snakemake still supports old pixelsize (deprecation log)

CHANGELOG.md

@@ -1,7 +1,7 @@
 ## [1.0.3] - tbd
 
 ### Breaking changes
-- `pixelsize` argument has been renamed to `pixel_size`
+- `pixelsize` argument has been renamed to `pixel_size` (the snakemake pipeline is only deprecating it for now)
 
 ### Added
 - The `phenocycler` reader can now also read `.tif` files (not just `.qptiff`)

sopa/cli/explorer.py

@@ -4,6 +4,10 @@
 
 app_explorer = typer.Typer()
 
+PIXELSIZE_DEPRECATED = (
+    "`pixelsize` is deprecated and will be removed in future versions. Use `pixel_size` instead."
+)
+
 
 @app_explorer.command()
 def write(
@@ -23,6 +27,10 @@ def write(
         0.2125,
         help="Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.",
     ),
+    pixelsize: float = typer.Option(
+        None,
+        help=PIXELSIZE_DEPRECATED,
+    ),
     lazy: bool = typer.Option(
         True,
         help="If `True`, will not load the full images in memory (except if the image memory is below `ram_threshold_gb`)",
@@ -41,6 +49,7 @@ def write(
     ),
 ):
     """Convert a spatialdata object to Xenium Explorer's inputs"""
+    import logging
     from pathlib import Path
 
     from sopa.io.explorer import write
@@ -51,6 +60,11 @@ def write(
     if output_path is None:
         output_path = Path(sdata_path).with_suffix(".explorer")
 
+    if pixelsize is not None:
+        log = logging.getLogger(__name__)
+        log.critical(PIXELSIZE_DEPRECATED)
+        pixel_size = pixelsize
+
     write(
         output_path,
         sdata,

workflow/Snakefile

@@ -186,7 +186,7 @@ rule image_write:
         mem_mb=64_000,
         partition="longq"
     params:
-        args_explorer = str(args["explorer"].where(keys=['lazy', 'ram_threshold_gb', 'pixel_size'])),
+        args_explorer = str(args["explorer"].where(keys=['lazy', 'ram_threshold_gb', 'pixel_size', 'pixelsize'])),
     shell:
         """
         sopa explorer write {paths.sdata_path} --output-path {paths.explorer_directory} {params.args_explorer} --mode '+i' --no-save-h5ad