test: remove hardcoded snemi fixture path

Author: akgohain

server_api/main.py

@@ -412,7 +412,7 @@ async def neuroglancer(req: Request):
         port = 4244
         neuroglancer.set_server_bind_address(ip, port)
         viewer = neuroglancer.Viewer()
-        # SNEMI (# 3d vol dim: z,y,x)
+        # Neuroglancer expects the EM volume axes in z, y, x order.
         res = neuroglancer.CoordinateSpace(
             names=["z", "y", "x"], units=["nm", "nm", "nm"], scales=scales
         )

tests/test_check_files_route.py

@@ -1,3 +1,4 @@
+import os
 import pathlib
 import unittest
 
@@ -6,7 +7,13 @@
 from server_api.main import app as server_api_app
 
 
-SNEMI_ROOT = pathlib.Path("/Users/adamg/seg.bio/testing_data/snemi")
+REPO_ROOT = pathlib.Path(__file__).resolve().parents[1]
+SNEMI_ROOT = pathlib.Path(
+    os.getenv(
+        "PYTC_TEST_SNEMI_ROOT",
+        REPO_ROOT.parent / "testing_data" / "snemi",
+    )
+)
 TEST_INPUT_PATH = SNEMI_ROOT / "image" / "test-input.tif"
 TRAIN_LABELS_PATH = SNEMI_ROOT / "seg" / "train-labels.tif"