Merge genaidev Into Dev

[ericspod]

Fixes # .

Description

At the moment this is a test to see if the conflicts and erroneously changed files can be resolved.

Types of changes

• [x] 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.

[ericspod]

I've set DCO to pass again. My email should be configured correctly now. I attempted the remediation commit but that added a second remediation entry for myself instead. The given instructions are perhaps incorrect?

[KumoLiu]

There are still many changes not related to the gen-ai-dev. Perhaps we should cherry-pick and make the merge clean? @ericspod @virginiafdez

[ericspod]

There are still many changes not related to the gen-ai-dev. Perhaps we should cherry-pick and make the merge clean? @ericspod @virginiafdez

I think the only unrelated changes now are some I made to fix some pylint errors I had encountered. The things that need fixing are from the conflict merging I tried to do.

[KumoLiu]

Hi @ericspod, could you please help fix this mypy issue, then I will help trigger more tests and merge this PR? https://github.com/Project-MONAI/MONAI/actions/runs/9867041090/job/27246782050?pr=7886#step:7:360 Thanks!

[ericspod]

Hi @KumoLiu I have gone through the PR with @virginiafdez and we're happy with it and all tests pass. A number of changes I did were to do with mypy code checking. The issue is that variables need to always exist in every code path, in many places variables are only assigned in one or another if-elif branch based on conditions that we know to be satisfied eventually. The code checker doesn't know this so the fix is to "declare" the variable first with an initial assignment.

[KumoLiu]

/build

[KumoLiu]

Hi @ericspod @virginiafdez, remaining issue in the blossom ci. ENV: torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu111

[2024-07-19T06:09:52.702Z] ======================================================================
[2024-07-19T06:09:52.702Z] ERROR: test_compatibility_with_monai_generative (tests.test_transformer.TestDecoderOnlyTransformer)
[2024-07-19T06:09:52.702Z] ----------------------------------------------------------------------
[2024-07-19T06:09:52.702Z] Traceback (most recent call last):
[2024-07-19T06:09:52.702Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_transformer.py", line 105, in test_compatibility_with_monai_generative
[2024-07-19T06:09:52.702Z]     net.load_old_state_dict(torch.load(weight_path), verbose=False)
[2024-07-19T06:09:52.702Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/networks/nets/transformer.py", line 141, in load_old_state_dict
[2024-07-19T06:09:52.702Z]     new_state_dict[f"{block}.attn.qkv.weight"] = torch.concat(
[2024-07-19T06:09:52.702Z] AttributeError: module 'torch' has no attribute 'concat'
[2024-07-19T06:09:52.702Z] 
[2024-07-19T06:09:52.702Z] ----------------------------------------------------------------------

[ericspod]

Hi @ericspod @virginiafdez, remaining issue in the blossom ci.

This should just be a matter of changing the alias concat to cat.

[KumoLiu]

/build

[KumoLiu]

/build

[ericspod]

@KumoLiu I think we're good now if you wanted to review anything I've commented on above.

[KumoLiu]

May need @virginiafdez approve to merge the PR.

[virginiafdez]

Done! I didn't add any comment because I checked this with Eric yesterday.

---

From: YunLiu @.> Sent: 19 July 2024 16:31 To: Project-MONAI/MONAI @.> Cc: Virginia Fernandez @.>; Mention @.> Subject: Re: [Project-MONAI/MONAI] Merge genaidev Into Dev (PR #7886)

May need @virginiafdezhttps://github.com/virginiafdez approve to merge the PR.

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