Merge branch 'master' into enh/add_caching_action

.github/workflows/ruff-formatting.yml

@@ -0,0 +1,38 @@
+name: Ruff formatting
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 12 * * 0"  # Weekly at noon UTC on Sundays
+
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Check with Ruff
+        id: ruff-check
+        uses: chartboost/ruff-action@v1
+        with:
+            src: './elephant'
+            args: 'format --check'
+        continue-on-error: true
+
+      - name: Fix with Ruff
+        uses: chartboost/ruff-action@v1
+        if : ${{ steps.ruff-check.outcome == 'failure' }}
+        with:
+            src: './elephant'
+            args: 'format --verbose'
+
+      - name: Create PR
+        uses: peter-evans/create-pull-request@v5
+        if : ${{ steps.ruff-check.outcome == 'failure' }}
+        with:
+            commit-message: ruff formatting
+            title: Ruff formatting
+            body: Reformatting code with ruff
+            branch: ruff-formatting

elephant/test/test_neo_tools.py

@@ -1163,40 +1163,52 @@ def test__get_all_spiketrains__spiketrain(self):
     #     assert_same_sub_schema(targ, res0)
 
     def test__get_all_spiketrains__segment(self):
+        # Generate a simple segment object containing one spike train,
+        # supporting objects of type Segment and SpikeTrain.
         obj = generate_one_simple_segment(
-            supported_objects=[neo.core.Segment, neo.core.SpikeTrain])
-        targ = copy.deepcopy(obj)
-        obj.spiketrains.append(obj.spiketrains[0])
-
+            nb_spiketrain=1,
+            supported_objects=[neo.core.Segment, neo.core.SpikeTrain]
+        )
+        # Append a deep copy of the first spike train in the segment's
+        # spike train list to itself.
+        obj.spiketrains.append(copy.deepcopy(obj.spiketrains[0]))
+        # Call the function get_all_spiketrains with the segment object
         res0 = nt.get_all_spiketrains(obj)
-
-        targ = targ.spiketrains
-
-        self.assertTrue(len(res0) > 0)
-
-        self.assertEqual(len(targ), len(res0))
-
-        assert_same_sub_schema(targ, res0)
+        # Assert that the length of the result res0 is equal to 2.
+        # This checks if the function correctly returns two spike trains,
+        # including the original and its copy.
+        self.assertTrue(len(res0) == 2)
 
     def test__get_all_spiketrains__block(self):
+        # Generate a simple block with 3 segments
         obj = generate_one_simple_block(
             nb_segment=3,
-            supported_objects=[
-                neo.core.Block, neo.core.Segment, neo.core.SpikeTrain])
+            supported_objects=[neo.core.Block,
+                               neo.core.Segment,
+                               neo.core.SpikeTrain]
+        )
+
+        # Deep copy the generated block for comparison
         targ = copy.deepcopy(obj)
 
-        iobj1 = obj.segments[0]
-        obj.segments.append(iobj1)
+        # Manipulate the block by appending a spiketrain from one segment to
+        # another
         iobj2 = obj.segments[0].spiketrains[1]
         obj.segments[1].spiketrains.append(iobj2)
+
+        # Get all spiketrains from the modified block
         res0 = nt.get_all_spiketrains(obj)
 
+        # Convert the target deep copy to a SpikeTrainList
         targ = SpikeTrainList(targ.list_children_by_class('SpikeTrain'))
 
-        self.assertTrue(len(res0) > 0)
-
-        self.assertEqual(len(targ), len(res0))
-
+        # Perform assertions to validate the results
+        self.assertTrue(
+            len(res0) > 0,
+            "The result of get_all_spiketrains should not be empty.")
+        self.assertEqual(
+            len(targ), len(res0),
+            "The lengths of the SpikeTrainList and result should be equal.")
         assert_same_sub_schema(targ, res0)
 
