Merge remote-tracking branch 'upstream/main' into mypy

README.md

@@ -1,6 +1,10 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![codecov](https://codecov.io/gh/SIMEXP/giga_connectome/branch/main/graph/badge.svg?token=P4EGV7NKZ8)](https://codecov.io/gh/SIMEXP/giga_connectome)
+[![.github/workflows/test.yml](https://github.com/SIMEXP/giga_connectome/actions/workflows/test.yml/badge.svg)](https://github.com/SIMEXP/giga_connectome/actions/workflows/test.yml)
+[![pre-commit](https://github.com/SIMEXP/giga_connectome/actions/workflows/run_precommit.yml/badge.svg)](https://github.com/SIMEXP/giga_connectome/actions/workflows/run_precommit.yml)
 [![Documentation Status](https://readthedocs.org/projects/giga-connectome/badge/?version=stable)](https://giga-connectome.readthedocs.io/en/latest/?badge=stable)
+![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)
+
 # giga_connectome
 
 This is a BIDS-App to extract signal from a parcellation with nilearn,

docs/source/changes.md

@@ -28,6 +28,7 @@ Released August 2023
 
 ### Changes
 
+- [EHN] If an output file already exists, it will be overwritten and warning is logged. (@Remi-Gau)
 - [EHN] Default atlas is now MIST. (@htwangtw)
 - [EHN] When using the `participant` analysis level, the output is one file per subject, rather than one file per scan. (@htwangtw)
 

giga_connectome/utils.py

@@ -185,28 +185,14 @@ def get_subject_lists(
     return []
 
 
-def check_path(path: Path) -> Path:
-    """Check if given path (file or dir) already exists, and if so returns a
-    new path with _<n> appended (n being the number of paths with the same name
-    that exist already).
-    """
-    path = path.resolve()
-    ext = path.suffix
-    path_parent = path.parent
+def check_path(path: Path):
+    """Check if given path (file or dir) already exists.
 
+    If so, a warning is logged.
+    """
+    path = path.absolute()
     if path.exists():
-        similar_paths = [
-            str(p).replace(ext, "")
-            for p in path_parent.glob(f"{path.stem}_*{ext}")
-        ]
-        existing_numbers = [
-            int(p.split("_")[-1])
-            for p in similar_paths
-            if p.split("_")[-1].isdigit()
-        ]
-        n = str(max(existing_numbers) + 1) if existing_numbers else "1"
-        path = path_parent / f"{path.stem}_{n}{ext}"
-
-        gc_log.debug(f"Specified path already exists, using {path} instead.")
-
-    return path
+        gc_log.warning(
+            f"Specified path already exists:\n\t{path}\n"
+            "Old file will be overwritten"
+        )

giga_connectome/workflow.py

@@ -79,7 +79,7 @@ def workflow(args: argparse.Namespace) -> None:
                 f"sub-{subject}_atlas-{atlas['name']}"
                 f"_desc-{strategy['name']}.h5"
             )
-            connectome_path = utils.check_path(connectome_path)
+            utils.check_path(connectome_path)
 
             gc_log.info(f"Generate subject level connectomes: sub-{subject}")
 
@@ -106,7 +106,7 @@ def workflow(args: argparse.Namespace) -> None:
     connectome_path = (
         output_dir / f"atlas-{atlas['name']}_desc-{strategy['name']}.h5"
     )
-    connectome_path = utils.check_path(connectome_path)
+    utils.check_path(connectome_path)
 
     gc_log.info(connectome_path)
     gc_log.info("Generate subject level connectomes")