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Fix deprecated argument in 'scipy.sparse.linalg.cg'#7897

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ericspod merged 20 commits into
Project-MONAI:devfrom
KumoLiu:cg
Jul 6, 2024
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Fix deprecated argument in 'scipy.sparse.linalg.cg'#7897
ericspod merged 20 commits into
Project-MONAI:devfrom
KumoLiu:cg

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@KumoLiu KumoLiu commented Jul 2, 2024

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Fixes #7896

Description

  • 'scipy.sparse.linalg.cg' keyword argument tol is deprecated in favor of rtol and will be removed in SciPy v1.14.0. Until then, if set, it will override rtol. So update to use rtol in cg.

  • Drop python 3.8 test in packaging and premerge-gpu-test.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
KumoLiu added 2 commits July 2, 2024 13:01
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented Jul 2, 2024

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/build

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented Jul 2, 2024

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/build

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@YanxuanLiu

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/build

@KumoLiu

KumoLiu commented Jul 2, 2024

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Hi @ericspod and @Nic-Ma, I dropped Python3.8 test in ".github/workflows/pythonapp.yml" since scipy requires Python>=3.9.
fb28a3f#diff-cbf97851bdfebccf2fcdd8848c6a93adb8d8affd5c6b1faf00238d528c3ef6cb

Since 3.8 has come to an end, do you have any concern on this change?

@KumoLiu

KumoLiu commented Jul 2, 2024

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/build

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KumoLiu commented Jul 2, 2024

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/build

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KumoLiu commented Jul 2, 2024

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/build

KumoLiu added 2 commits July 2, 2024 22:56
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented Jul 4, 2024

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/build

KumoLiu added 2 commits July 4, 2024 13:37
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented Jul 4, 2024

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/build

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KumoLiu commented Jul 4, 2024

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/build

KumoLiu added 4 commits July 4, 2024 18:07
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
KumoLiu and others added 6 commits July 5, 2024 17:41
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented Jul 5, 2024

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/build

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KumoLiu commented Jul 5, 2024

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Add a numpy version requirement as a workaround in this commit: 5ce2be9
Since multiprocessing with numpy 1.26.4 has some issue in Python3.0. Refer to
https://github.com/pytorch/pytorch/blob/e7ab7b83bc36825c102987a26b4a199f97674561/.ci/docker/common/install_conda.sh#L83

@ericspod ericspod merged commit 64ea76d into Project-MONAI:dev Jul 6, 2024
@KumoLiu KumoLiu deleted the cg branch July 17, 2024 09:03
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cg() got an unexpected keyword argument 'tol'

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