### Description

Adds (optional) kernel_size parameter to UpSample, used for deconv
(convolution transpose up-sampling).

This allows to upsample, e.g to upscale to 2x with a kernel_size 3.
(currently the default is to upscale to 2x with a kernel size 2)

if this parameter is not set, the behavior is the same as before


### 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.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: myron <[email protected]>

Fixes #4812 


### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: a-parida12 <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5251

### Description
replace `None` with `"none"` in the readers

### 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`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Can Zhao <[email protected]>

Fixes #5250.

### Description

Fixed bug that allow_low_quality_matches in set_regular_matcher was
always set to True and it's not using value from the argument, in
retinanet.

### 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`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Can Zhao <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Co-authored-by: monai-bot <[email protected]>

<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.34.0 →
v2.38.2](asottile/pyupgrade@v2.34.0...v2.38.2)
- [github.com/asottile/yesqa: v1.3.0 →
v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/hadialqattan/pycln: v1.3.5 →
v2.1.1](hadialqattan/pycln@v1.3.5...v2.1.1)
<!--pre-commit.ci end-->

Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5253 

### Description
enhance computing offset for spacing

### 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`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #4320
it seems we also have sufficient modules to close #3542


### 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: Wenqi Li <[email protected]>

# Patching CVE-2007-4559

Hi, we are security researchers from the Advanced Research Center at
[Trellix](https://www.trellix.com). We have began a campaign to patch a
widespread bug named CVE-2007-4559. CVE-2007-4559 is a 15 year old bug
in the Python tarfile package. By using extract() or extractall() on a
tarfile object without sanitizing input, a maliciously crafted .tar file
could perform a directory path traversal attack. We found at least one
unsantized extractall() in your codebase and are providing a patch for
you via pull request. The patch essentially checks to see if all tarfile
members will be extracted safely and throws an exception otherwise. We
encourage you to use this patch or your own solution to secure against
CVE-2007-4559. Further technical information about the vulnerability can
be found in this
[blog](https://www.trellix.com/en-us/about/newsroom/stories/research/tarfile-exploiting-the-world.html).

If you have further questions you may contact us through this projects
lead researcher [Kasimir Schulz](mailto:[email protected]).

Signed-off-by: monai-bot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <[email protected]>

This adds an additional UpSample mode DECONVGROUP to upsample with
groupwise convolution transpose.
Unit tests are passed too. 
 

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: myron <[email protected]>

Signed-off-by: binliu <[email protected]>

Fixes #5187 .

### Description

Updated the docstring of the is_pad parameter in flexible-unet.

### 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]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #4206

### Description
Currently ninja+jit is not tested on the cpu-only cases,
this adds ninja (optional dep.) and premerge tests on ubuntu for ninja +
jit extension.

### Status
**Ready**

### 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: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5090

### Description
update version numbers

### 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: Wenqi Li <[email protected]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5176.

### Description
Remove batch dim in `SobelGradients` and `SobelGradientsd` to make it
consistent with other post transforms.

### 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]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5177.

### Description

Add channel dim in `ComputeHoVerMaps` and `ComputeHoVerMapsd` to make it
consistent with other transforms.

### 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]>
Co-authored-by: Behrooz Hashemian <[email protected]>

Fixes #5031.

### Description
Update federated learning figure. Using SVG format. Also removes from
svg from gitignore.

### 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: Holger Roth <[email protected]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5209.

### Description
Fix typo in `RandScaleIntensityd`

### 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).
- [x] In-line docstrings updated.

Signed-off-by: KumoLiu <[email protected]>

fixes #5193 
fixes #5204

### Description

revise the import error messages and ignore a torchaudio warning.

### 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`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

…ey()` default (#5213)

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5211
Fixes #5214

### Description
- set device based on the first item:
```py
device = self.rand_2d_elastic.device
if device is None and isinstance(d[first_key], torch.Tensor):
    device = d[first_key].device  # type: ignore
    self.rand_2d_elastic.set_device(device)
```

- simplied transform `first_key()` default to a tuple

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #3844

### Description
adding the flexibility for skipping the transform if the pixdim is in
the specified range

### 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: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #4264 .

### Description

This PR adds the antialiasing option for `Resized` transform.

### 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: Yiheng Wang <[email protected]>

…les (#5224)

### Description

Some users may have models that take adjoint information. This PR allows
the adjoint information to be passed through the visualisation classes
to the model via `**kwargs`.

