Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

monai generative: refactor autoencoderkl #7552

Merged
merged 125 commits into from
Apr 23, 2024
Merged

monai generative: refactor autoencoderkl #7552

merged 125 commits into from
Apr 23, 2024

Conversation

marksgraham
Copy link
Contributor

@marksgraham marksgraham commented Mar 15, 2024 •
edited
Loading

Part of the refactoring in #7227

Description

Refactors autoencoderkl. Changes are:

  • Introduce CastToTempType class for upsampling
  • Downsample block removed and replaced by a Sequential
  • The attention block now uses MONAI's SABlock, allowing a lot of code to be removed
  • Added a load_old_state_dict that allows for models trained on MONAI Generative to be loaded in to this model, especially important given some of the MONAI Generative's model zoo uses this model. I have tested this works locally.

I discussed with @ericspod inheriting from AutoEncoder but after experimentation have decided against it as it introduced changes that made it very hard to ensure we could load model's trained in MONAI Generative.

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.

KumoLiu and others added 30 commits December 4, 2023 03:50
@KumoLiu
wholeBody_ct_segmentation failed to be download (Project-MONAI#7280)
2fc0126 
Fixes model-zoo#537



### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
update the Python version requirements for transformers (Project-MONA…
88f8dd2 
…I#7275)

Part of Project-MONAI#7250.

### Description
Fix the Python version for transformers smaller than 3.10.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: KumoLiu <[email protected]>
@kvttt @KumoLiu
7263 add diffusion loss (Project-MONAI#7272)
d5585c3 
Fixes Project-MONAI#7263.

### Description

Add diffusion loss. I also made a [demo
notebook](https://github.com/kvttt/deep-atlas/blob/main/diffusion_loss_scale_test.ipynb)
to provide some explanations and analyses of diffusion loss.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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).
- [x] 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: kaibo <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@heyufan1995
Fix swinunetrv2 2D bug (Project-MONAI#7302)
8212458 
Fixes # .

### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: heyufan1995 <[email protected]>
@KumoLiu
Fix RuntimeError in DataAnalyzer (Project-MONAI#7310)
b1c8b42 
Fixes Project-MONAI#7309

### Description

`DataAnalyzer` only catch error when data is on GPU, add catching error
when data is on CPU.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@KumoLiu
Support specified filenames in Saveimage (Project-MONAI#7318)
6126a6e 
Fixes Project-MONAI#7317 

### Description

Add support specified filename for users to save like nibabel.save.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@KumoLiu
Fix typo (Project-MONAI#7321)
4c546b3 
Fix typo.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@binliunls
fix optimizer pararmeter issue (Project-MONAI#7322)
01a0ee1 
Fixes # .

### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: binliu <[email protected]>
@KumoLiu @atbenmurray
Fix lazy ignored in SpatialPadd (Project-MONAI#7316)
90d2acb 
Fixes Project-MONAI#7314 Project-MONAI#7315.


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: Ben Murray <[email protected]>
@KumoLiu
Update openslide-python version (Project-MONAI#7344)
f5327ad
@KumoLiu
Upgrade the version of transformers (Project-MONAI#7343)
b3d7a48 
Fixes Project-MONAI#7338

