Merge branch 'main' into fix/sponsor

.pre-commit-config.yaml

@@ -9,11 +9,11 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.7.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0
+      rev: v3.0.1
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -27,7 +27,7 @@ repos:
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.277
+      rev: v0.0.282
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

Dockerfile

@@ -0,0 +1,12 @@
+FROM condaforge/mambaforge
+
+RUN mamba install python=3.10
+
+# complex dependencies that needs to be solved with conda
+RUN mamba install -c conda-forge gcc libgdal gxx imagecodecs -y
+
+# satellite spatialdata projects
+RUN pip install --no-cache-dir \
+    spatialdata \
+    spatialdata-io \
+    spatialdata-plot

src/spatialdata/_core/operations/rasterize.py

@@ -357,10 +357,7 @@ def _get_corrected_affine_matrix(
     if "z" in target_axes_unordered:
         target_axes = ("c", "z", "y", "x") if "c" in target_axes_unordered else ("z", "y", "x")
     else:
-        if "c" in target_axes_unordered:
-            target_axes = ("c", "y", "x")
-        else:
-            target_axes = ("y", "x")
+        target_axes = ("c", "y", "x") if "c" in target_axes_unordered else ("y", "x")
     target_spatial_axes = get_spatial_axes(target_axes)
     assert len(target_spatial_axes) == len(axes)
     assert len(target_spatial_axes) == len(axes)

src/spatialdata/transformations/ngff/ngff_coordinate_system.py

@@ -73,9 +73,9 @@ def __repr__(self) -> str:
 
     @staticmethod
     def from_dict(coord_sys: CoordSystem_t) -> NgffCoordinateSystem:
-        if "name" not in coord_sys.keys():
+        if "name" not in coord_sys:
             raise ValueError("`coordinate_system` MUST have a name.")
-        if "axes" not in coord_sys.keys():
+        if "axes" not in coord_sys:
             raise ValueError("`coordinate_system` MUST have axes.")
 
         if TYPE_CHECKING:
@@ -87,11 +87,11 @@ def from_dict(coord_sys: CoordSystem_t) -> NgffCoordinateSystem:
         axes = []
         for axis in coord_sys["axes"]:
             # for axis in sorted_axes:
-            if "name" not in axis.keys():
+            if "name" not in axis:
                 raise ValueError("Each axis MUST have a name.")
-            if "type" not in axis.keys():
+            if "type" not in axis:
                 raise ValueError("Each axis MUST have a type.")
-            if "unit" not in axis.keys() and axis["type"] not in ["channel", "array"]:
+            if "unit" not in axis and axis["type"] not in ["channel", "array"]:
                 raise ValueError("Each axis is either of type channel either MUST have a unit.")
             kw = {}
             if "unit" in axis:

src/spatialdata/transformations/operations.py

@@ -4,7 +4,6 @@
 from typing import TYPE_CHECKING, Optional, Union
 
 import networkx as nx
-import numpy
 import numpy as np
 from dask.dataframe import DataFrame as DaskDataFrame
 from geopandas import GeoDataFrame