From 5c9561696aaae2987e53d397f941a63ab12ef4a3 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Tue, 2 Jan 2024 09:40:56 +0000
Subject: [PATCH 1/9] overrides typing

---
 mcmc/mcmc_cholesky_vertex.py                     | 12 ++++++++----
 mcmc/mcmc_coordinator_vertex.py                  | 16 ++++++++++------
 mcmc/mcmc_model.py                               |  9 ++++++---
 mcmc/mcmc_root_finder_vertex.py                  | 12 ++++++++----
 mcmc/mcmc_vertex.py                              | 14 +++++++++-----
 mcmc_examples/arma/arma_fixed_point_model.py     |  7 ++++---
 mcmc_examples/arma/arma_float_model.py           |  7 ++++---
 mcmc_examples/arma/arma_model.py                 |  7 ++++---
 .../lighthouse/lighthouse_fixed_point_model.py   |  7 ++++---
 .../lighthouse/lighthouse_float_model.py         |  7 ++++---
 mcmc_examples/lighthouse/lighthouse_model.py     |  7 ++++---
 11 files changed, 65 insertions(+), 40 deletions(-)

diff --git a/mcmc/mcmc_cholesky_vertex.py b/mcmc/mcmc_cholesky_vertex.py
index 7e95fc7..7d4aae2 100644
--- a/mcmc/mcmc_cholesky_vertex.py
+++ b/mcmc/mcmc_cholesky_vertex.py
@@ -17,11 +17,14 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from pacman.model.placements import Placement
+
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
 from spinn_front_end_common.abstract_models\
     .abstract_generates_data_specification \
     import AbstractGeneratesDataSpecification
+from spinn_front_end_common.interface.ds import DataSpecificationGenerator
 from spinn_front_end_common.utilities.utility_objs.executable_type \
     import ExecutableType
 
@@ -61,20 +64,21 @@ def __init__(
 
     @property
     @overrides(MachineVertex.sdram_required)
-    def sdram_required(self):
+    def sdram_required(self) -> ConstantSDRAM:
         return ConstantSDRAM(self._n_parameter_bytes)
 
     @overrides(AbstractHasAssociatedBinary.get_binary_file_name)
-    def get_binary_file_name(self):
+    def get_binary_file_name(self) -> str:
         return "mcmc_cholesky.aplx"
 
     @overrides(AbstractHasAssociatedBinary.get_binary_start_type)
-    def get_binary_start_type(self):
+    def get_binary_start_type(self) -> ExecutableType:
         return ExecutableType.SYNC
 
     @overrides(
         AbstractGeneratesDataSpecification.generate_data_specification)
-    def generate_data_specification(self, spec, placement):
+    def generate_data_specification(
+            self, spec: DataSpecificationGenerator, placement: Placement):
 
         # Reserve and write the parameters region
         spec.reserve_memory_region(
diff --git a/mcmc/mcmc_coordinator_vertex.py b/mcmc/mcmc_coordinator_vertex.py
index b285dc2..1b8b084 100644
--- a/mcmc/mcmc_coordinator_vertex.py
+++ b/mcmc/mcmc_coordinator_vertex.py
@@ -17,13 +17,16 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from pacman.model.placements import Placement
+
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
 from spinn_front_end_common.abstract_models\
     .abstract_generates_data_specification \
     import AbstractGeneratesDataSpecification
 from spinn_front_end_common.data import FecDataView
-from spinn_front_end_common.interface.ds import DataType
+from spinn_front_end_common.interface.ds import (
+    DataSpecificationGenerator, DataType)
 from spinn_front_end_common.utilities.utility_objs.executable_type \
     import ExecutableType
 from spinn_utilities.progress_bar import ProgressBar
@@ -187,22 +190,23 @@ def acknowledge_partition_name(self):
 
     @property
     @overrides(MachineVertex.sdram_required)
-    def sdram_required(self):
+    def sdram_required(self) -> ConstantSDRAM:
         sdram = self._N_PARAMETER_BYTES + self._data_size
         sdram += len(self._mcmc_vertices) * self._KEY_ELEMENT_TYPE.size
         return ConstantSDRAM(sdram)
 
     @overrides(AbstractHasAssociatedBinary.get_binary_file_name)
-    def get_binary_file_name(self):
+    def get_binary_file_name(self) -> str:
         return "mcmc_coordinator.aplx"
 
