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]>

…5813)

part of #5804.

### Description

This adds a simple attribute access for ConfigParser so

```python
from monai.bundle import ConfigParser
parser = ConfigParser({"a":"b"})
a = parser.get_parsed_content("a")
```
can be rewritten to
```python
from monai.bundle import ConfigParser
parser = ConfigParser({"a":"b"})
a = parser.a
```
This only works for variables/methods that are not included in
ConfigParser so e.g. `parser.config` would still get the whole config.
This PR only supports shallow attribute accesses, since the returned
value will be a `dict` where you need to use `["key"]` to get the
content.

### 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`.

Signed-off-by: Felix Schnabel <[email protected]>

running the 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).

Fixes #5823.

### Description
This PR types following decorators:
- `deprecated`
- `deprecated_arg`
- `deprecated_arg_default`

Found
[here](https://github.com/Project-MONAI/MONAI/blob/dev/monai/utils/deprecate_utils.py).
It also fixes any typing issues that occurred because of the additional
typing.

Secondly, it fixes untyped decorator usage of the `ignite` library
(because of `optional_import`) for
[Workflow](https://github.com/Project-MONAI/MONAI/blob/34d713f9887a85f140630a75e9261b89f0005c84/monai/engines/workflow.py#L45)
and
[IgniteMetric](https://github.com/Project-MONAI/MONAI/blob/f9d472af05ceb56513771ea2faccebb79edc1a7a/monai/handlers/ignite_metric.py#L36).

### 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] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.

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

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

Fixes #5833


### 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: Wenqi Li <[email protected]>

Fixes #5835.

### Description
Use `from __future__ import annotations` in all source files using
annotations, so we have consistent usage (and not only in ~5 files).
The new annotations are also more readable e.g.
`Optional[Union[List[str], str]]` vs. `list[str] | str | None`.

Secondly, this issue includes changing `from typing import Callable,
Sequence, ...` to `from collections.abc import Callable, Sequence, ...`
since the ones in the `typing` module are deprecated. They are
interchangeable even for `isinstance` checks (see also [this
stackoverflow
thread](https://stackoverflow.com/questions/62547848/should-isinstance-check-against-typing-or-collections-abc)).

### 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] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.

Signed-off-by: Felix Schnabel <[email protected]>

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

fixes #5779

### 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.


review torch 1.12 tests and upgrade to the latest (1.13+)

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

### Description

This PR exclude `CuCIM`, `CuCIMD`, `RandCuCIM`, and `RandCuCIMD` wrapper
transfrom from `get_transform_backends` as they are not supposed to
support torch or numpy necessarily.

### 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: Behrooz <[email protected]>

Signed-off-by: Mikael Brudfors
[[email protected]](mailto:[email protected])

part of #5740

### Description


Makes the binary and categorical metrics from MetricsReloaded available
in MONAI via a wrapper module (`monai/metrics/wrapper.py`).

This module allows to use the MetricsReloaded metrics as, e.g.:
```py
import torch
from monai.metrics import MetricsReloadedBinary

metric_name = "Cohens Kappa"
metric = MetricsReloadedBinary(metric_name=metric_name)

# first iteration
# shape [batch=1, channel=1, 2, 2]
y_pred = torch.tensor([[[[1.0, 0.0], [0.0, 1.0]]]])
y = torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]])
print(metric(y_pred, y))

# second iteration
# shape [batch=1, channel=1, 2, 2]
y_pred = torch.tensor([[[[1.0, 0.0], [0.0, 0.0]]]])
y = torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]])
print(metric(y_pred, y))

# aggregate
# shape ([batch=2, channel=1])
print(metric.aggregate(reduction="none"))  # tensor([[0.5], [0.2]])

# reset
metric.reset()
```

Tests of all metrics are in `tests/test_metrics_reloaded.py`.

Note that MetricsReloaded is an optional dependency of MONAI; so in
order to use the wrapper, MONAI needs to be installed with:
```sh
pip install '.[metricsreloaded]'
```

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

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

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

Fixes #5844

- improves the error message when slicing data with inconsistent
metadata
- fixes an indexing case:
```
x = MetaTensor(np.zeros((10, 3, 4)))
x[slice(1, 0)]  # should return zero length data
```

### 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]>

Fixes #5855

### 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.


Test pre-merge pipeline only!

### Description

We noted it was possible to instantiate classes derived from DenseNet
only if spatial_dims, in_channels, and out_channels parameters were
passed by keywords.
Passing them via positional scheme was not working.
This small bug should be fixed now.

