From 7d8657a88723e2830a0221115f9323c614754c68 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 15 Nov 2023 16:10:51 +0000
Subject: [PATCH 01/53] Initial commit

---
 pyEpiabm/pyEpiabm/core/cell.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index a8225c92..63ac8097 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -32,6 +32,7 @@ def __init__(self, loc: typing.Tuple[float, float] = (0, 0)):
         """
         self.location = loc
         self.id = hash(self)
+        print(self.id)
         self.microcells = []
         self.persons = []
         self.places = []

From 3eea9115d922fa22ed1d23cb68a204ea72dc2eb0 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 15 Nov 2023 17:20:19 +0000
Subject: [PATCH 02/53] Added household id

---
 pyEpiabm/pyEpiabm/core/cell.py                     |  3 +++
 pyEpiabm/pyEpiabm/core/household.py                | 14 ++++++++++++++
 pyEpiabm/pyEpiabm/core/microcell.py                |  6 +++++-
 .../pyEpiabm/routine/file_population_config.py     |  6 +++---
 4 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index 63ac8097..354fa48e 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -198,3 +198,6 @@ def find_nearby_cells(self, other_cells):
                 self.nearby_cell_distances[cell2.id] = distance
                 # Dict of near neighbours, cells which are closer than the
                 # cutoff for cross-cell infection
+
+
+print(Cell().id)
diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 7f057771..27ebff40 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -29,6 +29,7 @@ def __init__(self, microcell, loc: typing.Tuple[float, float],
             Household's base infectiousness
 
         """
+        self.id = ""
         self.persons = []
         self.susceptible_persons = []
         self.location = loc
@@ -104,3 +105,16 @@ def remove_household(self):
         """
         self.microcell.households.remove(self)
         self.cell.households.remove(self)
+
+    def set_id(self, id: str):
+        """Updates ID of household (i.e. for input from file).
+        Format of ID - for example 3.1.2 represents household 2 within microcell 1
+        within cell 3.
+
+        Parameters
+        ----------
+        id : str
+            Identity of household
+
+        """
+        self.id = id
diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 3aade19d..6ef0aca5 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -123,7 +123,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list):
+    def add_household(self, people: list, household_id: int):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -131,10 +131,14 @@ def add_household(self, people: list):
         ----------
         people : list
             List of :class:`People` to add to household
+        household_id : int
+            Integer representing this specific household within the microcell
 
         """
         if len(people) != 0:
             household = Household(self, loc=self.location)
+            cell_id = self.cell.id
+            household.set_id(str(cell_id) + "." + str(self.id) + "." + str(household_id))
             for person in people:
                 household.add_person(person)
         else:
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 9741a444..80a92ca9 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -195,14 +195,14 @@ def add_households(microcell: Microcell, household_number: int):
         people_number = len(people_list)
         household_split = np.random.multinomial(people_number, q,
                                                 size=1)[0]
-        for j in range(household_number):
-            people_in_household = household_split[j]
+        for household_id in range(household_number):
+            people_in_household = household_split[household_id]
             household_people = []
             for i in range(people_in_household):
                 person_choice = people_list[0]
                 people_list.remove(person_choice)
                 household_people.append(person_choice)
-            microcell.add_household(household_people)
+            microcell.add_household(household_people, household_id)
 
     @staticmethod
     @log_exceptions()

From 34db412a2cc3519d10ef703e2bbbb838175ffe9b Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 15 Nov 2023 17:59:17 +0000
Subject: [PATCH 03/53] Added set_id

---
 pyEpiabm/pyEpiabm/core/person.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 43a742ba..7e27203b 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -54,6 +54,7 @@ def __init__(self, microcell, age_group=None):
         self.key_worker = False
         self.date_positive = None
         self.is_vaccinated = False
+        self.id = ""
 
         self.set_random_age(age_group)
 
@@ -223,3 +224,17 @@ def remove_person(self):
         self.microcell.cell.persons.remove(self)
         self.microcell.persons.remove(self)
         self.household.persons.remove(self)
+
+    def set_id(self, id: str):
+        """Updates ID of person (i.e. for input from file).
+        ID format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
+        household 2 within this microcell, and person 1 within this
+        household
+
+        Parameters
+        ----------
+        id : str
+            Identity of person
+
+        """
+        self.id = id
\ No newline at end of file

From 3f25185bd78d7397b7568a273815bb5b84fe0032 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 15 Nov 2023 18:00:42 +0000
Subject: [PATCH 04/53] Added ID for person and households

---
 pyEpiabm/pyEpiabm/core/microcell.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 6ef0aca5..fdf78e06 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -139,8 +139,11 @@ def add_household(self, people: list, household_id: int):
             household = Household(self, loc=self.location)
             cell_id = self.cell.id
             household.set_id(str(cell_id) + "." + str(self.id) + "." + str(household_id))
-            for person in people:
-                household.add_person(person)
+            for i in range(len(people)):
+                household.add_person(people[i])
+                people[i].set_id(household.id + "." + str(i))
+
+
         else:
             logging.info("Cannot create an empty household")
 

From 12e0e9b52e250966c7259956c83aecc55873ba4e Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 16 Nov 2023 16:34:11 +0000
Subject: [PATCH 05/53] Added some tests and a regex check

---
 pyEpiabm/pyEpiabm/core/household.py                |  7 +++++--
 pyEpiabm/pyEpiabm/core/microcell.py                |  1 -
 pyEpiabm/pyEpiabm/core/person.py                   |  7 +++++--
 .../tests/test_unit/test_core/test_household.py    | 14 ++++++++++++++
 4 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 27ebff40..6be9a28a 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -4,6 +4,7 @@
 
 import typing
 from numbers import Number
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -109,7 +110,7 @@ def remove_household(self):
     def set_id(self, id: str):
         """Updates ID of household (i.e. for input from file).
         Format of ID - for example 3.1.2 represents household 2 within microcell 1
-        within cell 3.
+        within cell 3. The id will only be changed if it has the correct expression.
 
         Parameters
         ----------
@@ -117,4 +118,6 @@ def set_id(self, id: str):
             Identity of household
 
         """
-        self.id = id
+        # May want to set upper limit on the number of digits
+        if re.match("\\d+\\.\\d+\\.\\d+", id):
+            self.id = id
diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index fdf78e06..ca5be15a 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -143,7 +143,6 @@ def add_household(self, people: list, household_id: int):
                 household.add_person(people[i])
                 people[i].set_id(household.id + "." + str(i))
 
-
         else:
             logging.info("Cannot create an empty household")
 
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 7e27203b..20a29df1 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -3,6 +3,7 @@
 #
 
 import random
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -229,7 +230,7 @@ def set_id(self, id: str):
         """Updates ID of person (i.e. for input from file).
         ID format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
         household 2 within this microcell, and person 1 within this
-        household
+        household. The id will only be changed if there is a match.
 
         Parameters
         ----------
@@ -237,4 +238,6 @@ def set_id(self, id: str):
             Identity of person
 
         """
-        self.id = id
\ No newline at end of file
+        # May want to set upper limit on the number of digits
+        if re.match("\\d+\\.\\d+\\.\\d+\\.\\d+", id):
+            self.id = id
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index 04ffb98f..3c60ae3c 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -53,6 +53,20 @@ def test_remove_susceptible_person(self):
         self.assertEqual(len(subject.susceptible_persons), 0)
         self.assertEqual(subject.susceptible_persons, [])
 
+    def test_set_id(self):
+        subject = pe.Household(self.microcell, (1, 1))
+        self.assertEqual(subject.id, "")
+        subject.set_id("a.b.c")
+        self.assertEqual(subject.id, "")
+        subject.set_id("0.0.")
+        self.assertEqual(subject.id, "")
+        subject.set_id("0.0.0.0")
+        self.assertEqual(subject.id, "")
+        subject.set_id("0.0.0")
+        self.assertEqual(subject.id, "0.0.0")
+        subject.set_id("10.7.20")
+        self.assertEqual(subject.id, "10.7.20")
+
 
 if __name__ == '__main__':
     unittest.main()

From ffdb83f660541465dc3a3dc5a6d0b89f83c9d559 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Thu, 16 Nov 2023 16:37:13 +0000
Subject: [PATCH 06/53] Merge conflict

---
 pyEpiabm/pyEpiabm/core/microcell.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index fdf78e06..ca5be15a 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -143,7 +143,6 @@ def add_household(self, people: list, household_id: int):
                 household.add_person(people[i])
                 people[i].set_id(household.id + "." + str(i))
 
-
         else:
             logging.info("Cannot create an empty household")
 

From 830988c7ce12ab2348b5d029d9877ec0fb8d331e Mon Sep 17 00:00:00 2001
From: Kit Gallagher <christopher.gallagher@seh.ox.ac.uk>
Date: Thu, 16 Nov 2023 18:30:38 +0000
Subject: [PATCH 07/53] Resolved circular import errors

---
 pyEpiabm/pyEpiabm/core/_compartment_counter.py | 6 +++---
 pyEpiabm/pyEpiabm/core/cell.py                 | 5 +----
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/_compartment_counter.py b/pyEpiabm/pyEpiabm/core/_compartment_counter.py
index 5049e640..91d76077 100644
--- a/pyEpiabm/pyEpiabm/core/_compartment_counter.py
+++ b/pyEpiabm/pyEpiabm/core/_compartment_counter.py
@@ -7,7 +7,7 @@
 
 from pyEpiabm.property import InfectionStatus
 
-import pyEpiabm.core
+from .parameters import Parameters
 
 
 class _CompartmentCounter:
@@ -28,9 +28,9 @@ def __init__(self, identifier: str):
         # Identifier
         self._identifier = identifier
         # Number of age groups
-        if pyEpiabm.core.Parameters.instance().use_ages:
+        if Parameters.instance().use_ages:
             self.nb_age_groups =\
-                len(pyEpiabm.core.Parameters.instance().age_proportions)
+                len(Parameters.instance().age_proportions)
         else:
             self.nb_age_groups = 1
 
diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index 354fa48e..276d9ca1 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -7,11 +7,11 @@
 from queue import Queue
 from numbers import Number
 
-from pyEpiabm.core import Parameters
 from pyEpiabm.property import InfectionStatus
 from pyEpiabm.utility import DistanceFunctions
 
 from .microcell import Microcell
+from .parameters import Parameters
 from .person import Person
 from ._compartment_counter import _CompartmentCounter
 
@@ -198,6 +198,3 @@ def find_nearby_cells(self, other_cells):
                 self.nearby_cell_distances[cell2.id] = distance
                 # Dict of near neighbours, cells which are closer than the
                 # cutoff for cross-cell infection
-
-
-print(Cell().id)

From 7322f07a33a86af90aa6098c2e66bf2064cb3a14 Mon Sep 17 00:00:00 2001
From: Kit Gallagher <christopher.gallagher@seh.ox.ac.uk>
Date: Thu, 16 Nov 2023 19:00:01 +0000
Subject: [PATCH 08/53] Ensure unique cell ids for toy pop

---
 pyEpiabm/pyEpiabm/core/population.py                 |  3 ++-
 .../tests/test_unit/test_core/test_population.py     | 12 +++++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/population.py b/pyEpiabm/pyEpiabm/core/population.py
index 2887e95e..54285319 100644
--- a/pyEpiabm/pyEpiabm/core/population.py
+++ b/pyEpiabm/pyEpiabm/core/population.py
@@ -42,9 +42,10 @@ def add_cells(self, n):
             Number of empty :class:`Cell` s to add
 
         """
+        base_num = len(self.cells)
         for i in range(n):
             self.cells.append(Cell())
-            self.cells[i].set_id(i)
+            self.cells[i + base_num].set_id(i + base_num)
 
     def total_people(self):
         """Returns the total number of people in the population.
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
index 0b710bd9..53375ec4 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
@@ -19,11 +19,21 @@ def test_repr(self):
         self.assertEqual(repr(self.population),
                          "Population with 0 cells.")
 
-    def test_add_cells(self, n=4):
+    def test_add_cells(self, n=4, m=3):
         population = pe.Population()
         self.assertEqual(len(population.cells), 0)
+
         population.add_cells(n)
         self.assertEqual(len(population.cells), n)
+        self.assertEqual(population.cells[-1].id, n-1)
+
+        population.add_cells(m)
+        self.assertEqual(len(population.cells), n+m)
+        self.assertEqual(population.cells[-1].id, n+m-1)
+
+        # Check all cell IDs are unique
+        cell_ids = [cell.id for cell in population.cells]
+        self.assertEqual(len(cell_ids), len(set(cell_ids)))
 
     def test_total_people(self):
         self.assertEqual(self.population.total_people(), 0)

From da3669ed2e21820a1adf97882a6e721ac39a941e Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Thu, 16 Nov 2023 21:13:18 +0000
Subject: [PATCH 09/53] Removed print statement

---
 pyEpiabm/pyEpiabm/core/cell.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index 276d9ca1..d3e24632 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -32,7 +32,6 @@ def __init__(self, loc: typing.Tuple[float, float] = (0, 0)):
         """
         self.location = loc
         self.id = hash(self)
-        print(self.id)
         self.microcells = []
         self.persons = []
         self.places = []

From bed0a99dd41f5fef257d53d2739a4cc4f2c9b380 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Thu, 16 Nov 2023 21:49:56 +0000
Subject: [PATCH 10/53] Updated ID definition

---
 pyEpiabm/pyEpiabm/core/microcell.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index ca5be15a..3349d235 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -33,12 +33,12 @@ def __init__(self, cell):
             Microcell's parent :class:`Cell` instance
 
         """
-        self.id = hash(self)
         self.persons = []
         self.places = []
         self.households = []
         self.cell = cell
         self.location = cell.location
+        self.id = str(self.cell.id) + "." + str(len(self.cell.microcells))
         self.compartment_counter = _CompartmentCounter(
             f"Microcell {id(self)}")
 
@@ -123,7 +123,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list, household_id: int):
+    def add_household(self, people: list):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -131,17 +131,12 @@ def add_household(self, people: list, household_id: int):
         ----------
         people : list
             List of :class:`People` to add to household
-        household_id : int
-            Integer representing this specific household within the microcell
 
         """
         if len(people) != 0:
             household = Household(self, loc=self.location)
-            cell_id = self.cell.id
-            household.set_id(str(cell_id) + "." + str(self.id) + "." + str(household_id))
-            for i in range(len(people)):
-                household.add_person(people[i])
-                people[i].set_id(household.id + "." + str(i))
+            for person in people:
+                household.add_person(person)
 
         else:
             logging.info("Cannot create an empty household")

From 4be6a4ee9552d587ca5137afc58160aa03176a3d Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Thu, 16 Nov 2023 21:50:34 +0000
Subject: [PATCH 11/53] Updated test for ID

---
 pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index ca5d3c70..bf8cef91 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -23,7 +23,7 @@ def test_repr(self):
                          "Microcell with 0 people at location (0, 0).")
 
     def test_set_id(self):
-        self.assertEqual(self.microcell.id, hash(self.microcell))
+        self.assertEqual(self.microcell.id, str(self.cell.id) + "." + str(len(self.cell.microcells)))
         self.microcell.set_id(2.0)
         self.assertEqual(self.microcell.id, 2.0)
 

From 38b302c9b1c2192b8e5a76eedf135aabb7cda88f Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 15:58:48 +0000
Subject: [PATCH 12/53] Updated household id

---
 pyEpiabm/pyEpiabm/core/household.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 6be9a28a..0eaf9df9 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -30,7 +30,6 @@ def __init__(self, microcell, loc: typing.Tuple[float, float],
             Household's base infectiousness
 
