Add in-memory flag to zarr_rechunk command line

pytools/zarr_rechunk.py

@@ -25,15 +25,18 @@
     default=False,
     help="Use the preferred compressor when recompressing.",
 )
+@click.option(
+    "--in-memory", is_flag=True, show_default=True, default=False, help="Use in-memory zarr store when recompressing."
+)
 @click.version_option(__version__)
-def main(input_zarr, log_level, chunk_size, recompress):
+def main(input_zarr, log_level, chunk_size, recompress, in_memory):
     logging.basicConfig(format="%(levelname)s: %(message)s", level=logging.getLevelName(log_level))
 
     compressor = Blosc(cname="zstd", clevel=5, shuffle=Blosc.SHUFFLE)
     z = HedwigZarrImages(input_zarr, read_only=False)
 
     for k in z.get_series_keys():
-        z[k].rechunk(chunk_size, compressor=compressor if recompress else None)
+        z[k].rechunk(chunk_size, compressor=compressor if recompress else None, in_memory=in_memory)
 
 
 if __name__ == "__main__":