### Example:
Before my fix:
```
import monai
net = monai.networks.nets.DenseNet(3,1,2) # Working
net = monai.networks.nets.DenseNet121(3,1,2) # NOT woking
net = monai.networks.nets.DenseNet121(spatial_dims=3, in_channels=1, out_channels=2) # Woking
```

After my fix:
```
import monai
net = monai.networks.nets.DenseNet121(3,1,2) # Woking
```

Thanks to @robsver for pointing this issue out.

### 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 #5852

### Description
1. the following partial instantiate doesn't work
```py
config = {"import statements": "$import math", 
          "calc": {"_target_": "math.isclose", "a": 0.001, "b": 0.001}}
print(ConfigParser(config).calc())
```
with an error message:
```
Component to instantiate must represent a valid class or function, but got math.isclose.
Traceback (most recent call last):
  File "test.py", line 4, in <module>
    print(ConfigParser(config).calc())
TypeError: isclose() missing required argument 'a' (pos 1)
```

because `math.isclose` is a builtin type but not a function:

```py
import inspect
inspect.isfunction(math.isclose)  # False
inspect.isbuiltin(math.isclose)  # True
```

the `partial` should support `callable` including builtin functions


2. also this PR supports `_target_` of reference object's methods such
as partial init:
```py
"forward": {"_target_": "$@model().forward", "x": "$torch.rand(1, 3, 256, 256)"}
```

### 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]>

Add ITK to the list of optional dependencies.

### Types of changes
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [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: Dženan Zukić <[email protected]>

Fixes #1840 .

### Description

I integrated the trainable bilateral filter layer (TBF) in the MONAI
repository as a new PyTorch filter layer. The TBF contains an analytical
gradient derivation toward its filter parameters and its noisy input
image which enables gradient-based optimization within the PyTorch
graph. See [here](https://doi.org/10.1002/mp.15718) for more details on
the gradient derivation. Unit tests were added that check the filter
output as well as the gradient computation.

### 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: Fabian Wagner <[email protected]>

Fixes #5862.

### Description

if `untyped_storage()` is present (pytorch 2) use it, else use
`storage()`.

### 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: Richard Brown <[email protected]>

Fixes #5865 

### 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: Suraj Pai <[email protected]>

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

Fixes #5875 .

### Description

Add warning in `RandHistogramShift` when the image's intensity is a
single value.

### 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: KumoLiu <[email protected]>

Fixes Project-MONAI/research-contributions#235

### Description
- also add `from monai.networks.utils import has_nvfuser_instance_norm`,
so that it can be used by external algos.

the current import failure was triggered here

https://github.com/NVIDIA/apex/blob/0da3ffb92ee6fbe5336602f0e3989db1cd16f880/apex/normalization/instance_norm.py#L15-L16

### 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]>

### Description

For torchvision models, the parameter `pretrained` is deprecated since
0.13 and may be removed in the future. Our `TorchVisionFC` model has
been using this parameter. This PR updated `TorchVisionFC` to remove
calling pretrained and instead to call `weights` with appropriate
defaults without any change in the functionality (backward compatible).

### 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`.

---------

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

### Description
https://github.com/charliermarsh/ruff

### 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>

Fixes #6404



### 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]>

Fixes
https://blossom.nvidia.com/dlmed-clara-jenkins/blue/organizations/jenkins/Monai-notebooks/detail/Monai-notebooks/814/pipeline/132.

### Description

-
Project-MONAI/research-contributions@23ea143


### 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: Mingxin Zheng <[email protected]>

Bug fix of bcprun commandline format

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]>

…tinaNet (#6393)

Fixes #6330  .

### Description

add support of list for 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`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

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

Fixes #6409


### 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]>

…6411)

Fixes #6410 .

### Description

- Add allow_skip switch let user determine if it is okay to skip some
Algo
- Force the integration to test all algorithms, especially SegresNet2D

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

---------

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

Fixes #5903 .

### Description

This PR added support to automatically set MLFlow `run_name` in the
MonaiAlgo.

### 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]>

Fixes # .

### Description

Fixed the problem with import_bundle_history with algo trained outside
autorunner. If outside autorunner, the algo_object.pkl will not have
score meta, and import_bundle_history will not recognize the algo as
trained. Changed that to read progress.yaml.

Fixed the OOM problem during ensembling. Move to CPU if OOM. Also do not
append prediction tensors to list and return. Save each predictions
separately and return the save path.

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

### Description

According to the discussion with @holgerroth and @wyli , to make the
args of `MonaiAlgo` more clear, this PR adjusted the order. In the
future versions, we will simplify to only use `TrainWorflow` and
`EvalWorkflow` and deprecate bundle related args.

### 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]>

fixes #6249

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

---------

Signed-off-by: Walter Hugo Lopez Pinaya <[email protected]>
Co-authored-by: Pedro F. da Costa <[email protected]>
Co-authored-by: Mark Graham <[email protected]>

Fixes #6420 .