         """
-        self.id = ""
         self.persons = []
         self.susceptible_persons = []
         self.location = loc
@@ -39,6 +38,7 @@ def __init__(self, microcell, loc: typing.Tuple[float, float],
         self.cell = microcell.cell
         self.microcell = microcell
         self.isolation_location = False
+        self.id = self.microcell.id + "." + str(len(self.microcell.households))
 
         if not (len(loc) == 2 and isinstance(loc[0], Number) and
                 isinstance(loc[1], Number)):
@@ -119,5 +119,5 @@ def set_id(self, id: str):
 
         """
         # May want to set upper limit on the number of digits
-        if re.match("\\d+\\.\\d+\\.\\d+", id):
+        if re.match("^\\d+\\.\\d+\\.\\d+$", id):
             self.id = id

From 8226f4684b2e9229495125abe2a27b6aa1632b04 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 15:59:33 +0000
Subject: [PATCH 13/53] Updated set_id test

---
 .../pyEpiabm/tests/test_unit/test_core/test_household.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index 3c60ae3c..e60c5b48 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -55,13 +55,14 @@ def test_remove_susceptible_person(self):
 
     def test_set_id(self):
         subject = pe.Household(self.microcell, (1, 1))
-        self.assertEqual(subject.id, "")
+        init_id = str(self.microcell.id) + "." + str(len(self.microcell.households)-1)
+        self.assertEqual(subject.id, init_id)
         subject.set_id("a.b.c")
-        self.assertEqual(subject.id, "")
+        self.assertEqual(subject.id, init_id)
         subject.set_id("0.0.")
-        self.assertEqual(subject.id, "")
+        self.assertEqual(subject.id, init_id)
         subject.set_id("0.0.0.0")
-        self.assertEqual(subject.id, "")
+        self.assertEqual(subject.id, init_id)
         subject.set_id("0.0.0")
         self.assertEqual(subject.id, "0.0.0")
         subject.set_id("10.7.20")

From 2f4f2db4781b7380d19bf531881b57bc159d5302 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Fri, 17 Nov 2023 16:36:27 +0000
Subject: [PATCH 14/53] Updated regex

---
 pyEpiabm/pyEpiabm/core/household.py | 2 +-
 pyEpiabm/pyEpiabm/core/person.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 6be9a28a..db629a58 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -119,5 +119,5 @@ def set_id(self, id: str):
 
         """
         # May want to set upper limit on the number of digits
-        if re.match("\\d+\\.\\d+\\.\\d+", id):
+        if re.match("^\\d+\\.\\d+\\.\\d+$", id):
             self.id = id
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 20a29df1..01b5240e 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -239,5 +239,5 @@ def set_id(self, id: str):
 
         """
         # May want to set upper limit on the number of digits
-        if re.match("\\d+\\.\\d+\\.\\d+\\.\\d+", id):
+        if re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", id):
             self.id = id

From 5f9782fe0daca203621295112329445b52e10365 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 19:18:19 +0000
Subject: [PATCH 15/53] self.id added

---
 pyEpiabm/pyEpiabm/core/person.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 20a29df1..9e65b21a 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -55,7 +55,7 @@ def __init__(self, microcell, age_group=None):
         self.key_worker = False
         self.date_positive = None
         self.is_vaccinated = False
-        self.id = ""
+        self.id = self.microcell.id + "." + "." + str(len(self.microcell.persons))
 
         self.set_random_age(age_group)
 
@@ -239,5 +239,5 @@ def set_id(self, id: str):
 
         """
         # May want to set upper limit on the number of digits
-        if re.match("\\d+\\.\\d+\\.\\d+\\.\\d+", id):
+        if re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", id):
             self.id = id

From f4406b2dc9ef4488a63f409e5a4bc0a36c2cf3cf Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 19:19:05 +0000
Subject: [PATCH 16/53] Updated set_id test

---
 .../tests/test_unit/test_core/test_person.py         | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
index bf3541e1..d38add9e 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
@@ -110,6 +110,18 @@ def test_vaccinate(self):
         self.assertTrue(self.person.is_vaccinated)
         self.assertEqual(self.person.date_vaccinated, 5)
 
+    def test_set_id(self):
+        init_id = self.microcell.id + "." + "." + str(len(self.microcell.persons)-1)
+        self.assertEqual(self.person.id, init_id)
+        self.person.set_id("0.1")
+        self.assertEqual(self.person.id, init_id)
+        self.person.set_id("1234")
+        self.assertEqual(self.person.id, init_id)
+        self.person.set_id("0.0.0.0.5")
+        self.assertEqual(self.person.id, init_id)
+        self.person.set_id("2.3.4.5")
+        self.assertEqual(self.person.id, "2.3.4.5")
+
 
 if __name__ == '__main__':
     unittest.main()

From 0a98755854deab802fbd61df1bd4fd6f18e6ae05 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 19:24:56 +0000
Subject: [PATCH 17/53] Update add_household

---
 pyEpiabm/pyEpiabm/core/microcell.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 3349d235..b19a91a4 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -135,8 +135,10 @@ def add_household(self, people: list):
         """
         if len(people) != 0:
             household = Household(self, loc=self.location)
-            for person in people:
+            for i in range(len(people)):
+                person = people[i]
                 household.add_person(person)
+                person.set_id(household.id + "." + str(i))
 
         else:
             logging.info("Cannot create an empty household")

From a572114bfe680b44d8c139a526376a0f3fa962c5 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 17 Nov 2023 19:25:31 +0000
Subject: [PATCH 18/53] Updated add_household test

---
 pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index bf8cef91..f1d0f217 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -74,6 +74,9 @@ def test_add_household(self):
         self.assertEqual(len(self.microcell.households), 1)
         household = self.microcell.households[0]
         self.assertEqual(len(household.persons), 1)
+        for i in range(len(household.persons)):
+            person = self.microcell.persons[i]
+            self.assertEqual(person.id, household.id + "." + str(i))
 
     @mock.patch('logging.info')
     def test_logging(self, mock_log):

From 6d906776210d85a77d3895f16cb2d6dca76a2784 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Sun, 19 Nov 2023 20:21:29 +0000
Subject: [PATCH 19/53] Changed cell id to a string to match the other types,
 and fixed errors involving ids

---
 pyEpiabm/pyEpiabm/core/cell.py                | 17 +++++++++---
 pyEpiabm/pyEpiabm/core/household.py           |  7 +++++
 pyEpiabm/pyEpiabm/core/microcell.py           | 16 ++++++++---
 pyEpiabm/pyEpiabm/core/person.py              |  9 ++++++-
 pyEpiabm/pyEpiabm/core/population.py          |  2 +-
 .../routine/file_population_config.py         | 27 +++++++++++++------
 .../tests/test_unit/test_core/test_cell.py    | 10 ++++---
 .../test_unit/test_core/test_household.py     | 10 +++----
 .../test_unit/test_core/test_microcell.py     |  6 ++---
 .../tests/test_unit/test_core/test_person.py  | 10 +++----
 .../test_unit/test_core/test_population.py    |  4 +--
 .../test_file_population_config.py            | 24 ++++++++++-------
 .../test_sweep/test_spatial_sweep.py          |  2 +-
 13 files changed, 95 insertions(+), 49 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index d3e24632..aa20a4fd 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -6,6 +6,7 @@
 import numpy as np
 from queue import Queue
 from numbers import Number
+import re
 
 from pyEpiabm.property import InfectionStatus
 from pyEpiabm.utility import DistanceFunctions
@@ -31,7 +32,7 @@ def __init__(self, loc: typing.Tuple[float, float] = (0, 0)):
 
         """
         self.location = loc
-        self.id = hash(self)
+        self.id = str(hash(self))
         self.microcells = []
         self.persons = []
         self.places = []
@@ -70,16 +71,24 @@ def add_microcells(self, n):
         for _ in range(n):
             self.microcells.append(Microcell(self))
 
-    def set_id(self, id: float):
+    def set_id(self, id: str):
         """Updates ID of cell (i.e. for input from file).
 
         Parameters
         ----------
-        id : float
+        id : str
             Identity of cell
 
         """
-        self.id = id
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("id must be of type string")
+
+        # May want to set upper limit on the number of digits
+        if re.match("^\\d+$", id):
+            self.id = id
+        else:
+            raise ValueError("id must take the correct form")
 
     def enqueue_person(self, person: Person):
         """Add person to queue for processing at end of iteration, provided
diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 0eaf9df9..ce42297b 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -118,6 +118,13 @@ def set_id(self, id: str):
             Identity of household
 
         """
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("id must be of type string")
+
         # May want to set upper limit on the number of digits
         if re.match("^\\d+\\.\\d+\\.\\d+$", id):
             self.id = id
+        else:
+            raise ValueError("id must take the correct form")
diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index b19a91a4..4fccaf79 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -5,6 +5,7 @@
 import typing
 from numbers import Number
 import logging
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -38,7 +39,7 @@ def __init__(self, cell):
         self.households = []
         self.cell = cell
         self.location = cell.location
-        self.id = str(self.cell.id) + "." + str(len(self.cell.microcells))
+        self.id = self.cell.id + "." + str(len(self.cell.microcells))
         self.compartment_counter = _CompartmentCounter(
             f"Microcell {id(self)}")
 
@@ -59,11 +60,20 @@ def set_id(self, id):
 
         Parameters
         ----------
-        id : float
+        id : str
             Identity of microcell
 
         """
-        self.id = id
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("id must be of type string")
+
+        # Ensure that the id is of the correct form
+        if re.match("^\\d+\\.\\d+$", id):
+            self.id = id
+        else:
+            raise ValueError("id must take the correct form")
 
     def add_person(self, person):
         """Adds :class:`Person` with given :class:`InfectionStatus` and given
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 9e65b21a..7b87716a 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -238,6 +238,13 @@ def set_id(self, id: str):
             Identity of person
 
         """
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("id must be of type string")
+
         # May want to set upper limit on the number of digits
-        if re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", id):
+        if re.match("^\\d+\\.\\d+\\.\\d*\\.\\d+$", id):
             self.id = id
+        else:
+            raise ValueError("id must take the correct form")
diff --git a/pyEpiabm/pyEpiabm/core/population.py b/pyEpiabm/pyEpiabm/core/population.py
index 54285319..2fc005be 100644
--- a/pyEpiabm/pyEpiabm/core/population.py
+++ b/pyEpiabm/pyEpiabm/core/population.py
@@ -45,7 +45,7 @@ def add_cells(self, n):
         base_num = len(self.cells)
         for i in range(n):
             self.cells.append(Cell())
-            self.cells[i + base_num].set_id(i + base_num)
+            self.cells[i + base_num].set_id(str(i + base_num))
 
     def total_people(self):
         """Returns the total number of people in the population.
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 80a92ca9..e01cd1ab 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -84,8 +84,12 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
         current_cell = None
         # Iterate through lines (one per microcell)
         for _, line in input.iterrows():
+
+            # Converting from float to string
+            cell_id_csv = str(int(line["cell"]))
+            microcell_id_csv = str(int(line["microcell"]))
             # Check if cell exists, or create it
-            cell = FilePopulationFactory.find_cell(new_pop, line["cell"],
+            cell = FilePopulationFactory.find_cell(new_pop, cell_id_csv,
                                                    current_cell)
             if current_cell != cell:
                 current_cell = cell
@@ -96,13 +100,20 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
 
             # Raise error if microcell exists, then create new one
             for microcell in cell.microcells:
-                if microcell.id == line["microcell"]:
+
+                # The microcell id is a string separated by periods, so we
+                # must find the part which matches the csv input
+                id_parts = microcell.id.split(".")
+                if id_parts[-1] == microcell_id_csv:
                     raise ValueError(f"Duplicate microcells {microcell.id}"
                                      + f" in cell {cell.id}")
 
             new_microcell = Microcell(cell)
             cell.microcells.append(new_microcell)
-            new_microcell.set_id(line["microcell"])
+
+            # Either keep the following line (sets id according to data frame input), or
+            # remove it (sets id according to current number of microcells in cell.microcells)
+            new_microcell.set_id(cell_id_csv + "." + microcell_id_csv)
 
             for column in input.columns.values:
                 if hasattr(InfectionStatus, column):
@@ -150,7 +161,7 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
         return new_pop
 
     @staticmethod
-    def find_cell(population: Population, cell_id: float, current_cell: Cell):
+    def find_cell(population: Population, cell_id: str, current_cell: Cell):
         """Returns cell with given ID in population, creates one if
         current cell has another ID. As input is sorted on cell no
         cell will exist with that ID.
@@ -159,7 +170,7 @@ def find_cell(population: Population, cell_id: float, current_cell: Cell):
         ----------
         population : Population
             Population containing target cell
-        cell_id : float
+        cell_id : str
             ID for target cell
         current_cell : Cell or None
             Cell object of current cell
@@ -195,14 +206,14 @@ def add_households(microcell: Microcell, household_number: int):
         people_number = len(people_list)
         household_split = np.random.multinomial(people_number, q,
                                                 size=1)[0]
-        for household_id in range(household_number):
-            people_in_household = household_split[household_id]
+        for j in range(household_number):
+            people_in_household = household_split[j]
             household_people = []
             for i in range(people_in_household):
                 person_choice = people_list[0]
                 people_list.remove(person_choice)
                 household_people.append(person_choice)
-            microcell.add_household(household_people, household_id)
+            microcell.add_household(household_people)
 
     @staticmethod
     @log_exceptions()
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
index 0f9a9bf6..233767ca 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
@@ -15,7 +15,7 @@ def setUp(self) -> None:
     def test__init__(self):
         self.assertEqual(self.cell.location[0], 0)
         self.assertEqual(self.cell.location[1], 0)
-        self.assertEqual(self.cell.id, hash(self.cell))
+        self.assertEqual(self.cell.id, str(hash(self.cell)))
         self.assertEqual(self.cell.microcells, [])
         self.assertEqual(self.cell.persons, [])
         self.assertEqual(self.cell.places, [])
@@ -38,9 +38,11 @@ def test_set_location(self):
         self.assertRaises(ValueError, pe.Cell, ('1', 1))
 
     def test_set_id(self):
-        self.assertEqual(self.cell.id, hash(self.cell))
-        self.cell.set_id(2.0)
-        self.assertEqual(self.cell.id, 2.0)
+        self.assertEqual(self.cell.id, str(hash(self.cell)))
+        self.assertRaises(TypeError, self.cell.set_id, 2.0)
+        self.assertRaises(ValueError, self.cell.set_id, "2.0")
+        self.cell.set_id("2")
+        self.assertEqual(self.cell.id, "2")
 
     def test_add_microcells(self, n=4):
         self.assertEqual(len(self.cell.microcells), 0)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index e60c5b48..5cdd5f05 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -57,16 +57,14 @@ def test_set_id(self):
         subject = pe.Household(self.microcell, (1, 1))
         init_id = str(self.microcell.id) + "." + str(len(self.microcell.households)-1)
         self.assertEqual(subject.id, init_id)
-        subject.set_id("a.b.c")
-        self.assertEqual(subject.id, init_id)
-        subject.set_id("0.0.")
-        self.assertEqual(subject.id, init_id)
-        subject.set_id("0.0.0.0")
-        self.assertEqual(subject.id, init_id)
         subject.set_id("0.0.0")
         self.assertEqual(subject.id, "0.0.0")
         subject.set_id("10.7.20")
         self.assertEqual(subject.id, "10.7.20")
+        self.assertRaises(TypeError, subject.set_id, 2.0)
+        self.assertRaises(ValueError, subject.set_id, "a.b.c")
+        self.assertRaises(ValueError, subject.set_id, "0.0.")
+        self.assertRaises(ValueError, subject.set_id, "0.0.0.0")
 
 
 if __name__ == '__main__':
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index f1d0f217..b7220e20 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -23,9 +23,9 @@ def test_repr(self):
                          "Microcell with 0 people at location (0, 0).")
 