Also combined the test files of GradCAM and GradCAM++ as they were the
same.

### 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).
- [x] New tests added to cover the changes.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.

Signed-off-by: Richard Brown <[email protected]>

### Description

We should be using `PY_EXE` in runtests as opposed to raw `pip`.

### 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).

Signed-off-by: Richard Brown <[email protected]>

Fixes #5232 .

### Description

According to user's feedback, this PR enhanced the MONAI bundle doc page
to include tutorial examples and model-zoo info.

### 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: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5163

### Description

enhance metatensor compatibility for `OneOf`

### 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`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5233 .

### Description

This PR added file existing check for the logging config, requested by
@holgerroth .

### 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: Nic Ma <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5225 .

### Description
1. fix 1d data error in `VarAutoEncoder`
2. add `use_sigmoid` flag

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: KumoLiu <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

1. Fix the issue #5227 
2. fix a small code flaw

Signed-off-by: David <[email protected]>

Signed-off-by: Holger Roth <[email protected]>

Fixes #5195.

### Description

Add support for MonaiAlgo to be run with torchrun for multi-gpu
training.

### 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: Holger Roth <[email protected]>

Fixes #5218 

### Description

This PR moves `HoVerNet` Mode and Branch outside of the module and make
them independent `StrEnums`.

### 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).
- [x] 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.

Signed-off-by: Behrooz <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ers` (#5732)

Fixes #.

### Description

- When the image is large, the number of instances may exceed np.uint8,
so the default dtype should set to `np.int64`
- a workaround way to add `FillHoles` before
`generate_instance_contour`, may prevent the issue when instances
contain hole

### 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]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5750.

### Description
Change dim in Sobel gradient which have been discussed in
#5503.

### 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]>

Signed-off-by: Sachidanand Alle <[email protected]>

Current MLFlow Handler fails when you invoke 2 train requests back to
back with different URI. Or multiple train requests within the same
process. This is mainly for using global array where it saves active
experiment, active run and others share the same. This will cause
conflicts between 2 invokes with 2 different URI.

Fixes
------
- Use MLFlow Client to create experiment/runs instead of global
functions.
- Save the current run through the lifecycle of handler. If any handler
has the same experiment name and same run name, the metrics all will be
merged as part of the same run (e.g. train and validation handler).
- If the run name is not provided (fall back on default) then last
active run within the same experiment (sorted based on start time) is
used for adding the metrics.

The above two conditions will help create similar behavior compared to
using `mlflow.active_run()`


Verified
---------
- Running single and multi gpu training on bundles
  - spleen_ct_segmentation_v0.1.0
  - spleen_deepedit_annotation_v0.1.0
  - swin_unetr_btcv_segmentation_v0.1.0
- Running Training workflows for both single and multi gpu in MONAI
Label
- Verified against running shared/single tracking URI (where all the
experiments get saved)
- Verified against individual eval/mlruns per bundle/workflow

> I suggest, original owner of this handler to verify/test all the
behaviors that were currently supported.

