add actual (portable) data tests for single and multi image pyramid generation

.github/workflows/publish_pypi.yml

@@ -83,7 +83,7 @@ jobs:
           CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
           CIBW_BEFORE_TEST_LINUX: dnf -y install maven java
-          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy
+          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy pytest
           CIBW_TEST_COMMAND: python -W default -m unittest discover -s {project}/tests -v
 
       - name: Install Dependencies
@@ -143,7 +143,7 @@ jobs:
             DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} &&
             MACOSX_DEPLOYMENT_TARGET=11.0 DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel} -e libc++ -e libunwind
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
-          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy
+          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy pytest
           CIBW_TEST_COMMAND: python -W default -m unittest discover -s {project}/tests -v
 
       - name: Install Dependencies

.github/workflows/wheel_build.yml

@@ -82,7 +82,7 @@ jobs:
           CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
           CIBW_BEFORE_TEST_LINUX: dnf -y install maven java
-          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy
+          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy pytest
           CIBW_TEST_COMMAND: python -W default -m unittest discover -s {project}/tests -v
 
       - name: Upload Artifact
@@ -139,7 +139,7 @@ jobs:
             DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} &&
             MACOSX_DEPLOYMENT_TARGET=11.0 DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel} -e libc++ -e libunwind
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
-          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy
+          CIBW_TEST_REQUIRES: bfio>=2.4.0 tensorstore numpy pytest
           CIBW_TEST_COMMAND: python -W default -m unittest discover -s {project}/tests -v
 
       - name: Upload Artifact

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel", "looseversion", "versioneer", "cmake"]
+requires = ["setuptools>=61.0", "wheel", "looseversion", "versioneer", "pytest", "cmake"]
 build-backend = "setuptools.build_meta"

pytest.ini

@@ -0,0 +1,10 @@
+[pytest]
+testpaths =
+    tests/python
+python_files =
+    test_*.py
+addopts =
+    --ignore=tests/python/test_read.py
+    --ignore=tests/python/test_pytest_bridge.py
+markers =
+    integration: integration tests that touch disk/network

tests/python/io_utils.py

@@ -0,0 +1,37 @@
+from dataclasses import dataclass
+from pathlib import Path
+import subprocess
+
+
+
+@dataclass(frozen=True)
+class PolusTestDataRepo:
+    repo_url: str = "https://github.com/sameeul/polus-test-data.git"
+    repo_dir: Path = Path("polus-test-data")
+    default_branch: str = "main"
+
+
+def ensure_repo_cloned(repo: PolusTestDataRepo, depth: int = 1) -> Path:
+    """
+    Ensure the repo exists locally. If not, clone it.
+    Returns the local repo directory.
+    """
+    if repo.repo_dir.exists():
+        return repo.repo_dir
+
+    repo.repo_dir.parent.mkdir(parents=True, exist_ok=True)
+    subprocess.run(
+        ["git", "clone", "--depth", str(depth), repo.repo_url, str(repo.repo_dir)],
+        check=True,
+    )
+    return repo.repo_dir
+
+
+def get_local_file_path(repo_dir: Path, rel_path: Path) -> Path:
+    """
+    Resolve a path inside the repo and validate it exists.
+    """
+    local_path = (repo_dir / rel_path).resolve()
+    if not local_path.exists():
+        raise FileNotFoundError(f"File not found: {local_path}")
+    return local_path

tests/python/multi_images.py

@@ -0,0 +1,58 @@
+from pathlib import Path
+from typing import Mapping
+from types import MappingProxyType
+
+from argolid import PyramidGenerartor
+DEFAULT_DOWNSAMPLE_METHODS = MappingProxyType({1: "mean"})
+from .io_utils import ensure_repo_cloned, PolusTestDataRepo
+
+
+def generate_pyramid_from_repo_path(
+    *,
+    repo: PolusTestDataRepo,
+    file_pattern: str,
+    image_name: str = "test_image",
+    output_dir: str | Path,
+    min_dim: int = 1024,
+    vis_type: str = "Viv",
+    downsample_methods: Mapping[int, str] = DEFAULT_DOWNSAMPLE_METHODS,
+) -> None:
+    """
+    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")
+
+    output_dir = Path(output_dir)
+    output_dir.parent.mkdir(parents=True, exist_ok=True)
+
+    pyr_gen = PyramidGenerartor()
+    pyr_gen.generate_from_image_collection(
+        input_dir,
+        file_pattern,
+        image_name,
+        str(output_dir),
+        min_dim,
+        vis_type,
+        dict(downsample_methods),
+    )
+
+
+def main() -> None:
+    repo = PolusTestDataRepo()
+    file_pattern = "x{x:d}_y{y:d}_c{c:d}.ome.tiff"
+    output_dir = Path("output") / "2D_pyramid_assembled"
+
+    generate_pyramid_from_repo_path(
+        repo=repo,
+        file_pattern=file_pattern,
+        image_name="test_image",
+        output_dir=output_dir,
+        min_dim=1024,
+        vis_type="Viv",
+        downsample_methods={1: "mean"},
+    )
+
+
+if __name__ == "__main__":
+    main()

