Merge branch 'dev' into cb_clean_code

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
     hooks:
     -   id: black
 -   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         name: isort (python)

.readthedocs.yaml

@@ -9,11 +9,12 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
     post_create_environment:
-      # Install Poetry
-      - pip install poetry
+      # Install Poetry 1.7
+      # TODO: Investigate why pipeline is broken with 1.8
+      - pip install poetry==1.7.1
       # Do not use virtual environments
       - poetry config virtualenvs.create false
       # Install docs group of dependencies

clinicadl/generate/generate.py

@@ -277,7 +277,7 @@ def generate_trivial_dataset(
             try:
                 mask_path_tar = fetch_file(FILE1, cache_clinicadl)
                 tar_file = tarfile.open(mask_path_tar)
-                print("File: " + mask_path_tar)
+                print(f"File: {mask_path_tar}")
                 try:
                     tar_file.extractall(cache_clinicadl)
                     tar_file.close()

clinicadl/random_search/random_search_utils.py

@@ -45,9 +45,9 @@ def get_space_dict(launch_directory: Path) -> Dict[str, Any]:
     # Default of specific options of random search
     space_dict.setdefault("d_reduction", "MaxPooling")
     space_dict.setdefault("network_normalization", "BatchNorm")
-    space_dict.setdefault("channels_limit", "512")
-    space_dict.setdefault("n_conv", "1")
-    space_dict.setdefault("wd_bool", "True")
+    space_dict.setdefault("channels_limit", 512)
+    space_dict.setdefault("n_conv", 1)
+    space_dict.setdefault("wd_bool", True)
 
     train_default = build_train_dict(toml_path, space_dict["network_task"])
 

clinicadl/utils/clinica_utils.py

@@ -1138,20 +1138,21 @@ def _sha256(path: Path):
     return sha256hash.hexdigest()
 
 
-def fetch_file(remote: RemoteFileStructure, dirname: Optional[Path]) -> Path:
+
+def fetch_file(remote: RemoteFileStructure, dirname: Path) -> Path:
     """Download a specific file and save it into the resources folder of the package.
 
     Parameters
     ----------
     remote : RemoteFileStructure
         Structure containing url, filename and checksum.
 
-    dirname : str
+    dirname : Path
         Absolute path where the file will be downloaded.
 
     Returns
     -------
-    file_path : str
+    file_path : Path
         Absolute file path.
     """
 

clinicadl/utils/maps_manager/maps_manager_utils.py

@@ -266,4 +266,4 @@ def remove_unused_tasks(
 #                     toml_dict[key] = value.as_posix()
 #         if isinstance(value, Path):
 #             toml_dict[key] = value.as_posix()
-#     return toml_dict
+#     return toml_dict