Error Description
---------

Error stack when you run two train workflows with in the same process
(simply one after another).
```
[2022-12-13 21:08:11,095] [4047823] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/localhome/sachi/.local/lib/python3.10/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/fastapi/applications.py", line 199, in __call__
    await super().__call__(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/middleware/errors.py", line 181, in __call__
    raise exc from None
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/middleware/errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/middleware/cors.py", line 78, in __call__
    await self.app(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/exceptions.py", line 82, in __call__
    raise exc from None
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/routing.py", line 580, in __call__
    await route.handle(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/routing.py", line 241, in handle
    await self.app(scope, receive, send)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/starlette/routing.py", line 52, in app
    response = await func(request)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/fastapi/routing.py", line 219, in app
    raw_response = await run_endpoint_function(
  File "/localhome/sachi/.local/lib/python3.10/site-packages/fastapi/routing.py", line 152, in run_endpoint_function
    return await dependant.call(**values)
  File "/localhome/sachi/Projects/monailabel/monailabel/endpoints/train.py", line 96, in api_run_model
    return run_model(model, params, run_sync, enqueue)
  File "/localhome/sachi/Projects/monailabel/monailabel/endpoints/train.py", line 55, in run_model
    res, detail = AsyncTask.run("train", request=request, params=params, force_sync=run_sync, enqueue=enqueue)
  File "/localhome/sachi/Projects/monailabel/monailabel/utils/async_tasks/task.py", line 43, in run
    return instance.train(request), None
  File "/localhome/sachi/Projects/monailabel/monailabel/interfaces/app.py", line 422, in train
    result = task(request, self.datastore())
  File "/localhome/sachi/Projects/monailabel/monailabel/tasks/train/basic_train.py", line 458, in __call__
    res = self.train(0, world_size, req, datalist)
  File "/localhome/sachi/Projects/monailabel/monailabel/tasks/train/basic_train.py", line 545, in train
    context.trainer.run()
  File "/localhome/sachi/Projects/MONAI/monai/engines/trainer.py", line 53, in run
    super().run()
  File "/localhome/sachi/Projects/MONAI/monai/engines/workflow.py", line 281, in run
    super().run(data=self.data_loader, max_epochs=self.state.max_epochs)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 892, in run
    return self._internal_run()
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 935, in _internal_run
    return next(self._internal_run_generator)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 993, in _internal_run_as_gen
    self._handle_exception(e)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 636, in _handle_exception
    self._fire_event(Events.EXCEPTION_RAISED, e)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "/localhome/sachi/Projects/MONAI/monai/handlers/stats_handler.py", line 181, in exception_raised
    raise e
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 946, in _internal_run_as_gen
    self._fire_event(Events.STARTED)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/ignite/engine/engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "/localhome/sachi/Projects/MONAI/monai/handlers/mlflow_handler.py", line 183, in start
    self._delete_exist_param_in_dict(attrs)
  File "/localhome/sachi/Projects/MONAI/monai/handlers/mlflow_handler.py", line 141, in _delete_exist_param_in_dict
    log_data = self.client.get_run(cur_run.info.run_id).data
  File "/localhome/sachi/.local/lib/python3.10/site-packages/mlflow/tracking/client.py", line 150, in get_run
    return self._tracking_client.get_run(run_id)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/mlflow/tracking/_tracking_service/client.py", line 72, in get_run
    return self.store.get_run(run_id)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/mlflow/store/tracking/file_store.py", line 623, in get_run
    run_info = self._get_run_info(run_id)
  File "/localhome/sachi/.local/lib/python3.10/site-packages/mlflow/store/tracking/file_store.py", line 646, in _get_run_info
    raise MlflowException(
mlflow.exceptions.MlflowException: Run '1765aea084a3417586d052d9d8240039' not found
FAILED                                                                                                                                                           [ 72%]

```


### 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: Sachidanand Alle <[email protected]>

### Description

Enable auto3dseg maximize gpu utilization based on gpus in higher API
levels.

### 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: Dong Yang <[email protected]>
Signed-off-by: dongy <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Dong Yang <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: dongy <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

part of #5626
changelog updates

### 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: Wenqi Li <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Co-authored-by: monai-bot <[email protected]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5714.

### Description
Add warning in `GenerateSuccinctContour` and skip invalid instance.

### 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]>

Signed-off-by: binliu <[email protected]>
### Description

Add a multi-thread unit test for mlflow handler.

### 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]>

…reate_test_image_2d (#5627)

Signed-off-by: OeslleLucena <[email protected]>

Fixes #5373.

### Description
Change the `synthetic.py` script to have the (height, width, depth)
format.
Edit all the tests that uses `create_test_image_3d` to match the new
format.

### 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.
- [x] 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: OeslleLucena <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

part of #5626


### 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: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Signed-off-by: Wenqi Li <[email protected]>


### 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: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5679  and #5320

### Description

This PR adds the support of download bundles from ngc:
https://catalog.ngc.nvidia.com/models?filters=&orderBy=scoreDESC&query=monai
In addition, when "version" is not provided, it changes to download the
latest version in default.

### 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: Yiheng Wang <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

part of #5626


### 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: Wenqi Li <[email protected]>

… reflect unification of epoch-based training (#5763)

Signed-off-by: dongy <[email protected]>

### Description

- Update ALGO_HASH to support `num_workers` override
- Update test cases.

### 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).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.

Signed-off-by: dongy <[email protected]>
Co-authored-by: dongy <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5770 .

### Description

This PR enables the `remove_prefix` arg in `monai.bundle.load`

### 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: Yiheng Wang <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

  - update citation.cff
  - update weekly-preview version number
  - closes #5626

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5776 


### 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: Wenqi Li <[email protected]>

Fixes #5793 .