### Description

transformers' version is pinned to v4.22 since
Project-MONAI#5157.
Updated the version refer to
huggingface/transformers#21678.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@dependabot
Bump github/codeql-action from 2 to 3 (Project-MONAI#7354)
02973f0 
Bumps [github/codeql-action](https://github.com/github/codeql-action)
from 2 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/github/codeql-action/releases">github/codeql-action's
releases</a>.</em></p>
<blockquote>
<h2>CodeQL Bundle v2.15.5</h2>
<p>Bundles CodeQL CLI v2.15.5</p>
<ul>
<li>(<a
href="https://github.com/github/codeql-cli-binaries/blob/HEAD/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql-cli-binaries/releases/tag/v2.15.5">release</a>)</li>
</ul>
<p>Includes the following CodeQL language packs from <a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5"><code>github/codeql@codeql-cli/v2.15.5</code></a>:</p>
<ul>
<li><code>codeql/cpp-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/cpp/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/cpp/ql/src">source</a>)</li>
<li><code>codeql/cpp-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/cpp/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/cpp/ql/lib">source</a>)</li>
<li><code>codeql/csharp-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/csharp/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/csharp/ql/src">source</a>)</li>
<li><code>codeql/csharp-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/csharp/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/csharp/ql/lib">source</a>)</li>
<li><code>codeql/go-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/go/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/go/ql/src">source</a>)</li>
<li><code>codeql/go-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/go/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/go/ql/lib">source</a>)</li>
<li><code>codeql/java-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/java/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/java/ql/src">source</a>)</li>
<li><code>codeql/java-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/java/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/java/ql/lib">source</a>)</li>
<li><code>codeql/javascript-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/javascript/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/javascript/ql/src">source</a>)</li>
<li><code>codeql/javascript-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/javascript/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/javascript/ql/lib">source</a>)</li>
<li><code>codeql/python-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/python/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/python/ql/src">source</a>)</li>
<li><code>codeql/python-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/python/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/python/ql/lib">source</a>)</li>
<li><code>codeql/ruby-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/ruby/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/ruby/ql/src">source</a>)</li>
<li><code>codeql/ruby-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/ruby/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/ruby/ql/lib">source</a>)</li>
<li><code>codeql/swift-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/swift/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/swift/ql/src">source</a>)</li>
<li><code>codeql/swift-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/swift/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.5/swift/ql/lib">source</a>)</li>
</ul>
<h2>CodeQL Bundle v2.15.4</h2>
<p>Bundles CodeQL CLI v2.15.4</p>
<ul>
<li>(<a
href="https://github.com/github/codeql-cli-binaries/blob/HEAD/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql-cli-binaries/releases/tag/v2.15.4">release</a>)</li>
</ul>
<p>Includes the following CodeQL language packs from <a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4"><code>github/codeql@codeql-cli/v2.15.4</code></a>:</p>
<ul>
<li><code>codeql/cpp-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/cpp/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/cpp/ql/src">source</a>)</li>
<li><code>codeql/cpp-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/cpp/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/cpp/ql/lib">source</a>)</li>
<li><code>codeql/csharp-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/csharp/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/csharp/ql/src">source</a>)</li>
<li><code>codeql/csharp-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/csharp/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/csharp/ql/lib">source</a>)</li>
<li><code>codeql/go-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/go/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/go/ql/src">source</a>)</li>
<li><code>codeql/go-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/go/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/go/ql/lib">source</a>)</li>
<li><code>codeql/java-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/java/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/java/ql/src">source</a>)</li>
<li><code>codeql/java-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/java/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/java/ql/lib">source</a>)</li>
<li><code>codeql/javascript-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/javascript/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/javascript/ql/src">source</a>)</li>
<li><code>codeql/javascript-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/javascript/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/javascript/ql/lib">source</a>)</li>
<li><code>codeql/python-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/python/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/python/ql/src">source</a>)</li>
<li><code>codeql/python-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/python/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/python/ql/lib">source</a>)</li>
<li><code>codeql/ruby-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/ruby/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/ruby/ql/src">source</a>)</li>
<li><code>codeql/ruby-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/ruby/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/ruby/ql/lib">source</a>)</li>
<li><code>codeql/swift-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/swift/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/swift/ql/src">source</a>)</li>
<li><code>codeql/swift-all</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/swift/ql/lib/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.4/swift/ql/lib">source</a>)</li>
</ul>
<h2>CodeQL Bundle</h2>
<p>Bundles CodeQL CLI v2.15.3</p>
<ul>
<li>(<a
href="https://github.com/github/codeql-cli-binaries/blob/HEAD/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql-cli-binaries/releases/tag/v2.15.3">release</a>)</li>
</ul>
<p>Includes the following CodeQL language packs from <a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.3"><code>github/codeql@codeql-cli/v2.15.3</code></a>:</p>
<ul>
<li><code>codeql/cpp-queries</code> (<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.3/cpp/ql/src/CHANGELOG.md">changelog</a>,
<a
href="https://github.com/github/codeql/tree/codeql-cli/v2.15.3/cpp/ql/src">source</a>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
changelog</a>.</em></p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/github/codeql-action/commit/e0c2b0a8a0cf7360f5f17b1ee83b98565e81cbaf"><code>e0c2b0a</code></a>
change version numbers inside processing function as well</li>
<li><a
href="https://github.com/github/codeql-action/commit/8e4a6c7a903526fda317aa47e226cbd5a4f1d358"><code>8e4a6c7</code></a>
improve handling of changelog processing for backports</li>
<li><a
href="https://github.com/github/codeql-action/commit/511f073971a2ce589ceea100a90831c5ca4310bb"><code>511f073</code></a>
Merge pull request <a