### Description

Fix version in requirements.txt

### 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: Mingxin Zheng <[email protected]>

Fixes #6417 .

### Description

- Move the logics of creating ensemble output dir from `ensemble` to
`__init__` in EnsembleRunner to avoid processes competing with each
other in dir creation
- Add checks in AutoRunner `set_image_save_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).
- [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: Mingxin Zheng <[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]>

Fixes #6426

### Description
only warn when checking the most recent applied operations

### 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 #6222

### Description
nonbreaking change extending the current mode+padding mode combinations.

### 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 #6433 .

### Description

- Move the SaveImage Transform setters back to `ensemble` method to
ensure DDP is initiated
- Use RankFilter to suppress logging for rank >0
- Minor updates such as renaming and 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).
- [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: Mingxin Zheng <[email protected]>

If you run the following pipeline with lazy resampling it breaks as the
pending info contains a 3x3 affine transform and there are 4x4 affine
transforms already in the list:

```
[Flip(0), Flip(1), Rotate90(1), Zoom(0.8), NormalizeIntensity()]
```

Although it could be fixed by ensuring that Zoom always puts out a 4x4
affine, the more flexible and pragmatic solution is to promote 2d affine
transforms to 3d affine transforms as a matter of course. This way we
never have the issue that a given transform (particularly potential 3rd
party transforms modified for lazy execution) can subsequently cause
this problem.



### 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: Ben Murray <[email protected]>

Fixes #6435 .

### Description

In this PR, the changes are
- Make `template_path` a property that's available for all Algo classes
to find the path to instantiate the class. The default value of
`template_path` is None.
- Enhance `algo_from_pickle` function by making it search in a few
candidate directories to instantiate the `Algo` class if needed.
- Remove checking if an algo instance is `BundleAlgo` in HPO logics
because `template_path` is universal for all `Algo` now.
- Update out-of-date docstring for AutoRunner

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

---------

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

- auto adjust buffer_dim for images with small last time, such as
768x768x128 CTs
- fixes a small bug when buffered mode is not attempted



### 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]>

Fixes #6442 .

### Description

This PR is used to fix the thread safe issue of DynUNet. Created list in
forward function is replaced by a tensor.

### 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]>

Fixes #6424 .

### Description

This PR added support to register customized app required properties to
the `BundleWorkflow`, then check and access the properties.

### 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: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fixes #6415  .

### Description

Fix the mlflow handler bug. When running a bundle with ` MLFLowHandler`
back to back without assigning the run name , the later run info will be
recorded into the former run, although the former run is finished. This
PR checks the status of runs and filters the finished ones.