     @overrides(AbstractHasAssociatedBinary.get_binary_start_type)
-    def get_binary_start_type(self):
+    def get_binary_start_type(self) -> ExecutableType:
         return ExecutableType.SYNC
 
     @overrides(
         AbstractGeneratesDataSpecification.generate_data_specification)
-    def generate_data_specification(self, spec, placement):
+    def generate_data_specification(
+            self, spec: DataSpecificationGenerator, placement: Placement):
         routing_info = FecDataView.get_routing_infos()
 
         # Reserve and write the parameters region
@@ -265,7 +269,7 @@ def generate_data_specification(self, spec, placement):
         spec.end_specification()
 
     @overrides(MachineVertex.get_n_keys_for_partition)
-    def get_n_keys_for_partition(self, partition_id):
+    def get_n_keys_for_partition(self, partition_id: str) -> int:
         return self._n_sequences
 
     def read_samples(self, buffer_manager):
diff --git a/mcmc/mcmc_model.py b/mcmc/mcmc_model.py
index a8d2e0f..888c8a5 100644
--- a/mcmc/mcmc_model.py
+++ b/mcmc/mcmc_model.py
@@ -13,28 +13,31 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.abstract_base import AbstractBase
 from spinn_utilities.abstract_base import abstractmethod
+from mcmc.mcmc_parameter import MCMCParameter
+from mcmc.mcmc_state_variable import MCMCStateVariable
 
 
 class MCMCModel(object, metaclass=AbstractBase):
 
     @abstractmethod
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         """ Get the parameters of the model
 
         :rtype: list of :py:class:`mcmc.mcmc_parameter.MCMCParameter`
         """
 
     @abstractmethod
-    def get_state_variables(self):
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         """ Get the state variables of the model
 
         :rtype: list of :py:class:`mcmc.mcmc_state_variable.MCMCStateVariable`
         """
 
     @abstractmethod
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         """ Get the name of the binary compiled with this model
 
         :rtype: str
diff --git a/mcmc/mcmc_root_finder_vertex.py b/mcmc/mcmc_root_finder_vertex.py
index ba922a8..a2fde6f 100644
--- a/mcmc/mcmc_root_finder_vertex.py
+++ b/mcmc/mcmc_root_finder_vertex.py
@@ -17,11 +17,14 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from pacman.model.placements import Placement
+
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
 from spinn_front_end_common.abstract_models\
     .abstract_generates_data_specification \
     import AbstractGeneratesDataSpecification
+from spinn_front_end_common.interface.ds import DataSpecificationGenerator
 from spinn_front_end_common.utilities.utility_objs.executable_type \
     import ExecutableType
 
@@ -60,20 +63,21 @@ def __init__(
 
     @property
     @overrides(MachineVertex.sdram_required)
-    def sdram_required(self):
+    def sdram_required(self) -> ConstantSDRAM:
         return ConstantSDRAM(self._n_parameter_bytes)
 
     @overrides(AbstractHasAssociatedBinary.get_binary_file_name)
-    def get_binary_file_name(self):
+    def get_binary_file_name(self) -> str:
         return "mcmc_root_finder.aplx"
 
     @overrides(AbstractHasAssociatedBinary.get_binary_start_type)
-    def get_binary_start_type(self):
+    def get_binary_start_type(self) -> ExecutableType:
         return ExecutableType.SYNC
 
     @overrides(
         AbstractGeneratesDataSpecification.generate_data_specification)
-    def generate_data_specification(self, spec, placement):
+    def generate_data_specification(
+            self, spec: DataSpecificationGenerator, placement: Placement):
 
         # Reserve and write the parameters region
         spec.reserve_memory_region(
diff --git a/mcmc/mcmc_vertex.py b/mcmc/mcmc_vertex.py
index e625a59..f5a0c9b 100644
--- a/mcmc/mcmc_vertex.py
+++ b/mcmc/mcmc_vertex.py
@@ -17,6 +17,8 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from pacman.model.placements import Placement
+
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
 from spinn_front_end_common.abstract_models\
@@ -25,7 +27,8 @@
 from spinn_front_end_common.data import FecDataView
 from spinn_front_end_common.interface.buffer_management.buffer_models\
     .abstract_receive_buffers_to_host import AbstractReceiveBuffersToHost
-from spinn_front_end_common.interface.ds import DataType
+from spinn_front_end_common.interface.ds import (
+    DataSpecificationGenerator, DataType)
 from spinn_front_end_common.utilities import helpful_functions
 from spinn_front_end_common.interface.buffer_management \
     import recording_utilities
@@ -195,20 +198,21 @@ def cholesky_result_partition_name(self):
 