href="https://redirect.github.com/github/codeql-action/issues/2033">#2033</a>
from github/dependabot/npm_and_yarn/npm-0a98872b3d</li>
<li><a
href="https://github.com/github/codeql-action/commit/ebf5a837135e243d2654e281549af1ee7dc107aa"><code>ebf5a83</code></a>
Merge pull request <a
href="https://redirect.github.com/github/codeql-action/issues/2035">#2035</a>
from github/mergeback/v3.22.11-to-main-b374143c</li>
<li><a
href="https://github.com/github/codeql-action/commit/7813bda958fdd91160a45ff6cdb3a723b381c8c6"><code>7813bda</code></a>
Update checked-in dependencies</li>
<li><a
href="https://github.com/github/codeql-action/commit/2b2fb6b1dc9a83da2dd429ce0c83af9380973083"><code>2b2fb6b</code></a>
Update changelog and version after v3.22.11</li>
<li><a
href="https://github.com/github/codeql-action/commit/b374143c1149a9115d881581d29b8390bbcbb59c"><code>b374143</code></a>
Merge pull request <a
href="https://redirect.github.com/github/codeql-action/issues/2034">#2034</a>
from github/update-v3.22.11-64e61baea</li>
<li><a
href="https://github.com/github/codeql-action/commit/95591babe868195080e3ca2c641042066f097f3d"><code>95591ba</code></a>
Merge branch 'main' into dependabot/npm_and_yarn/npm-0a98872b3d</li>
<li><a
href="https://github.com/github/codeql-action/commit/e2b5cc75ce46a4a33dbafa57e19019d6bd5a67be"><code>e2b5cc7</code></a>
Update changelog for v3.22.11</li>
<li>See full diff in <a
href="https://github.com/github/codeql-action/compare/v2...v3">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=github/codeql-action&package-manager=github_actions&previous-version=2&new-version=3)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump actions/upload-artifact from 3 to 4 (Project-MONAI#7350)
38ac573 
Bumps
[actions/upload-artifact](https://github.com/actions/upload-artifact)
from 3 to 4.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's
releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h2>What's Changed</h2>
<p>The release of upload-artifact@v4 and download-artifact@v4 are major
changes to the backend architecture of Artifacts. They have numerous
performance and behavioral improvements.</p>
<p>For more information, see the <a
href="https://github.com/actions/toolkit/tree/main/packages/artifact"><code>@​actions/artifact</code></a>
documentation.</p>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/vmjoseph"><code>@​vmjoseph</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/upload-artifact/pull/464">actions/upload-artifact#464</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/upload-artifact/compare/v3...v4.0.0">https://github.com/actions/upload-artifact/compare/v3...v4.0.0</a></p>
<h2>v3.1.3</h2>
<h2>What's Changed</h2>
<ul>
<li>chore(github): remove trailing whitespaces by <a
href="https://github.com/ljmf00"><code>@​ljmf00</code></a> in <a
href="https://redirect.github.com/actions/upload-artifact/pull/313">actions/upload-artifact#313</a></li>
<li>Bump <code>@​actions/artifact</code> version to v1.1.2 by <a
href="https://github.com/bethanyj28"><code>@​bethanyj28</code></a> in <a
href="https://redirect.github.com/actions/upload-artifact/pull/436">actions/upload-artifact#436</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/upload-artifact/compare/v3...v3.1.3">https://github.com/actions/upload-artifact/compare/v3...v3.1.3</a></p>
<h2>v3.1.2</h2>
<ul>
<li>Update all <code>@actions/*</code> NPM packages to their latest
versions- <a
href="https://redirect.github.com/actions/upload-artifact/issues/374">#374</a></li>
<li>Update all dev dependencies to their most recent versions - <a
href="https://redirect.github.com/actions/upload-artifact/issues/375">#375</a></li>
</ul>
<h2>v3.1.1</h2>
<ul>
<li>Update actions/core package to latest version to remove
<code>set-output</code> deprecation warning <a
href="https://redirect.github.com/actions/upload-artifact/issues/351">#351</a></li>
</ul>
<h2>v3.1.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Bump <code>@​actions/artifact</code> to v1.1.0 (<a
href="https://redirect.github.com/actions/upload-artifact/pull/327">actions/upload-artifact#327</a>)
<ul>
<li>Adds checksum headers on artifact upload (<a
href="https://redirect.github.com/actions/toolkit/pull/1095">actions/toolkit#1095</a>)
(<a
href="https://redirect.github.com/actions/toolkit/pull/1063">actions/toolkit#1063</a>)</li>
</ul>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/upload-artifact/commit/c7d193f32edcb7bfad88892161225aeda64e9392"><code>c7d193f</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-artifact/issues/466">#466</a>
from actions/v4-beta</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/13131bb095770b4070a7477c3cd2d96e1c16d9f4"><code>13131bb</code></a>
licensed cache</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/4a6c273b9834f66a1d05c170dc3f80f9cdb9def1"><code>4a6c273</code></a>
Merge branch 'main' into v4-beta</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/f391bb91a3d3118aeca171c365bb319ece276b37"><code>f391bb9</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-artifact/issues/465">#465</a>
from actions/robherley/v4-documentation</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/9653d03c4b74c32144e02dae644fea70e079d4b3"><code>9653d03</code></a>
Apply suggestions from code review</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/875b63076402f25ef9d52c294c86ba4f97810575"><code>875b630</code></a>
add limitations section</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/ecb21463e93740a6be75c3116242169bfdbcb15a"><code>ecb2146</code></a>
add compression example</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/5e7604f84a055838f64ed68bb9904751523081ae"><code>5e7604f</code></a>
trim some repeated info</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/d6437d07581fe318a364512e6cf6b1dca6b4f92c"><code>d6437d0</code></a>
naming</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/1b561557037b4957d7d184e9aac02bec86c771eb"><code>1b56155</code></a>
s/v4-beta/v4/g</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/upload-artifact/compare/v3...v4">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/upload-artifact&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump actions/setup-python from 4 to 5 (Project-MONAI#7351)
454f89c 
Bumps [actions/setup-python](https://github.com/actions/setup-python)
from 4 to 5.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/setup-python/releases">actions/setup-python's
releases</a>.</em></p>
<blockquote>
<h2>v5.0.0</h2>
<h2>What's Changed</h2>
<p>In scope of this release, we update node version runtime from node16
to node20 (<a
href="https://redirect.github.com/actions/setup-python/pull/772">actions/setup-python#772</a>).
Besides, we update dependencies to the latest versions.</p>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0">https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0</a></p>
<h2>v4.8.0</h2>
<h2>What's Changed</h2>
<p>In scope of this release we added support for GraalPy (<a
href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a>).
You can use this snippet to set up GraalPy:</p>
<pre lang="yaml"><code>steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 
  with:
    python-version: 'graalpy-22.3' 
- run: python my_script.py
</code></pre>
<p>Besides, the release contains such changes as:</p>
<ul>
<li>Trim python version when reading from file by <a
href="https://github.com/FerranPares"><code>@​FerranPares</code></a> in
<a
href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
<li>Use non-deprecated versions in examples by <a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
<li>Change deprecation comment to past tense by <a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/723">actions/setup-python#723</a></li>
<li>Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/743">actions/setup-python#743</a></li>
<li>advanced-usage.md: Encourage the use actions/checkout@v4 by <a
href="https://github.com/cclauss"><code>@​cclauss</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/729">actions/setup-python#729</a></li>
<li>Examples now use checkout@v4 by <a
