Merge pull request #39 from iamcipherdev/fix/zarr-format-check-subset-concat-2026-10-15

fix(cli): validate --zarr-format in subset and concat

Author: Claptar

src/adata/cli.py

@@ -347,6 +347,10 @@ def subset(
         adata subset data.h5ad -o out.h5ad -q "n_counts > 1000 and cluster in A,B"
         adata subset data.h5ad -o out.h5ad --var-query "highly_variable == True"
     """
+    if zarr_format is not None and zarr_format not in (2, 3):
+        console.print("[bold red]Error:[/] --zarr-format must be 2 or 3.")
+        raise typer.Exit(code=1)
+
     if obs is None and var is None and obs_query is None and var_query is None:
         console.print(
             "[bold red]Error:[/] Provide at least one of --obs, --var, "
@@ -447,6 +451,10 @@ def concat(
         adata concat *.h5ad -o merged.h5ad --join outer --label sample
         adata concat a.h5ad b.h5ad -o m.h5ad --keys a,b --index-unique - --uns-merge same
     """
+    if zarr_format is not None and zarr_format not in (2, 3):
+        console.print("[bold red]Error:[/] --zarr-format must be 2 or 3.")
+        raise typer.Exit(code=1)
+
     for name, value in (("--merge", merge), ("--uns-merge", uns_merge)):
         if value is not None and value not in MERGE_CHOICES:
             console.print(

tests/test_commands_coverage.py

@@ -297,6 +297,28 @@ def test_create_rejects_a_bad_zarr_format(temp_dir):
     assert "must be 2 or 3" in _out(result)
 
 
+def test_subset_rejects_a_bad_zarr_format(store, temp_dir):
+    path, _ = store
+    result = runner.invoke(
+        app,
+        ["subset", str(path), "-o", str(temp_dir / "o.h5ad"),
+         "-q", "obs_names", "--zarr-format", "4"],
+    )
+    assert result.exit_code == 1
+    assert "must be 2 or 3" in _out(result)
+
+
+def test_concat_rejects_a_bad_zarr_format(store, temp_dir):
+    path, _ = store
+    result = runner.invoke(
+        app,
+        ["concat", str(path), str(path), "-o", str(temp_dir / "o.h5ad"),
+         "--zarr-format", "4"],
+    )
+    assert result.exit_code == 1
+    assert "must be 2 or 3" in _out(result)
+
+
 def test_create_requires_a_size_or_a_name_file(temp_dir):
     result = runner.invoke(app, ["create", str(temp_dir / "x.h5ad"), "--n-var", "2"])
     assert result.exit_code == 1