### 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: binliu <[email protected]>

Bumps
[peter-evans/create-or-update-comment](https://github.com/peter-evans/create-or-update-comment)
from 2 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/peter-evans/create-or-update-comment/releases">peter-evans/create-or-update-comment's
releases</a>.</em></p>
<blockquote>
<h2>Create or Update Comment v3.0.0</h2>
<h2>What's new</h2>
<ul>
<li>Now supports replacing reactions on a comment by setting input
<code>reactions-edit-mode</code> to <code>replace</code>. The default
behaviour has not changed and will <code>append</code> reactions.</li>
<li>Chose how the action should append the comment body with input
<code>append-separator</code>. The default behaviour is to add a
<code>newline</code>. Other options are <code>space</code> and
<code>none</code>.</li>
<li><code>body-file</code> is deprecated in favour of
<code>body-path</code>. The behaviour is unchanged.</li>
</ul>
<h2>What's Changed</h2>
<ul>
<li>v3 by <a
href="https://github.com/peter-evans"><code>@​peter-evans</code></a> in
<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/161">peter-evans/create-or-update-comment#161</a></li>
<li>Update some links in the README by <a
href="https://github.com/Kurt-von-Laven"><code>@​Kurt-von-Laven</code></a>
in <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/152">peter-evans/create-or-update-comment#152</a></li>
<li>9 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/Kurt-von-Laven"><code>@​Kurt-von-Laven</code></a>
made their first contribution in <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/152">peter-evans/create-or-update-comment#152</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/peter-evans/create-or-update-comment/compare/v2.1.1...v3.0.0">https://github.com/peter-evans/create-or-update-comment/compare/v2.1.1...v3.0.0</a></p>
<h2>Create or Update Comment v2.1.1</h2>
<p>⚙️ Fixes the recent Json5 vulnerability.</p>
<h2>What's Changed</h2>
<ul>
<li>11 dependency updates by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/peter-evans/create-or-update-comment/compare/v2.1.0...v2.1.1">https://github.com/peter-evans/create-or-update-comment/compare/v2.1.0...v2.1.1</a></p>
<h2>Create or Update Comment v2.1.0</h2>
<p>⭐ Adds input <code>body-file</code>, the path to a file containing
the comment body.</p>
<h2>What's Changed</h2>
<ul>
<li>Replace set-output by <a
href="https://github.com/peter-evans"><code>@​peter-evans</code></a> in
<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/130">peter-evans/create-or-update-comment#130</a></li>
<li>Bump chuhlomin/render-template from 1.5 to 1.6 by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/132">peter-evans/create-or-update-comment#132</a></li>
<li>Support reading body from a file by <a
href="https://github.com/umanghome"><code>@​umanghome</code></a> in <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/115">peter-evans/create-or-update-comment#115</a></li>
<li>Add input body-file by <a
href="https://github.com/peter-evans"><code>@​peter-evans</code></a> in
<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/133">peter-evans/create-or-update-comment#133</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/umanghome"><code>@​umanghome</code></a>
made their first contribution in <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/115">peter-evans/create-or-update-comment#115</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/peter-evans/create-or-update-comment/compare/v2.0.1...v2.1.0">https://github.com/peter-evans/create-or-update-comment/compare/v2.0.1...v2.1.0</a></p>
<h2>Create or Update Comment v2.0.1</h2>
<p>⚙️ Bumps <code>@actions/core</code> to transition away from <a
href="https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/">deprecated
runner commands</a>.</p>
<h2>What's Changed</h2>
<ul>
<li>Add workflow permissions by <a
href="https://github.com/peter-evans"><code>@​peter-evans</code></a> in
<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/pull/120">peter-evans/create-or-update-comment#120</a></li>
<li>9 dependency updates by <a
href="https://github.com/github-actions"><code>@​github-actions</code></a>
and <a
href="https://github.com/dependabot">https://github.com/dependabot</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/peter-evans/create-or-update-comment/compare/v2.0.0...v2.0.1">https://github.com/peter-evans/create-or-update-comment/compare/v2.0.0...v2.0.1</a></p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/3383acd359705b10cb1eeef05c0e88c056ea4666"><code>3383acd</code></a>
v3 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/161">#161</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/9c6357680f5ea232e8afaf4efc0cc92367110d78"><code>9c63576</code></a>
Bump peter-evans/create-pull-request from 4 to 5 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/163">#163</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/3d6c0b9c6c6128c3f7fc6f873c0218915585ff51"><code>3d6c0b9</code></a>
ci: add missing checkout step</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/1fcda994df6b557d6ae3d3afbd8b4c55bbd14f29"><code>1fcda99</code></a>
ci: add test v3 workflow</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/5f728c3dae25f329afbe34ee4d08eef25569d79f"><code>5f728c3</code></a>
Bump peter-evans/enable-pull-request-automerge from 2 to 3 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/160">#160</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/fd9e73cdb111244f59c4bdf94994545011a0d89c"><code>fd9e73c</code></a>
Bump eslint from 8.36.0 to 8.37.0 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/159">#159</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/384c114887453534544cab66743e0ed42a1342a8"><code>384c114</code></a>
Bump eslint from 8.35.0 to 8.36.0 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/155">#155</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/44526e38b60c3be1ea27a6cd6f7359f7ce3f6bc8"><code>44526e3</code></a>
Bump jest from 29.4.3 to 29.5.0 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/154">#154</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/b1fa5d531f73c67e1ab3962d1c16764f188066a6"><code>b1fa5d5</code></a>
Bump eslint from 8.34.0 to 8.35.0 (<a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/153">#153</a>)</li>
<li><a
href="https://github.com/peter-evans/create-or-update-comment/commit/c5a7a9808bb4d6de79278436482399ce9a4de9d5"><code>c5a7a98</code></a>
Merge pull request <a
href="https://redirect.github.com/peter-evans/create-or-update-comment/issues/152">#152</a>
from Kurt-von-Laven/patch-1</li>
<li>Additional commits viewable in <a
href="https://github.com/peter-evans/create-or-update-comment/compare/v2...v3">compare
view</a></li>
</ul>
</details>
<br />


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</details>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Adds an option to hide warning messages of EnsureSameShaped 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: myron <[email protected]>

…nt (#6457)

Fixes #6456.

### Description

- Make the test images also depend on GPUs
- Improve docstring for infer

### 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).
- [ ] 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: Mingxin Zheng <[email protected]>

…_dir (#6448)

Fixes #6447 
Fixes #6443

### Description

- Put the documentation together
- Add missing docstring
- num_gpus is not the right way to do mGPU training
- improve logging (no more `logging.warning("[info] ...")`)
- fix work_dir

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

---------

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