href="https://github.com/simonw"><code>@​simonw</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/738">actions/setup-python#738</a></li>
<li>Update actions/checkout to v4 by <a
href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
in <a
href="https://redirect.github.com/actions/setup-python/pull/761">actions/setup-python#761</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a
href="https://github.com/FerranPares"><code>@​FerranPares</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
<li><a href="https://github.com/timfel"><code>@​timfel</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a></li>
<li><a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4...v4.8.0">https://github.com/actions/setup-python/compare/v4...v4.8.0</a></p>
<h2>v4.7.1</h2>
<h2>What's Changed</h2>
<ul>
<li>Bump word-wrap from 1.2.3 to 1.2.4 by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/702">actions/setup-python#702</a></li>
<li>Add range validation for toml files by <a
href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
in <a
href="https://redirect.github.com/actions/setup-python/pull/726">actions/setup-python#726</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4...v4.7.1">https://github.com/actions/setup-python/compare/v4...v4.7.1</a></p>
<h2>v4.7.0</h2>
<p>In scope of this release, the support for reading python version from
pyproject.toml was added (<a
href="https://redirect.github.com/actions/setup-python/pull/669">actions/setup-python#669</a>).</p>
<pre lang="yaml"><code>      - name: Setup Python
        uses: actions/setup-python@v4
&lt;/tr&gt;&lt;/table&gt; 
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/setup-python/commit/0a5c61591373683505ea898e09a3ea4f39ef2b9c"><code>0a5c615</code></a>
Update action to node20 (<a
href="https://redirect.github.com/actions/setup-python/issues/772">#772</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/0ae58361cdfd39e2950bed97a1e26aa20c3d8955"><code>0ae5836</code></a>
Add example of GraalPy to docs (<a
href="https://redirect.github.com/actions/setup-python/issues/773">#773</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/b64ffcaf5b410884ad320a9cfac8866006a109aa"><code>b64ffca</code></a>
update actions/checkout to v4 (<a
href="https://redirect.github.com/actions/setup-python/issues/761">#761</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/8d2896179abf658742de432b3f203d2c2d86a587"><code>8d28961</code></a>
Examples now use checkout@v4 (<a
href="https://redirect.github.com/actions/setup-python/issues/738">#738</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/7bc6abb01e0555719edc2dbca70a2fde309e5e56"><code>7bc6abb</code></a>
advanced-usage.md: Encourage the use actions/checkout@v4 (<a
href="https://redirect.github.com/actions/setup-python/issues/729">#729</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/e8111cec9d3dc15220d8a3b638f08419f57b906a"><code>e8111ce</code></a>
Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 (<a
href="https://redirect.github.com/actions/setup-python/issues/743">#743</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/a00ea43da65e7c04d2bdae58b3afecd77057eb9e"><code>a00ea43</code></a>
add fix for graalpy ci (<a
href="https://redirect.github.com/actions/setup-python/issues/741">#741</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/8635b1ccc5934e73ed3510980fd2e7790b85839b"><code>8635b1c</code></a>
Change deprecation comment to past tense (<a
href="https://redirect.github.com/actions/setup-python/issues/723">#723</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/f6cc428f535856f9c23558d01765a42a4d6cf758"><code>f6cc428</code></a>
Use non-deprecated versions in examples (<a
href="https://redirect.github.com/actions/setup-python/issues/724">#724</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/5f2af211d616f86005883b44826180b21abb4060"><code>5f2af21</code></a>
Add GraalPy support (<a
href="https://redirect.github.com/actions/setup-python/issues/694">#694</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/setup-python/compare/v4...v5">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/setup-python&package-manager=github_actions&previous-version=4&new-version=5)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump actions/download-artifact from 3 to 4 (Project-MONAI#7352)
db6e81d 
Bumps
[actions/download-artifact](https://github.com/actions/download-artifact)
from 3 to 4.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/download-artifact/releases">actions/download-artifact's
releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h2>What's Changed</h2>
<p>The release of upload-artifact@v4 and download-artifact@v4 are major
changes to the backend architecture of Artifacts. They have numerous
performance and behavioral improvements.</p>
<p>For more information, see the <a
href="https://github.com/actions/toolkit/tree/main/packages/artifact"><code>@​actions/artifact</code></a>
documentation.</p>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/bflad"><code>@​bflad</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/download-artifact/pull/194">actions/download-artifact#194</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/download-artifact/compare/v3...v4.0.0">https://github.com/actions/download-artifact/compare/v3...v4.0.0</a></p>
<h2>v3.0.2</h2>
<ul>
<li>Bump <code>@actions/artifact</code> to v1.1.1 - <a
href="https://redirect.github.com/actions/download-artifact/pull/195">actions/download-artifact#195</a></li>
<li>Fixed a bug in Node16 where if an HTTP download finished too quickly
(&lt;1ms, e.g. when it's mocked) we attempt to delete a temp file that
has not been created yet <a
href="hhttps://redirect.github.com/actions/toolkit/pull/1278">actions/toolkit#1278</a></li>
</ul>
<h2>v3.0.1</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/download-artifact/pull/178">Bump
<code>@​actions/core</code> to 1.10.0</a></li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/download-artifact/commit/f44cd7b40bfd40b6aa1cc1b9b5b7bf03d3c67110"><code>f44cd7b</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/download-artifact/issues/259">#259</a>
from actions/robherley/glob-downloads</li>
<li><a
href="https://github.com/actions/download-artifact/commit/3181fe853d2c9a606cd326853bf4c5b8ced5df02"><code>3181fe8</code></a>
add some migration docs</li>
<li><a
href="https://github.com/actions/download-artifact/commit/aaaac7b403f278b6b7eebdca69ca1658616f1c57"><code>aaaac7b</code></a>
licensed cache</li>
<li><a
href="https://github.com/actions/download-artifact/commit/7c9182f0e18dadedfbca3189ab7a22a416aa6714"><code>7c9182f</code></a>
update readme</li>
<li><a
href="https://github.com/actions/download-artifact/commit/b94e7015566b40b2de5eeeda514f239968da2dd7"><code>b94e701</code></a>
licensed cache</li>
<li><a
href="https://github.com/actions/download-artifact/commit/0b55470e40ab7435f445813ebc18b1107ecf7e32"><code>0b55470</code></a>
add test case for globbed downloads to same directory</li>
<li><a
href="https://github.com/actions/download-artifact/commit/0b51c2ef9042b581aded9711127e4a6d5f71c550"><code>0b51c2e</code></a>
update prettier/eslint versions</li>
<li><a
href="https://github.com/actions/download-artifact/commit/c4c6db724f9510b2b3cff5ebcc417c87a2b2fa97"><code>c4c6db7</code></a>
support globbing artifact list &amp; merging download directory</li>
<li><a
href="https://github.com/actions/download-artifact/commit/1bd0606e08fcaa4c28afc1fc7d45830ab5482dac"><code>1bd0606</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/download-artifact/issues/252">#252</a>
from stchr/patch-1</li>
<li><a
href="https://github.com/actions/download-artifact/commit/eff4d42b1f6ff704c7a0f37152ed8793673560ef"><code>eff4d42</code></a>
fix default for run-id</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/download-artifact/compare/v3...v4">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/download-artifact&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump peter-evans/slash-command-dispatch from 3.0.1 to 3.0.2 (Project-…
8fa6931 
…MONAI#7353)

