squashed

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.8
+  python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0

region_grower/atlas_helper.py

@@ -2,6 +2,7 @@
 
 This helper allows simple lookups without having to reason in term of [PH][1-6] and [PH]y.
 """
+
 import operator
 from pathlib import Path
 from typing import List
@@ -31,16 +32,24 @@ def __init__(self, atlas: Atlas, region_structure_path: str):
         if region_structure_path is not None and Path(region_structure_path).exists():
             with open(region_structure_path, "r", encoding="utf-8") as region_file:
                 self.region_structure = yaml.safe_load(region_file)
+                self.region_structure_base_path = Path(region_structure_path).parent
         else:
-            raise ValueError("Please provide an existing region_structure file.")
+            raise ValueError(f"region_structure file not found at {region_structure_path}.")
 
         self.regions = list(self.region_structure.keys())
         self.layers = {}
         for region in self.regions:
             self.layers[region] = self.region_structure[region]["layers"]
-        self.y = atlas.load_data("[PH]y")
+        try:
+            self.y = atlas.load_data("[PH]y")
+        except:
+            self.y = None
+
         self.brain_regions = atlas.load_data("brain_regions")
-        self.orientations = atlas.load_data("orientation", cls=OrientationField)
+        try:
+            self.orientations = atlas.load_data("orientation", cls=OrientationField)
+        except:
+            self.orientations = None
 
     def layer_thickness(self, layer: Union[int, str]) -> Atlas:
         """Returns an atlas of the layer thickness."""

region_grower/cli.py

@@ -195,6 +195,12 @@ def generate_distributions(
     is_flag=True,
     default=False,
 )
+@click.option(
+    "--resume",
+    help="Resume synthesis, do not synthesize if file exists (default: False)",
+    is_flag=True,
+    default=False,
+)
 @click.option(
     "--max-drop-ratio",
     help="Max drop ratio for any mtype (default: 0)",
@@ -284,6 +290,12 @@ def generate_distributions(
     is_flag=True,
     default=False,
 )
+@click.option(
+    "--synthesize-axons",
+    help="Display the versions of all the accessible modules in a logger entry",
+    is_flag=True,
+    default=False,
+)
 def synthesize_morphologies(**kwargs):  # pylint: disable=too-many-arguments, too-many-locals
     """Synthesize morphologies."""
     if mpi_enabled and kwargs.get("with_mpi", False):  # pragma: no cover