python3Packages.stytra: fix tests

pkgs/development/python-modules/stytra/0000-workaround-pyqtgraph.patch

@@ -0,0 +1,26 @@
+diff --git a/stytra/gui/fishplots.py b/stytra/gui/fishplots.py
+index 49ef1fe..fd1cc50 100644
+--- a/stytra/gui/fishplots.py
++++ b/stytra/gui/fishplots.py
+@@ -13,7 +13,7 @@ from lightparam.gui import ParameterGui
+ from scipy.ndimage.filters import gaussian_filter1d
+ 
+ 
+-class StreamingPositionPlot(pg.GraphicsWindow):
++class StreamingPosition(pg.GraphicsView):
+     """Plot that displays the virtual position of the fish"""
+ 
+     def __init__(self, *args, data_accumulator, n_points=500, **kwargs):
+diff --git a/stytra/utilities.py b/stytra/utilities.py
+index f79c4db..feaa7ef 100644
+--- a/stytra/utilities.py
++++ b/stytra/utilities.py
+@@ -239,7 +239,7 @@ def recursive_update(d, u):
+     :return:
+     """
+     for k, v in u.items():
+-        if isinstance(v, collections.Mapping):
++        if isinstance(v, collections.ChainMap):
+             d[k] = recursive_update(d.get(k, {}), v)
+         else:
+             d[k] = v

pkgs/development/python-modules/stytra/default.nix

@@ -33,8 +33,7 @@
 buildPythonPackage rec {
   pname = "stytra";
   version = "0.8.34";
-  format = "setuptools";
+  pyproject = true;
-
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
@@ -42,10 +41,10 @@ buildPythonPackage rec {
     sha256 = "aab9d07575ef599a9c0ae505656e3c03ec753462df3c15742f1f768f2b578f0a";
   };
 
-  # crashes python
+  patches = [
-  preCheck = ''
+    # https://github.com/portugueslab/stytra/issues/87
-    rm stytra/tests/test_z_experiments.py
+    ./0000-workaround-pyqtgraph.patch
-  '';
+  ];
 
   propagatedBuildInputs = [
     opencv4
@@ -79,6 +78,11 @@ buildPythonPackage rec {
     pyserial
   ];
 
+  disabledTestPaths = [
+    # Crashes python
+    "stytra/tests/test_z_experiments.py"
+  ];
+
   meta = with lib; {
     description = "A modular package to control stimulation and track behaviour";
     homepage = "https://github.com/portugueslab/stytra";