Bumps
[peter-evans/slash-command-dispatch](https://github.com/peter-evans/slash-command-dispatch)
from 3.0.1 to 3.0.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/peter-evans/slash-command-dispatch/releases">peter-evans/slash-command-dispatch's
releases</a>.</em></p>
<blockquote>
<h2>Slash Command Dispatch v3.0.2</h2>
<h2>What's Changed</h2>
<ul>
<li>fix: replace use of any type by <a
href="https://github.com/peter-evans"><code>@​peter-evans</code></a> in
<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/152">peter-evans/slash-command-dispatch#152</a></li>
<li>fixing link to <code>Get a pull request</code> by <a
href="https://github.com/Borda"><code>@​Borda</code></a> in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/270">peter-evans/slash-command-dispatch#270</a></li>
<li>Update getting-started.md due to changes in Github UI by <a
href="https://github.com/martin-displayr"><code>@​martin-displayr</code></a>
in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/289">peter-evans/slash-command-dispatch#289</a></li>
<li>[Security] Fix GraphQL query to get a collaborator's permission by
<a href="https://github.com/0xn3va"><code>@​0xn3va</code></a> in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/301">peter-evans/slash-command-dispatch#301</a></li>
<li>129 dependency updates by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/Borda"><code>@​Borda</code></a> made
their first contribution in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/270">peter-evans/slash-command-dispatch#270</a></li>
<li><a
href="https://github.com/martin-displayr"><code>@​martin-displayr</code></a>
made their first contribution in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/289">peter-evans/slash-command-dispatch#289</a></li>
<li><a href="https://github.com/0xn3va"><code>@​0xn3va</code></a> made
their first contribution in <a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/pull/301">peter-evans/slash-command-dispatch#301</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/peter-evans/slash-command-dispatch/compare/v3.0.1...v3.0.2">https://github.com/peter-evans/slash-command-dispatch/compare/v3.0.1...v3.0.2</a></p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/f996d7b7aae9059759ac55e978cff76d91853301"><code>f996d7b</code></a>
Fix the CollaboratorPermission GraphQL query (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/301">#301</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/05b97d641c7ed206082e7984193d314070260d44"><code>05b97d6</code></a>
build(deps-dev): bump <code>@​types/node</code> from 16.18.65 to
16.18.67 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/300">#300</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/8e7007329b5b0d971d44b9558606eed52edbdda6"><code>8e70073</code></a>
build(deps-dev): bump eslint from 8.54.0 to 8.55.0 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/299">#299</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/bd00135609f8bb0e709eea67f2a294f928fd1e7a"><code>bd00135</code></a>
build(deps-dev): bump <code>@​types/node</code> from 16.18.62 to
16.18.65 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/298">#298</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/ee873b6d3d1e6ae67120bcfb3e807c1d11502741"><code>ee873b6</code></a>
build(deps-dev): bump eslint from 8.53.0 to 8.54.0 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/296">#296</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/44abc47f988dc0de6261fb54747b79de67b6af0d"><code>44abc47</code></a>
build(deps-dev): bump <code>@​types/node</code> from 16.18.61 to
16.18.62 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/295">#295</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/19ad7b830c1554acf2ccefe7f3ff5566750d5e9b"><code>19ad7b8</code></a>
build(deps-dev): bump <code>@​types/node</code> from 16.18.60 to
16.18.61 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/294">#294</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/29a9815e9ffe9a5b9b4367e4b76770bcb468a7e7"><code>29a9815</code></a>
build(deps-dev): bump prettier from 3.0.3 to 3.1.0 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/293">#293</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/ade03097a3cb6e69e3ed86210ec745493dacf6bc"><code>ade0309</code></a>
build(deps-dev): bump eslint from 8.52.0 to 8.53.0 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/292">#292</a>)</li>
<li><a
href="https://github.com/peter-evans/slash-command-dispatch/commit/fc8222e6761738cc303ace6ed030f7fe63d6da0c"><code>fc8222e</code></a>
build(deps-dev): bump <code>@​types/node</code> from 16.18.59 to
16.18.60 (<a
href="https://redirect.github.com/peter-evans/slash-command-dispatch/issues/291">#291</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/peter-evans/slash-command-dispatch/compare/v3.0.1...v3.0.2">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=peter-evans/slash-command-dispatch&package-manager=github_actions&previous-version=3.0.1&new-version=3.0.2)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@KumoLiu @ericspod
Give more useful exception when batch is considered during matrix mul…
445d750 
…tiplication (Project-MONAI#7326)