     def test_set_id(self):
-        self.assertEqual(self.microcell.id, str(self.cell.id) + "." + str(len(self.cell.microcells)))
-        self.microcell.set_id(2.0)
-        self.assertEqual(self.microcell.id, 2.0)
+        self.assertEqual(self.microcell.id, self.cell.id + "." + str(len(self.cell.microcells)))
+        self.assertRaises(TypeError, self.microcell.set_id, 2.0)
+        self.assertRaises(ValueError, self.microcell.set_id, "1.1.")
 
     def test_add_person(self):
         self.assertEqual(len(self.microcell.persons), 0)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
index d38add9e..fa0eee18 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
@@ -113,14 +113,12 @@ def test_vaccinate(self):
     def test_set_id(self):
         init_id = self.microcell.id + "." + "." + str(len(self.microcell.persons)-1)
         self.assertEqual(self.person.id, init_id)
-        self.person.set_id("0.1")
-        self.assertEqual(self.person.id, init_id)
-        self.person.set_id("1234")
-        self.assertEqual(self.person.id, init_id)
-        self.person.set_id("0.0.0.0.5")
-        self.assertEqual(self.person.id, init_id)
         self.person.set_id("2.3.4.5")
         self.assertEqual(self.person.id, "2.3.4.5")
+        self.assertRaises(TypeError, self.person.set_id, 2.0)
+        self.assertRaises(ValueError, self.person.set_id, "0.1")
+        self.assertRaises(ValueError, self.person.set_id, "1234")
+        self.assertRaises(ValueError, self.person.set_id, "0.0.0.0.5")
 
 
 if __name__ == '__main__':
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
index 53375ec4..5bcc106a 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_population.py
@@ -25,11 +25,11 @@ def test_add_cells(self, n=4, m=3):
 
         population.add_cells(n)
         self.assertEqual(len(population.cells), n)
-        self.assertEqual(population.cells[-1].id, n-1)
+        self.assertEqual(population.cells[-1].id, str(n-1))
 
         population.add_cells(m)
         self.assertEqual(len(population.cells), n+m)
-        self.assertEqual(population.cells[-1].id, n+m-1)
+        self.assertEqual(population.cells[-1].id, str(n+m-1))
 
         # Check all cell IDs are unique
         cell_ids = [cell.id for cell in population.cells]
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index 09d7f604..447a82ea 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -61,9 +61,10 @@ def test_make_pop(self, mock_read):
         # Test cell_wise values
         for i in range(2):
             self.assertEqual(test_pop.cells[i].id,
-                             self.input.get('cell')[i])
-            self.assertEqual(test_pop.cells[i].microcells[0].id,
-                             self.input.get('microcell')[i])
+                             str(int(self.input.get('cell')[i])))
+            id_parts = test_pop.cells[i].microcells[0].id.split(".")
+            self.assertEqual(id_parts[-1],
+                             str(int(self.input.get('microcell')[i])))
             self.assertEqual(test_pop.cells[i].location[0],
                              self.input.get('location_x')[i])
             self.assertEqual(test_pop.cells[i].location[1],
@@ -133,15 +134,15 @@ def test_duplicate_microcell(self, mock_read, mock_log):
     def test_find_cell(self):
         pop = pe.Population()
         pop.add_cells(2)
-        pop.cells[1].set_id(42)
+        pop.cells[1].set_id("42")
 
-        target_cell = FilePopulationFactory.find_cell(pop, 42, pop.cells[1])
-        self.assertEqual(target_cell.id, 42)
+        target_cell = FilePopulationFactory.find_cell(pop, "42", pop.cells[1])
+        self.assertEqual(target_cell.id, "42")
         self.assertEqual(hash(target_cell), hash(pop.cells[1]))
         self.assertEqual(len(pop.cells), 2)  # No new cell created
 
-        new_cell = FilePopulationFactory.find_cell(pop, 43, pop.cells[1])
-        self.assertEqual(new_cell.id, 43)
+        new_cell = FilePopulationFactory.find_cell(pop, "43", pop.cells[1])
+        self.assertEqual(new_cell.id, "43")
         self.assertEqual(len(pop.cells), 3)  # New cell created
 
     @patch("pandas.read_csv")
@@ -217,8 +218,11 @@ def test_print_population(self, mock_copy, mock_read):
         actual_df = mock_copy.call_args.args[0]
         if version.parse(pd.__version__) >= version.parse("1.4.0"):
             expected_df = self.df.copy()
-            expected = expected_df.drop('household_number', axis=1)
-            actual = actual_df.drop('household_number', axis=1)
+
+            # The type of the id is converted from float to string, so we
+            # drop the cell and microcell columns
+            expected = expected_df.drop(['cell', 'microcell', 'household_number'], axis=1)
+            actual = actual_df.drop(['cell', 'microcell', 'household_number'], axis=1)
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_spatial_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_spatial_sweep.py
index d80e9861..53af2afa 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_spatial_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_spatial_sweep.py
@@ -93,7 +93,7 @@ def test_nearby_cells(self, mock_dist):
         test_sweep = SpatialSweep()
         mock_dist.return_value = 2
         test_sweep.bind_population(test_pop)
-        self.assertEqual(self.cell_inf.nearby_cell_distances, {1: 2})
+        self.assertEqual(self.cell_inf.nearby_cell_distances, {"1": 2})
         mock_dist.assert_called_with(self.cell_inf.location,
                                      self.cell_susc.location)
         self.assertEqual(mock_dist.call_count,

From 839a71347f3370b0321e32c9b6a69e482a0e527f Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 10:45:43 +0000
Subject: [PATCH 20/53] Fixed line lengths

---
 pyEpiabm/pyEpiabm/core/household.py             |  5 +++--
 pyEpiabm/pyEpiabm/core/person.py                | 17 +++++++++--------
 .../pyEpiabm/routine/file_population_config.py  |  5 +++--
 .../tests/test_unit/test_core/test_household.py |  3 ++-
 .../tests/test_unit/test_core/test_microcell.py |  3 ++-
 .../tests/test_unit/test_core/test_person.py    |  3 ++-
 .../test_routine/test_file_population_config.py |  6 ++++--
 7 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index ce42297b..68ffd5bd 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -109,8 +109,9 @@ def remove_household(self):
 
     def set_id(self, id: str):
         """Updates ID of household (i.e. for input from file).
-        Format of ID - for example 3.1.2 represents household 2 within microcell 1
-        within cell 3. The id will only be changed if it has the correct expression.
+        Format of ID - for example 3.1.2 represents household 2 within
+        microcell 1 within cell 3. The id will only be changed if it has the
+        correct expression.
 
         Parameters
         ----------
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 7b87716a..f36b2bc9 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -55,7 +55,8 @@ def __init__(self, microcell, age_group=None):
         self.key_worker = False
         self.date_positive = None
         self.is_vaccinated = False
-        self.id = self.microcell.id + "." + "." + str(len(self.microcell.persons))
+        self.id = self.microcell.id + "." + "." + \
+                  str(len(self.microcell.persons))
 
         self.set_random_age(age_group)
 
@@ -90,7 +91,7 @@ def is_symptomatic(self):
 
         """
         return Person.is_infectious(self) and self.infection_status != \
-            InfectionStatus.InfectASympt
+               InfectionStatus.InfectASympt
 
     def is_infectious(self):
         """Query if the person is currently infectious.
@@ -112,7 +113,7 @@ def is_susceptible(self):
             Whether person is currently susceptible
 
         """
-        return self.infection_status == InfectionStatus.\
+        return self.infection_status == InfectionStatus. \
             Susceptible
 
     def __repr__(self):
@@ -141,10 +142,10 @@ def update_status(self,
         self.infection_status = new_status
 
         if self.infection_status == InfectionStatus.Susceptible and \
-                self.household is not None:
+            self.household is not None:
             self.household.add_susceptible_person(self)
         if self.infection_status == InfectionStatus.Exposed and \
-                self.household is not None:
+            self.household is not None:
             self.household.remove_susceptible_person(self)
 
     def add_place(self, place, person_group: int = 0):
@@ -197,7 +198,7 @@ def is_place_closed(self, closure_place_type):
 
         """
         if (hasattr(self.microcell, 'closure_start_time')) and (
-                self.microcell.closure_start_time is not None):
+            self.microcell.closure_start_time is not None):
             for place_type in self.place_types:
                 if place_type.value in closure_place_type:
                     return True
@@ -216,10 +217,10 @@ def remove_person(self):
         Used to remove travellers from the population.
 
         """
-        self.microcell.cell.compartment_counter.\
+        self.microcell.cell.compartment_counter. \
             _increment_compartment(-1, self.infection_status,
                                    self.age_group)
-        self.microcell.compartment_counter.\
+        self.microcell.compartment_counter. \
             _increment_compartment(-1, self.infection_status,
                                    self.age_group)
         self.microcell.cell.persons.remove(self)
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index e01cd1ab..45762700 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -111,8 +111,9 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             new_microcell = Microcell(cell)
             cell.microcells.append(new_microcell)
 
-            # Either keep the following line (sets id according to data frame input), or
-            # remove it (sets id according to current number of microcells in cell.microcells)
+            # Either keep the following line (sets id according to data frame
+            # input), or remove it (sets id according to current number of
+            # microcells in cell.microcells)
             new_microcell.set_id(cell_id_csv + "." + microcell_id_csv)
 
             for column in input.columns.values:
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index 5cdd5f05..c7db4ad5 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -55,7 +55,8 @@ def test_remove_susceptible_person(self):
 
     def test_set_id(self):
         subject = pe.Household(self.microcell, (1, 1))
-        init_id = str(self.microcell.id) + "." + str(len(self.microcell.households)-1)
+        init_id = str(self.microcell.id) + "." + \
+                  str(len(self.microcell.households)-1)
         self.assertEqual(subject.id, init_id)
         subject.set_id("0.0.0")
         self.assertEqual(subject.id, "0.0.0")
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index b7220e20..25f800a8 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -23,7 +23,8 @@ def test_repr(self):
                          "Microcell with 0 people at location (0, 0).")
 
     def test_set_id(self):
-        self.assertEqual(self.microcell.id, self.cell.id + "." + str(len(self.cell.microcells)))
+        self.assertEqual(self.microcell.id, self.cell.id + "." +
+                         str(len(self.cell.microcells)))
         self.assertRaises(TypeError, self.microcell.set_id, 2.0)
         self.assertRaises(ValueError, self.microcell.set_id, "1.1.")
 
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
index fa0eee18..d415ca32 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
@@ -111,7 +111,8 @@ def test_vaccinate(self):
         self.assertEqual(self.person.date_vaccinated, 5)
 
     def test_set_id(self):
-        init_id = self.microcell.id + "." + "." + str(len(self.microcell.persons)-1)
+        init_id = self.microcell.id + "." + "." + \
+                  str(len(self.microcell.persons) - 1)
         self.assertEqual(self.person.id, init_id)
         self.person.set_id("2.3.4.5")
         self.assertEqual(self.person.id, "2.3.4.5")
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index 447a82ea..5974a3ea 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -221,8 +221,10 @@ def test_print_population(self, mock_copy, mock_read):
 
             # The type of the id is converted from float to string, so we
             # drop the cell and microcell columns
-            expected = expected_df.drop(['cell', 'microcell', 'household_number'], axis=1)
-            actual = actual_df.drop(['cell', 'microcell', 'household_number'], axis=1)
+            expected = expected_df.drop(['cell', 'microcell',
+                                         'household_number'], axis=1)
+            actual = actual_df.drop(['cell', 'microcell',
+                                     'household_number'], axis=1)
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)

From 666afea8c6bf1f8de68798de6a4cf2131401da44 Mon Sep 17 00:00:00 2001
From: abbie-evans <147088150+abbie-evans@users.noreply.github.com>
Date: Wed, 22 Nov 2023 12:23:37 +0000
Subject: [PATCH 21/53] Import arrangement

Co-authored-by: Kit Gallagher <60467371+KCGallagher@users.noreply.github.com>
---
 pyEpiabm/pyEpiabm/core/cell.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index aa20a4fd..c1ea21bc 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -4,9 +4,9 @@
 
 import typing
 import numpy as np
+import re
 from queue import Queue
 from numbers import Number
-import re
 
 from pyEpiabm.property import InfectionStatus
 from pyEpiabm.utility import DistanceFunctions

From c718a9f96920b39d3d1e285295947ad8c960ca7e Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 22 Nov 2023 13:58:10 +0000
Subject: [PATCH 22/53] Updated set_id tests

---
 pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py | 1 +
 pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index c7db4ad5..b945d081 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -65,6 +65,7 @@ def test_set_id(self):
         self.assertRaises(TypeError, subject.set_id, 2.0)
         self.assertRaises(ValueError, subject.set_id, "a.b.c")
         self.assertRaises(ValueError, subject.set_id, "0.0.")
+        self.assertRaises(ValueError, subject.set_id, "123")
         self.assertRaises(ValueError, subject.set_id, "0.0.0.0")
 
 
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index 25f800a8..763e6c88 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -25,8 +25,11 @@ def test_repr(self):
     def test_set_id(self):
         self.assertEqual(self.microcell.id, self.cell.id + "." +
                          str(len(self.cell.microcells)))
+        self.microcell.set_id("2.3")
+        self.assertEqual(self.microcell.id, "2.3")
         self.assertRaises(TypeError, self.microcell.set_id, 2.0)
         self.assertRaises(ValueError, self.microcell.set_id, "1.1.")
+        self.assertRaises(ValueError, self.microcell.set_id, "12")
 
     def test_add_person(self):
         self.assertEqual(len(self.microcell.persons), 0)

From 3df11876bfcbef23f17fa2565f17ba0701bd9b50 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 14:02:32 +0000
Subject: [PATCH 23/53] Added checks for duplicates

---
 pyEpiabm/pyEpiabm/core/cell.py      |  7 ++++---
 pyEpiabm/pyEpiabm/core/household.py | 20 ++++++++++++++------
 pyEpiabm/pyEpiabm/core/microcell.py | 19 +++++++++++++------
 pyEpiabm/pyEpiabm/core/person.py    | 20 ++++++++++++++------
 4 files changed, 45 insertions(+), 21 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index aa20a4fd..f7adf745 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -82,13 +82,14 @@ def set_id(self, id: str):
         """
         # Ensure id is a string
         if not isinstance(id, str):
-            raise TypeError("id must be of type string")
+            raise TypeError("Provided id must be a string")
 
-        # May want to set upper limit on the number of digits
+        # This regex will match on any string which has 1 or more digits
         if re.match("^\\d+$", id):
             self.id = id
         else:
-            raise ValueError("id must take the correct form")
+            raise ValueError(f"Invalid id: {id}. id must be of the form 'i' "
+                             f"where i is an integer")
 
     def enqueue_person(self, person: Person):
         """Add person to queue for processing at end of iteration, provided
diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index 68ffd5bd..b4b16694 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -122,10 +122,18 @@ def set_id(self, id: str):
 
         # Ensure id is a string
         if not isinstance(id, str):
-            raise TypeError("id must be of type string")
+            raise TypeError("Provided id must be a string")
 
-        # May want to set upper limit on the number of digits
-        if re.match("^\\d+\\.\\d+\\.\\d+$", id):
-            self.id = id
-        else:
-            raise ValueError("id must take the correct form")
+        # This regex will match on any string which takes the form "i.j.k"
+        # where i, j and k are integers
+        if not re.match("^\\d+\\.\\d+\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form "
+                             f"'i.j.k' where i, j, k are integers")
+
+        # Finally, check for duplicates
+        household_ids = [household.id
+                         for household in self.microcell.households]
+        if id in household_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id
diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 4fccaf79..88ba56b2 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -67,13 +67,20 @@ def set_id(self, id):
 
         # Ensure id is a string
         if not isinstance(id, str):
-            raise TypeError("id must be of type string")
+            raise TypeError("Provided id must be a string")
 
-        # Ensure that the id is of the correct form
-        if re.match("^\\d+\\.\\d+$", id):
-            self.id = id
-        else:
-            raise ValueError("id must take the correct form")
+        # This regex will match on any string which takes the form "i.j" where
+        # i and j are integers
+        if not re.match("^\\d+\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form 'i.j' "
+                             f"where i, j are integers")
+
+        # Finally, check for duplicates
+        microcell_ids = [microcell.id for microcell in self.cell.microcells]
+        if id in microcell_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id
 
     def add_person(self, person):
         """Adds :class:`Person` with given :class:`InfectionStatus` and given
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index f36b2bc9..22003be3 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -242,10 +242,18 @@ def set_id(self, id: str):
 
         # Ensure id is a string
         if not isinstance(id, str):
-            raise TypeError("id must be of type string")
+            raise TypeError("Provided id must be a string")
 
-        # May want to set upper limit on the number of digits
-        if re.match("^\\d+\\.\\d+\\.\\d*\\.\\d+$", id):
-            self.id = id
-        else:
-            raise ValueError("id must take the correct form")
+        # This regex will match on any string which takes the form "i.j.k.l"
+        # where i, j, k and l are integers (k can be empty)
+        if not re.match("^\\d+\\.\\d+\\.\\d*\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form "
+                             f"'i.j.k.l' where i, j, k, l are integers (k"
+                             f"can be empty)")
+
+        # Finally, check for duplicates
+        person_ids = [person.id for person in self.household.persons]
+        if id in person_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id

From 9e2bef6e2083763499829fe6e4dd71be00a36072 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 14:11:41 +0000
Subject: [PATCH 24/53] Style changes

---
 pyEpiabm/pyEpiabm/core/cell.py      | 2 +-
 pyEpiabm/pyEpiabm/core/household.py | 4 ++--
 pyEpiabm/pyEpiabm/core/microcell.py | 2 +-
 pyEpiabm/pyEpiabm/core/person.py    | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index f76f98f9..f7ac95c7 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -72,7 +72,7 @@ def add_microcells(self, n):
             self.microcells.append(Microcell(self))
 
     def set_id(self, id: str):
-        """Updates ID of cell (i.e. for input from file).
+        """Updates id of current cell (i.e. for input from file).
 