     @property
     @overrides(MachineVertex.sdram_required)
-    def sdram_required(self):
+    def sdram_required(self) -> ConstantSDRAM:
         return ConstantSDRAM(self._sdram_usage)
 
     @overrides(AbstractHasAssociatedBinary.get_binary_file_name)
-    def get_binary_file_name(self):
+    def get_binary_file_name(self) -> str:
         return self._model.get_binary_name()
 
     @overrides(AbstractHasAssociatedBinary.get_binary_start_type)
-    def get_binary_start_type(self):
+    def get_binary_start_type(self) -> ExecutableType:
         return ExecutableType.SYNC
 
     @overrides(
         AbstractGeneratesDataSpecification.generate_data_specification)
-    def generate_data_specification(self, spec, placement):
+    def generate_data_specification(
+            self, spec: DataSpecificationGenerator, placement: Placement):
 
         routing_info = FecDataView.get_routing_infos()
         # Reserve and write the recording regions
diff --git a/mcmc_examples/arma/arma_fixed_point_model.py b/mcmc_examples/arma/arma_fixed_point_model.py
index 29b182d..59d06a4 100644
--- a/mcmc_examples/arma/arma_fixed_point_model.py
+++ b/mcmc_examples/arma/arma_fixed_point_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from spinn_front_end_common.interface.ds import DataType
@@ -41,11 +42,11 @@ def __init__(
         self._q_jump_scale = q_jump_scale
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "arma.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         return [
             MCMCParameter(self._parameters, DataType.S1615),  # array ?
             MCMCParameter(self._p_jump_scale, DataType.S1615),
@@ -53,7 +54,7 @@ def get_parameters(self):
         ]
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         return [
             MCMCStateVariable("order_p", 10, DataType.S1615),  # check type
             MCMCStateVariable("order_q", 10, DataType.S1615)
diff --git a/mcmc_examples/arma/arma_float_model.py b/mcmc_examples/arma/arma_float_model.py
index 63632a2..a0f358b 100644
--- a/mcmc_examples/arma/arma_float_model.py
+++ b/mcmc_examples/arma/arma_float_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from mcmc.mcmc_model import MCMCModel
@@ -40,11 +41,11 @@ def __init__(
         self._cholesky = cholesky
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "arma.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         # Best here to convert the arrays into individual values
         return_params = []
         for i in range(len(self._jump_scale)):
@@ -54,7 +55,7 @@ def get_parameters(self):
         return return_params
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self)-> List[MCMCStateVariable]:
         # Best here to convert the arrays into individual values
         return_state_vars = []
         for i in range(len(self._parameters)):
diff --git a/mcmc_examples/arma/arma_model.py b/mcmc_examples/arma/arma_model.py
index cb530c0..1093ea4 100644
--- a/mcmc_examples/arma/arma_model.py
+++ b/mcmc_examples/arma/arma_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from mcmc.mcmc_model import MCMCModel
@@ -42,11 +43,11 @@ def __init__(
         self._q_jump_scale = q_jump_scale
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "arma.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         # It's probably best here to convert the arrays into individual values?
         return_params = []
         for i in range(len(self._p_jump_scale)):
@@ -59,7 +60,7 @@ def get_parameters(self):
         return return_params
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self)-> List[MCMCStateVariable]:
         # It's probably best here to convert the arrays into individual values?
         return_state_vars = []
         for i in range(len(self._parameters)):
diff --git a/mcmc_examples/lighthouse/lighthouse_fixed_point_model.py b/mcmc_examples/lighthouse/lighthouse_fixed_point_model.py
index 89ee579..1deb7fb 100644
--- a/mcmc_examples/lighthouse/lighthouse_fixed_point_model.py
+++ b/mcmc_examples/lighthouse/lighthouse_fixed_point_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from spinn_front_end_common.interface.ds import DataType
@@ -51,11 +52,11 @@ def __init__(
         self._cholesky = cholesky
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "lighthouse.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         return [
             MCMCParameter(self._alpha_jump_scale, DataType.S1615),
             MCMCParameter(self._beta_jump_scale, DataType.S1615),
@@ -66,7 +67,7 @@ def get_parameters(self):
         ]
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         return [
             MCMCStateVariable("alpha", 0.0, DataType.S1615),
             MCMCStateVariable("beta", 1.0, DataType.S1615)
diff --git a/mcmc_examples/lighthouse/lighthouse_float_model.py b/mcmc_examples/lighthouse/lighthouse_float_model.py
index 77c857a..1427b66 100644
--- a/mcmc_examples/lighthouse/lighthouse_float_model.py
+++ b/mcmc_examples/lighthouse/lighthouse_float_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from mcmc.mcmc_model import MCMCModel
@@ -51,11 +52,11 @@ def __init__(
         self._cholesky = cholesky
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "lighthouse.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self)  -> List[MCMCParameter]:
         return [
             MCMCParameter(self._alpha_jump_scale, numpy.float32),
             MCMCParameter(self._beta_jump_scale, numpy.float32),
@@ -66,7 +67,7 @@ def get_parameters(self):
         ]
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         return [
             MCMCStateVariable("alpha", 0.0, numpy.float32),
             MCMCStateVariable("beta", 1.0, numpy.float32)
diff --git a/mcmc_examples/lighthouse/lighthouse_model.py b/mcmc_examples/lighthouse/lighthouse_model.py
index 3129aea..78466fd 100644
--- a/mcmc_examples/lighthouse/lighthouse_model.py
+++ b/mcmc_examples/lighthouse/lighthouse_model.py
@@ -13,6 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
 from spinn_utilities.overrides import overrides
 