Fixes Project-MONAI#7323

### Description

Give more useful exception when batch is considered during matrix
multiplication.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>
@KumoLiu
Fix incorrectly size compute in auto3dseg analyzer (Project-MONAI#7374)
d7137cf 
Fixes Project-MONAI#7222

### Description
remove int convert here.

https://github.com/Project-MONAI/MONAI/blob/8fa6931b14ba9617a595fff1d396ac44cc82e207/monai/auto3dseg/analyzer.py#L259

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@kvttt
7380 mention demo in bending energy and diffusion docstrings (Project…
e1ffa7e 
…-MONAI#7381)

Fixes Project-MONAI#7380.

### Description

Mention
[demo](https://github.com/Project-MONAI/tutorials/blob/main/modules/bending_energy_diffusion_loss_notes.ipynb)
in bending energy and diffusion docstrings.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: kaibo <[email protected]>
@KumoLiu
Pin gdown version to v4.6.3 (Project-MONAI#7384)
25f1901 
Workaround for Project-MONAI#7382 Project-MONAI#7383

### Description

Based on the comment
[here](wkentaro/gdown#291 (comment)),
pin the gdown version as a workaround. Will review this one once gdown
has some update internal.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: YunLiu <[email protected]>
@KumoLiu
Fix Premerge (Project-MONAI#7397)
78295c7 
Fixes Project-MONAI#7396


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@vlaminckaxel
Track applied operations in image filter (Project-MONAI#7395)
80be1c3 
Fixes Project-MONAI#7394 

### Description

When ImageFilter is in the transformation sequence it didn't pass the
applied_operations.
Now it is passed when present.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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).
- [x] 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: axel.vlaminck <[email protected]>
@KumoLiu @ericspod @pre-commit-ci
Add compile support in SupervisedTrainer and SupervisedEvaluator (
facf176 
Project-MONAI#7375)

Fixes # .