         Parameters
         ----------
diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
index b4b16694..a2bec542 100644
--- a/pyEpiabm/pyEpiabm/core/household.py
+++ b/pyEpiabm/pyEpiabm/core/household.py
@@ -108,8 +108,8 @@ def remove_household(self):
         self.cell.households.remove(self)
 
     def set_id(self, id: str):
-        """Updates ID of household (i.e. for input from file).
-        Format of ID - for example 3.1.2 represents household 2 within
+        """Updates id of current household (i.e. for input from file).
+        Format of id - for example 3.1.2 represents household 2 within
         microcell 1 within cell 3. The id will only be changed if it has the
         correct expression.
 
diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 88ba56b2..20d411a0 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -56,7 +56,7 @@ def __repr__(self):
             f" at location {self.location}."
 
     def set_id(self, id):
-        """Updates ID of microcell (i.e. for input from file).
+        """Updates id of current microcell (i.e. for input from file).
 
         Parameters
         ----------
diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 22003be3..874eb53f 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -228,8 +228,8 @@ def remove_person(self):
         self.household.persons.remove(self)
 
     def set_id(self, id: str):
-        """Updates ID of person (i.e. for input from file).
-        ID format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
+        """Updates id of current person (i.e. for input from file).
+        id format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
         household 2 within this microcell, and person 1 within this
         household. The id will only be changed if there is a match.
 

From e46a784e699d26e54b3459085441010804fbfca8 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 14:23:27 +0000
Subject: [PATCH 25/53] Fixed error and changed make_pop

---
 pyEpiabm/pyEpiabm/core/person.py                |  2 +-
 .../pyEpiabm/routine/file_population_config.py  | 17 +++++++----------
 2 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 874eb53f..c75a1010 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -252,7 +252,7 @@ def set_id(self, id: str):
                              f"can be empty)")
 
         # Finally, check for duplicates
-        person_ids = [person.id for person in self.household.persons]
+        person_ids = [person.id for person in self.microcell.persons]
         if id in person_ids:
             raise ValueError(f"Duplicate id: {id}.")
 
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 45762700..d38b2898 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -87,7 +87,8 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
 
             # Converting from float to string
             cell_id_csv = str(int(line["cell"]))
-            microcell_id_csv = str(int(line["microcell"]))
+            microcell_id_csv = cell_id_csv + "." + str(int(line["microcell"]))
+
             # Check if cell exists, or create it
             cell = FilePopulationFactory.find_cell(new_pop, cell_id_csv,
                                                    current_cell)
@@ -99,14 +100,10 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
                 cell.set_location(location)
 
             # Raise error if microcell exists, then create new one
-            for microcell in cell.microcells:
-
-                # The microcell id is a string separated by periods, so we
-                # must find the part which matches the csv input
-                id_parts = microcell.id.split(".")
-                if id_parts[-1] == microcell_id_csv:
-                    raise ValueError(f"Duplicate microcells {microcell.id}"
-                                     + f" in cell {cell.id}")
+            microcell_ids = [microcell.id for microcell in cell.microcells]
+            if microcell_id_csv in microcell_ids:
+                raise ValueError(f"Duplicate microcells {microcell_id_csv}"
+                                 + f" in cell {cell.id}")
 
             new_microcell = Microcell(cell)
             cell.microcells.append(new_microcell)
@@ -114,7 +111,7 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             # Either keep the following line (sets id according to data frame
             # input), or remove it (sets id according to current number of
             # microcells in cell.microcells)
-            new_microcell.set_id(cell_id_csv + "." + microcell_id_csv)
+            new_microcell.set_id(microcell_id_csv)
 
             for column in input.columns.values:
                 if hasattr(InfectionStatus, column):

From a983def64e125dcaa1a9103d128e84fb81dd19c6 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 22 Nov 2023 14:48:31 +0000
Subject: [PATCH 26/53] Added tests for uniqueness of id

---
 .../pyEpiabm/tests/test_unit/test_core/test_household.py   | 7 +++++--
 .../pyEpiabm/tests/test_unit/test_core/test_microcell.py   | 5 +++++
 pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py | 5 +++++
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index b945d081..ad8bc870 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -58,8 +58,6 @@ def test_set_id(self):
         init_id = str(self.microcell.id) + "." + \
                   str(len(self.microcell.households)-1)
         self.assertEqual(subject.id, init_id)
-        subject.set_id("0.0.0")
-        self.assertEqual(subject.id, "0.0.0")
         subject.set_id("10.7.20")
         self.assertEqual(subject.id, "10.7.20")
         self.assertRaises(TypeError, subject.set_id, 2.0)
@@ -67,6 +65,11 @@ def test_set_id(self):
         self.assertRaises(ValueError, subject.set_id, "0.0.")
         self.assertRaises(ValueError, subject.set_id, "123")
         self.assertRaises(ValueError, subject.set_id, "0.0.0.0")
+        subject.set_id("1.1.1")
+        self.microcell.households.append(subject)
+        new_household = pe.Household(self.microcell, (1, 2))
+        self.cell.microcells.append(new_household)
+        self.assertRaises(ValueError, new_household.set_id, "1.1.1")
 
 
 if __name__ == '__main__':
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index 763e6c88..408a4889 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -30,6 +30,11 @@ def test_set_id(self):
         self.assertRaises(TypeError, self.microcell.set_id, 2.0)
         self.assertRaises(ValueError, self.microcell.set_id, "1.1.")
         self.assertRaises(ValueError, self.microcell.set_id, "12")
+        self.microcell.set_id("0.0")
+        self.cell.microcells.append(self.microcell)
+        new_microcell = pe.Microcell(self.cell)
+        self.cell.microcells.append(new_microcell)
+        self.assertRaises(ValueError, new_microcell.set_id, "0.0")
 
     def test_add_person(self):
         self.assertEqual(len(self.microcell.persons), 0)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
index d415ca32..7c24f88c 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_person.py
@@ -120,6 +120,11 @@ def test_set_id(self):
         self.assertRaises(ValueError, self.person.set_id, "0.1")
         self.assertRaises(ValueError, self.person.set_id, "1234")
         self.assertRaises(ValueError, self.person.set_id, "0.0.0.0.5")
+        self.person.set_id("1.1.1.1")
+        self.microcell.persons.append(self.person)
+        new_person = pe.Person(self.microcell)
+        self.microcell.persons.append(new_person)
+        self.assertRaises(ValueError, new_person.set_id, "1.1.1.1")
 
 
 if __name__ == '__main__':

From 182cdb65f38e8c0c403c2f8a322c2c3dd7cdaf5b Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 15:10:58 +0000
Subject: [PATCH 27/53] Fixes of duplicate ids

---
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py  | 7 +++++++
 pyEpiabm/pyEpiabm/routine/file_population_config.py | 4 ----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index f0d1e592..a7eb77bd 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -75,6 +75,13 @@ def __call__(self, time):
                                     selected_household = random.choice(
                                         existing_households)
                                     selected_household.add_person(person)
+
+                                    # Have to update the person's id to
+                                    # account for their new household
+                                    person.set_id(selected_household.id +
+                                                  "." +
+                                                  len(selected_household
+                                                      .persons))
                                 else:
                                     person.household.isolation_location = \
                                         False
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index d38b2898..a9fe79fa 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -107,10 +107,6 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
 
             new_microcell = Microcell(cell)
             cell.microcells.append(new_microcell)
-
-            # Either keep the following line (sets id according to data frame
-            # input), or remove it (sets id according to current number of
-            # microcells in cell.microcells)
             new_microcell.set_id(microcell_id_csv)
 
             for column in input.columns.values:

From 18a666d3333b94d647c3ec44f074e05a1e32d560 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 15:13:25 +0000
Subject: [PATCH 28/53] Fixes of duplicate ids

---
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index a7eb77bd..7e04bcaf 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -80,8 +80,8 @@ def __call__(self, time):
                                     # account for their new household
                                     person.set_id(selected_household.id +
                                                   "." +
-                                                  len(selected_household
-                                                      .persons))
+                                                  str(len(selected_household
+                                                          .persons)))
                                 else:
                                     person.household.isolation_location = \
                                         False

From 6a8ddd61365842e9b87e7823c5807a1c73055284 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 15:45:08 +0000
Subject: [PATCH 29/53] Checked that the actual dataframe in
 test_file_population_config matches the expected

---
 pyEpiabm/pyEpiabm/core/person.py                       |  2 +-
 .../test_routine/test_file_population_config.py        | 10 ++++------
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index c75a1010..69619cf3 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -231,7 +231,7 @@ def set_id(self, id: str):
         """Updates id of current person (i.e. for input from file).
         id format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
         household 2 within this microcell, and person 1 within this
-        household. The id will only be changed if there is a match.
+        household. The id will only be changed if it is of the correct format.
 
         Parameters
         ----------
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index 5974a3ea..5d8ad175 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -216,15 +216,13 @@ def test_print_population(self, mock_copy, mock_read):
 
         FilePopulationFactory.print_population(test_pop, 'output.csv')
         actual_df = mock_copy.call_args.args[0]
+        actual_df['cell'] = pd.Series([1.0, 2.0])
+        actual_df['microcell'] = pd.Series([1.0, 1.0])
         if version.parse(pd.__version__) >= version.parse("1.4.0"):
             expected_df = self.df.copy()
 
-            # The type of the id is converted from float to string, so we
-            # drop the cell and microcell columns
-            expected = expected_df.drop(['cell', 'microcell',
-                                         'household_number'], axis=1)
-            actual = actual_df.drop(['cell', 'microcell',
-                                     'household_number'], axis=1)
+            expected = expected_df.drop(['household_number'], axis=1)
+            actual = actual_df.drop(['household_number'], axis=1)
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)

From ecea0bd4839bb92b3c503df6a963c0e1b5062c36 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 15:49:34 +0000
Subject: [PATCH 30/53] Pandas version check

---
 .../test_unit/test_routine/test_file_population_config.py     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index 5d8ad175..c8d639e2 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -216,13 +216,13 @@ def test_print_population(self, mock_copy, mock_read):
 
         FilePopulationFactory.print_population(test_pop, 'output.csv')
         actual_df = mock_copy.call_args.args[0]
-        actual_df['cell'] = pd.Series([1.0, 2.0])
-        actual_df['microcell'] = pd.Series([1.0, 1.0])
         if version.parse(pd.__version__) >= version.parse("1.4.0"):
             expected_df = self.df.copy()
 
             expected = expected_df.drop(['household_number'], axis=1)
             actual = actual_df.drop(['household_number'], axis=1)
+            actual_df['cell'] = pd.Series([1.0, 2.0])
+            actual_df['microcell'] = pd.Series([1.0, 1.0])
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)

From e21a57dc068798747c36348cf3f78b698d763caa Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 15:57:15 +0000
Subject: [PATCH 31/53] Fixed error

---
 .../test_unit/test_routine/test_file_population_config.py     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index c8d639e2..a01b15a1 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -221,8 +221,8 @@ def test_print_population(self, mock_copy, mock_read):
 
             expected = expected_df.drop(['household_number'], axis=1)
             actual = actual_df.drop(['household_number'], axis=1)
-            actual_df['cell'] = pd.Series([1.0, 2.0])
-            actual_df['microcell'] = pd.Series([1.0, 1.0])
+            actual['cell'] = pd.Series([1.0, 2.0])
+            actual['microcell'] = pd.Series([1.0, 1.0])
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)

From b8bde2c23bceaa79663946520641b3cf0b656722 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 16:02:47 +0000
Subject: [PATCH 32/53] Added duplicates test for cells

---
 pyEpiabm/pyEpiabm/core/cell.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
index f7ac95c7..93869609 100644
--- a/pyEpiabm/pyEpiabm/core/cell.py
+++ b/pyEpiabm/pyEpiabm/core/cell.py
@@ -71,13 +71,15 @@ def add_microcells(self, n):
         for _ in range(n):
             self.microcells.append(Microcell(self))
 
-    def set_id(self, id: str):
+    def set_id(self, id: str, cells: typing.List):
         """Updates id of current cell (i.e. for input from file).
 
         Parameters
         ----------
         id : str
             Identity of cell
+        cells : list
+            List of all current cells
 
         """
         # Ensure id is a string
@@ -85,12 +87,17 @@ def set_id(self, id: str):
             raise TypeError("Provided id must be a string")
 
         # This regex will match on any string which has 1 or more digits
-        if re.match("^\\d+$", id):
-            self.id = id
-        else:
+        if not re.match("^\\d+$", id):
             raise ValueError(f"Invalid id: {id}. id must be of the form 'i' "
                              f"where i is an integer")
 
+        # Finally, check for duplicates
+        cell_ids = [cell.id for cell in cells]
+        if id in cell_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id
+
     def enqueue_person(self, person: Person):
         """Add person to queue for processing at end of iteration, provided
         they are not already recovered (and so may be infected).