 from mcmc.mcmc_model import MCMCModel
@@ -51,11 +52,11 @@ def __init__(
         self._cholesky = cholesky
 
     @overrides(MCMCModel.get_binary_name)
-    def get_binary_name(self):
+    def get_binary_name(self) -> str:
         return "lighthouse.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self):
+    def get_parameters(self) -> List[MCMCParameter]:
         return [
             MCMCParameter(self._alpha_jump_scale, numpy.float64),
             MCMCParameter(self._beta_jump_scale, numpy.float64),
@@ -66,7 +67,7 @@ def get_parameters(self):
         ]
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self):
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         return [
             MCMCStateVariable("alpha", 0.0, numpy.float64),
             MCMCStateVariable("beta", 1.0, numpy.float64)

From 27cd769fa1e03a68552e060735ce94418184ecbd Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Tue, 2 Jan 2024 09:47:00 +0000
Subject: [PATCH 2/9] flake8

---
 mcmc_examples/arma/arma_float_model.py             | 2 +-
 mcmc_examples/arma/arma_model.py                   | 2 +-
 mcmc_examples/lighthouse/lighthouse_float_model.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/mcmc_examples/arma/arma_float_model.py b/mcmc_examples/arma/arma_float_model.py
index a0f358b..2fd623b 100644
--- a/mcmc_examples/arma/arma_float_model.py
+++ b/mcmc_examples/arma/arma_float_model.py
@@ -55,7 +55,7 @@ def get_parameters(self) -> List[MCMCParameter]:
         return return_params
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self)-> List[MCMCStateVariable]:
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         # Best here to convert the arrays into individual values
         return_state_vars = []
         for i in range(len(self._parameters)):
diff --git a/mcmc_examples/arma/arma_model.py b/mcmc_examples/arma/arma_model.py
index 1093ea4..3b7e6f8 100644
--- a/mcmc_examples/arma/arma_model.py
+++ b/mcmc_examples/arma/arma_model.py
@@ -60,7 +60,7 @@ def get_parameters(self) -> List[MCMCParameter]:
         return return_params
 