### Description

Add `compile` support in `SupervisedTrainer` and `SupervisedEvaluator`.
Convert to `torch.Tensor` internally.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@KumoLiu @pre-commit-ci
Fix CUDA_VISIBLE_DEVICES setting ignored (Project-MONAI#7408)
abe2e31 
Fixes Project-MONAI#7407

### Description

Move `optional import cucim` inside the function to avoid using all
GPUs.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@KumoLiu
Fix Incorrect updated affine in NrrdReader and update docstring in …
6c9e49e 
…`ITKReader` (Project-MONAI#7415)

Fixes Project-MONAI#7414
Fixes Project-MONAI#7371


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@KumoLiu
Ignore E704 after update black (Project-MONAI#7422)
df4cf92 
Fixes Project-MONAI#7421

### Description
https://pypi.org/project/black/24.1.1/

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: YunLiu <[email protected]>
@marksgraham
Merge branch 'dev' into gen-ai-dev
7086b36
@marksgraham
Merge branch 'gen-ai-dev' of github.com:marksgraham/MONAI into gen-ai…
61a9f73 
…-dev
@marksgraham
Merge branch 'dev' into gen-ai-dev
81d34c6
@KumoLiu
update rm -rf /opt/hostedtoolcache avoid change the python version (P…
cd36c1c 
…roject-MONAI#7424)

Fixes Project-MONAI#7416

### Description

update `rm -rf /opt/hostedtoolcache` avoid change the python version

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
monai-bot and others added 4 commits April 19, 2024 05:28
@monai-bot
Auto3DSeg algo_template hash update (Project-MONAI#7674)
ffd4454 
Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>
@freddiewanah @KumoLiu
Fixed four test issues within test code. (Project-MONAI#7662)
224c47a 
### Description

This PR fixed the three issues within the test code that could cause
problems during CICD.

Three issues:

tests/test_pad_collation.py line 120: supposed to be assertEqual, but
not assertTure? or it will always be true.
tests/test_to_numpy.py line 74: Same as above.
tests/test_auto3dseg.py line 370: typo? two same asserts next to each
other.
tests/test_compose.py line 719, 725, 727: Should be assertEqual instead
of assertTrue

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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`.
- [x] 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: Han Wang <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@freddiewanah @KumoLiu
Adapt to use assert raises (Project-MONAI#7670)
7a6b69f 
### Description

Some test cases use try/except command, instead of catch exceptions with
assertRaise. This will cause extra execution time according to the
experimental tests.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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`.
- [x] 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: Han Wang <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@SomeUserName1 @KumoLiu
MedicalNetPerceptualSimilarity: Add multi-channel (Project-MONAI#7568)
03a5fa6 
Fixes Project-MONAI#7567 .

### Description
MedicalNetPerceptualSimilarity: Add multi-channel support for 3Dvolumes.
The current version of the code in the dev branch already largely
supports that besides the following:
medicalnet_* require inputs to have a single channel. 
This PR passes the multi-channel volume channel-wise to the networks and
concatenates the resulting feature vectors.
The existing code takes care of averaging over channels and spatially.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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).
- [x] 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: Fabian Klopfer <[email protected]>
Co-authored-by: YunLiu <[email protected]>
KumoLiu
KumoLiu reviewed Apr 19, 2024
View reviewed changes
Copy link
Contributor

@KumoLiu KumoLiu left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the PR. Overall looks good to me.
Several comments inline. Not much seems to need changing, so perhaps we can do the next one. After @ericspod returns, if there are no comments, I will try to merge this one. Thanks.

monai/networks/blocks/upsample.py Outdated Show resolved Hide resolved
monai/networks/blocks/upsample.py Show resolved Hide resolved
monai/networks/nets/autoencoderkl.py Outdated Show resolved Hide resolved
monai/networks/nets/autoencoderkl.py Outdated Show resolved Hide resolved
monai/networks/nets/autoencoderkl.py Outdated Show resolved Hide resolved
monai/networks/nets/spade_autoencoderkl.py Outdated Show resolved Hide resolved
monai/networks/nets/autoencoderkl.py Show resolved Hide resolved
tests/test_autoencoderkl.py Show resolved Hide resolved
tests/test_spade_autoencoderkl.py Show resolved Hide resolved
KumoLiu and others added 7 commits April 22, 2024 09:07
@KumoLiu
Workaround for B909 in flake8-bugbear (Project-MONAI#7691)
c6bf8e9 
Workaround for Project-MONAI#7690

### Description
Updated with flake8-bugbear, causing the B909 error. A workaround fix
was made for the flake8-bugbear version because the 24.4.21 update
contained some false positives.
Fore more information, see
PyCQA/flake8-bugbear#467

