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install imagecodecs and openslide-python dependencies so additional tests will run #634

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merged 13 commits into from
Dec 4, 2023
Merged

install imagecodecs and openslide-python dependencies so additional tests will run #634

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dbaebab
install imagecodecs and openslide-python dependencies needed by a sma…
grlee77 Nov 17, 2023
cac9f41
try setting LD_LIBRARY_PATH to include libopenslide location
grlee77 Nov 17, 2023
ccaa73c
print openslide location during wheel testing
grlee77 Nov 17, 2023
9b042e1
install libopenslide-dev on x86_64
grlee77 Nov 17, 2023
099fb01
Update ci/test_wheel.sh
grlee77 Nov 18, 2023
103e119
Merge branch 'branch-23.12' into grelee/install-additional-test-case-…
grlee77 Nov 18, 2023
b644477
call apt update first
grlee77 Nov 18, 2023
29a5e14
skip the specific test cases that fail on CI
grlee77 Nov 20, 2023
55dbf6e
remove debug/testing lines from the test_wheel.sh script
grlee77 Nov 20, 2023
68bb75d
Merge branch 'branch-23.12' into grelee/install-additional-test-case-…
jakirkham Nov 29, 2023
6a318cd
skip clara module tests on CUDA 11 only
grlee77 Dec 1, 2023
9cce4bf
Merge branch 'branch-24.02' into grelee/install-additional-test-case-…
jakirkham Dec 1, 2023
829dd9c
Merge branch 'branch-24.02' into grelee/install-additional-test-case-…
jakirkham Dec 4, 2023
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10 changes: 8 additions & 2 deletions ci/test_wheel.sh
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Expand Up @@ -13,6 +13,12 @@ python -m pip install $(echo ./dist/cucim*.whl)[test]
if [[ "$(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

# TODO: fix and remove two test cases skipped here
# test_cache_hit_miss currently fails
# test_converter passes, but a segfault occurs on pytest exit when it is enabled
python -m pytest ./python/cucim -k "not test_converter and not test_cache_hit_miss"
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Would it be possible to move these to PyTest decorators?

We could also use skipif to more carefully restrict when they are skipped

@pytest.mark.skip(reason="currently fails")
def test_cache_hit_miss():
    ...
 
@pytest.mark.skip(reason="passes, but a segfault occurs on pytest exit when it is enabled")
def test_converter():
    ...

fi
7 changes: 3 additions & 4 deletions dependencies.yaml
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Expand Up @@ -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
2 changes: 2 additions & 0 deletions python/cucim/pyproject.toml
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Expand Up @@ -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",
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