Replace from source dependency bunch with on-the-fly git clone for PyPI

.gitignore

@@ -25,6 +25,7 @@ fundus_image_toolbox/fovea_od_localization/models/*
 fundus_image_toolbox/quality_prediction/models/*
 fundus_image_toolbox/quality_prediction/data/*
 fundus_image_toolbox/vessel_segmentation/segmentation/*
+fundus_image_toolbox/vessel_segmentation/bunch/
 fundus.jpg
 
 # Others

fundus_image_toolbox/vessel_segmentation/clone.py

@@ -16,11 +16,10 @@ def clone_repo(
     branch="main",
     target_dir=f"./segmentation",
 ):
-    # Clone Segmentation Quality Control repo
     os.makedirs(target_dir, exist_ok=True)
     if not os.listdir(target_dir):
         print(
-            f"The vessel segmentation folder is missing. Downloading it from {link}..."
+            f"Module missing, downloading it from {link}..."
         )
         pwd = os.getcwd()
         os.system(f"git clone {link} {target_dir}")
@@ -33,6 +32,9 @@ def clone_repo(
             pass
         os.chdir(pwd)
 
+def adjust_imports(target_dir):
+    # Make imports of segmentation module relative
+    if os.path.exists(target_dir):
         print("Adjusting imports...")
         add_dots_to_imports_in_folder(target_dir)
         replace_args(target_dir)
@@ -63,11 +65,11 @@ def add_dots_to_imports(file_path):
 
                 # Check if is a local file in same directory
                 if os.path.exists(os.path.join(this_dir, fname)):
-                    print(os.path.join(this_dir, fname + ".py"))
+                    # print(os.path.join(this_dir, fname + ".py"))
                     is_local_file = True
                 # Check if is a local folder in parent directory
                 elif os.path.exists(os.path.join(par_dir, fname)):
-                    print(os.path.join(par_dir, fname))
+                    # print(os.path.join(par_dir, fname))
                     is_local_folder = True
 
             c = ".." if is_local_folder else "."
@@ -83,8 +85,8 @@ def add_dots_to_imports(file_path):
                 imports = terms[-1].split(",")
                 imports = [i.replace(" ", "") for i in imports]
 
-                print("parents: ", parents)
-                print("imports: ", imports)
+                # print("parents: ", parents)
+                # print("imports: ", imports)
 
                 if len(parents) > 0:
                     file.write(
@@ -101,7 +103,7 @@ def add_dots_to_imports_in_folder(folder_path):
     for root, _, files in os.walk(folder_path):
         for file in files:
             if file.endswith(".py"):
-                print("########\n", file)
+                # print("########\n", file)
                 add_dots_to_imports(os.path.join(root, file))
 
 def replace_args(folder_path):

fundus_image_toolbox/vessel_segmentation/inference.py

@@ -18,13 +18,26 @@
     from .segmentation.utils.notebook_utils import clahe_equalized, get_ensemble
     from .segmentation.utils.model_definition import FR_UNet
 except ImportError:
-    from .clone import clone_repo
+    from .clone import clone_repo, adjust_imports
 
     this_dir = Path(__file__).resolve().parent
-    clone_repo(target_dir=(this_dir / "segmentation").__str__())
+    target_dir = (this_dir / "segmentation").__str__()
+    clone_repo(target_dir=target_dir)
+    adjust_imports(target_dir)
     from .segmentation.utils.notebook_utils import clahe_equalized, get_ensemble
     from .segmentation.utils.model_definition import FR_UNet
 
+try:
+    # The pickled model is a bunch object but PyPI's bunch is too old.
+    import bunch
+except ImportError:
+    from .clone import clone_repo
+
+    this_dir = Path(__file__).resolve().parent
+    clone_repo(target_dir=(this_dir / "bunch").__str__(), link="https://github.com/dsc/bunch", branch="master", commit="85ed6841bf5754867703e67324a4c82b66f1cd4b")
+    sys.path.append((this_dir / "bunch").__str__())
+    import bunch
+
 
 class Parser(ArgumentParser):
     def error(self, message):

pyproject.toml

@@ -16,7 +16,6 @@ authors = [
 requires-python = ">=3.9"
 dependencies = [
     "albumentations",
-    "bunch @ git+https://github.com/dsc/bunch",
     "captum>=0.7.0",
     "gdown>=5.2.0",
     "imgaug>=0.4.0",
@@ -59,4 +58,4 @@ include-package-data = true
 where = ["."]
 
 [tool.uv.workspace]
-members = ["."]
+members = ["."]

todos.md

@@ -13,7 +13,7 @@
 
     [x] circle_crop
 
-[ ] Vessel Segmentation: Ask Patrick & Jerry if they could get rid of "bunch" dependency: "bunch" prevents the use of python >= 3.10. 31.1.205: Relaxed it using the development version from git.
+[ ] Vessel Segmentation: Ask Patrick & Jerry if they could get rid of "bunch" dependency: "bunch" prevents the use of python >= 3.10. 31.1.205: PyPI does not accept bunch as a git dependency as there's an older version on PyPI. Hence now we clone it for the segmentation code on the fly.
 
 [ ] Once Sarah has refactored her image cropping code to yield an image as output, add it to circle_crop, s.t. one can choose between the two algorithms