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

Signed-off-by: YunLiu <[email protected]>
@marksgraham @KumoLiu
Update monai/networks/blocks/upsample.py
a9cee62 
Co-authored-by: YunLiu <[email protected]>
Signed-off-by: Mark Graham <[email protected]>
@marksgraham @KumoLiu
Update monai/networks/nets/autoencoderkl.py
37a286f 
Co-authored-by: YunLiu <[email protected]>
Signed-off-by: Mark Graham <[email protected]>
@marksgraham @KumoLiu
Update monai/networks/nets/autoencoderkl.py
618da31 
Co-authored-by: YunLiu <[email protected]>
Signed-off-by: Mark Graham <[email protected]>
@KumoLiu @pre-commit-ci
Fix AttributeError in 'PerceptualLoss' (Project-MONAI#7693)
178ebc8 
Fixes Project-MONAI#7692

### Description

Fix AttributeError in 'PerceptualLoss' 

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@marksgraham
Requested changes
46c39dc
@marksgraham
Adds 3d cases
a3bc49e 
Signed-off-by: Mark Graham <[email protected]>
@KumoLiu KumoLiu requested a review from ericspod April 22, 2024 15:17
@KumoLiu
Copy link
Contributor

KumoLiu commented Apr 22, 2024

Will set DCO pass for this pr: https://github.com/Project-MONAI/MONAI/pull/7552/checks?check_run_id=24109528540

Do you have any concern? @Nic-Ma @ericspod @marksgraham

@KumoLiu
Copy link
Contributor

KumoLiu commented Apr 22, 2024

And @marksgraham, could you please take a look at the ci error, looks like many tests failed. Thanks!

@marksgraham
Code formatting
90d96ca 
Signed-off-by: Mark Graham <[email protected]>
@marksgraham
Attempted fix for upsampling
7d3cc2d 
Signed-off-by: Mark Graham <[email protected]>
@marksgraham
Nice without negation
2356591 
Signed-off-by: Mark Graham <[email protected]>
@marksgraham
Copy link
Contributor Author

@KumoLiu fixed the CI, shall i merge in dev to get your fix for the code format error?

KumoLiu and others added 5 commits April 23, 2024 09:28
@KumoLiu
Always convert input to C-order in distance_transform_edt (Project-MO…
ac9b186 
…NAI#7675)

Fixes Project-MONAI#7660

`indices_` may not always be a shallow copy for F-order input as it
constantly converts to C-order

https://github.com/Project-MONAI/MONAI/blob/ffd4454b576abd4eaae30b364f41c213e30dca4c/monai/transforms/utils.py#L2209

https://github.com/Project-MONAI/MONAI/blob/ffd4454b576abd4eaae30b364f41c213e30dca4c/monai/utils/type_conversion.py#L262

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.

---------

Signed-off-by: YunLiu <[email protected]>
@monai-bot @KumoLiu
Auto3DSeg algo_template hash update (Project-MONAI#7695)
a59676f 
Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@freddiewanah @KumoLiu
Merge similar test components with parameterized (Project-MONAI#7663)
ec6aa33 
### Description

I noticed some test cases contain same duplicated asserts. Having
multiple asserts in one test cases can cause potential issues like when
the first assert fails, the test case stops and won't check the second
assert. By using @parameterized.expand, this issue can be resolved and
the caching also saves execution time.

Added sign-offs from  Project-MONAI#7648 

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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`.
- [x] 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: Han Wang <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@k-sukharev @KumoLiu
Add ResNet backbones for FlexibleUNet (Project-MONAI#7571)
dc58e5c 
Fixes Project-MONAI#7570.

### Description

Add ResNet backbones (with option to use pretrained Med3D weights) for
FlexibleUNet.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Konstantin Sukharev <[email protected]>
Co-authored-by: YunLiu <[email protected]>
@marksgraham
Merge dev
45992f8
@KumoLiu
Copy link
Contributor

KumoLiu commented Apr 23, 2024

Hi @ericspod, do you have any other comment on this pr otherwise I think we can merge this one?

BTW, next time let we merge dev in a seperate PR which could avoid too much files changed.

Thanks!

@KumoLiu
Copy link
Contributor

KumoLiu commented Apr 23, 2024

/build

@ericspod
Copy link
Member

@KumoLiu I had discussed things with @marksgraham and we've concluded that whatever refactors we can do are great but there's a lot we can't without breaking compatibility. I'm confident this code is good in general since we've been using it within the other repo for a while now.

We definitely need a cleaner approach to syncing with dev in these feature branches since 810 changes files is a lot! I hope this doesn't pollute the git history when we go to merge this feature branch.

Thanks both!

@KumoLiu KumoLiu enabled auto-merge (squash) April 23, 2024 14:58
@KumoLiu KumoLiu merged commit ba188e2 into Project-MONAI:gen-ai-dev Apr 23, 2024
28 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@KumoLiu KumoLiu KumoLiu left review comments

@ericspod ericspod ericspod approved these changes

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

@atbenmurray atbenmurray Awaiting requested review from atbenmurray

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.