add correct hooks for unittest and install pytest as deps in CI

Author: Vasu Jaganath

.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

pytest.ini

@@ -5,5 +5,6 @@ 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

@@ -8,7 +8,7 @@
 class PolusTestDataRepo:
     repo_url: str = "https://github.com/sameeul/polus-test-data.git"
     repo_dir: Path = Path("polus-test-data")
-    default_branch: str = "main"  # used only if you later add pull/update logic
+    default_branch: str = "main"
 
 
 def ensure_repo_cloned(repo: PolusTestDataRepo, depth: int = 1) -> Path:

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

@@ -22,11 +22,9 @@ def test_single_image_pyramid(tmp_path: Path) -> None:
         output_dir=out_dir,
     )
 
-    shapes = assert_is_argolid_omexml_zarr_pyramid(out_dir, expect_levels=2)
     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]}"
-

tests/python/zarr_assertions.py

@@ -43,7 +43,6 @@ def find_argolid_root(out_dir: Path) -> Path:
         return candidates[0]
 
     if len(candidates) > 1:
-        # deterministic choice, newest wins
         return max(candidates, key=lambda p: p.stat().st_mtime)
 
     raise FileNotFoundError(
@@ -85,7 +84,7 @@ def assert_is_argolid_omexml_zarr_pyramid(out_dir: Path, expect_levels: int | No
     series0 = data["0"]
     assert isinstance(series0, zarr.Group)
 
-    # levels can be arrays or groups, depending on how the writer stored them
+    # levels can be arrays or groups
     level_names = sorted(
         [k for k in series0.keys() if str(k).isdigit()],
         key=lambda s: int(s),
@@ -122,7 +121,6 @@ def assert_is_argolid_omexml_zarr_pyramid(out_dir: Path, expect_levels: int | No
 
         raise AssertionError(f"Unexpected type at level {lvl}: {type(node)}")
 
-    # after shapes computed:
     assert shapes, "No shapes collected from pyramid levels"
     y0, x0 = shapes[0][-2], shapes[0][-1]
     assert y0 > 0 and x0 > 0, "Each array must have non-zero shape"