### Description

This PR provides a workaround for the incompatible sphinx 6.0.0

### 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: Yiheng Wang <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <[email protected]>

VarAutoEncoder.__init__() got an unexpected keyword argument
'dimensions' because now it is called spatial_dims.

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5775 .

### Description

This PR fixes the issue of `_get_latest_bundle_version` on Windows
(`os.path.join` will produce backslash which will create a wrong url)
Thanks @SachidanandAlle for finding this issue.

### 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: Yiheng Wang <[email protected]>

<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 →
v4.4.0](pre-commit/pre-commit-hooks@v4.3.0...v4.4.0)
- [github.com/asottile/pyupgrade: v2.38.2 →
v3.3.1](asottile/pyupgrade@v2.38.2...v3.3.1)
- [github.com/hadialqattan/pycln: v2.1.1 →
v2.1.2](hadialqattan/pycln@v2.1.1...v2.1.2)
<!--pre-commit.ci end-->

fixes #5805

Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Signed-off-by: kbressem <[email protected]>

Fixes #3178

### Description
As discussed in #3178, this PR adds a more general interface to apply
simple convolutions to images. This PR (re-)implements 2D and 3D
versions for mean filtering, edge detection, outline detection, mask
dilatation and image sharpening.

### Detailed description
The main transform is `ImageFilter`. It comes with some preset filters
that can be initialized using a string. Available presets are `["mean",
"laplace", "elliptical", "sobel", "sharpen", "median", "gauss",
"savitzky_golay"]`. For example, a transformation for mean filtering can
be created with:

```python
mean_filter = ImageFilter("mean", 3)
```
`ImageFilter` automatically detects whether the input is 2D or 3D and
creates the appropriate filter on the first call. This filter will then
be used in future calls of the transformation, so switching between 2D
and 3D images is not supported.

The initialization form string is only a convenience function. All
preset filters are also available in
`monai.networks.layers.simplelayers` as `nn.Module` subclasses.
ImageFilter` can also be created directly from an `nn.Module`. For
example, to create a transformation for mean filtering, the following is
also possible:

```python
filter_3d = MeanFilter(spatial_dims=3, size=3)
mean_filter = ImageFilter(filter_3d)
```

In this example, however, the filter size is predefined and is not
automatically derived from the input.
In addition, it is also possible to use custom filters with
`ImageFilter` using a `torch.Tensor` or `numpy.ndarray`. For example:

```python
filter_3d = torch.ones(3,3,3)
mean_filter = ImageFilter(filter_3d)
```

`RandImageFilter` is a randomizable variant of `ImageFilter` that
executes with probability `p` on each call. Both `ImageFilter` and
`RandImageFilter` also have dictionary versions.



### 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.
- [x] 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: kbressem <[email protected]>

Fixes #5653.

### Description

A new utility decorator that enables us to warn users of a changing
default argument.
Current implementation does the following:
- If version < since no warning will be printed.
- If the default argument is explicitly set by the caller no warning
will be printed.
- If since <= version < replaced a warning like this will be printed:
"Default of argument `{name}` has been deprecated since version
`{since}` from `{old_default}` to `{new_default}`. It will be changed in
version `{replaced}`."
- If replaced <= version a warning like this will be printed: "Default
of argument `{name}` was changed in version `{changed}` from
`{old_default}` to `{new_default}`."
- It doesn't validate the `old_default`, so you can even use this in
scenarios where the default is actually `None` but set later in the
function. This also enables us to set `old_default` to any string if the
default is e.g. not printable.
- The only validation that will throw an error is, if the `new_default`
== the actual default and version < replaced. Which means, that somebody
replaced the value already, before the version was incremented. Apart
from that also any value for `new_default` can be set, giving the same
advantages as for the `old_default`.

### 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).
- [x] New tests added to cover the changes.
- [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: Felix Schnabel <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5782

### Description
- adds 'mode' and 'align_corners' options to the blocks and nets
- fixes a few typos

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5624 
Fixes #5816 

### Description

- undo the workaround
(29a34ad)
- smaller test case tests/test_auto3dseg_ensemble.py

### 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: Wenqi Li <[email protected]>

Signed-off-by: KumoLiu <[email protected]>

Fixes #5609.

### Description
Update the docstring for `HoVerNet` and `UpSample`.

### 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`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: KumoLiu <[email protected]>