Merge pull request #1562 from SpiNNakerManchester/tspy

Typing of Integration test

Author: Christian-B

.github/workflows/python_actions.yml

@@ -32,6 +32,6 @@ jobs:
       coverage-package: spynnaker
       flake8-packages: spynnaker unittests spynnaker_integration_tests proxy_integration_tests
       pylint-packages: spynnaker
-      mypy-packages:  spynnaker_integration_tests proxy_integration_tests
-      mypy-full-packages: spynnaker unittests
+      mypy-packages: proxy_integration_tests
+      mypy-full-packages: spynnaker unittests spynnaker_integration_tests
       cfg-file: spynnaker

mypy.bash

@@ -27,4 +27,4 @@ spalloc="../spalloc/spalloc_client"
 fec="../SpiNNFrontEndCommon/spinn_front_end_common"
 test_base="../TestBase/spinnaker_testbase"
 
-mypy --python-version 3.8 $utils $machine $man $pacman $spalloc $fec $test_base spynnaker unittests
+mypy --python-version 3.8 $utils $machine $man $pacman $spalloc $fec $test_base spynnaker unittests spynnaker_integration_tests

mypyd.bash

@@ -27,4 +27,5 @@ spalloc="../spalloc/spalloc_client"
 fec="../SpiNNFrontEndCommon/spinn_front_end_common"
 test_base="../TestBase/spinnaker_testbase"
 
-mypy --python-version 3.8 --disallow-untyped-defs $utils $machine $man $pacman $spalloc $fec $test_base spynnaker unittests
+mypy --python-version 3.8 --disallow-untyped-defs $utils $machine $man $pacman $spalloc $fec $test_base spynnaker unittests spynnaker_integration_tests
+

pyproject.toml

@@ -17,5 +17,5 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [[tool.mypy.overrides]]
-module = ["matplotlib", "matplotlib.*", "pyNN.*", "quantities", "neo", "scipy", "scipy.*", "lazyarray"]
+module = ["matplotlib", "matplotlib.*", "pyNN.*", "quantities", "neo", "neo.*", "scipy", "scipy.*", "lazyarray"]
 ignore_missing_imports = true

spynnaker_integration_tests/conftest.py

@@ -12,13 +12,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import Iterator
+
 import pytest
+from _pytest.fixtures import SubRequest
 from spynnaker.pyNN.data.spynnaker_data_view import SpynnakerDataView
 import pyNN.spiNNaker as sim
 
 
 @pytest.fixture(autouse=True)
-def check_end_is_called(request):
+def check_end_is_called(request: SubRequest) -> Iterator[None]:
     """ Fixture for all tests, to make sure end is used!
     """
     yield

spynnaker_integration_tests/scripts/checker.py

@@ -12,8 +12,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from neo import AnalogSignal, SpikeTrain
+from spynnaker.pyNN.models.populations import Population
 
-def check_neuron_data(spikes, v, exc, expected_spikes, simtime, label, index):
+
+def check_neuron_data(
+        spikes: SpikeTrain, v: AnalogSignal, exc: AnalogSignal,
+        expected_spikes: int, simtime: int, label: str, index: int) -> None:
 
     if len(spikes) != expected_spikes:
         raise AssertionError(
@@ -56,7 +61,7 @@ def check_neuron_data(spikes, v, exc, expected_spikes, simtime, label, index):
                         index, t, t_delta, label, v[t], target_v - 1))
 
 
-def check_data(pop, expected_spikes, simtime):
+def check_data(pop: Population, expected_spikes: int, simtime: int) -> None:
     neo = pop.get_data("all")
     spikes = neo.segments[0].spiketrains
     v = neo.segments[0].filter(name="v")[0]

spynnaker_integration_tests/scripts/pattern_spiker.py

@@ -11,9 +11,15 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+
+from types import ModuleType
+from typing import List, Optional
 import numpy
 import math
-from spynnaker.pyNN.models.populations import PopulationView
+from neo import AnalogSignal
+from neo.core.spiketrainlist import SpikeTrainList
+
+from spynnaker.pyNN.models.populations import (Population, PopulationView)
 
 
 class PatternSpiker(object):
@@ -29,9 +35,12 @@ class PatternSpiker(object):
                  -50.73040771484375, -50.450927734375, -50.185089111328125]
     V_COUNT = len(V_PATTERN)
 
-    def create_population(self, sim, n_neurons, label,
-                          spike_rate=None, spike_rec_indexes=None,
-                          v_rate=None, v_rec_indexes=None):
+    def create_population(
+            self, sim: ModuleType, n_neurons: int, label: str,
+            spike_rate: Optional[int] = None,
+            spike_rec_indexes: Optional[List[int]] = None,
+            v_rate: Optional[int] = None,
+            v_rec_indexes: Optional[List[int]] = None) -> Population:
 
         v_start = self.V_PATTERN * int(math.ceil(n_neurons/self.V_COUNT))
         v_start = v_start[:n_neurons]
@@ -51,11 +60,13 @@ def create_population(self, sim, n_neurons, label,
             view.record(['v'], sampling_interval=v_rate)
         return pop
 
-    def check_v(self, v, label, v_rate, v_rec_indexes, is_view, missing):
+    def check_v(self, v: AnalogSignal, label: str, v_rate: Optional[int],
+                v_rec_indexes: Optional[List[int]], is_view: bool,
+                missing: bool) -> None:
         if v_rate is None:
             v_rate = 1
         if v_rec_indexes is None:
-            v_rec_indexes = range(len(v[0]))
+            v_rec_indexes = list(range(len(v[0])))
         else:
             actual_indexes = list(v.annotations["channel_names"])
 
@@ -85,7 +96,9 @@ def check_v(self, v, label, v_rate, v_rec_indexes, is_view, missing):
                             self.V_PATTERN[(t + neuron) % self.V_COUNT]))
 
     def check_spikes(
-            self, spikes, simtime, label, spike_rate, spike_rec_indexes):
+            self, spikes: SpikeTrainList, simtime: int, label: str,
+            spike_rate: Optional[int],
+            spike_rec_indexes: Optional[List[int]]) -> None:
         for neuron in range(len(spikes)):
             if spike_rec_indexes and neuron not in spike_rec_indexes:
                 continue
@@ -111,8 +124,13 @@ def check_spikes(
                         "Found {} but expected {}".format(
                             neuron, label, spikes[neuron], adjusted_spikes, ))
 
-    def check(self, pop, simtime, spike_rate=None, spike_rec_indexes=None,
-              v_rate=None, v_rec_indexes=None, is_view=False, missing=False):
+    def check(
+            self, pop: Population, simtime: int,
+            spike_rate: Optional[int] = None,
+            spike_rec_indexes: Optional[List[int]] = None,
+            v_rate: Optional[int] = None,
+            v_rec_indexes: Optional[List[int]] = None, is_view: bool = False,
+            missing: bool = False) -> None:
         if is_view:
             neo = pop.get_data("spikes")
             spikes = neo.segments[0].spiketrains

spynnaker_integration_tests/scripts/synfire_npop_run.py

@@ -18,11 +18,13 @@
 Synfirechain-like example
 """
 import numpy
+from numpy.typing import NDArray
 import pyNN.spiNNaker as p
 from spinnaker_testbase.root_test_case import RootTestCase
 
 
-def do_synfire_npop(nNeurons, n_pops, neurons_per_core, runtime=25000):
+def do_synfire_npop(nNeurons: int, n_pops: int, neurons_per_core: int,
+                    runtime: int = 25000) -> NDArray[numpy.floating]:
     """
     Runs the script Does the run based on the parameters