     def test__get_all_spiketrains__list(self):
@@ -1207,8 +1219,6 @@ def test__get_all_spiketrains__list(self):
                     neo.core.Block, neo.core.Segment, neo.core.SpikeTrain])
             for _ in range(3)]
         targ = copy.deepcopy(obj)
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].spiketrains[1]
         obj[2].segments[1].spiketrains.append(iobj2)
         obj.append(obj[-1])
@@ -1232,8 +1242,6 @@ def test__get_all_spiketrains__tuple(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].spiketrains[1]
         obj[2].segments[1].spiketrains.append(iobj2)
         obj.append(obj[-1])
@@ -1256,8 +1264,6 @@ def test__get_all_spiketrains__iter(self):
                     neo.core.Block, neo.core.Segment, neo.core.SpikeTrain])
             for _ in range(3)]
         targ = copy.deepcopy(obj)
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].spiketrains[1]
         obj[2].segments[1].spiketrains.append(iobj2)
         obj.append(obj[-1])
@@ -1281,8 +1287,6 @@ def test__get_all_spiketrains__dict(self):
                     neo.core.Block, neo.core.Segment, neo.core.SpikeTrain])
             for _ in range(3)]
         targ = copy.deepcopy(obj)
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].spiketrains[1]
         obj[2].segments[1].spiketrains.append(iobj2)
         obj.append(obj[-1])
@@ -1333,8 +1337,6 @@ def test__get_all_events__block(self):
                 neo.core.Block, neo.core.Segment, neo.core.Event])
         targ = copy.deepcopy(obj)
 
-        iobj1 = obj.segments[0]
-        obj.segments.append(iobj1)
         iobj2 = obj.segments[0].events[1]
         obj.segments[1].events.append(iobj2)
         res0 = nt.get_all_events(obj)
@@ -1356,8 +1358,6 @@ def test__get_all_events__list(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].events[1]
         obj[2].segments[1].events.append(iobj2)
         obj.append(obj[-1])
@@ -1381,8 +1381,6 @@ def test__get_all_events__tuple(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].events[1]
         obj[2].segments[1].events.append(iobj2)
         obj.append(obj[0])
@@ -1406,8 +1404,6 @@ def test__get_all_events__iter(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].events[1]
         obj[2].segments[1].events.append(iobj2)
         obj.append(obj[0])
@@ -1431,8 +1427,6 @@ def test__get_all_events__dict(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].events[1]
         obj[2].segments[1].events.append(iobj2)
         obj.append(obj[0])
@@ -1482,10 +1476,6 @@ def test__get_all_epochs__block(self):
                 neo.core.Block, neo.core.Segment, neo.core.Epoch])
         targ = copy.deepcopy(obj)
 
-        iobj1 = obj.segments[0]
-        obj.segments.append(iobj1)
-        iobj2 = obj.segments[0].epochs[1]
-        obj.segments[1].epochs.append(iobj2)
         res0 = nt.get_all_epochs(obj)
 
         targ = targ.list_children_by_class('Epoch')
@@ -1505,8 +1495,6 @@ def test__get_all_epochs__list(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].epochs[1]
         obj[2].segments[1].epochs.append(iobj2)
         obj.append(obj[-1])
@@ -1530,8 +1518,6 @@ def test__get_all_epochs__tuple(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].epochs[1]
         obj[2].segments[1].epochs.append(iobj2)
         obj.append(obj[0])
@@ -1555,8 +1541,6 @@ def test__get_all_epochs__iter(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].epochs[1]
         obj[2].segments[1].epochs.append(iobj2)
         obj.append(obj[0])
@@ -1580,8 +1564,6 @@ def test__get_all_epochs__dict(self):
             for _ in range(3)]
         targ = copy.deepcopy(obj)
         obj.append(obj[-1])
-        iobj1 = obj[2].segments[0]
-        obj[2].segments.append(iobj1)
         iobj2 = obj[1].segments[2].epochs[1]
         obj[2].segments[1].epochs.append(iobj2)
         obj.append(obj[0])

elephant/test/test_trials.py

@@ -29,7 +29,7 @@ def _create_trials_block(n_trials: int = 0,
             n_spiketrains=n_spiketrains)
         analogsignals = [AnalogSignal(signal=[.01, 3.3, 9.3], units='uV',
                                       sampling_rate=1 * pq.Hz)
-                         ] * n_analogsignals
+                         for _ in range(n_analogsignals)]
         for spiketrain in spiketrains:
             segment.spiketrains.append(spiketrain)
         for analogsignal in analogsignals: