update autoformatting (Project-MONAI#54)

* update autoformatting

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

* update config

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

* update config

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

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

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

.pre-commit-config.yaml

@@ -9,31 +9,51 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-yaml
-      - id: check-docstring-first
-      - id: check-executables-have-shebangs
       - id: check-toml
       - id: check-case-conflict
       - id: check-added-large-files
         args: ['--maxkb=1024']
       - id: detect-private-key
+      - id: forbid-new-submodules
+      - id: pretty-format-json
+        args: ['--autofix', '--no-sort-keys', '--indent=4']
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
 
-  #- repo: https://github.com/asottile/pyupgrade
-  #  rev: v2.23.2
-  #  hooks:
-  #    - id: pyupgrade
-  #      args: [--py36-plus]
-  #      name: Upgrade code
+  # - repo: https://github.com/asottile/pyupgrade
+  #   rev: v2.31.1
+  #   hooks:
+  #     - id: pyupgrade
+  #       args: [--py36-plus]
+  #       name: Upgrade code
+  #       exclude: |
+  #         (?x)^(
+  #             versioneer.py|
+  #             monai/_version.py
+  #         )$
 
-  #- repo: https://github.com/asottile/yesqa
-  #  rev: v1.2.3
-  #  hooks:
-  #    - id: yesqa
-  #      name: Unused noqa
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.3.0
+    hooks:
+      - id: yesqa
+        name: Unused noqa
+        additional_dependencies:
+          - flake8>=3.8.1
+          - flake8-bugbear
+          - flake8-comprehensions
+          - flake8-executable
+          - flake8-pyi
+          - pep8-naming
+        exclude: |
+          (?x)^(
+              monai/__init__.py|
+              docs/source/conf.py
+          )$
 
   #- repo: https://github.com/PyCQA/isort
   #  rev: 5.9.3

DiNTS/README.md

@@ -112,4 +112,4 @@ To further fuse the output segmetnation masks, user needs to create a `.json` fi
   pages={4126--4135},
   year={2020}
 }
-```
+```

DiNTS/run_ensemble.sh

@@ -30,4 +30,4 @@ python -m torch.distributed.launch --nproc_per_node=${NUM_GPUS_PER_NODE} \
                                         "${FOLDER_0}/Seg_Fold1_test" \
                                         "${FOLDER_0}/Seg_Fold2_test" \
                                         "${FOLDER_0}/Seg_Fold3_test" \
-                                        "${FOLDER_0}/Seg_Fold4_test" \
+                                        "${FOLDER_0}/Seg_Fold4_test" \

DiNTS/run_infer_multi-gpu.sh

@@ -41,4 +41,4 @@ do
                             --output_root=${OUTPUT_ROOT} \
                             --prob \
                             --root=${DATA_ROOT}
-done
+done

DiNTS/run_install_monai.sh

@@ -9,4 +9,4 @@ pip uninstall --yes monai
 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai
 
 pip uninstall --yes tqdm
-pip install tqdm
+pip install tqdm

README.md

@@ -2,12 +2,12 @@
 
 **Contribution Guidelines:**
 
-1. Contributions are required to be published and have successfully undergone peer-review (If the contributing person is not the author of the work, no approval from the authors of the paper is required, but the contribution needs to be clearly labeled as a “Third-party contribution”). 
+1. Contributions are required to be published and have successfully undergone peer-review (If the contributing person is not the author of the work, no approval from the authors of the paper is required, but the contribution needs to be clearly labeled as a “Third-party contribution”).
+
+2. The implementation is required to feature MONAI components to a substantial extent.
 
-2. The implementation is required to feature MONAI components to a substantial extent. 
-
 3. The implementation is required to include a boilerplate shell script (to be published) allowing code-reviewers to execute the code and reproduce the paper’s results with one click.
 
-4. Under the hood, code quality does not have to match standards of the MONAI main repository, as the Research Contribution repository aims at a fast track for code change proposals and demonstrating cutting-edge research ideas. 
+4. Under the hood, code quality does not have to match standards of the MONAI main repository, as the Research Contribution repository aims at a fast track for code change proposals and demonstrating cutting-edge research ideas.
 
 5. New contributions will be given a MONAI version tag (visible in the associated Readme) according to the utilized version of MONAI. This avoids the need to maintain compatibility of contributions for following MONAI releases.

SkullRec/README.md

@@ -138,5 +138,3 @@ and,
   publisher={Springer}
 }
 ```
-
-

SwinUNETR/BRATS21/README.md

@@ -4,4 +4,3 @@ A swin transformer-based model for volumetric (3D) brain tumor segmentation task
 
 # References
 [1] Hatamizadeh, Ali, et al. "Swin UNETR: Shifted Window Transformers for 3D Semantic Segmentation of Brain Tumors.", 2021.
-

lamp-automated-model-parallelism/unet_pipe.py

@@ -24,7 +24,7 @@
 class Stash(nn.Module):
     def forward(self, input: torch.Tensor):
         yield stash("skip", input)
-        return input  # noqa  using yield together with return
+        return input  # using yield together with return
 
 
 @skippable(stash=[], pop=["skip"])