Build: Bump NeuroTS and fix tests accordingly

requirements/base.pip

@@ -18,7 +18,7 @@ morphio>=3.3.6,<4
 neuroc>=0.2.8,<1
 neurocollage>=0.3.3
 neurom>=3.2.2,<4
-neurots>=3.5,<4
+neurots>=3.6,<4
 numpy>=1.24.1
 pandas>=1.5.3
 placement_algorithm>=2.3.1

src/synthesis_workflow/extra/make_map.py

@@ -21,8 +21,11 @@ def get_annotations(cells, column, input_annotation, mode="mean"):
     tmp = pd.DataFrame(_voxels.astype(int), columns=v_inds)
     if mode == "mean":
         _values = cells[[column]].join(tmp).groupby(v_inds).mean().reset_index()
-    if mode == "sum":
+    elif mode == "sum":
         _values = cells[[column]].join(tmp).groupby(v_inds).sum().reset_index()
+    else:
+        msg = f"Unknown mode '{mode}' (should be either 'mean' or 'sum')"
+        raise ValueError(msg)
     _ids = tuple(_values[v_inds].to_numpy().transpose())
     annotation.raw[_ids] = _values[column].to_list()
     return annotation

src/synthesis_workflow/validation.py

@@ -468,6 +468,8 @@ def _plot_density_profile(
             ax.legend(loc="best")
         elif isinstance(circuit, VacuumCircuit):
             plot_df = _get_vacuum_depths_df(circuit, mtype)
+        else:
+            plot_df = None
 
         with DisableLogger():
             sns.violinplot(x="neurite_type", y="y", data=plot_df, ax=ax, bw=0.1)

tests/data/in_small_O1/out/synthesis/apical_points.yaml

@@ -2,49 +2,49 @@
 216363698b529b4a97b750923ceb3ffd: null
 4462ebfc5f915ef09cfbac6e7687a66e: null
 48f165d57b00c7f4781ef86f5c8cc1ab:
-- 1.0846096277236938
-- 200.81143188476562
-- 3.6691887378692627
+- -14.394819259643555
+- 194.89781188964844
+- 9.01955795288086
 4dad2986ce8349606a06e9ab85a0bcc1:
-- 6.183896064758301
-- 196.69227600097656
-- 1.9936573505401611
+- -1.07305908203125
+- 195.03805541992188
+- -7.569953918457031
 5bc8fbbcbde5c0994164d8399f767c45: null
 6018366cf658f7a75ed34fe53a096533: null
 6513270e269e0d37f2a74de452e6b438: null
 72e63ac7a95383221f70d5dc2e675fc7:
-- -10.834639549255371
-- 196.5214385986328
-- -20.68924331665039
+- 4.626476764678955
+- 194.84230041503906
+- 20.284626007080078
 7b89296c6dcbac5008577eb1924770d3:
-- 29.904052734375
-- 189.7825164794922
-- -0.43575024604797363
+- -8.819189071655273
+- 194.1275177001953
+- -14.387084007263184
 8575062102fbcd4f357fbc5af71a1bfc:
-- 7.837672233581543
-- 198.6809539794922
-- 3.10603404045105
+- -1.843111515045166
+- 195.61419677734375
+- 12.465193748474121
 87751d4ca8501e2c44dcda6a797d76de:
-- -3.613675355911255
-- 193.3195037841797
-- 0.663608193397522
+- -3.984039545059204
+- 197.0111541748047
+- -6.497995376586914
 b8a1abcd1a6916c74da4f9fc3c6da5d7: null
 c15521b1b3dca50a9daa37e51b591d75:
-- 6.65926456451416
-- 198.2982177734375
-- 1.4248672723770142
+- -0.25705447793006897
+- 199.17787170410156
+- 11.141695022583008
 cd613e30d8f16adf91b7584a2265b1f5: null
 d95bafc8f2a4d27bdcf4bb99f4bea973: null
 db5b5fab8f4d3e27dda1494c73cf256d:
-- -2.8398842811584473
-- 197.15805053710938
-- -15.908510208129883
+- 26.932884216308594
+- 195.74429321289062
+- -1.293025255203247
 e3e70682c2094cac629f6fbed82c07cd: null
 e539a78bc8eff3460b12ae6ead581e57:
-- -5.473010063171387
-- 198.32235717773438
-- -3.1372883319854736
+- 9.035844802856445
+- 195.72015380859375
+- 7.5418572425842285
 e8d79f49af6d114c4a6f188a424e617b:
-- -21.98592758178711
-- 198.70675659179688
-- -13.453657150268555
+- 21.528072357177734
+- 197.24026489257812
+- 9.389350891113281