All tests pass

tests/neurax_identical/test_swc.py

@@ -20,7 +20,9 @@ def test_swc_cell():
     t_max = 5.0  # ms
     current = nx.step_current(0.5, 1.0, 0.2, dt, t_max)
 
-    cell = nx.read_swc("../morph.swc", nseg=2, max_branch_len=300.0)
+    dirname = os.path.dirname(__file__)
+    fname = os.path.join(dirname, "../morph.swc")
+    cell = nx.read_swc(fname, nseg=2, max_branch_len=300.0)
     cell.insert(HHChannel())
     cell.branch(1).comp(0.0).record()
     cell.branch(1).comp(0.0).stimulate(current)
@@ -54,8 +56,10 @@ def test_swc_net():
     t_max = 5.0  # ms
     current = nx.step_current(0.5, 1.0, 0.2, dt, t_max)
 
-    cell1 = nx.read_swc("../morph.swc", nseg=2, max_branch_len=300.0)
-    cell2 = nx.read_swc("../morph.swc", nseg=2, max_branch_len=300.0)
+    dirname = os.path.dirname(__file__)
+    fname = os.path.join(dirname, "../morph.swc")
+    cell1 = nx.read_swc(fname, nseg=2, max_branch_len=300.0)
+    cell2 = nx.read_swc(fname, nseg=2, max_branch_len=300.0)
 
     connectivities = [
         nx.Connectivity(GlutamateSynapse(), [nx.Connection(0, 0, 0.0, 1, 0, 0.0)])

tests/neurax_vs_neuron/test_cell.py

@@ -35,7 +35,6 @@ def test_similarity():
 
 
 def _run_neurax(i_delay, i_dur, i_amp, dt, t_max):
-
     nseg_per_branch = 8
     comp = nx.Compartment().initialize()
     branch = nx.Branch([comp for _ in range(nseg_per_branch)]).initialize()
@@ -54,7 +53,9 @@ def _run_neurax(i_delay, i_dur, i_amp, dt, t_max):
     cell.set_states("n", 0.3644787002343737)
     cell.set_states("voltages", -62.0)
 
-    cell.branch(0).comp(0.0).stimulate(nx.step_current(i_delay, i_dur, i_amp, dt, t_max))
+    cell.branch(0).comp(0.0).stimulate(
+        nx.step_current(i_delay, i_dur, i_amp, dt, t_max)
+    )
     cell.branch(0).comp(0.0).record()
     cell.branch(1).comp(1.0).record()
     cell.branch(2).comp(1.0).record()

tests/neurax_vs_neuron/test_comp.py

@@ -35,7 +35,6 @@ def test_similarity():
 
 
 def _run_neurax(i_delay, i_dur, i_amp, dt, t_max):
-
     comp = nx.Compartment().initialize()
     comp.insert(HHChannel())
 

tests/test_swc.py

@@ -18,7 +18,8 @@
 
 
 def test_swc_reader_lengths():
-    fname = "morph.swc"
+    dirname = os.path.dirname(__file__)
+    fname = os.path.join(dirname, "morph.swc")
 
     _, pathlengths, _, _ = nx.utils.swc.swc_to_neurax(fname, max_branch_len=2000.0)
     pathlengths = np.asarray(pathlengths)[1:]
@@ -56,7 +57,8 @@ def test_swc_radius():
     range_16 = np.linspace(non_split / 2, 1 - non_split / 2, nseg)
 
     # Can not use full morphology because of branch sorting.
-    fname = "morph_250.swc"
+    dirname = os.path.dirname(__file__)
+    fname = os.path.join(dirname, "morph_250.swc")
 
     _, pathlen, radius_fns, _ = nx.utils.swc.swc_to_neurax(
         fname, max_branch_len=2000.0, sort=False
@@ -100,8 +102,8 @@ def test_swc_voltages():
     It tests whether, on average over time and recordings, the voltage is off by less
     than 1.5 mV.
     """
-
-    fname = "morph.swc"  # n120
+    dirname = os.path.dirname(__file__)
+    fname = os.path.join(dirname, "morph.swc")  # n120
 
     i_delay = 2.0
     i_dur = 5.0