Use Path.resolve() consistently to prevent UNC/drive letter ambiguity (#304)

* Use Path.resolve() consistently to prevent UNC/drive letter ambiguity

* Ignore VSCode files

* Black linting

* Try causing a relative path error by using a drive alias

* More consistently call resolve on returned paths and fix tests to compare resolved paths

Author: ethanbb

.github/workflows/windows-conda.yml

@@ -32,6 +32,9 @@ jobs:
           
       - shell: bash -l {0}
         run: |
+          # make a drive letter alias so we can test canonical path resolution
+          subst Z: .
+          cd /z
           conda activate mescore
           mamba install pytest
           caimanmanager install

.gitignore

@@ -138,3 +138,6 @@ dmypy.json
 tests/tmp
 tests/videos
 tests/ground_truths*
+
+# VSCode
+.vscode/

mesmerize_core/algorithms/cnmf.py

@@ -33,7 +33,7 @@ def run_algo(batch_path, uuid, data_path: str = None):
     input_movie_path = str(df.paths.resolve(input_movie_path))
 
     # make output dir
-    output_dir = Path(batch_path).parent.joinpath(str(uuid))
+    output_dir = Path(batch_path).parent.joinpath(str(uuid)).resolve()
     output_dir.mkdir(parents=True, exist_ok=True)
 
     params = item["params"]
@@ -96,14 +96,14 @@ def run_algo(batch_path, uuid, data_path: str = None):
         print("performing eval")
         cnm.estimates.evaluate_components(images, cnm.params, dview=dview)
 
-        output_path = output_dir.joinpath(f"{uuid}.hdf5").resolve()
+        output_path = output_dir.joinpath(f"{uuid}.hdf5")
 
         cnm.save(str(output_path))
 
         Cn = cm.local_correlations(images, swap_dim=False)
         Cn[np.isnan(Cn)] = 0
 
-        corr_img_path = output_dir.joinpath(f"{uuid}_cn.npy").resolve()
+        corr_img_path = output_dir.joinpath(f"{uuid}_cn.npy")
         np.save(str(corr_img_path), Cn, allow_pickle=False)
 
         # output dict for dataframe row (pd.Series)

mesmerize_core/algorithms/cnmfe.py

@@ -29,7 +29,7 @@ def run_algo(batch_path, uuid, data_path: str = None):
     # resolve full path
     input_movie_path = str(df.paths.resolve(input_movie_path))
 
-    output_dir = Path(batch_path).parent.joinpath(str(uuid))
+    output_dir = Path(batch_path).parent.joinpath(str(uuid)).resolve()
     output_dir.mkdir(parents=True, exist_ok=True)
 
     params = item["params"]
@@ -87,7 +87,7 @@ def run_algo(batch_path, uuid, data_path: str = None):
         print("evaluating components")
         cnm.estimates.evaluate_components(images, cnm.params, dview=dview)
 
-        cnmf_hdf5_path = output_dir.joinpath(f"{uuid}.hdf5").resolve()
+        cnmf_hdf5_path = output_dir.joinpath(f"{uuid}.hdf5")
         cnm.save(str(cnmf_hdf5_path))
 
         # save output paths to outputs dict

mesmerize_core/batch_utils.py

@@ -49,7 +49,7 @@ def set_parent_raw_data_path(path: Union[Path, str]) -> Path:
         raise NotADirectoryError(
             "The directory passed to `set_parent_raw_data_path()` does not exist.\n"
         )
-    PARENT_DATA_PATH = path
+    PARENT_DATA_PATH = path.resolve()
 
     return PARENT_DATA_PATH
 
@@ -65,15 +65,15 @@ def get_parent_raw_data_path() -> Path:
 
     """
     global PARENT_DATA_PATH
-    return PARENT_DATA_PATH
+    return PARENT_DATA_PATH.resolve()
 
 
 class _BasePathExtensions:
     def __init__(self, data: Union[pd.DataFrame, pd.Series]):
         self._data = data
 
     def set_batch_path(self, path: Union[str, Path]):
-        self._data.attrs["batch_path"] = Path(path)
+        self._data.attrs["batch_path"] = Path(path).resolve()
 
     def get_batch_path(self) -> Path:
         """
@@ -84,9 +84,11 @@ def get_batch_path(self) -> Path:
         Path
             full path to the batch dataframe file as a Path object
         """
-        if "batch_path" in self._data.attrs.keys():
-            if self._data.attrs["batch_path"] is not None:
-                return self._data.attrs["batch_path"]
+        if (
+            "batch_path" in self._data.attrs.keys()
+            and self._data.attrs["batch_path"] is not None
+        ):
+            return Path(self._data.attrs["batch_path"]).resolve()
         else:
             raise ValueError("Batch path is not set")
 
@@ -133,24 +135,23 @@ def split(self, path: Union[str, Path]):
             (<batch_dir> or <raw_data_dir>, <relative_path>)
 
         """
-        path = Path(path)
+        path = Path(path).resolve()
         # check if input movie is within batch dir
-        if self.get_batch_path().parent in path.parents:
-            return self.get_batch_path().parent, path.relative_to(
-                self.get_batch_path().parent
-            )
+        batch_parent = self.get_batch_path().parent
+        if batch_parent in path.parents:
+            return batch_parent, path.relative_to(batch_parent)
 
         # else check if in parent raw data dir
-        elif get_parent_raw_data_path() is not None:
-            if get_parent_raw_data_path() in path.parents:
-                return get_parent_raw_data_path(), path.relative_to(
-                    get_parent_raw_data_path()
-                )
+        else:
+            raw_data_path = get_parent_raw_data_path()
+            if raw_data_path is not None:
+                if raw_data_path in path.parents:
+                    return raw_data_path, path.relative_to(raw_data_path)
 
         raise NotADirectoryError(
             f"Could not split `path`:\n{path}"
-            f"\nnot relative to either batch path:\n{self.get_batch_path()}"
-            f"\nor parent raw data path:\n{get_parent_raw_data_path()}"
+            f"\nnot relative to either batch path:\n{batch_parent}"
+            f"\nor parent raw data path:\n{raw_data_path if raw_data_path is not None else '(not set)'}"
         )
 
 
@@ -258,6 +259,6 @@ def create_batch(path: Union[str, Path], remove_existing: bool = False) -> pd.Da
 def get_full_raw_data_path(path: Union[Path, str]) -> Path:
     path = Path(path)
     if PARENT_DATA_PATH is not None:
-        return PARENT_DATA_PATH.joinpath(path)
+        path = PARENT_DATA_PATH.joinpath(path)
 
-    return path
+    return path.resolve()  # needed in case path is absolute but not canonical