Merge branch 'main' into anndataR

Author: Artur-man

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
-Depends: R (>= 4.4)
-Version: 0.99.23
+Depends: R (>= 4.5)
+Version: 0.99.24
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufracturer
     data and writing to .zarr, on-disk representation of images/labels as

R/read.R

@@ -1,30 +1,32 @@
 #
-allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7", 
-"pillow==11.1.0", "anndata==0.11.3", "annotated_types==0.7.0", "asciitree==0.3.3", 
-"attr==0.3.2", "certifi==2025.01.31", "charset_normalizer==3.4.1", 
-"click==8.1.8", "cloudpickle==3.1.1", "cycler==0.12.1", "dask==2024.4.1", 
-"dask_image==2024.5.3", "datashader==0.17.0", 
-"deprecated==1.2.18", "distributed==2024.4.1", 
-"flowio==1.3.0", "fsspec==2025.2.0", "geopandas==1.0.1", "h5py==3.12.1", 
-"idna==3.10", "imagecodecs==2024.12.30", "imageio==2.37.0", "jinja2==3.1.5", 
-"joblib==1.4.2", "kiwisolver==1.4.8", "lazy_loader==0.4", "legacy_api_wrap==1.4.1", 
-"llvmlite==0.44.0", "locket==1.0.0", "markupsafe==3.0.2", "matplotlib==3.10.0", 
-"more_itertools==10.3.0", "msgpack==1.1.0", "multipledispatch==0.6.0", 
-"multiscale_spatial_image==2.0.2", "natsort==8.4.0", "networkx==3.4.2", 
-"numba==0.61.0", "numcodecs==0.15.1", "numpy==2.1.3", "ome_types==0.5.3", 
-"ome_zarr==0.10.3", "packaging==24.2", "pandas==2.2.3", "param==2.2.0", 
-"pims==0.7", "platformdirs==4.3.6", "psutil==7.0.0", "pyarrow==19.0.0", 
-"pyct==0.5.0", "pydantic==2.10.6", "pydantic_compat==0.1.2", 
-"pydantic_core==2.27.2", "pygments==2.19.1", "pyparsing==3.2.1", 
-"pyproj==3.7.0", "pytz==2025.1", "readfcs==2.0.1", "requests==2.32.3", 
-"rich==13.9.4", "scanpy==1.11.0", "scipy==1.15.1", "setuptools==75.8.0", 
-"shapely==2.0.7", "six==1.17.0", "scikit-image==0.25.1", "scikit-learn==1.5.2", 
-"slicerator==1.1.0", "sortedcontainers==2.4.0", "spatial_image==1.1.0", 
-"tblib==3.0.0", "threadpoolctl==3.5.0", "tifffile==2025.1.10", 
-"toolz==1.0.0", "tornado==6.4.2", "tqdm==4.67.1", 
-"typing_extensions==4.12.2", "urllib3==2.3.0", "wrapt==1.17.2", 
-"xarray==2024.11.0", "xarray_dataclasses==1.9.1", "xarray_schema==0.0.3", 
-"zarr==2.18.4", "zict==3.0.0")
+# allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7", 
+# "pillow==11.1.0", "anndata==0.11.3", "annotated_types==0.7.0", "asciitree==0.3.3", 
+# "attr==0.3.2", "certifi==2025.01.31", "charset_normalizer==3.4.1", 
+# "click==8.1.8", "cloudpickle==3.1.1", "cycler==0.12.1", "dask==2024.4.1", 
+# "dask_image==2024.5.3", "datashader==0.17.0", 
+# "deprecated==1.2.18", "distributed==2024.4.1", 
+# "flowio==1.3.0", "fsspec==2025.2.0", "geopandas==1.0.1", "h5py==3.12.1", 
+# "idna==3.10", "imagecodecs==2024.12.30", "imageio==2.37.0", "jinja2==3.1.5", 
+# "joblib==1.4.2", "kiwisolver==1.4.8", "lazy_loader==0.4", "legacy_api_wrap==1.4.1", 
+# "llvmlite==0.44.0", "locket==1.0.0", "markupsafe==3.0.2", "matplotlib==3.10.0", 
+# "more_itertools==10.3.0", "msgpack==1.1.0", "multipledispatch==0.6.0", 
+# "multiscale_spatial_image==2.0.2", "natsort==8.4.0", "networkx==3.4.2", 
+# "numba==0.61.0", "numcodecs==0.15.1", "numpy==2.1.3", "ome_types==0.5.3", 
+# "ome_zarr==0.10.3", "packaging==24.2", "pandas==2.2.3", "param==2.2.0", 
+# "pims==0.7", "platformdirs==4.3.6", "psutil==7.0.0", "pyarrow==19.0.0", 
+# "pyct==0.5.0", "pydantic==2.10.6", "pydantic_compat==0.1.2", 
+# "pydantic_core==2.27.2", "pygments==2.19.1", "pyparsing==3.2.1", 
+# "pyproj==3.7.0", "pytz==2025.1", "readfcs==2.0.1", "requests==2.32.3", 
+# "rich==13.9.4", "scanpy==1.11.0", "scipy==1.15.1", "setuptools==75.8.0", 
+# "shapely==2.0.7", "six==1.17.0", "scikit-image==0.25.1", "scikit-learn==1.5.2", 
+# "slicerator==1.1.0", "sortedcontainers==2.4.0", "spatial_image==1.1.0", 
+# "tblib==3.0.0", "threadpoolctl==3.5.0", "tifffile==2025.1.10", 
+# "toolz==1.0.0", "tornado==6.4.2", "tqdm==4.67.1", 
+# "typing_extensions==4.12.2", "urllib3==2.3.0", "wrapt==1.17.2", 
+# "xarray==2024.11.0", "xarray_dataclasses==1.9.1", "xarray_schema==0.0.3", 
+# "zarr==2.18.4", "zict==3.0.0")
+allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0", 
+         "spatialdata_plot==0.2.14", "setuptools==75.8.0")
 # notes from VJC -- readSpatialData was modified below so
 # that if anndataR = FALSE, spatialdata.read_zarr is used
 # to get the whole zarr store, and then the tables are
@@ -119,7 +121,7 @@ readShape <- function(x, ...) {
 #' @importFrom basilisk BasiliskEnvironment
 .env <- BasiliskEnvironment(
     pkgname="SpatialData", envname="anndata_env",
-    packages=c( "python==3.12.0", "zarr==2.18.4" ),
+    packages=c( "python==3.13.0"),
     pip=allp)
 
 #' @importFrom reticulate import

R/tx_to_ext.R

@@ -24,12 +24,15 @@
 #' @examples
 #' src <- system.file("extdata", "blobs.zarr", package="SpatialData")
 #' td <- tempfile()
-#' do_tx_to_ext(
-#'   srcdir=src, dest=td, 
-#'   coordinate_system="global",
-#'   maintain_positioning=FALSE, 
-#'   target_width=400.)
-#' (sd <- readSpatialData(td))
+#' # TODO: for now this example converts to a zarr v3 so we comment out, 
+#' # check again later
+#' 
+#' # do_tx_to_ext(
+#' #  srcdir=src, dest=td, 
+#' #  coordinate_system="global",
+#' #  maintain_positioning=FALSE, 
+#' #  target_width=400.)
+#' # (sd <- readSpatialData(td))
 #' 
 #' @export
 do_tx_to_ext <- function(srcdir, dest, coordinate_system, ...) {