From 337b6a5eb37cfba3e71a587c2124d16a28105fa3 Mon Sep 17 00:00:00 2001
From: FloWuenne <flowuenne@gmail.com>
Date: Fri, 21 Jul 2023 16:43:18 +0200
Subject: [PATCH 1/2] Added first simple version of CLI script.

---
 src/spatialdata_io/__main__.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 src/spatialdata_io/__main__.py

diff --git a/src/spatialdata_io/__main__.py b/src/spatialdata_io/__main__.py
new file mode 100644
index 00000000..a5e9b508
--- /dev/null
+++ b/src/spatialdata_io/__main__.py
@@ -0,0 +1,19 @@
+import os
+import click
+import spatialdata_io
+
+@click.command()
+@click.argument('input_path', type=click.Path(exists=True))
+@click.argument('output_path', type=click.Path())
+@click.option('--reader_name', type=click.Choice(['codex', 'cosmx', 'curio', 'mcmicro', 'merscope', 'metaspace', 'resolve', 'steinbock', 'visium', 'xenium']), help='name of the reader to use', required=True)
+def main(input_path, output_path, reader_name):
+    if os.path.exists(output_path):
+        print("Spatialdata object already exists! If you want to recompute it, please delete the existing Zarr store.")
+    else:
+        reader_func = getattr(spatialdata_io, reader_name)
+        sdata = reader_func(input_path) ## Can only handle mcmicro at the moment. Add logic for other readers!!!
+        sdata.write(output_path)
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 55118531f1aa0742283e82b31bfb2fd2f2191074 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 21 Jul 2023 20:02:10 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spatialdata_io/__main__.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/spatialdata_io/__main__.py b/src/spatialdata_io/__main__.py
index a5e9b508..2f0b4001 100644
--- a/src/spatialdata_io/__main__.py
+++ b/src/spatialdata_io/__main__.py
@@ -1,19 +1,29 @@
 import os
+
 import click
+
 import spatialdata_io
 
+
 @click.command()
-@click.argument('input_path', type=click.Path(exists=True))
-@click.argument('output_path', type=click.Path())
-@click.option('--reader_name', type=click.Choice(['codex', 'cosmx', 'curio', 'mcmicro', 'merscope', 'metaspace', 'resolve', 'steinbock', 'visium', 'xenium']), help='name of the reader to use', required=True)
+@click.argument("input_path", type=click.Path(exists=True))
+@click.argument("output_path", type=click.Path())
+@click.option(
+    "--reader_name",
+    type=click.Choice(
+        ["codex", "cosmx", "curio", "mcmicro", "merscope", "metaspace", "resolve", "steinbock", "visium", "xenium"]
+    ),
+    help="name of the reader to use",
+    required=True,
+)
 def main(input_path, output_path, reader_name):
     if os.path.exists(output_path):
         print("Spatialdata object already exists! If you want to recompute it, please delete the existing Zarr store.")
     else:
         reader_func = getattr(spatialdata_io, reader_name)
-        sdata = reader_func(input_path) ## Can only handle mcmicro at the moment. Add logic for other readers!!!
+        sdata = reader_func(input_path)  ## Can only handle mcmicro at the moment. Add logic for other readers!!!
         sdata.write(output_path)
 
 
-if __name__ == '__main__':
-    main()
\ No newline at end of file
+if __name__ == "__main__":
+    main()