From 8027168f7a5c587475347e9a9360a9703165a79d Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 22 Nov 2023 16:03:53 +0000
Subject: [PATCH 33/53] Added duplicates test for cells

---
 pyEpiabm/pyEpiabm/core/population.py                | 2 +-
 pyEpiabm/pyEpiabm/routine/file_population_config.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/population.py b/pyEpiabm/pyEpiabm/core/population.py
index 2fc005be..bf0fc368 100644
--- a/pyEpiabm/pyEpiabm/core/population.py
+++ b/pyEpiabm/pyEpiabm/core/population.py
@@ -45,7 +45,7 @@ def add_cells(self, n):
         base_num = len(self.cells)
         for i in range(n):
             self.cells.append(Cell())
-            self.cells[i + base_num].set_id(str(i + base_num))
+            self.cells[i + base_num].set_id(str(i + base_num), self.cells)
 
     def total_people(self):
         """Returns the total number of people in the population.
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index a9fe79fa..71266c27 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -179,7 +179,7 @@ def find_cell(population: Population, cell_id: str, current_cell: Cell):
             return current_cell
         new_cell = Cell()
         population.cells.append(new_cell)
-        new_cell.set_id(cell_id)
+        new_cell.set_id(cell_id, population.cells)
         return new_cell
 
     @staticmethod

From 705d1146bd275c6725e113a135a2a84791d057a6 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 22 Nov 2023 18:56:18 +0000
Subject: [PATCH 34/53] Update set_id test for duplicates

---
 .../pyEpiabm/tests/test_unit/test_core/test_cell.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
index 233767ca..d62720b3 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
@@ -38,11 +38,18 @@ def test_set_location(self):
         self.assertRaises(ValueError, pe.Cell, ('1', 1))
 
     def test_set_id(self):
+        cells = []
+        cell1 = pe.Cell()
         self.assertEqual(self.cell.id, str(hash(self.cell)))
-        self.assertRaises(TypeError, self.cell.set_id, 2.0)
-        self.assertRaises(ValueError, self.cell.set_id, "2.0")
-        self.cell.set_id("2")
+        self.assertRaises(TypeError, self.cell.set_id, id=2.0, cells=[cell1])
+        self.assertRaises(ValueError, self.cell.set_id, id="2.0", cells=[cell1])
+        self.cell.set_id(id="2", cells=[cell1])
         self.assertEqual(self.cell.id, "2")
+        cell1.set_id(id="1", cells=[cell1])
+        cells.append(cell1)
+        new_cell = pe.Cell((1,1))
+        cells.append(new_cell)
+        self.assertRaises(ValueError, new_cell.set_id, id="1", cells=[cell1])
 
     def test_add_microcells(self, n=4):
         self.assertEqual(len(self.cell.microcells), 0)

From 1cbc7bbcf2028616f0c41faa0b9baa67cc49f384 Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 22 Nov 2023 19:14:29 +0000
Subject: [PATCH 35/53] Added argument cells for use of cells set_id

---
 .../tests/test_unit/test_routine/test_file_population_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index a01b15a1..c784ae90 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -134,7 +134,7 @@ def test_duplicate_microcell(self, mock_read, mock_log):
     def test_find_cell(self):
         pop = pe.Population()
         pop.add_cells(2)
-        pop.cells[1].set_id("42")
+        pop.cells[1].set_id("42", cells=pop.cells)
 
         target_cell = FilePopulationFactory.find_cell(pop, "42", pop.cells[1])
         self.assertEqual(target_cell.id, "42")

From c7532d57c9a0fd80fe13f154cd3692e5e445b53d Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 22 Nov 2023 19:31:29 +0000
Subject: [PATCH 36/53] Attempt fix of indent error

---
 pyEpiabm/pyEpiabm/core/person.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index 69619cf3..ce46fc1b 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -142,7 +142,7 @@ def update_status(self,
         self.infection_status = new_status
 
         if self.infection_status == InfectionStatus.Susceptible and \
-            self.household is not None:
+                                 self.household is not None:
             self.household.add_susceptible_person(self)
         if self.infection_status == InfectionStatus.Exposed and \
             self.household is not None:

From ec769246a1bcac8dcf32c5cb1fb532550ddddddd Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Thu, 23 Nov 2023 07:54:42 +0000
Subject: [PATCH 37/53] Style fixes

---
 pyEpiabm/pyEpiabm/core/person.py                       | 10 +++++-----
 .../pyEpiabm/tests/test_unit/test_core/test_cell.py    |  5 +++--
 .../tests/test_unit/test_core/test_household.py        |  4 ++--
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
index ce46fc1b..84374ab6 100644
--- a/pyEpiabm/pyEpiabm/core/person.py
+++ b/pyEpiabm/pyEpiabm/core/person.py
@@ -56,7 +56,7 @@ def __init__(self, microcell, age_group=None):
         self.date_positive = None
         self.is_vaccinated = False
         self.id = self.microcell.id + "." + "." + \
-                  str(len(self.microcell.persons))
+            str(len(self.microcell.persons))
 
         self.set_random_age(age_group)
 
@@ -91,7 +91,7 @@ def is_symptomatic(self):
 
         """
         return Person.is_infectious(self) and self.infection_status != \
-               InfectionStatus.InfectASympt
+            InfectionStatus.InfectASympt
 
     def is_infectious(self):
         """Query if the person is currently infectious.
@@ -142,10 +142,10 @@ def update_status(self,
         self.infection_status = new_status
 
         if self.infection_status == InfectionStatus.Susceptible and \
-                                 self.household is not None:
+                self.household is not None:
             self.household.add_susceptible_person(self)
         if self.infection_status == InfectionStatus.Exposed and \
-            self.household is not None:
+                self.household is not None:
             self.household.remove_susceptible_person(self)
 
     def add_place(self, place, person_group: int = 0):
@@ -198,7 +198,7 @@ def is_place_closed(self, closure_place_type):
 
         """
         if (hasattr(self.microcell, 'closure_start_time')) and (
-            self.microcell.closure_start_time is not None):
+                self.microcell.closure_start_time is not None):
             for place_type in self.place_types:
                 if place_type.value in closure_place_type:
                     return True
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
index d62720b3..581dbb77 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_cell.py
@@ -42,12 +42,13 @@ def test_set_id(self):
         cell1 = pe.Cell()
         self.assertEqual(self.cell.id, str(hash(self.cell)))
         self.assertRaises(TypeError, self.cell.set_id, id=2.0, cells=[cell1])
-        self.assertRaises(ValueError, self.cell.set_id, id="2.0", cells=[cell1])
+        self.assertRaises(ValueError, self.cell.set_id, id="2.0",
+                          cells=[cell1])
         self.cell.set_id(id="2", cells=[cell1])
         self.assertEqual(self.cell.id, "2")
         cell1.set_id(id="1", cells=[cell1])
         cells.append(cell1)
-        new_cell = pe.Cell((1,1))
+        new_cell = pe.Cell((1, 1))
         cells.append(new_cell)
         self.assertRaises(ValueError, new_cell.set_id, id="1", cells=[cell1])
 
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
index ad8bc870..e702d5dd 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_household.py
@@ -55,8 +55,8 @@ def test_remove_susceptible_person(self):
 
     def test_set_id(self):
         subject = pe.Household(self.microcell, (1, 1))
-        init_id = str(self.microcell.id) + "." + \
-                  str(len(self.microcell.households)-1)
+        init_id = str(self.microcell.id) + "." \
+            + str(len(self.microcell.households)-1)
         self.assertEqual(subject.id, init_id)
         subject.set_id("10.7.20")
         self.assertEqual(subject.id, "10.7.20")

From 48a98d2f604414a9f0cf8f3915e3c31f1bd34848 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 23 Nov 2023 09:36:55 +0000
Subject: [PATCH 38/53] Changed csv read so that cell and microcell ids are
 read as integers, not floats

---
 .../pyEpiabm/intervention/travel_isolation.py |  2 ++
 .../routine/file_population_config.py         | 11 ++++----
 .../test_file_population_config.py            | 28 ++++++++++++-------
 3 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index 7e04bcaf..e046a018 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -82,6 +82,8 @@ def __call__(self, time):
                                                   "." +
                                                   str(len(selected_household
                                                           .persons)))
+                                    # Here we should keep track of this
+                                    # person's previous id
                                 else:
                                     person.household.isolation_location = \
                                         False
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 71266c27..32feb3f7 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -62,7 +62,8 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             logging.info(f"Set population random seed to: {random_seed}")
 
         # Read file into pandas dataframe
-        input = pd.read_csv(input_file)
+        input = pd.read_csv(input_file, dtype={"cell": int,
+                                               "microcell": int})
         loc_given = ("location_x" and "location_y" in input.columns.values)
         # Sort csv on cell and microcell ID
         input = input.sort_values(by=["cell", "microcell"])
@@ -83,11 +84,11 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
         # Store current cell
         current_cell = None
         # Iterate through lines (one per microcell)
-        for _, line in input.iterrows():
-
+        for line in input.itertuples():
+            line = line._asdict()
             # Converting from float to string
-            cell_id_csv = str(int(line["cell"]))
-            microcell_id_csv = cell_id_csv + "." + str(int(line["microcell"]))
+            cell_id_csv = str(line["cell"])
+            microcell_id_csv = cell_id_csv + "." + str(line["microcell"])
 
             # Check if cell exists, or create it
             cell = FilePopulationFactory.find_cell(new_pop, cell_id_csv,
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index c784ae90..ac49c8a2 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -13,7 +13,7 @@ class TestPopConfig(TestPyEpiabm):
     """
 
     def setUp(self) -> None:
-        self.input = {'cell': [1.0, 2.0], 'microcell': [1.0, 1.0],
+        self.input = {'cell': [1, 2], 'microcell': [1, 1],
                       'location_x': [0.0, 1.0], 'location_y': [0.0, 1.0],
                       'household_number': [1, 1], 'place_number': [1, 1],
                       'Susceptible': [8, 9], 'InfectMild': [2, 3]}
@@ -37,7 +37,9 @@ def test_make_pop(self, mock_read):
         mock_read.return_value = self.df
 
         test_pop = FilePopulationFactory.make_pop('test_input.csv')
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_once_with('test_input.csv',
+                                          dtype={"cell": int,
+                                                 "microcell": int})
 
         total_people = 0
         total_infectious = 0
@@ -61,10 +63,10 @@ def test_make_pop(self, mock_read):
         # Test cell_wise values
         for i in range(2):
             self.assertEqual(test_pop.cells[i].id,
-                             str(int(self.input.get('cell')[i])))
+                             str(self.input.get('cell')[i]))
             id_parts = test_pop.cells[i].microcells[0].id.split(".")
             self.assertEqual(id_parts[-1],
-                             str(int(self.input.get('microcell')[i])))
+                             str(self.input.get('microcell')[i]))
             self.assertEqual(test_pop.cells[i].location[0],
                              self.input.get('location_x')[i])
             self.assertEqual(test_pop.cells[i].location[1],
@@ -95,7 +97,9 @@ def test_invalid_input(self, mock_read, mock_log):
         FilePopulationFactory.make_pop('test_input.csv')
         mock_log.assert_called_once_with("ValueError in FilePopulation"
                                          + "Factory.make_pop()")
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_once_with('test_input.csv',
+                                          dtype={"cell": int,
+                                                 "microcell": int})
 
     @patch("pandas.read_csv")
     def test_disorderd_input(self, mock_read):
@@ -103,7 +107,7 @@ def test_disorderd_input(self, mock_read):
         and microcells.
         """
         # Read in disordered data
-        dict_extra = {'cell': [1.0, 3.0], 'microcell': [2.0, 1.0],
+        dict_extra = {'cell': [1, 3], 'microcell': [2, 1],
                       'location_x': [0.0, 2.0], 'location_y': [0.0, 2.0],
                       'household_number': [1, 1], 'place_number': [1, 1],
                       'Susceptible': [8, 9], 'InfectMild': [2, 3]}
@@ -129,7 +133,9 @@ def test_duplicate_microcell(self, mock_read, mock_log):
         FilePopulationFactory.make_pop('test_input.csv')
         mock_log.assert_called_once_with("ValueError in FilePopulation"
                                          + "Factory.make_pop()")
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_once_with('test_input.csv',
+                                          dtype={"cell": int,
+                                                 "microcell": int})
 
     def test_find_cell(self):
         pop = pe.Population()
@@ -180,7 +186,9 @@ def test_random_seed_param(self, mock_read, mock_random,
         mock_read.return_value = self.df
 
         FilePopulationFactory.make_pop('test_input.csv', random_seed=n)
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_once_with('test_input.csv',
+                                          dtype={"cell": int,
+                                                 "microcell": int})
 
         mock_random.assert_called_once_with(n)
         mock_np_random.assert_called_once_with(n)
@@ -221,8 +229,8 @@ def test_print_population(self, mock_copy, mock_read):
 
             expected = expected_df.drop(['household_number'], axis=1)
             actual = actual_df.drop(['household_number'], axis=1)
-            actual['cell'] = pd.Series([1.0, 2.0])
-            actual['microcell'] = pd.Series([1.0, 1.0])
+            actual['cell'] = pd.Series([1, 2])
+            actual['microcell'] = pd.Series([1, 1])
 
             pd.testing.assert_frame_equal(actual,
                                           expected, check_dtype=False)

From 7d8b8b08439fa2149e549eb5a46fb348324ce5c0 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 23 Nov 2023 18:22:38 +0000
Subject: [PATCH 39/53] Fixed some errors

---
 .../test_func/functional_testing_class.py     |  2 +-
 .../test_func/test_closure_functional.py      | 24 +++++++++++----
 .../test_func/test_distancing_functional.py   | 12 ++++++--
 .../test_func/test_isolation_functional.py    | 24 +++++++++++----
 .../test_func/test_quarantine_functional.py   | 30 +++++++++++--------
 .../tests/test_func/test_sim_functional.py    | 12 +++++---
 6 files changed, 71 insertions(+), 33 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_func/functional_testing_class.py b/pyEpiabm/pyEpiabm/tests/test_func/functional_testing_class.py
index 7dc77956..a12cba97 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/functional_testing_class.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/functional_testing_class.py
@@ -30,7 +30,7 @@ def setUpPopulation(self):
         """Can be called in setUp to create a default population,
         to test the impact of interventions.
         """
-        self.pop_params = {'cell': [1.0, 2.0], 'microcell': [1.0, 1.0],
+        self.pop_params = {'cell': [1, 2], 'microcell': [1, 1],
                            'location_x': [0.0, 1.0], 'location_y': [0.0, 1.0],
                            'household_number': [1, 1],
                            'Susceptible': [800, 900], 'InfectMild': [10, 0],
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
index 5a7a9742..c6155aff 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
@@ -54,7 +54,9 @@ def test_closure_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -83,7 +85,9 @@ def test_no_closure_type(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -112,7 +116,9 @@ def test_closure_type_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -141,7 +147,9 @@ def test_spatial_params_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -172,7 +180,9 @@ def test_microcell_threshold_extreme(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -200,7 +210,9 @@ def test_microcell_threshold_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
index dffbed91..f91f12ba 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
@@ -60,7 +60,9 @@ def test_distancing_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -88,7 +90,9 @@ def test_spatial_enhanced_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -117,7 +121,9 @@ def test_prob_lower(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
index 2a768094..30eaa1b5 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
@@ -54,7 +54,9 @@ def test_isolation_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -82,7 +84,9 @@ def test_threshold_num(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -109,7 +113,9 @@ def test_delay_days(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc().sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -137,7 +143,9 @@ def test_duration_days(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -164,7 +172,9 @@ def test_isolation_prob(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -191,7 +201,9 @@ def test_isolation_effectiveness(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
index aa2dcc79..b20059d1 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
@@ -17,6 +17,7 @@ class TestQuarantineFunctional(TestFunctional):
     household quarantine intervention simulations with known
     results/properties to ensure code functions as desired.
     """
+
     def setUp(self) -> None:
         TestFunctional.setUpPopulation()
 
@@ -32,17 +33,18 @@ def setUp(self) -> None:
             "isolation_house_effectiveness": 1},
 
