Merge pull request #43 from spirosmaggioros/main

Fixed pre-commit
CBICA · Oct 11, 2024 · b14ad71 · b14ad71
2 parents 692067c + cbe2b79
commit b14ad71
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Showing 4 changed files with 42 additions and 19 deletions.
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -12,6 +12,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - run: pip3 install pre-commit
       - run: pre-commit run --files NiChart_DLMUSE/*
diff --git a/NiChart_DLMUSE/SegmentImage.py b/NiChart_DLMUSE/SegmentImage.py
@@ -5,8 +5,12 @@
 
 
 def run_dlicv(
-    in_dir: str, in_suff: Any, out_dir: str, out_suff: Any, device: str,
-    extra_args: str = ""
+    in_dir: str,
+    in_suff: Any,
+    out_dir: str,
+    out_suff: Any,
+    device: str,
+    extra_args: str = "",
 ) -> None:
     # Call DLICV
     print("Running DLICV")
@@ -19,8 +23,12 @@ def run_dlicv(
 
 
 def run_dlmuse(
-    in_dir: str, in_suff: Any, out_dir: str, out_suff: Any, device: str,
-    extra_args: str = ""
+    in_dir: str,
+    in_suff: Any,
+    out_dir: str,
+    out_suff: Any,
+    device: str,
+    extra_args: str = "",
 ) -> None:
     # Call DLMUSE
     print("Running DLMUSE")

diff --git a/NiChart_DLMUSE/__main__.py b/NiChart_DLMUSE/__main__.py
@@ -145,7 +145,14 @@ def main() -> None:
     for i in range(len(subfolders)):
         curr_out_dir = out_dir + f"/split_{i}"
         curr_thread = threading.Thread(
-            target=run_pipeline, args=(subfolders[i], curr_out_dir, device, dlmuse_extra_args, dlicv_extra_args)
+            target=run_pipeline,
+            args=(
+                subfolders[i],
+                curr_out_dir,
+                device,
+                dlmuse_extra_args,
+                dlicv_extra_args,
+            ),
         )
         curr_thread.start()
         threads.append(curr_thread)
@@ -157,6 +164,5 @@ def main() -> None:
     remove_subfolders(in_data)
 
 
-
 if __name__ == "__main__":
     main()
diff --git a/NiChart_DLMUSE/dlmuse_pipeline.py b/NiChart_DLMUSE/dlmuse_pipeline.py
@@ -1,6 +1,6 @@
 import os
-from pathlib import Path
-import pkg_resources
+
+import pkg_resources  # type: ignore
 
 from .CalcROIVol import apply_create_roi_csv, combine_roi_csv
 from .MaskImage import apply_combine_masks, apply_mask_img
@@ -25,28 +25,37 @@
 #     "dicts",
 #     "MUSE_mapping_consecutive_indices.csv",
 # )
-#DICT_MUSE_NNUNET_MAP = os.path.join(
+# DICT_MUSE_NNUNET_MAP = os.path.join(
 #    Path(__file__).parent.parent,
 #    "shared",
 #    "dicts",
 #   "MUSE_mapping_consecutive_indices.csv",
-#)
-DICT_MUSE_NNUNET_MAP = pkg_resources.resource_filename('NiChart_DLMUSE',
-                                                        'shared/dicts/MUSE_mapping_consecutive_indices.csv')
+# )
+DICT_MUSE_NNUNET_MAP = pkg_resources.resource_filename(
+    "NiChart_DLMUSE", "shared/dicts/MUSE_mapping_consecutive_indices.csv"
+)
 LABEL_FROM = "IndexConsecutive"
 LABEL_TO = "IndexMUSE"
 
 DICT_MUSE_SINGLE = DICT_MUSE_NNUNET_MAP
 # DICT_MUSE_DERIVED = os.path.join(
 #     os.path.dirname(os.getcwd()), "shared", "dicts", "MUSE_mapping_derived_rois.csv"
 # )
-#DICT_MUSE_DERIVED = os.path.join(
+# DICT_MUSE_DERIVED = os.path.join(
 #    Path(__file__).parent.parent, "shared", "dicts", "MUSE_mapping_derived_rois.csv"
-#)
-DICT_MUSE_DERIVED = pkg_resources.resource_filename('NiChart_DLMUSE',
-                                                    'shared/dicts/MUSE_mapping_derived_rois.csv')
-
-def run_pipeline(in_data: str, out_dir: str, device: str, dlmuse_extra_args: str, dlicv_extra_args: str) -> None:
+# )
+DICT_MUSE_DERIVED = pkg_resources.resource_filename(
+    "NiChart_DLMUSE", "shared/dicts/MUSE_mapping_derived_rois.csv"
+)
+
+
+def run_pipeline(
+    in_data: str,
+    out_dir: str,
+    device: str,
+    dlmuse_extra_args: str,
+    dlicv_extra_args: str,
+) -> None:
     """
     NiChart pipeline
     """