add volume generator test

tests/python/io_utils.py

@@ -6,7 +6,7 @@
 
 @dataclass(frozen=True)
 class PolusTestDataRepo:
-    repo_url: str = "https://github.com/sameeul/polus-test-data.git"
+    repo_url: str = "https://github.com/sameeul//polus-test-data.git"
     repo_dir: Path = Path("polus-test-data")
     default_branch: str = "main"
 
@@ -21,7 +21,17 @@ def ensure_repo_cloned(repo: PolusTestDataRepo, depth: int = 1) -> Path:
 
     repo.repo_dir.parent.mkdir(parents=True, exist_ok=True)
     subprocess.run(
-        ["git", "clone", "--depth", str(depth), repo.repo_url, str(repo.repo_dir)],
+        [
+            "git",
+            "clone",
+            "--branch",
+            repo.default_branch,
+            "--single-branch",
+            "--depth",
+            str(depth),
+            repo.repo_url,
+            str(repo.repo_dir),
+        ],
         check=True,
     )
     return repo.repo_dir

tests/python/multi_images.py

@@ -21,7 +21,7 @@ def generate_pyramid_from_repo_path(
     Clone the repo if needed, locate the image file, then run Argolid pyramid generation.
     """
     repo_dir = ensure_repo_cloned(repo)
-    input_dir = str(repo_dir / "argolid")
+    input_dir = str(repo_dir / "argolid" / "2D")
 
     output_dir = Path(output_dir)
     output_dir.parent.mkdir(parents=True, exist_ok=True)

tests/python/test_single_image.py

@@ -18,7 +18,7 @@ def test_single_image_pyramid(tmp_path: Path) -> None:
 
     generate_pyramid_from_repo_file(
         repo=repo,
-        rel_image_path=Path("argolid") / "x0_y0_c1.ome.tiff",
+        rel_image_path=Path("argolid") / "2D" / "x0_y0_c1.ome.tiff",
         output_dir=out_dir,
     )
 

tests/python/test_volume_generator.py

@@ -0,0 +1,57 @@
+from pathlib import Path
+
+import pytest
+
+from argolid import VolumeGenerator
+from .io_utils import ensure_repo_cloned, PolusTestDataRepo
+
+
+@pytest.mark.parametrize(
+    "file_pattern,output_dir,image_name,group_by",
+    [
+        ("{z:d}.c{c:d}.ome.tiff", "volume_full", "test_volume", "c"),
+    ],
+)
+def test_generate_volume_creates_output(
+    tmp_path: Path,
+    file_pattern: str,
+    output_dir: str,
+    image_name: str,
+    group_by: str,
+) -> None:
+
+    repo = PolusTestDataRepo()
+    repo_dir = ensure_repo_cloned(repo)
+
+    input_dir = repo_dir / "argolid" / "3D"
+    assert input_dir.is_dir(), f"Missing test data dir: {input_dir}"
+
+    out_dir = tmp_path / output_dir
+
+    vg = VolumeGenerator(
+        source_dir=str(input_dir),
+        group_by=group_by,
+        file_pattern=file_pattern,
+        out_dir=str(out_dir),
+        image_name=image_name,
+    )
+
+    vg.generate_volume()
+
+    root = out_dir / image_name
+    assert root.is_dir(), f"Expected output root dir: {root}"
+
+    base_scale = root / "0"
+    assert base_scale.is_dir(), f"Expected base scale dir: {base_scale}"
+
+    # zarr markers
+    zarr_markers = [
+        root / ".zgroup",
+        root / ".zattrs",
+        base_scale / ".zgroup",
+        base_scale / ".zattrs",
+    ]
+    assert any(p.exists() for p in zarr_markers), (
+        "Expected at least one zarr metadata marker (.zgroup/.zattrs) "
+        f"under {root} or {base_scale}"
+    )