     @overrides(MCMCModel.get_state_variables)
-    def get_state_variables(self)-> List[MCMCStateVariable]:
+    def get_state_variables(self) -> List[MCMCStateVariable]:
         # It's probably best here to convert the arrays into individual values?
         return_state_vars = []
         for i in range(len(self._parameters)):
diff --git a/mcmc_examples/lighthouse/lighthouse_float_model.py b/mcmc_examples/lighthouse/lighthouse_float_model.py
index 1427b66..6fd681a 100644
--- a/mcmc_examples/lighthouse/lighthouse_float_model.py
+++ b/mcmc_examples/lighthouse/lighthouse_float_model.py
@@ -56,7 +56,7 @@ def get_binary_name(self) -> str:
         return "lighthouse.aplx"
 
     @overrides(MCMCModel.get_parameters)
-    def get_parameters(self)  -> List[MCMCParameter]:
+    def get_parameters(self) -> List[MCMCParameter]:
         return [
             MCMCParameter(self._alpha_jump_scale, numpy.float32),
             MCMCParameter(self._beta_jump_scale, numpy.float32),

From 8b755ebd5ebc4d53c66c1e8a684f89b2bcbd9ea2 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Mon, 8 Jan 2024 08:24:58 +0000
Subject: [PATCH 3/9] activate mypy

---
 .github/workflows/python_actions.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/python_actions.yml b/.github/workflows/python_actions.yml
index 72376f8..aa25c86 100644
--- a/.github/workflows/python_actions.yml
+++ b/.github/workflows/python_actions.yml
@@ -78,6 +78,9 @@ jobs:
       if: matrix.python-version == 3.12
       uses: ./support/actions/check-copyrights
 
+    - name: Lint with mypy
+      run: mypy $BASE_PKG
+
 #    # Add the following as required in the future
 #    - name: Validate XML
 #      if: matrix.python-version == 3.8

From 6ac0b567cdcbe4953e6de2ae143ee3d35365dbe4 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Mon, 8 Jan 2024 09:33:59 +0000
Subject: [PATCH 4/9] Install mypy

---
 .github/workflows/python_actions.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/python_actions.yml b/.github/workflows/python_actions.yml
index aa25c86..dddce43 100644
--- a/.github/workflows/python_actions.yml
+++ b/.github/workflows/python_actions.yml
@@ -39,6 +39,8 @@ jobs:
         path: support
     - name: Install pip, etc
       uses: ./support/actions/python-tools
+    - name: Install mypy
+      run: pip install mypy
 
     - name: Install Spinnaker Dependencies
       uses: ./support/actions/install-spinn-deps

From 5a33d4e5b32cf7b56054f8751bb2d41f527cdbc0 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Mon, 8 Jan 2024 13:08:39 +0000
Subject: [PATCH 5/9] add py.typed marker

---
 mcmc/py.typed | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 mcmc/py.typed

diff --git a/mcmc/py.typed b/mcmc/py.typed
new file mode 100644
index 0000000..91eaa0c
--- /dev/null
+++ b/mcmc/py.typed
@@ -0,0 +1,13 @@
+# Copyright (c) 2023 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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 9e9d4bfda0a4983b8ec57e8cb47dd74fa46e7d32 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Mon, 8 Jan 2024 16:20:09 +0000
Subject: [PATCH 6/9] mypy mcmc

---
 .github/workflows/python_actions.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python_actions.yml b/.github/workflows/python_actions.yml
index dddce43..4eeb97e 100644
--- a/.github/workflows/python_actions.yml
+++ b/.github/workflows/python_actions.yml
@@ -81,7 +81,7 @@ jobs:
       uses: ./support/actions/check-copyrights
 
     - name: Lint with mypy
-      run: mypy $BASE_PKG
+      run: mypy mcmc
 
 #    # Add the following as required in the future
 #    - name: Validate XML

From 83492b92faa76dc7c9dc0af7b2cff3e426831514 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Mon, 8 Jan 2024 16:37:25 +0000
Subject: [PATCH 7/9] typing fixes

---
 mcmc/mcmc_cholesky_vertex.py    | 12 ++++++------
 mcmc/mcmc_coordinator_vertex.py | 11 ++++++-----
 mcmc/mcmc_model.py              |  3 +++
 mcmc/mcmc_root_finder_vertex.py |  4 ++--
 mcmc/mcmc_vertex.py             |  5 +++--
 5 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/mcmc/mcmc_cholesky_vertex.py b/mcmc/mcmc_cholesky_vertex.py
index 7d4aae2..f20d2a3 100644
--- a/mcmc/mcmc_cholesky_vertex.py
+++ b/mcmc/mcmc_cholesky_vertex.py
@@ -13,11 +13,15 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from pacman.model.graphs.machine import MachineVertex
-from pacman.model.resources import ConstantSDRAM
+from enum import Enum
+
 from spinn_utilities.overrides import overrides
 
