improve pathing

Author: lappalainenj

flyvis/__init__.py

@@ -35,14 +35,14 @@ def timetz(*args):
 
 import datamate
 
+repo_dir = Path(__file__).parent.parent
+
 
 def resolve_root_dir():
     "Resolving the root directory in which all data is downloaded and stored."
 
     # Try to get root directory from environment variable
-    root_dir_env = os.getenv(
-        "FLYVIS_ROOT_DIR", str(Path(__file__).parent.parent / "data")
-    )
+    root_dir_env = os.getenv("FLYVIS_ROOT_DIR", str(repo_dir / "data"))
     return Path(root_dir_env).expanduser().absolute()
 
 
@@ -51,10 +51,10 @@ def resolve_root_dir():
 results_dir = root_dir / "results"
 renderings_dir = root_dir / "renderings"
 sintel_dir = root_dir / "SintelDataSet"
-connectome_file = root_dir / "connectome/fib25-fib19_v2.2.json"
-source_dir = (repo_dir := Path(__file__).parent.parent) / "flyvis"
+connectome_file = repo_dir / "data/connectome/fib25-fib19_v2.2.json"
+source_dir = repo_dir / "flyvis"
 config_dir = repo_dir / "config"
-script_dir = Path(__file__).parent.parent / "flyvis_cli"
+script_dir = repo_dir / "flyvis_cli"
 examples_dir = repo_dir / "examples"
 
 datamate.set_root_dir(root_dir)

flyvis/connectome/connectome.py

@@ -161,9 +161,18 @@ class ConnectomeFromAvgFilters(Directory):
         ```
     """
 
-    def __init__(self, file=flyvis.connectome_file, extent=15, n_syn_fill=1) -> None:
-        if not Path(file).exists():
+    def __init__(self, file=flyvis.connectome_file.name, extent=15, n_syn_fill=1) -> None:
+        # case 0: file is an absolute path
+        if (Path(file)).exists():
+            file = Path(file)
+        # case 1: file is specified relative to package directory
+        elif (flyvis.repo_dir / "data/connectome" / file).exists():
+            file = flyvis.repo_dir / "data/connectome" / file
+        # case 2: file is specified relative to root directory
+        elif (flyvis.root_dir / "connectome" / file).exists():
             file = flyvis.root_dir / "connectome" / file
+        else:
+            raise FileNotFoundError(f"Connectome file {file} not found.")
 
         # Load the connectome spec.
         spec = json.loads(Path(file).read_text())