             "household_quarantine": {
-            "start_time": 0,
-            "policy_duration": 365,
-            "case_threshold": 0,
-            "quarantine_delay": 0,
-            "quarantine_duration": 10,
-            "quarantine_house_compliant": 1.0,
-            "quarantine_individual_compliant": 1.0,
-            "quarantine_house_effectiveness": 1.1,
-            "quarantine_spatial_effectiveness": 0.1,
-            "quarantine_place_effectiveness": [0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
-        }
+                "start_time": 0,
+                "policy_duration": 365,
+                "case_threshold": 0,
+                "quarantine_delay": 0,
+                "quarantine_duration": 10,
+                "quarantine_house_compliant": 1.0,
+                "quarantine_individual_compliant": 1.0,
+                "quarantine_house_effectiveness": 1.1,
+                "quarantine_spatial_effectiveness": 0.1,
+                "quarantine_place_effectiveness": [0.1, 0.1, 0.1, 0.1, 0.1,
+                                                   0.1]
+            }
         }
 
     def test_quarantine_present(self, mock_read, mock_csv):
@@ -68,12 +70,14 @@ def test_quarantine_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
         HelperFunc().compare_susceptible_groups(
-             pop_isolation.cells, pop_quarantine.cells)
+            pop_isolation.cells, pop_quarantine.cells)
 
 
 if __name__ == '__main__':
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
index ec2112d9..bb6fdcc1 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
@@ -174,7 +174,7 @@ def test_segmented_infection(self, *mocks):
         outside their household (or microcell) without a spatial sweep.
         """
         mock_read, mock_csv = mocks[:2]
-        file_input = {'cell': [1.0, 2.0], 'microcell': [1.0, 1.0],
+        file_input = {'cell': [1, 2], 'microcell': [1, 1],
                       'location_x': [0.0, 1.0], 'location_y': [0.0, 1.0],
                       'household_number': [1, 1],
                       'Susceptible': [8, 9], 'InfectMild': [2, 0]}
@@ -189,7 +189,9 @@ def test_segmented_infection(self, *mocks):
                                                 self.file_params,
                                                 sweep_list)
 
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_with('test_input.csv',
+                                     dtype={"cell": int,
+                                            "microcell": int})
         mock_csv.assert_called_once()
 
         cell_data_0 = pop.cells[0].compartment_counter.retrieve()
@@ -209,7 +211,7 @@ def test_small_cutoff(self, *mocks):
         outside their cell when the cut-off is sufficiently small.
         """
         mock_read, mock_csv = mocks[:2]
-        file_input = {'cell': [1.0, 2.0], 'microcell': [1.0, 1.0],
+        file_input = {'cell': [1, 2], 'microcell': [1, 1],
                       'location_x': [0.0, 1.0], 'location_y': [0.0, 1.0],
                       'household_number': [1, 1],
                       'Susceptible': [8, 9], 'InfectMild': [2, 0]}
@@ -224,7 +226,9 @@ def test_small_cutoff(self, *mocks):
                                                 self.file_params,
                                                 sweep_list)
 
-        mock_read.assert_called_once_with('test_input.csv')
+        mock_read.assert_called_once_with('test_input.csv',
+                                          dtype={"cell": int,
+                                                 "microcell": int})
         mock_csv.assert_called_once()
 
         cell_data_0 = pop.cells[0].compartment_counter.retrieve()

From e3eb42cab4319b8af11acb251531fc613ff95b4f Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Fri, 24 Nov 2023 18:34:04 +0000
Subject: [PATCH 40/53] Updated error message

---
 pyEpiabm/pyEpiabm/routine/file_population_config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 32feb3f7..1b397ba8 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -103,8 +103,8 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             # Raise error if microcell exists, then create new one
             microcell_ids = [microcell.id for microcell in cell.microcells]
             if microcell_id_csv in microcell_ids:
-                raise ValueError(f"Duplicate microcells {microcell_id_csv}"
-                                 + f" in cell {cell.id}")
+                raise ValueError(f"Duplicate microcells: {microcell_id_csv}"
+                                 + f" already exists in cell {cell.id}")
 
             new_microcell = Microcell(cell)
             cell.microcells.append(new_microcell)

From da8895a9b34aa1404e6aadb05057337ee656fd98 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Mon, 27 Nov 2023 08:44:00 +0000
Subject: [PATCH 41/53] Removed parameter chaining in the mock_read

---
 .../routine/file_population_config.py         |  4 +--
 .../test_func/test_closure_functional.py      | 27 +++++++------------
 .../test_func/test_distancing_functional.py   | 15 +++++------
 .../test_func/test_isolation_functional.py    | 27 +++++++------------
 .../test_func/test_quarantine_functional.py   |  7 ++---
 .../tests/test_func/test_sim_functional.py    | 11 ++++----
 .../test_file_population_config.py            | 19 +++++--------
 7 files changed, 42 insertions(+), 68 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 1b397ba8..c5a05fbe 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -62,8 +62,8 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             logging.info(f"Set population random seed to: {random_seed}")
 
         # Read file into pandas dataframe
-        input = pd.read_csv(input_file, dtype={"cell": int,
-                                               "microcell": int})
+        input = pd.read_csv(filepath_or_buffer=input_file, dtype={"cell": int,
+                            "microcell": int})
         loc_given = ("location_x" and "location_y" in input.columns.values)
         # Sort csv on cell and microcell ID
         input = input.sort_values(by=["cell", "microcell"])
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
index c6155aff..e7fa9142 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_closure_functional.py
@@ -33,6 +33,9 @@ def setUp(self) -> None:
         }
         }
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     def test_closure_present(self, mock_read, mock_csv):
         """Place closure functional test to ensure more people will be
         susceptible when place closure intervention is present.
@@ -54,9 +57,7 @@ def test_closure_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -85,9 +86,7 @@ def test_no_closure_type(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -116,9 +115,7 @@ def test_closure_type_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -147,9 +144,7 @@ def test_spatial_params_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -180,9 +175,7 @@ def test_microcell_threshold_extreme(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -210,9 +203,7 @@ def test_microcell_threshold_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
index f91f12ba..eab00dd4 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_distancing_functional.py
@@ -39,6 +39,9 @@ def setUp(self) -> None:
         }
         }
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     def test_distancing_present(self, mock_read, mock_csv):
         """Social distancing functional test to ensure more people will be
         susceptible when social distancing intervention is present.
@@ -60,9 +63,7 @@ def test_distancing_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -90,9 +91,7 @@ def test_spatial_enhanced_large(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -121,9 +120,7 @@ def test_prob_lower(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
index 30eaa1b5..dc62ed4d 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_isolation_functional.py
@@ -33,6 +33,9 @@ def setUp(self) -> None:
             "isolation_house_effectiveness": 0}
         }
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     def test_isolation_present(self, mock_read, mock_csv):
         """Case isolation functional test to ensure more people will be
         susceptible when case isolation intervention is present.
@@ -54,9 +57,7 @@ def test_isolation_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -84,9 +85,7 @@ def test_threshold_num(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -113,9 +112,7 @@ def test_delay_days(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc().sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -143,9 +140,7 @@ def test_duration_days(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -172,9 +167,7 @@ def test_isolation_prob(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
@@ -201,9 +194,7 @@ def test_isolation_effectiveness(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
index b20059d1..e29049e9 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_quarantine_functional.py
@@ -47,6 +47,9 @@ def setUp(self) -> None:
             }
         }
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     def test_quarantine_present(self, mock_read, mock_csv):
         """Household quarantine functional test to ensure more people will be
         susceptible when household quarantine intervention is present.
@@ -70,9 +73,7 @@ def test_quarantine_present(self, mock_read, mock_csv):
             "test_input.csv", self.sim_params, self.file_params,
             HelperFunc.sweep_list_initialise())
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         self.assertEqual(mock_csv.call_count, 2)
 
         # Compare number of susceptible individuals for each age group
diff --git a/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py b/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
index bb6fdcc1..5905be5e 100644
--- a/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
+++ b/pyEpiabm/pyEpiabm/tests/test_func/test_sim_functional.py
@@ -33,6 +33,9 @@ def setUp(self) -> None:
                             "spatial_output": False,
                             "age_stratified": True}
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     @staticmethod
     def toy_simulation(pop_params, sim_params, file_params):
         # Create a population based on the parameters given.
@@ -189,9 +192,7 @@ def test_segmented_infection(self, *mocks):
                                                 self.file_params,
                                                 sweep_list)
 
-        mock_read.assert_called_with('test_input.csv',
-                                     dtype={"cell": int,
-                                            "microcell": int})
+        mock_read.assert_called_with(**self.read_params)
         mock_csv.assert_called_once()
 
         cell_data_0 = pop.cells[0].compartment_counter.retrieve()
@@ -226,9 +227,7 @@ def test_small_cutoff(self, *mocks):
                                                 self.file_params,
                                                 sweep_list)
 
-        mock_read.assert_called_once_with('test_input.csv',
-                                          dtype={"cell": int,
-                                                 "microcell": int})
+        mock_read.assert_called_once_with(**self.read_params)
         mock_csv.assert_called_once()
 
         cell_data_0 = pop.cells[0].compartment_counter.retrieve()
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
index ac49c8a2..74f8c720 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_file_population_config.py
@@ -20,6 +20,9 @@ def setUp(self) -> None:
         self.df = pd.DataFrame(self.input)
         pe.Parameters.instance().household_size_distribution = []
 
+        self.read_params = {"filepath_or_buffer": 'test_input.csv',
+                            "dtype": {"cell": int, "microcell": int}}
+
     @patch('logging.exception')
     def test_make_pop_no_file(self, mock_log):
         """Tests for when no file is specified.
@@ -37,9 +40,7 @@ def test_make_pop(self, mock_read):
         mock_read.return_value = self.df
 
         test_pop = FilePopulationFactory.make_pop('test_input.csv')
-        mock_read.assert_called_once_with('test_input.csv',
-                                          dtype={"cell": int,
-                                                 "microcell": int})
+        mock_read.assert_called_once_with(**self.read_params)
 
         total_people = 0
         total_infectious = 0
@@ -97,9 +98,7 @@ def test_invalid_input(self, mock_read, mock_log):
         FilePopulationFactory.make_pop('test_input.csv')
         mock_log.assert_called_once_with("ValueError in FilePopulation"
                                          + "Factory.make_pop()")
-        mock_read.assert_called_once_with('test_input.csv',
-                                          dtype={"cell": int,
-                                                 "microcell": int})
+        mock_read.assert_called_once_with(**self.read_params)
 
     @patch("pandas.read_csv")
     def test_disorderd_input(self, mock_read):
@@ -133,9 +132,7 @@ def test_duplicate_microcell(self, mock_read, mock_log):
         FilePopulationFactory.make_pop('test_input.csv')
         mock_log.assert_called_once_with("ValueError in FilePopulation"
                                          + "Factory.make_pop()")
-        mock_read.assert_called_once_with('test_input.csv',
-                                          dtype={"cell": int,
-                                                 "microcell": int})
+        mock_read.assert_called_once_with(**self.read_params)
 
     def test_find_cell(self):
         pop = pe.Population()
@@ -186,9 +183,7 @@ def test_random_seed_param(self, mock_read, mock_random,
         mock_read.return_value = self.df
 
         FilePopulationFactory.make_pop('test_input.csv', random_seed=n)
-        mock_read.assert_called_once_with('test_input.csv',
-                                          dtype={"cell": int,
-                                                 "microcell": int})
+        mock_read.assert_called_once_with(**self.read_params)
 
         mock_random.assert_called_once_with(n)
         mock_np_random.assert_called_once_with(n)

From 89806cb2707e6c582e2c21dcd446a3263506046c Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 29 Nov 2023 19:23:49 +0000
Subject: [PATCH 42/53] Modified add_household so that person id is only set if
 person does not already have household

---
 pyEpiabm/pyEpiabm/core/microcell.py           |  6 +++++-
 .../pyEpiabm/intervention/travel_isolation.py |  8 --------
 .../routine/file_population_config.py         | 19 +++++++++----------
 .../test_unit/test_core/test_microcell.py     |  7 +++++++
 4 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 20d411a0..afea4b98 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -155,7 +155,11 @@ def add_household(self, people: list):
             for i in range(len(people)):
                 person = people[i]
                 household.add_person(person)
-                person.set_id(household.id + "." + str(i))
+
+                # If the person already has a household, then do not change
+                # their id
+                if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id):
+                    person.set_id(household.id + "." + str(i))
 
         else:
             logging.info("Cannot create an empty household")
diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index e046a018..bf85760a 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -76,14 +76,6 @@ def __call__(self, time):
                                         existing_households)
                                     selected_household.add_person(person)
 
-                                    # Have to update the person's id to
-                                    # account for their new household
-                                    person.set_id(selected_household.id +
-                                                  "." +
-                                                  str(len(selected_household
-                                                          .persons)))
-                                    # Here we should keep track of this
-                                    # person's previous id
                                 else:
                                     person.household.isolation_location = \
                                         False
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index c5a05fbe..425b9a40 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -85,10 +85,9 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
         current_cell = None
         # Iterate through lines (one per microcell)
         for line in input.itertuples():
-            line = line._asdict()
             # Converting from float to string
-            cell_id_csv = str(line["cell"])
-            microcell_id_csv = cell_id_csv + "." + str(line["microcell"])
+            cell_id_csv = str(line.cell)
+            microcell_id_csv = cell_id_csv + "." + str(line.microcell)
 
             # Check if cell exists, or create it
             cell = FilePopulationFactory.find_cell(new_pop, cell_id_csv,
@@ -97,7 +96,7 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
                 current_cell = cell
 
             if loc_given:
-                location = (line["location_x"], line["location_y"])
+                location = (line.location_x, line.location_y)
                 cell.set_location(location)
 
             # Raise error if microcell exists, then create new one
@@ -113,7 +112,7 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
             for column in input.columns.values:
                 if hasattr(InfectionStatus, column):
                     value = getattr(InfectionStatus, column)
-                    for _ in range(int(line[column])):
+                    for _ in range(int(getattr(line, column))):
                         person = Person(new_microcell)
                         person.set_random_age()
                         new_microcell.add_person(person)
@@ -129,14 +128,14 @@ def make_pop(input_file: str, random_seed: int = None, time: float = 0):
 
             # Add households and places to microcell
             if len(Parameters.instance().household_size_distribution) == 0:
-                if (('household_number' in line) and
-                        (line["household_number"]) > 0):
-                    households = int(line["household_number"])
+                if (hasattr(line, 'household_number') and
+                        line.household_number > 0):
+                    households = int(line.household_number)
                     FilePopulationFactory.add_households(new_microcell,
                                                          households)
 
-            if ('place_number' in line) and (line["place_number"]) > 0:
-                new_microcell.add_place(int(line["place_number"]),
+            if hasattr(line, 'place_number') and line.place_number > 0:
+                new_microcell.add_place(int(line.place_number),
                                         cell.location,
                                         random.choice(list(PlaceType)))
 
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index 408a4889..95259301 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -87,6 +87,13 @@ def test_add_household(self):
             person = self.microcell.persons[i]
             self.assertEqual(person.id, household.id + "." + str(i))
 
+        # Check that if the person already has a household, then we cannot
+        # change their id when they move to a new one
+        person = self.microcell.persons[0]
+        household.persons.remove(person)
+        self.microcell.add_household([person])
+        self.assertEqual(person.id, household.id + ".0")
+
     @mock.patch('logging.info')
     def test_logging(self, mock_log):
         self.microcell.add_household(self.microcell.persons)

From 8345e24b67e1ae805e12acf592868f8a1c7274ee Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 29 Nov 2023 20:29:23 +0000
Subject: [PATCH 43/53] Added change_id parameter to the add_household function
 so that we can control when the id of a person is changed

---
 pyEpiabm/pyEpiabm/core/microcell.py           | 26 +++++++++-----
 .../pyEpiabm/intervention/travel_isolation.py |  2 +-
 .../routine/file_population_config.py         |  2 +-
 .../pyEpiabm/routine/toy_population_config.py |  2 +-
 .../pyEpiabm/sweep/initial_household_sweep.py |  3 +-
 .../test_unit/test_core/test_microcell.py     | 36 ++++++++++++-------
 .../test_travel_isolation.py                  |  2 +-
 .../test_initial_household_sweep.py           |  9 ++---
 .../test_unit/test_sweep/test_travel_sweep.py | 12 ++++---
 9 files changed, 60 insertions(+), 34 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index afea4b98..e55962fc 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -25,6 +25,7 @@ class Microcell:
         An instance of :class:`Cell`
 
     """
+
     def __init__(self, cell):
         """Constructor Method.
 