+from spinnman.model.enums import ExecutableType
+
+from pacman.model.graphs.machine import MachineVertex
 from pacman.model.placements import Placement
+from pacman.model.resources import ConstantSDRAM
 
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
@@ -25,10 +29,6 @@
     .abstract_generates_data_specification \
     import AbstractGeneratesDataSpecification
 from spinn_front_end_common.interface.ds import DataSpecificationGenerator
-from spinn_front_end_common.utilities.utility_objs.executable_type \
-    import ExecutableType
-
-from enum import Enum
 
 
 class MCMCCholeskyRegions(Enum):
diff --git a/mcmc/mcmc_coordinator_vertex.py b/mcmc/mcmc_coordinator_vertex.py
index 1b8b084..f0f576c 100644
--- a/mcmc/mcmc_coordinator_vertex.py
+++ b/mcmc/mcmc_coordinator_vertex.py
@@ -17,6 +17,8 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from spinnman.model.enums import ExecutableType
+
 from pacman.model.placements import Placement
 
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
@@ -27,8 +29,6 @@
 from spinn_front_end_common.data import FecDataView
 from spinn_front_end_common.interface.ds import (
     DataSpecificationGenerator, DataType)
-from spinn_front_end_common.utilities.utility_objs.executable_type \
-    import ExecutableType
 from spinn_utilities.progress_bar import ProgressBar
 
 import numpy
@@ -236,16 +236,17 @@ def generate_data_specification(
         spec.write_value(len(keys), data_type=DataType.UINT32)
 
         # Write the key
-        routing_info = routing_info.get_routing_info_from_pre_vertex(
+        vertex_routing_info = routing_info.get_routing_info_from_pre_vertex(
             self, self._data_partition_name)
-        spec.write_value(routing_info.key, data_type=DataType.UINT32)
+        assert vertex_routing_info is not None
+        spec.write_value(vertex_routing_info.key, data_type=DataType.UINT32)
 
         # Write the window size
         spec.write_value(self._window_size, data_type=DataType.UINT32)
 
         # Write the sequence mask
         spec.write_value(
-            ~routing_info.mask & 0xFFFFFFFF, data_type=DataType.UINT32)
+            ~vertex_routing_info.mask & 0xFFFFFFFF, data_type=DataType.UINT32)
 
         # Write the timer
         spec.write_value(self._send_timer, data_type=DataType.UINT32)
diff --git a/mcmc/mcmc_model.py b/mcmc/mcmc_model.py
index 888c8a5..c6d6b3c 100644
--- a/mcmc/mcmc_model.py
+++ b/mcmc/mcmc_model.py
@@ -28,6 +28,7 @@ def get_parameters(self) -> List[MCMCParameter]:
 
         :rtype: list of :py:class:`mcmc.mcmc_parameter.MCMCParameter`
         """
+        raise NotImplementedError
 
     @abstractmethod
     def get_state_variables(self) -> List[MCMCStateVariable]:
@@ -35,6 +36,7 @@ def get_state_variables(self) -> List[MCMCStateVariable]:
 
         :rtype: list of :py:class:`mcmc.mcmc_state_variable.MCMCStateVariable`
         """
+        raise NotImplementedError
 
     @abstractmethod
     def get_binary_name(self) -> str:
@@ -42,3 +44,4 @@ def get_binary_name(self) -> str:
 
         :rtype: str
         """
+        raise NotImplementedError
diff --git a/mcmc/mcmc_root_finder_vertex.py b/mcmc/mcmc_root_finder_vertex.py
index a2fde6f..97d490b 100644
--- a/mcmc/mcmc_root_finder_vertex.py
+++ b/mcmc/mcmc_root_finder_vertex.py
@@ -19,14 +19,14 @@
 
 from pacman.model.placements import Placement
 
+from spinnman.model.enums import ExecutableType
+
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
     import AbstractHasAssociatedBinary
 from spinn_front_end_common.abstract_models\
     .abstract_generates_data_specification \
     import AbstractGeneratesDataSpecification
 from spinn_front_end_common.interface.ds import DataSpecificationGenerator
-from spinn_front_end_common.utilities.utility_objs.executable_type \
-    import ExecutableType
 
 from enum import Enum
 
diff --git a/mcmc/mcmc_vertex.py b/mcmc/mcmc_vertex.py
index f5a0c9b..303f65c 100644
--- a/mcmc/mcmc_vertex.py
+++ b/mcmc/mcmc_vertex.py
@@ -17,6 +17,8 @@
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
 
