add --spot argument to CLI

Author: quentinblampey

docs/cli.md

@@ -107,6 +107,7 @@ $ spatialdata_xenium_explorer write [OPTIONS] SDATA_PATH
 * `--points-key TEXT`: Name of the transcripts (key of `sdata.points`). This argument doesn't need to be provided if there is only one points key.
 * `--gene-column TEXT`: Column name of the points dataframe containing the gene names
 * `--pixelsize FLOAT`: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.  [default: 0.2125]
+* `--spot / --no-spot`: Whether the technology is based on spots  [default: no-spot]
 * `--layer TEXT`: Layer of `sdata.table` where the gene counts are saved. If `None`, uses `sdata.table.X`.
 * `--lazy / --no-lazy`: If `True`, will not load the full images in memory (except if the image memory is below `ram_threshold_gb`)  [default: lazy]
 * `--ram-threshold-gb INTEGER`: Threshold (in gygabytes) from which image can be loaded in memory. If `None`, the image is never loaded in memory  [default: 4]

spatialdata_xenium_explorer/cli/app.py

@@ -31,6 +31,7 @@ def write(
         0.2125,
         help="Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.",
     ),
+    spot: bool = typer.Option(False, help="Whether the technology is based on spots"),
     layer: str = typer.Option(
         None,
         help="Layer of `sdata.table` where the gene counts are saved. If `None`, uses `sdata.table.X`.",
@@ -68,6 +69,7 @@ def write(
         points_key=points_key,
         gene_column=gene_column,
         pixelsize=pixelsize,
+        spot=spot,
         layer=layer,
         lazy=lazy,
         ram_threshold_gb=ram_threshold_gb,