@@ -53,7 +54,7 @@ def __repr__(self):
 
         """
         return f"Microcell with {len(self.persons)} people" + \
-            f" at location {self.location}."
+               f" at location {self.location}."
 
     def set_id(self, id):
         """Updates id of current microcell (i.e. for input from file).
@@ -140,7 +141,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list):
+    def add_household(self, people: list, change_id: bool):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -148,6 +149,9 @@ def add_household(self, people: list):
         ----------
         people : list
             List of :class:`People` to add to household
+        change_id : bool
+            Boolean representing whether we wish to set the id of the people
+            of the household when the function is called or not
 
         """
         if len(people) != 0:
@@ -158,17 +162,21 @@ def add_household(self, people: list):
 
                 # If the person already has a household, then do not change
                 # their id
-                if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id):
+                if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id) and \
+                    change_id:
                     person.set_id(household.id + "." + str(i))
+                else:
+                    logging.info(f"Person {person.id} has moved to household"
+                                 f"{household.id}")
 
         else:
             logging.info("Cannot create an empty household")
 
     def notify_person_status_change(
-            self,
-            old_status: InfectionStatus,
-            new_status: InfectionStatus,
-            age_group) -> None:
+        self,
+        old_status: InfectionStatus,
+        new_status: InfectionStatus,
+        age_group) -> None:
         """Notify Microcell that a person's status has changed.
 
         Parameters
@@ -201,8 +209,8 @@ def set_location(self, loc: typing.Tuple[float, float]):
 
     def count_icu(self):
         return sum(map(lambda person: person.infection_status ==
-                   InfectionStatus.InfectICU, self.persons))
+                                      InfectionStatus.InfectICU, self.persons))
 
     def count_infectious(self):
         return sum(map(lambda person: person.is_infectious() is
-                   True, self.persons))
+                                      True, self.persons))
diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index bf85760a..8930cf8a 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -94,7 +94,7 @@ def __call__(self, time):
                                     person.household.persons.remove(person)
                                     # Put in new household
                                     person.microcell.add_household([
-                                        person])
+                                        person], change_id=False)
                                     person.household.isolation_location = \
                                         True
                                 else:
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 425b9a40..6e8de039 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -207,7 +207,7 @@ def add_households(microcell: Microcell, household_number: int):
                 person_choice = people_list[0]
                 people_list.remove(person_choice)
                 household_people.append(person_choice)
-            microcell.add_household(household_people)
+            microcell.add_household(household_people, change_id=False)
 
     @staticmethod
     @log_exceptions()
diff --git a/pyEpiabm/pyEpiabm/routine/toy_population_config.py b/pyEpiabm/pyEpiabm/routine/toy_population_config.py
index bcdf389d..3cdefe3c 100644
--- a/pyEpiabm/pyEpiabm/routine/toy_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/toy_population_config.py
@@ -136,7 +136,7 @@ def add_households(population: Population, household_number: int):
                         person_choice = people_list[0]
                         people_list.remove(person_choice)
                         household_people.append(person_choice)
-                    microcell.add_household(household_people)
+                    microcell.add_household(household_people, change_id=True)
 
     @staticmethod
     def add_places(population: Population, place_number: float):
diff --git a/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py b/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
index 73d677d4..d7377afa 100644
--- a/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
+++ b/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
@@ -68,7 +68,8 @@ def household_allocation(self, population: Population):
                     people_in_household = []
                     for i in range(k, k + m):
                         people_in_household.append(microcell.persons[i])
-                    microcell.add_household(people_in_household)
+                    microcell.add_household(people_in_household,
+                                            change_id=True)
                     k += m
 
     def one_person_household_age(self, person: Person):
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index 95259301..0d08cc6c 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -79,24 +79,36 @@ def test_setup(self, n=5):
 
     def test_add_household(self):
         self.microcell.add_people(1)
-        self.microcell.add_household(self.microcell.persons)
+        self.microcell.add_household(self.microcell.persons, change_id=True)
         self.assertEqual(len(self.microcell.households), 1)
-        household = self.microcell.households[0]
-        self.assertEqual(len(household.persons), 1)
-        for i in range(len(household.persons)):
+        original_household = self.microcell.households[0]
+        self.assertEqual(len(original_household.persons), 1)
+        for i in range(len(original_household.persons)):
             person = self.microcell.persons[i]
-            self.assertEqual(person.id, household.id + "." + str(i))
+            self.assertEqual(person.id, original_household.id + "." + str(i))
 
-        # Check that if the person already has a household, then we cannot
-        # change their id when they move to a new one
-        person = self.microcell.persons[0]
-        household.persons.remove(person)
-        self.microcell.add_household([person])
-        self.assertEqual(person.id, household.id + ".0")
+        # Now add another original_household without changing
+        # the id of the person
+        self.microcell.add_household(self.microcell.persons, change_id=False)
+        self.assertEqual(original_household.persons[0].id,
+                         original_household.id + ".0")
 
     @mock.patch('logging.info')
     def test_logging(self, mock_log):
-        self.microcell.add_household(self.microcell.persons)
+        self.microcell.add_household(self.microcell.persons, change_id=True)
+        mock_log.assert_called_once()
+
+    @mock.patch('logging.info')
+    def test_logging_duplicates(self, mock_log):
+        # Check that if the person already has a household, then we cannot
+        # change their id when they move to a new one
+        self.microcell.add_people(1)
+        self.microcell.add_household(self.microcell.persons, change_id=True)
+        old_household = self.microcell.households[0]
+        person = self.microcell.persons[0]
+        old_household.persons.remove(person)
+        self.microcell.add_household([person], change_id=True)
+        self.assertEqual(person.id, old_household.id + ".0")
         mock_log.assert_called_once()
 
     def test_report(self):
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 2e0f277c..49612af6 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -83,7 +83,7 @@ def test___call__(self, mock_random):
             1, status=InfectionStatus.InfectASympt, age_group=7)
         person_introduced2 = self._microcell.persons[3]
         self._population.travellers.append(person_introduced2)
-        self._microcell.add_household([person_introduced2])
+        self._microcell.add_household([person_introduced2], change_id=False)
         person_introduced2.travel_end_time = 40
         self.travelisolation(time=21)
         self.assertTrue(person_introduced2.household.isolation_location)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
index 0daa8ed6..c8738760 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
@@ -384,10 +384,11 @@ def test_call(self, mock_log):
         test_sweep = pe.sweep.InitialHouseholdSweep()
         test_sweep.bind_population(self.test_population)
         microcell = self.test_population.cells[0].microcells[0]
-        microcell.add_household([self.person1])
-        microcell.add_household([self.person2, self.person3])
-        microcell.add_household([self.person4, self.person5, self.person6])
-        microcell.add_household([])
+        microcell.add_household([self.person1], change_id=True)
+        microcell.add_household([self.person2, self.person3], change_id=True)
+        microcell.add_household([self.person4, self.person5, self.person6],
+                                change_id=True)
+        microcell.add_household([], change_id=True)
 
         for cell in self.test_population.cells:
             for person in cell.persons:
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
index b9138bdc..f921a700 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
@@ -30,10 +30,14 @@ def setUp(self) -> None:
         self.microcell2 = self.cell.microcells[1]
         self.microcell1.add_people(15)
         self.microcell2.add_people(5)
-        self.microcell1.add_household(self.microcell1.persons.copy()[:10])
-        self.microcell1.add_household(self.microcell1.persons.copy()[10:])
-        self.microcell2.add_household(self.microcell1.persons.copy()[:3])
-        self.microcell2.add_household(self.microcell1.persons.copy()[3:])
+        self.microcell1.add_household(self.microcell1.persons.copy()[:10],
+                                      change_id=True)
+        self.microcell1.add_household(self.microcell1.persons.copy()[10:],
+                                      change_id=True)
+        self.microcell2.add_household(self.microcell1.persons.copy()[:3],
+                                      change_id=True)
+        self.microcell2.add_household(self.microcell1.persons.copy()[3:],
+                                      change_id=True)
         # By default all susceptible, make 2 infectious
         self.initial_infected_person1 = self.microcell1.persons[0]
         self.initial_infected_person1.update_status(InfectionStatus(4))

From f2074a7cef644e93bc0fb48da236eec4ef2aa1f8 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Wed, 29 Nov 2023 20:33:00 +0000
Subject: [PATCH 44/53] Error fix

---
 pyEpiabm/pyEpiabm/sweep/travel_sweep.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/sweep/travel_sweep.py b/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
index c45eab04..33fea5e9 100644
--- a/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
+++ b/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
@@ -151,7 +151,7 @@ def assign_microcell_and_household(self, number_individuals_introduced):
         microcells) with highest population density are selected. The
         individuals are assigned to one of these microcells by a uniform random
         choice between them. Individuals can end up in the same microcell.
-        Next, individuals are assigned to an wxisting or a new household within
+        Next, individuals are assigned to an existing or a new household within
         the selected microcell.
 
         Parameters
@@ -195,7 +195,7 @@ def assign_microcell_and_household(self, number_individuals_introduced):
                 selected_household.add_person(person)
             else:
                 # Create new household
-                selected_microcell.add_household([person])
+                selected_microcell.add_household([person], change_id=False)
 
     def check_leaving_individuals(self, time, person):
         """Check if individuals travel_end_time is reached. If interventions

From d32616606f46cdb94d572b0b67d8c05bad71a40b Mon Sep 17 00:00:00 2001
From: Abbie Evans <abbieevans75@gmail.com>
Date: Wed, 29 Nov 2023 21:45:59 +0000
Subject: [PATCH 45/53] Style fixes

---
 pyEpiabm/pyEpiabm/core/microcell.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index e55962fc..71cfc377 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -163,7 +163,7 @@ def add_household(self, people: list, change_id: bool):
                 # If the person already has a household, then do not change
                 # their id
                 if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id) and \
-                    change_id:
+                        change_id:
                     person.set_id(household.id + "." + str(i))
                 else:
                     logging.info(f"Person {person.id} has moved to household"
@@ -176,7 +176,7 @@ def notify_person_status_change(
         self,
         old_status: InfectionStatus,
         new_status: InfectionStatus,
-        age_group) -> None:
+            age_group) -> None:
         """Notify Microcell that a person's status has changed.
 
         Parameters
@@ -209,8 +209,8 @@ def set_location(self, loc: typing.Tuple[float, float]):
 
     def count_icu(self):
         return sum(map(lambda person: person.infection_status ==
-                                      InfectionStatus.InfectICU, self.persons))
+                       InfectionStatus.InfectICU, self.persons))
 
     def count_infectious(self):
         return sum(map(lambda person: person.is_infectious() is
-                                      True, self.persons))
+                       True, self.persons))

From 14cc1d2a850b070ef848de54ba451039df0bc586 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 11:07:36 +0000
Subject: [PATCH 46/53] Updated add_household to have a default value

---
 pyEpiabm/pyEpiabm/core/microcell.py                | 14 +++++++-------
 pyEpiabm/pyEpiabm/routine/toy_population_config.py |  2 +-
 pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py |  3 +--
 .../test_sweep/test_initial_household_sweep.py     |  9 ++++-----
 .../test_unit/test_sweep/test_travel_sweep.py      | 12 ++++--------
 5 files changed, 17 insertions(+), 23 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index e55962fc..806497e5 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -141,7 +141,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list, change_id: bool):
+    def add_household(self, people: list, change_id: bool = True):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -162,12 +162,12 @@ def add_household(self, people: list, change_id: bool):
 
                 # If the person already has a household, then do not change
                 # their id
-                if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id) and \
-                    change_id:
-                    person.set_id(household.id + "." + str(i))
-                else:
-                    logging.info(f"Person {person.id} has moved to household"
-                                 f"{household.id}")
+                if change_id:
+                    if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id):
+                        person.set_id(household.id + "." + str(i))
+                    else:
+                        logging.info(f"Person {person.id} has moved to "
+                                     f"household {household.id}")
 
         else:
             logging.info("Cannot create an empty household")
diff --git a/pyEpiabm/pyEpiabm/routine/toy_population_config.py b/pyEpiabm/pyEpiabm/routine/toy_population_config.py
index 3cdefe3c..bcdf389d 100644
--- a/pyEpiabm/pyEpiabm/routine/toy_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/toy_population_config.py
@@ -136,7 +136,7 @@ def add_households(population: Population, household_number: int):
                         person_choice = people_list[0]
                         people_list.remove(person_choice)
                         household_people.append(person_choice)
-                    microcell.add_household(household_people, change_id=True)
+                    microcell.add_household(household_people)
 
     @staticmethod
     def add_places(population: Population, place_number: float):
diff --git a/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py b/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
index d7377afa..73d677d4 100644
--- a/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
+++ b/pyEpiabm/pyEpiabm/sweep/initial_household_sweep.py
@@ -68,8 +68,7 @@ def household_allocation(self, population: Population):
                     people_in_household = []
                     for i in range(k, k + m):
                         people_in_household.append(microcell.persons[i])
-                    microcell.add_household(people_in_household,
-                                            change_id=True)
+                    microcell.add_household(people_in_household)
                     k += m
 
     def one_person_household_age(self, person: Person):
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
index c8738760..0daa8ed6 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_household_sweep.py
@@ -384,11 +384,10 @@ def test_call(self, mock_log):
         test_sweep = pe.sweep.InitialHouseholdSweep()
         test_sweep.bind_population(self.test_population)
         microcell = self.test_population.cells[0].microcells[0]
-        microcell.add_household([self.person1], change_id=True)
-        microcell.add_household([self.person2, self.person3], change_id=True)
-        microcell.add_household([self.person4, self.person5, self.person6],
-                                change_id=True)
-        microcell.add_household([], change_id=True)
+        microcell.add_household([self.person1])
+        microcell.add_household([self.person2, self.person3])
+        microcell.add_household([self.person4, self.person5, self.person6])
+        microcell.add_household([])
 
         for cell in self.test_population.cells:
             for person in cell.persons:
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
index f921a700..b9138bdc 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
@@ -30,14 +30,10 @@ def setUp(self) -> None:
         self.microcell2 = self.cell.microcells[1]
         self.microcell1.add_people(15)
         self.microcell2.add_people(5)
-        self.microcell1.add_household(self.microcell1.persons.copy()[:10],
-                                      change_id=True)
-        self.microcell1.add_household(self.microcell1.persons.copy()[10:],
-                                      change_id=True)
-        self.microcell2.add_household(self.microcell1.persons.copy()[:3],
-                                      change_id=True)
-        self.microcell2.add_household(self.microcell1.persons.copy()[3:],
-                                      change_id=True)
+        self.microcell1.add_household(self.microcell1.persons.copy()[:10])
+        self.microcell1.add_household(self.microcell1.persons.copy()[10:])
+        self.microcell2.add_household(self.microcell1.persons.copy()[:3])
+        self.microcell2.add_household(self.microcell1.persons.copy()[3:])
         # By default all susceptible, make 2 infectious
         self.initial_infected_person1 = self.microcell1.persons[0]
         self.initial_infected_person1.update_status(InfectionStatus(4))

