Create Exemplar workflow

setup.py

@@ -36,10 +36,10 @@
     "diff-pdf-visually>=1.5.1",
     "dir-content-diff>=1.2",
     "mock>=3",
-    "pytest>=6",
-    "pytest-cov>=3",
-    "pytest-html>=2",
-    "pytest-xdist>=2",
+    "pytest>=7",
+    "pytest-cov>=4",
+    "pytest-html>=3",
+    "pytest-xdist>=3.0.2",
 ]
 
 setup(

src/morphology_workflows/curation.py

@@ -1,4 +1,5 @@
 """Curation functions."""
+
 import json
 import logging
 import shutil
@@ -497,7 +498,13 @@ def recenter(row, data_dir):
 def orient(row, data_dir, pia_direction="y"):
     """Orient a morphology such that the original pia_direcion is along y."""
     new_morph_path = data_dir / Path(row.morph_path).name
-    _convert = {"x": [1.0, 0, 0], "z": [0.0, 0.0, 1.0]}
+    _convert = {
+        "x": [1.0, 0, 0],
+        "z": [0.0, 0.0, 1.0],
+        "-x": [-1.0, 0, 0],
+        "-y": [0.0, -1.0, 0.0],
+        "-z": [0.0, 0.0, -1.0],
+    }
     morph = Morphology(row.morph_path)
     if pia_direction != "y":
         rotation_matrix = rotation_matrix_from_vectors(_convert[pia_direction], [0.0, 1.0, 0.0])