tests/python/single_image.py

@@ -0,0 +1,57 @@
+from pathlib import Path
+from typing import Mapping
+from types import MappingProxyType
+
+from argolid import PyramidGenerartor
+from .io_utils import ensure_repo_cloned, get_local_file_path, PolusTestDataRepo
+
+
+DEFAULT_DOWNSAMPLE_METHODS: Mapping[int, str] = MappingProxyType({1: "mean"})
+
+
+def generate_pyramid_from_repo_file(
+    *,
+    repo: PolusTestDataRepo,
+    rel_image_path: Path,
+    output_dir: str | Path,
+    min_dim: int = 1024,
+    vis_type: str = "Viv",
+    downsample_methods: Mapping[int, str] = DEFAULT_DOWNSAMPLE_METHODS,
+) -> None:
+    """
+    Clone the repo if needed, locate the image file, then run Argolid pyramid generation.
+    """
+    repo_dir = ensure_repo_cloned(repo)
+    input_file = str(get_local_file_path(repo_dir, rel_image_path))
+
+    output_dir = Path(output_dir)
+    output_dir.parent.mkdir(parents=True, exist_ok=True)
+
+    pyr_gen = PyramidGenerartor()
+    pyr_gen.generate_from_single_image(
+        input_file,
+        str(output_dir),
+        min_dim,
+        vis_type,
+        dict(downsample_methods),
+    )
+
+
+def main() -> None:
+    repo = PolusTestDataRepo()
+
+    rel_image_path = Path("argolid") / "x0_y0_c1.ome.tiff"
+    output_dir = Path("output") / "one_image_ome_zarr"
+
+    generate_pyramid_from_repo_file(
+        repo=repo,
+        rel_image_path=rel_image_path,
+        output_dir=output_dir,
+        min_dim=1024,
+        vis_type="Viv",
+        downsample_methods={1: "mean"},
+    )
+
+
+if __name__ == "__main__":
+    main()

tests/python/test_multi_images.py

@@ -0,0 +1,34 @@
+import shutil
+from pathlib import Path
+
+import pytest
+
+from .io_utils import PolusTestDataRepo
+from .multi_images import generate_pyramid_from_repo_path
+from .zarr_assertions import assert_is_argolid_omexml_zarr_pyramid
+
+
+@pytest.mark.integration
+def test_stitched_image_collection_pyramid(tmp_path: Path) -> None:
+    if shutil.which("git") is None:
+        pytest.skip("git not available")
+
+    repo = PolusTestDataRepo(repo_dir=tmp_path / "polus-test-data")
+    out_dir = tmp_path / "out"
+
+    generate_pyramid_from_repo_path(
+        repo=repo,
+        file_pattern="x{x:d}_y{y:d}_c{c:d}.ome.tiff",
+        image_name="stitched_image",
+        output_dir=out_dir,
+        min_dim=1024,
+        vis_type="Viv",
+        downsample_methods={1: "mean"},
+    )
+
+    shapes = assert_is_argolid_omexml_zarr_pyramid(out_dir / "stitched_image.zarr" , expect_levels=2)
+
+    # ensure at least one spatial dimension shrinks between level 0 and 1
+    y0, x0 = shapes[0][-2], shapes[0][-1]
+    y1, x1 = shapes[1][-2], shapes[1][-1]
+    assert (y1 < y0) or (x1 < x0), f"Expected level 1 to be downsampled vs level 0, got L0={shapes[0]} L1={shapes[1]}"

tests/python/test_pytest_bridge.py

@@ -0,0 +1,32 @@
+import os
+import subprocess
+import sys
+import unittest
+from pathlib import Path
+
+
+if "PYTEST_CURRENT_TEST" in os.environ:
+    raise unittest.SkipTest("pytest bridge should not run under pytest")
+
+class TestPytestSuite(unittest.TestCase):
+    """Run pytest-based tests under unittest-driven CI."""
+    def test_pytest(self) -> None:
+        "The entry point of pytest execution"
+        tests_python = Path(__file__).resolve().parent  # tests/python
+
+        env = os.environ.copy()
+        env["PYTEST_DISABLE_PLUGIN_AUTOLOAD"] = "1"
+
+        subprocess.run(
+            [
+                sys.executable,
+                "-m",
+                "pytest",
+                "-vv",
+                "-s",
+                str(tests_python),
+            ],
+            check=True,
+            env=env,
+            timeout=900,
+        )

tests/python/test_single_image.py

@@ -0,0 +1,30 @@
+import shutil
+from pathlib import Path
+
+import pytest
+
+from .io_utils import PolusTestDataRepo
+from .single_image import generate_pyramid_from_repo_file
+from .zarr_assertions import assert_is_argolid_omexml_zarr_pyramid
+
+
+@pytest.mark.integration
+def test_single_image_pyramid(tmp_path: Path) -> None:
+    if shutil.which("git") is None:
+        pytest.skip("git not available")
+
+    repo = PolusTestDataRepo(repo_dir=tmp_path / "polus-test-data")
+    out_dir = tmp_path / "out" / "single_image"
+
+    generate_pyramid_from_repo_file(
+        repo=repo,
+        rel_image_path=Path("argolid") / "x0_y0_c1.ome.tiff",
+        output_dir=out_dir,
+    )
+
+    shapes = assert_is_argolid_omexml_zarr_pyramid(out_dir, expect_levels=2)
+
+    # ensure at least one spatial dimension shrinks between level 0 and 1
+    y0, x0 = shapes[0][-2], shapes[0][-1]
+    y1, x1 = shapes[1][-2], shapes[1][-1]
+    assert (y1 < y0) or (x1 < x0), f"Expected level 1 to be downsampled vs level 0, got L0={shapes[0]} L1={shapes[1]}"