install imagecodecs and openslide-python dependencies so additional t…

…ests will run (#634)

This MR may initially fail during wheel testing due to #626, as a few test cases relying on these packages were not being run at the time #619 was merged.

Authors:
  - Gregory Lee (https://github.com/grlee77)
  - https://github.com/jakirkham

Approvers:
  - Ray Douglass (https://github.com/raydouglass)
  - Gigon Bae (https://github.com/gigony)
  - https://github.com/jakirkham

URL: #634

ci/test_wheel.sh

@@ -9,10 +9,21 @@ RAPIDS_PY_WHEEL_NAME="cucim_${RAPIDS_PY_CUDA_SUFFIX}" rapids-download-wheels-fro
 # echo to expand wildcard before adding `[extra]` requires for pip
 python -m pip install $(echo ./dist/cucim*.whl)[test]
 
+CUDA_MAJOR_VERSION=${RAPIDS_CUDA_VERSION:0:2}
+
 # Run smoke tests for aarch64 pull requests
 if [[ "$(arch)" == "aarch64" && ${RAPIDS_BUILD_TYPE} == "pull-request" ]]; then
     python ./ci/wheel_smoke_test.py
 else
-    # TODO: revisit enabling imagecodecs package during testing
-    python -m pytest ./python/cucim
+
+    DEBIAN_FRONTEND=noninteractive apt update
+    DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends libopenslide0
+
+    if [[ ${CUDA_MAJOR_VERSION} == "11" ]]; then
+        # Omit I/O-related tests in ./python/cucim/tests due to known CUDA bug
+        # with dynamic loading of libcufile.
+        python -m pytest ./python/cucim/src/
+    else
+        python -m pytest ./python/cucim
+    fi
 fi

dependencies.yaml

@@ -262,10 +262,9 @@ dependencies:
             - opencv-python-headless>=4.6
       - output_types: [requirements, pyproject]
         packages:
-          # temporarily remove imagecodecs / openslide-python from wheel tests
-          # # skip packages on arm64 that don't provide a wheel
-          # - imagecodecs>=2021.6.8; platform_machine=='x86_64'
-          # - openslide-python>=1.1.2; platform_machine=='x86_64'
+          # skip packages on arm64 that don't provide a wheel
+          - imagecodecs>=2021.6.8; platform_machine=='x86_64'
+          - openslide-python>=1.1.2; platform_machine=='x86_64'
           - matplotlib
           - opencv-python-headless>=4.6
           - click

python/cucim/pyproject.toml

@@ -62,8 +62,10 @@ Tracker = "https://github.com/rapidsai/cucim/issues"
 test = [
     "GPUtil>=1.4.0",
     "click",
+    "imagecodecs>=2021.6.8; platform_machine=='x86_64'",
     "matplotlib",
     "opencv-python-headless>=4.6",
+    "openslide-python>=1.1.2; platform_machine=='x86_64'",
     "pooch>=1.6.0",
     "psutil>=5.8.0",
     "pytest-cov>=2.12.1",

python/cucim/tests/unit/clara/test_image_cache.py

@@ -196,6 +196,7 @@ def test_reserve_more_cache_memory():
     assert cache.miss_count == 0
 
 
+@pytest.mark.skip(reason="currently fails (gh-626)")
 def test_cache_hit_miss(testimg_tiff_stripe_32x24_16_jpeg):
     from cucim import CuImage
     from cucim.clara.cache import preferred_memory_capacity