scientific python spec0

.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
 

.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

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",
@@ -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/_utils_rust.pyi

@@ -1,7 +1,8 @@
+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/lazykde/_LazyKDE.py

@@ -1,6 +1,6 @@
 from collections.abc import Iterable
 from itertools import chain
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Self
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -18,7 +18,6 @@
 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, _RangeTuple2D
 from .._utils import _raise_module_load_error, _validate_n_threads, validate_threads