Merge pull request #5 from CBICA/spiros-dev

Fixed pre-commit | Correct torch version | Building workflows and badges
CBICA · Dec 11, 2024 · 085d142 · 085d142
2 parents cad0ddc + fa8f1c8
commit 085d142
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Showing 6 changed files with 14 additions and 8 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/DLWMLS/__main__.py b/DLWMLS/__main__.py
@@ -246,7 +246,7 @@ def main() -> None:
     model_folder = os.path.join(
         Path(__file__).parent,
         "nnunet_results",
-        "Dataset004_Dataset003_qcedCorrected/nnUNetTrainer__nnUNetPlans__3d_fullres"
+        "Dataset004_Dataset003_qcedCorrected/nnUNetTrainer__nnUNetPlans__3d_fullres",
         # "Dataset%s_Dataset%s_dlwmlsICVAll/nnUNetTrainer__nnUNetPlans__%s"
         # "Dataset%s_Task%s_DLWMLSV2/nnUNetTrainer__nnUNetPlans__%s/"
         # % (args.d, args.d, args.c),

diff --git a/DLWMLS/utils.py b/DLWMLS/utils.py
@@ -37,6 +37,9 @@ def rename_and_copy_files(src_folder: str, des_folder: str) -> Tuple[dict, dict]
         shutil.copy2(old_name, new_name)
         rename_dict[filename] = rename_file
         rename_back_dict[rename_back] = filename.split(".nii")[0] + "_WMLS.nii.gz"
-        print("%s will be renamed to %s" % (old_name, filename.split(".nii")[0] + "_WMLS.nii.gz"))
+        print(
+            "%s will be renamed to %s"
+            % (old_name, filename.split(".nii")[0] + "_WMLS.nii.gz")
+        )
 
     return rename_dict, rename_back_dict
diff --git a/README.md b/README.md
@@ -1,5 +1,8 @@
 # DLWMLS - Deep Learning White Matter Lesion Segmentation
 
+![MacOS Build](https://github.com/CBICA/DLWMLS/actions/workflows/macos-build.yml/badge.svg)
+![Ubuntu Build](https://github.com/CBICA/DLWMLS/actions/workflows/ubuntu-build.yml/badge.svg)
+
 ## Overview
 
 DLWMLS uses a trained [nnUNet](https://github.com/MIC-DKFZ/nnUNet) model to segment White Matter Lesions (WML) from ICV-segmented (see DLICV method) and LPS oriented brain images (Nifti/.nii.gz format).
@@ -17,7 +20,7 @@ pip install -e .
 ```
 
 ### Installing PyTorch
-Depending on your system configuration and supported CUDA version, you may need to follow the [PyTorch Installation Instructions](https://pytorch.org/get-started/locally/). 
+Depending on your system configuration and supported CUDA version, you may need to follow the [PyTorch Installation Instructions](https://pytorch.org/get-started/locally/).
 
 ## Usage
 
@@ -34,7 +37,7 @@ DLWMLS -h
 ```
 
 ## \[Windows Users\] Troubleshooting model download failures
-Our model download process creates several deep directory structures. If you are on Windows and your model download process fails, it may be due to Windows file path limitations. 
+Our model download process creates several deep directory structures. If you are on Windows and your model download process fails, it may be due to Windows file path limitations.
 
 To enable long path support in Windows 10, version 1607, and later, the registry key `HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem LongPathsEnabled (Type: REG_DWORD)` must exist and be set to 1.
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
-torch>=2.2.1
-nnunetv2>=2.2.1
+torch==2.2.1
+nnunetv2==2.5.1
 argparse
 huggingface_hub
 pathlib
diff --git a/setup.py b/setup.py
@@ -20,9 +20,9 @@
     download_url="https://github.com/CBICA/DLWMLS/",
     url="https://github.com/CBICA/DLWMLS/",
     packages=find_packages(exclude=["tests", ".github"]),
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     install_requires=[
-        "torch>=2.2.1",
+        "torch<=2.2.1",
         "nnunetv2>=2.2.1",
         "argparse",
         "huggingface_hub",