Adds ruff precommit autofixes (#6402)

### 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 <wenqil@nvidia.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -26,6 +26,12 @@ repos:
         args: ['--autofix', '--no-sort-keys', '--indent=4']
       - id: end-of-file-fixer
       - id: mixed-line-ending
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.261
+    hooks:
+    -   id: ruff
+        args:
+        - --fix
 
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.3.1
@@ -53,8 +59,6 @@ repos:
           - flake8>=3.8.1
           - flake8-bugbear
           - flake8-comprehensions
-          - flake8-executable
-          - flake8-pyi
           - pep8-naming
         exclude: |
           (?x)^(
@@ -68,30 +72,3 @@ repos:
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]
-
-  #- repo: https://github.com/PyCQA/isort
-  #  rev: 5.9.3
-  #  hooks:
-  #    - id: isort
-  #      name: Format imports
-
-  # - repo: https://github.com/psf/black
-  #   rev: 21.7b0
-  #   hooks:
-  #     - id: black
-  #       name: Format code
-
-  #- repo: https://github.com/executablebooks/mdformat
-  #  rev: 0.7.8
-  #  hooks:
-  #    - id: mdformat
-  #      additional_dependencies:
-  #        - mdformat-gfm
-  #        - mdformat_frontmatter
-  #      exclude: CHANGELOG.md
-
-  # - repo: https://github.com/PyCQA/flake8
-  #   rev: 3.9.2
-  #   hooks:
-  #     - id: flake8
-  #       name: Check PEP8

monai/networks/utils.py

@@ -64,7 +64,6 @@
 
 logger = get_logger(module_name=__name__)
 
-global _has_nvfuser
 _has_nvfuser = None
 
 
@@ -914,7 +913,7 @@ def convert_to_trt(
     if not dynamic_batchsize:
         warnings.warn(f"There is no dynamic batch range. The converted model only takes {input_shape} shape input.")
 
-    if (not (dynamic_batchsize is None)) and (len(dynamic_batchsize) != 3):
+    if (dynamic_batchsize is not None) and (len(dynamic_batchsize) != 3):
         warnings.warn(f"The dynamic batch range sequence should have 3 elements, but got {dynamic_batchsize} elements.")
 
     device = device if device else 0

monai/transforms/utility/array.py

@@ -1640,13 +1640,11 @@ def _check_filter_format(self, filter: str | NdarrayOrTensor | nn.Module, filter
                 raise ValueError("`filter_size` should be a single uneven integer.")
             if filter not in self.supported_filters:
                 raise NotImplementedError(f"{filter}. Supported filters are {self.supported_filters}.")
-        elif isinstance(filter, torch.Tensor) or isinstance(filter, np.ndarray):
+        elif isinstance(filter, (torch.Tensor, np.ndarray)):
             if filter.ndim not in [1, 2, 3]:
                 raise ValueError("Only 1D, 2D, and 3D filters are supported.")
             self._check_all_values_uneven(filter.shape)
-        elif isinstance(filter, (nn.Module, Transform)):
-            pass
-        else:
+        elif not isinstance(filter, (nn.Module, Transform)):
             raise TypeError(
                 f"{type(filter)} is not supported."
                 "Supported types are `class 'str'`, `class 'torch.Tensor'`, `class 'np.ndarray'`, "

monai/utils/aliases.py

@@ -81,7 +81,8 @@ def resolve_name(name):
     if obj is None:
         # Get all modules having the declaration/import, need to check here that getattr returns something which doesn't
         # equate to False since in places __getattr__ returns 0 incorrectly:
-        # https://github.com/tensorflow/tensorboard/blob/a22566561d2b4fea408755a951ac9eaf3a156f8e/tensorboard/compat/tensorflow_stub/pywrap_tensorflow.py#L35  # noqa: B950
+        # https://github.com/tensorflow/tensorboard/blob/a22566561d2b4fea408755a951ac9eaf3a156f8e/
+        # tensorboard/compat/tensorflow_stub/pywrap_tensorflow.py#L35
         mods = [m for m in list(sys.modules.values()) if getattr(m, name, None)]
 
         if len(mods) > 0:  # found modules with this declaration or import

pyproject.toml

@@ -36,6 +36,11 @@ exclude = '''
 all = true
 exclude = "monai/bundle/__main__.py"
 
+[tool.ruff]
+line-length = 133
+ignore-init-module-imports = true
+ignore = ["F401", "E741"]
+
 [tool.pytype]
 # Space-separated list of files or directories to exclude.
 exclude = ["versioneer.py", "_version.py"]

requirements-dev.txt

@@ -13,8 +13,6 @@ lmdb
 flake8>=3.8.1
 flake8-bugbear
 flake8-comprehensions
-flake8-executable
-pylint!=2.13  # https://github.com/PyCQA/pylint/issues/5969
 mccabe
 pep8-naming
 pycodestyle

runtests.sh

@@ -533,7 +533,8 @@ then
     # ensure that the necessary packages for code format testing are installed
     if ! is_pip_installed pylint
     then
-        install_deps
+        echo "Pip installing pylint ..."
+        ${cmdPrefix}${PY_EXE} -m pip install pylint>2.16
     fi
     ${cmdPrefix}${PY_EXE} -m pylint --version