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BUG: Fix PathMNIST tests and add automatic rerun for CIFAR tests #319

Merged

kenza-bouzid merged 47 commits into main from kenzab/mount_pathmnist_tests

Apr 26, 2022

Contributor

kenza-bouzid commented Apr 21, 2022 •

edited

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No longer rely on medmnist package to download PathMNIST dataset
Downloading PathMNIST on the fly from hi-ml
Add pytest marker flaky to automatically rerun CIFAR tests
Upgrade cucim
add --max_run_duration parameter to limit aml test runs

kenza-bouzid added 13 commits

April 19, 2022 15:59


          add max_run_duration

4919f1a


          wip mounting dataset on the fly

2ac6778


          get workspace separately

78ddd86

wip

ce3eaf0

wip

cefed6a

wip

f67fabd


          Revert "wip"

38ca9e7

This reverts commit f67fabd.


          Revert "wip"

4da9057

This reverts commit cefed6a.

wip

040efe6


          Merge remote-tracking branch 'origin/main' into kenzab/mount_pathmnis…

e0302a4

…t_tests


          fix tests

25d2c2c


          add automatic rerun for cifar tests

1be5f39


          update requirements

99efcd7

ant0nsc approved these changes

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hi-ml-histopathology/testhisto/testhisto/mocks/base_data_generator.py Outdated Show resolved Hide resolved

test_requirements.txt Outdated Show resolved Hide resolved

kenza-bouzid added 16 commits

April 22, 2022 13:35

wip

539c98e


          linting

2e72823


          sort requirements

d2f22ae


          fix path

6448add


          add logs

24c8360


          download instead of mount

9e22077


          upgrade monai

19332a4


          rebase env

8bb7c13


          try with cuCIM backend

5e94b02

wip

9fe6ea4


          remove slides test in cpu mode

de0e764


          fix tests

acaa158


          upgrade cucim

dd7228a


          fix typo

acbb076


          add flaky marker

6a2441c


          teardown tests

413ab8b


          rename param

97ae3f5

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/mocks/base_data_generator.py Outdated Show resolved Hide resolved


          rename tmp_path param to avoid confusing with pytest fixture

vale-salvatelli reviewed

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hi-ml-histopathology/environment.yml Show resolved Hide resolved

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/mocks/slides_generator.py Outdated Show resolved Hide resolved

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/mocks/tiles_generator.py Outdated Show resolved Hide resolved

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Contributor

vale-salvatelli left a comment

Looks good to me. Left a couple of minor comments

hi-ml-histopathology/testhisto/testhisto/mocks/base_data_generator.py Outdated Show resolved Hide resolved

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/mocks/tiles_generator.py Outdated Show resolved Hide resolved


          Update hi-ml-histopathology/testhisto/testhisto/mocks/base_data_gener…

9ddf43c

…ator.py

Co-authored-by: vale-salvatelli <vale-salvatelli@users.noreply.github.com>

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hi-ml-azure/src/health_azure/utils.py Outdated Show resolved Hide resolved

kenza-bouzid added 3 commits

April 26, 2022 09:10


          fix paths

a318448


          add clarifying variables

aab2138


          fix imports

3d11f18

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/models/test_deepmil.py Outdated Show resolved Hide resolved

mebristo reviewed

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hi-ml-histopathology/testhisto/testhisto/models/test_deepmil.py Show resolved Hide resolved


          rebase context manager

78ea9ba

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kenza-bouzid and others added 3 commits

April 26, 2022 09:26


          add logs

e5e912d


          fix docstring

dfdf652


          remove trailing space

80853b1

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hi-ml-histopathology/testhisto/testhisto/models/test_deepmil.py Outdated Show resolved Hide resolved

kenza-bouzid added 4 commits

April 26, 2022 10:42


          fix typo

b5021f1


          Merge remote-tracking branch 'origin/main' into kenzab/mount_pathmnis…

a8d44d7

…t_tests


          Merge remote-tracking branch 'origin/main' into kenzab/mount_pathmnis…

52bc608

…t_tests


          update tmp_path_to_pathmnist_dataset

d837411

mebristo approved these changes

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kenza-bouzid merged commit b47b901 into main

kenza-bouzid deleted the kenzab/mount_pathmnist_tests branch

April 26, 2022 14:25

kenza-bouzid mentioned this pull request

Add a max_run_duration flag for the GPU tests #309

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