11.1", features = ["serde"] }
 zarrs         = { version = "0.16.4", features = ["ndarray", "gzip"] }

README.md

@@ -34,7 +34,7 @@ conda install bioconda::sainsc
 ```
 
 For detailed installation instructions please refer to the
-[documentation](https://sainsc.readthedocs.io/en/stable/installation.html).
+[documentation](https://sainsc.readthedocs.io/page/installation.html).
 
 ## Documentation
 

pyproject.toml

@@ -8,24 +8,23 @@ name            = "sainsc"
 description     = "Segmentation-free Analysis of In Situ Capture data"
 readme          = { file = "README.md", content-type = "text/markdown" }
 license         = { file = "LICENSE" }
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dynamic         = ["version"]
 
 authors = [
     { name = "Niklas Müller-Bötticher", email = "[email protected]" },
 ]
 dependencies = [
     "anndata>=0.9",
-    "matplotlib",
+    "matplotlib>=3.7",
     "matplotlib-scalebar",
     "numba>=0.44",
-    "numpy>=1.21",
-    "pandas",
+    "numpy>=1.24",
+    "pandas>=2.0",
     "polars[pandas]>=1",
-    "scikit-image>=0.18",
-    "scipy>=1.9",
+    "scikit-image>=0.20",
+    "scipy>=1.10",
     "seaborn>=0.11",
-    "typing-extensions>=4",
 ]
 classifiers = [
     "Intended Audience :: Science/Research",
@@ -53,10 +52,10 @@ data = ["pooch>=1"]
 dev = ["sainsc[data,docs,spatialdata]", "pre-commit"]
 
 [project.urls]
-homepage      = "https://github.com/HiDiHlabs/sainsc"
-documentation = "https://sainsc.readthedocs.io"
-repository    = "https://github.com/HiDiHlabs/sainsc"
-
+Homepage      = "https://github.com/HiDiHlabs/sainsc"
+Documentation = "https://sainsc.readthedocs.io"
+Repository    = "https://github.com/HiDiHlabs/sainsc"
+Issues        = "https://github.com/HiDiHlabs/sainsc/issues"
 
 [tool]
 
@@ -75,16 +74,16 @@ target = "sainsc._utils_rust"
 profile = "black"
 
 [tool.black]
-target-version = ["py310", "py311", "py312"]
+target-version = ["py311", "py312", "py313"]
 
 [tool.ruff]
-target-version = "py310"
+target-version = "py311"
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["E402"]
 
 [tool.mypy]
-python_version         = "3.10"
+python_version         = "3.11"
 ignore_missing_imports = true
 warn_no_return         = false
 packages               = "sainsc"

sainsc/__init__.py

@@ -7,7 +7,8 @@
 
 del PackageNotFoundError, version
 
+from . import io, lazykde, utils
 from ._utils_rust import GridCounts
 from .lazykde import LazyKDE
 
-__all__ = ["GridCounts", "LazyKDE"]
+__all__ = ["io", "lazykde", "utils", "GridCounts", "LazyKDE"]

sainsc/_utils_rust.pyi

@@ -1,9 +1,9 @@
 from pathlib import Path
+from typing import Self
 
 import numpy as np
 from numpy.typing import NDArray
 from polars import DataFrame
-from typing_extensions import Self
 
 from ._typealias import _Csx, _CsxArray
 

sainsc/io/_io.py

@@ -232,7 +232,6 @@ def read_Xenium(
         :py:attr:`sainsc.io.XENIUM_CTRLS` by default.
         For Xenium v3 parquet files the data is automatically filtered with the
         'is_gene' column, as well.
-    column.
     n_threads : int | None, optional
         Number of threads used for reading file and processing. If `None` or 0 this will
         default to the number of available CPUs.

sainsc/lazykde/_LazyKDE.py

@@ -1,7 +1,7 @@
 from collections.abc import Iterable
 from itertools import chain
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Self
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -19,7 +19,6 @@
 from numpy.typing import NDArray
 from scipy.sparse import coo_array, csc_array, csr_array
 from skimage.feature import peak_local_max
-from typing_extensions import Self
 
 from .._typealias import _Cmap, _Csx, _CsxArray, _Local_Max, _PathLike, _RangeTuple2D
 from .._utils import _raise_module_load_error, _validate_n_threads, validate_threads
@@ -30,7 +29,7 @@
     kde_at_coord,
     sparse_kde_csx_py,
 )
-from ._kernel import gaussian_kernel
+from ..utils import gaussian_kernel
 from ._utils import (
     SCALEBAR_PARAMS,
     CosineCelltypeCallable,
@@ -1281,7 +1280,7 @@ def celltype_map(self) -> NDArray[np.signedinteger] | None:
         """
         return self._celltype_map
 
-    def __str__(self) -> str:
+    def __repr__(self) -> str:
         repr = [
             f"LazyKDE ({self.n_threads} threads)",
             f"genes: {len(self.genes)}",

sainsc/lazykde/__init__.py

@@ -2,8 +2,7 @@
 This module contains functionality for performing the various analysis steps of sainsc.
 """
 
-from ._kernel import epanechnikov_kernel, gaussian_kernel
 from ._LazyKDE import LazyKDE
 from ._utils import SCALEBAR_PARAMS
 
-__all__ = ["SCALEBAR_PARAMS", "LazyKDE", "epanechnikov_kernel", "gaussian_kernel"]
+__all__ = ["SCALEBAR_PARAMS", "LazyKDE"]

sainsc/utils/__init__.py

@@ -2,6 +2,7 @@
 This module contains additional utility functionality supporting the analysis.
 """
 
+from ._kernel import epanechnikov_kernel, gaussian_kernel
 from ._signatures import celltype_signatures
 
-__all__ = ["celltype_signatures"]
+__all__ = ["celltype_signatures", "epanechnikov_kernel", "gaussian_kernel"]

src/gridcounts.rs

@@ -278,7 +278,7 @@ impl GridCounts {
         Ok(((HashMap::new(),), HashMap::new()))
     }
 
-    fn __str__(&self) -> String {
+    fn __repr__(&self) -> String {
         let mut repr = vec![
             format!("GridCounts ({} threads)", self.n_threads),
             format!("genes: {}", self.counts.len()),