+from spinnman.model.enums import ExecutableType
+
 from pacman.model.placements import Placement
 
 from spinn_front_end_common.abstract_models.abstract_has_associated_binary \
@@ -32,8 +34,6 @@
 from spinn_front_end_common.utilities import helpful_functions
 from spinn_front_end_common.interface.buffer_management \
     import recording_utilities
-from spinn_front_end_common.utilities.utility_objs.executable_type \
-    import ExecutableType
 
 from enum import Enum
 import numpy
@@ -262,6 +262,7 @@ def generate_data_specification(
         if (self._model.root_finder):
             routing_info_rf = routing_info.get_routing_info_from_pre_vertex(
                 self, self._parameter_partition_name)
+            assert routing_info_rf is not None
             spec.write_value(routing_info_rf.key, data_type=DataType.UINT32)
         else:
             spec.write_value(0, data_type=DataType.UINT32)

From a709d9e5ef034bcc67d67ddb6ce3efef915d2cd6 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Tue, 9 Jan 2024 07:12:08 +0000
Subject: [PATCH 8/9] typing

---
 mcmc/mcmc_coordinator_vertex.py | 4 +++-
 mcmc/mcmc_vertex.py             | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/mcmc/mcmc_coordinator_vertex.py b/mcmc/mcmc_coordinator_vertex.py
index f0f576c..c2131bf 100644
--- a/mcmc/mcmc_coordinator_vertex.py
+++ b/mcmc/mcmc_coordinator_vertex.py
@@ -13,6 +13,8 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from typing import List
+
 from pacman.model.graphs.machine import MachineVertex
 from pacman.model.resources import ConstantSDRAM
 from spinn_utilities.overrides import overrides
@@ -217,7 +219,7 @@ def generate_data_specification(
 
         # Get the placement of the vertices and find out how many chips
         # are needed
-        keys = list()
+        keys: List[int] = list()
         for vertex in self._mcmc_vertices:
             mcmc_placement = FecDataView.get_placement_of_vertex(vertex)
             self._mcmc_placements.append(mcmc_placement)
diff --git a/mcmc/mcmc_vertex.py b/mcmc/mcmc_vertex.py
index 303f65c..5a4f3ec 100644
--- a/mcmc/mcmc_vertex.py
+++ b/mcmc/mcmc_vertex.py
@@ -270,6 +270,7 @@ def generate_data_specification(
         if (self._model.cholesky):
             routing_info_ch = routing_info.get_routing_info_from_pre_vertex(
                 self, self._cholesky_partition_name)
+            assert routing_info_ch is not None
             spec.write_value(routing_info_ch.key, data_type=DataType.UINT32)
         else:
             spec.write_value(0, data_type=DataType.UINT32)

From d2646b3c8a49c39fdfdff3def6be447c185e2d56 Mon Sep 17 00:00:00 2001
From: "Christian Y. Brenninkmeijer"
 <christian.brenninkmeijer@manchester.ac.uk>
Date: Tue, 9 Jan 2024 07:28:54 +0000
Subject: [PATCH 9/9] check for None

---
 mcmc/mcmc_coordinator_vertex.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mcmc/mcmc_coordinator_vertex.py b/mcmc/mcmc_coordinator_vertex.py
index c2131bf..6e42ba0 100644
--- a/mcmc/mcmc_coordinator_vertex.py
+++ b/mcmc/mcmc_coordinator_vertex.py
@@ -226,7 +226,8 @@ def generate_data_specification(
             if self._is_receiver_placement(mcmc_placement):
                 key = routing_info.get_first_key_from_pre_vertex(
                     vertex, self._acknowledge_partition_name)
-                keys.append(key)
+                if key is not None:
+                    keys.append(key)
         keys.sort()
 
         # Write the data size in words