From 63aad2336b81e04a61a8d8bd9071d5f4c575f993 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 16:03:01 +0000
Subject: [PATCH 47/53] Made changes travel_sweep to ensure that the ids of
 travellers are set

---
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py           | 2 +-
 pyEpiabm/pyEpiabm/sweep/travel_sweep.py                      | 4 +++-
 .../test_unit/test_intervention/test_travel_isolation.py     | 3 ++-
 .../pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py | 5 +++--
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index 8930cf8a..bf85760a 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -94,7 +94,7 @@ def __call__(self, time):
                                     person.household.persons.remove(person)
                                     # Put in new household
                                     person.microcell.add_household([
-                                        person], change_id=False)
+                                        person])
                                     person.household.isolation_location = \
                                         True
                                 else:
diff --git a/pyEpiabm/pyEpiabm/sweep/travel_sweep.py b/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
index 33fea5e9..9e7c8ba7 100644
--- a/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
+++ b/pyEpiabm/pyEpiabm/sweep/travel_sweep.py
@@ -193,9 +193,11 @@ def assign_microcell_and_household(self, number_individuals_introduced):
                     [h for h in selected_microcell.households if not
                      h.isolation_location])
                 selected_household.add_person(person)
+                person.set_id(selected_household.id + "." +
+                              str(len(selected_household.persons) - 1))
             else:
                 # Create new household
-                selected_microcell.add_household([person], change_id=False)
+                selected_microcell.add_household([person])
 
     def check_leaving_individuals(self, time, person):
         """Check if individuals travel_end_time is reached. If interventions
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 49612af6..912d8fd5 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -82,8 +82,9 @@ def test___call__(self, mock_random):
         self._microcell.add_people(
             1, status=InfectionStatus.InfectASympt, age_group=7)
         person_introduced2 = self._microcell.persons[3]
+        person_introduced2.set_id("0.0.2.0")
         self._population.travellers.append(person_introduced2)
-        self._microcell.add_household([person_introduced2], change_id=False)
+        self._microcell.add_household([person_introduced2])
         person_introduced2.travel_end_time = 40
         self.travelisolation(time=21)
         self.assertTrue(person_introduced2.household.isolation_location)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
index b9138bdc..9fb0f8bd 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_travel_sweep.py
@@ -131,12 +131,13 @@ def test_assign_microcell_and_household(self):
         self.travelsweep(time=1)
         self.assertEqual(len(self.microcell1.persons), 16)
         self.assertEqual(len(self.microcell1.households), 3)
+        self.assertEqual(self.microcell1.persons[-1].id, "0.0.2.0")
 
     def test_remove_leaving_individual(self):
         """Remove individuals introduced after their travel_end_time has
         passed and check if they are not in isolation and/or quarantine.
         If so, keep them in the population until isolation_start_time and/or
-        quaratine_start_time has also passed. Check if the population size
+        quarantine_start_time has also passed. Check if the population size
         is as expected at the considered time points.
 
         """
@@ -152,7 +153,7 @@ def test_remove_leaving_individual(self):
         # Remove after end time and isolation and quarantine over
         self.travelsweep.travel_params['ratio_introduce_cases'] = 0.5
         self.travelsweep.travel_params['duration_travel_stay'] = [2, 2]
-        # Introduce individual staying untill day 16
+        # Introduce individual staying until day 16
         self.travelsweep(time=14)
         introduced_person = self.cell.persons[-1]
         introduced_person.travel_isolation_start_time = 18

From 15978f3eb74e4b9fef499f07a92bfcd8e629c11d Mon Sep 17 00:00:00 2001
From: abbie-evans <147088150+abbie-evans@users.noreply.github.com>
Date: Thu, 30 Nov 2023 17:13:24 +0000
Subject: [PATCH 48/53] Update for loop in add_household

Co-authored-by: Kit Gallagher <60467371+KCGallagher@users.noreply.github.com>
---
 pyEpiabm/pyEpiabm/core/microcell.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index de834cf4..898c8781 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -156,8 +156,7 @@ def add_household(self, people: list, change_id: bool = True):
         """
         if len(people) != 0:
             household = Household(self, loc=self.location)
-            for i in range(len(people)):
-                person = people[i]
+            for i, person in enumerate(people):
                 household.add_person(person)
 
                 # If the person already has a household, then do not change

From ea0a512fff46e6029d70b89ed417a72c6eb164e2 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 17:57:18 +0000
Subject: [PATCH 49/53] Changed add_household to have an override_person_id
 boolean attribute to determine whether we want the id overridden or not

---
 pyEpiabm/pyEpiabm/core/microcell.py           | 24 +++++++++----------
 .../pyEpiabm/intervention/travel_isolation.py |  2 +-
 .../routine/file_population_config.py         |  2 +-
 .../test_unit/test_core/test_microcell.py     | 22 ++++++++---------
 .../test_travel_isolation.py                  |  3 ++-
 5 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index de834cf4..a9392dce 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -141,7 +141,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list, change_id: bool = True):
+    def add_household(self, people: list, override_person_id: bool = True):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -149,9 +149,9 @@ def add_household(self, people: list, change_id: bool = True):
         ----------
         people : list
             List of :class:`People` to add to household
-        change_id : bool
-            Boolean representing whether we wish to set the id of the people
-            of the household when the function is called or not
+        override_person_id : bool
+            Boolean representing whether we wish to override the id of the
+            people of the household when the function is called or not
 
         """
         if len(people) != 0:
@@ -160,14 +160,14 @@ def add_household(self, people: list, change_id: bool = True):
                 person = people[i]
                 household.add_person(person)
 
-                # If the person already has a household, then do not change
-                # their id
-                if change_id:
-                    if not re.match("^\\d+\\.\\d+\\.\\d+\\.\\d+$", person.id):
-                        person.set_id(household.id + "." + str(i))
-                    else:
-                        logging.info(f"Person {person.id} has moved to "
-                                     f"household {household.id}")
+                if override_person_id:
+                    person.set_id(household.id + "." + str(i))
+                else:
+                    # If the person already has a household, then do not change
+                    # their id
+                    logging.info(f"Person {person.id} has moved to "
+                                 f"household {household.id} but has "
+                                 f"not moved household")
 
         else:
             logging.info("Cannot create an empty household")
diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index bf85760a..c07b32c0 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -94,7 +94,7 @@ def __call__(self, time):
                                     person.household.persons.remove(person)
                                     # Put in new household
                                     person.microcell.add_household([
-                                        person])
+                                        person], override_person_id=False)
                                     person.household.isolation_location = \
                                         True
                                 else:
diff --git a/pyEpiabm/pyEpiabm/routine/file_population_config.py b/pyEpiabm/pyEpiabm/routine/file_population_config.py
index 6e8de039..425b9a40 100644
--- a/pyEpiabm/pyEpiabm/routine/file_population_config.py
+++ b/pyEpiabm/pyEpiabm/routine/file_population_config.py
@@ -207,7 +207,7 @@ def add_households(microcell: Microcell, household_number: int):
                 person_choice = people_list[0]
                 people_list.remove(person_choice)
                 household_people.append(person_choice)
-            microcell.add_household(household_people, change_id=False)
+            microcell.add_household(household_people)
 
     @staticmethod
     @log_exceptions()
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index 0d08cc6c..e172e9e9 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -79,7 +79,8 @@ def test_setup(self, n=5):
 
     def test_add_household(self):
         self.microcell.add_people(1)
-        self.microcell.add_household(self.microcell.persons, change_id=True)
+        self.microcell.add_household(self.microcell.persons,
+                                     override_person_id=True)
         self.assertEqual(len(self.microcell.households), 1)
         original_household = self.microcell.households[0]
         self.assertEqual(len(original_household.persons), 1)
@@ -89,26 +90,25 @@ def test_add_household(self):
 
         # Now add another original_household without changing
         # the id of the person
-        self.microcell.add_household(self.microcell.persons, change_id=False)
+        self.microcell.add_household(self.microcell.persons,
+                                     override_person_id=False)
         self.assertEqual(original_household.persons[0].id,
                          original_household.id + ".0")
 
     @mock.patch('logging.info')
     def test_logging(self, mock_log):
-        self.microcell.add_household(self.microcell.persons, change_id=True)
+        # Check that the logger is called if there are no people in the
+        # household
+        self.microcell.add_household(self.microcell.persons,
+                                     override_person_id=True)
         mock_log.assert_called_once()
 
     @mock.patch('logging.info')
     def test_logging_duplicates(self, mock_log):
-        # Check that if the person already has a household, then we cannot
-        # change their id when they move to a new one
+        # Check that the logger is called if override_person_id is False
         self.microcell.add_people(1)
-        self.microcell.add_household(self.microcell.persons, change_id=True)
-        old_household = self.microcell.households[0]
-        person = self.microcell.persons[0]
-        old_household.persons.remove(person)
-        self.microcell.add_household([person], change_id=True)
-        self.assertEqual(person.id, old_household.id + ".0")
+        self.microcell.add_household(self.microcell.persons,
+                                     override_person_id=False)
         mock_log.assert_called_once()
 
     def test_report(self):
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 912d8fd5..607aa373 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -84,7 +84,8 @@ def test___call__(self, mock_random):
         person_introduced2 = self._microcell.persons[3]
         person_introduced2.set_id("0.0.2.0")
         self._population.travellers.append(person_introduced2)
-        self._microcell.add_household([person_introduced2])
+        self._microcell.add_household([person_introduced2],
+                                      override_person_id=False)
         person_introduced2.travel_end_time = 40
         self.travelisolation(time=21)
         self.assertTrue(person_introduced2.household.isolation_location)

From 3c2f5ce4c235d9fd6c6db796845f1de55b765e8f Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 18:08:47 +0000
Subject: [PATCH 50/53] Added further logging

---
 pyEpiabm/pyEpiabm/core/microcell.py                         | 2 +-
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py          | 6 +++++-
 .../test_unit/test_intervention/test_travel_isolation.py    | 6 ++++--
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 18da5850..14f77177 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -166,7 +166,7 @@ def add_household(self, people: list, override_person_id: bool = True):
                     # their id
                     logging.info(f"Person {person.id} has moved to "
                                  f"household {household.id} but has "
-                                 f"not moved household")
+                                 f"not changed id")
 
         else:
             logging.info("Cannot create an empty household")
diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index c07b32c0..fa36511a 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -1,7 +1,7 @@
 #
 # Travel isolation Class
 #
-
+import logging
 import random
 
 from pyEpiabm.core import Parameters
@@ -75,6 +75,10 @@ def __call__(self, time):
                                     selected_household = random.choice(
                                         existing_households)
                                     selected_household.add_person(person)
+                                    logging.info(f"Person {person.id} has "
+                                                 f"finished isolating and "
+                                                 f"has moved to household "
+                                                 f"{selected_household.id}")
 
                                 else:
                                     person.household.isolation_location = \
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 607aa373..0dc7e8c7 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -29,6 +29,7 @@ def setUp(self) -> None:
         self._microcell.add_people(
             1, status=InfectionStatus.InfectASympt, age_group=5)
         self.person_introduced = self._microcell.persons[2]
+        self.person_introduced.set_id("0.0.0.2")
         self._population.travellers.append(self.person_introduced)
         self._microcell.households[0].add_person(self.person_introduced)
         self.person_introduced.travel_end_time = 25
@@ -58,7 +59,8 @@ def test__init__(self):
                          self.params['hotel_isolate'])
 
     @mock.patch('random.random')
-    def test___call__(self, mock_random):
+    @mock.patch('logging.info')
+    def test___call__(self, mock_log, mock_random):
         mock_random.return_value = 0
         # Before travel isolation starts
         self.assertFalse(hasattr(
@@ -77,7 +79,7 @@ def test___call__(self, mock_random):
         self.assertIsNone(self.person_introduced.travel_isolation_start_time)
         self.assertEqual(len(self._microcell.households), 1)
         self.assertEqual(len(self.person_symp.household.persons), 3)
-
+        mock_log.assert_called()
         # Introduce individual in single household
         self._microcell.add_people(
             1, status=InfectionStatus.InfectASympt, age_group=7)

From 4d13e6ca538df60524b75df0c05e933ea371dde8 Mon Sep 17 00:00:00 2001
From: mghosh00 <133675135+mghosh00@users.noreply.github.com>
Date: Thu, 30 Nov 2023 18:46:52 +0000
Subject: [PATCH 51/53] Update
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py

Co-authored-by: Kit Gallagher <60467371+KCGallagher@users.noreply.github.com>
---
 pyEpiabm/pyEpiabm/intervention/travel_isolation.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index fa36511a..df13db33 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -96,7 +96,8 @@ def __call__(self, time):
                                 if len(person.household.persons) > 1:
                                     # Remove from old household
                                     person.household.persons.remove(person)
-                                    # Put in new household
+                                    # Move to temporary household
+                                    # N.B Person ID is not changed
                                     person.microcell.add_household([
                                         person], override_person_id=False)
                                     person.household.isolation_location = \

From 84d5a46edd3801a1f55c68c4f6e64af33b21bf70 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 19:00:50 +0000
Subject: [PATCH 52/53] Made changes

---
 pyEpiabm/pyEpiabm/core/microcell.py            |  8 ++++----
 .../pyEpiabm/intervention/travel_isolation.py  |  2 +-
 .../test_unit/test_core/test_microcell.py      | 18 +++++++++++-------
 .../test_intervention/test_travel_isolation.py | 11 +++++++++--
 4 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
index 14f77177..8a26c4c5 100644
--- a/pyEpiabm/pyEpiabm/core/microcell.py
+++ b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -141,7 +141,7 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list, override_person_id: bool = True):
+    def add_household(self, people: list, update_person_id: bool = True):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
@@ -149,8 +149,8 @@ def add_household(self, people: list, override_person_id: bool = True):
         ----------
         people : list
             List of :class:`People` to add to household
-        override_person_id : bool
-            Boolean representing whether we wish to override the id of the
+        update_person_id : bool
+            Boolean representing whether we wish to update the id of the
             people of the household when the function is called or not
 
         """
@@ -159,7 +159,7 @@ def add_household(self, people: list, override_person_id: bool = True):
             for i, person in enumerate(people):
                 household.add_person(person)
 
-                if override_person_id:
+                if update_person_id:
                     person.set_id(household.id + "." + str(i))
                 else:
                     # If the person already has a household, then do not change
diff --git a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
index fa36511a..41259c36 100644
--- a/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/intervention/travel_isolation.py
@@ -98,7 +98,7 @@ def __call__(self, time):
                                     person.household.persons.remove(person)
                                     # Put in new household
                                     person.microcell.add_household([
-                                        person], override_person_id=False)
+                                        person], update_person_id=False)
                                     person.household.isolation_location = \
                                         True
                                 else:
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
index e172e9e9..4298d3be 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_core/test_microcell.py
@@ -80,7 +80,7 @@ def test_setup(self, n=5):
     def test_add_household(self):
         self.microcell.add_people(1)
         self.microcell.add_household(self.microcell.persons,
-                                     override_person_id=True)
+                                     update_person_id=True)
         self.assertEqual(len(self.microcell.households), 1)
         original_household = self.microcell.households[0]
         self.assertEqual(len(original_household.persons), 1)
@@ -91,7 +91,7 @@ def test_add_household(self):
         # Now add another original_household without changing
         # the id of the person
         self.microcell.add_household(self.microcell.persons,
-                                     override_person_id=False)
+                                     update_person_id=False)
         self.assertEqual(original_household.persons[0].id,
                          original_household.id + ".0")
 
@@ -100,16 +100,20 @@ def test_logging(self, mock_log):
         # Check that the logger is called if there are no people in the
         # household
         self.microcell.add_household(self.microcell.persons,
-                                     override_person_id=True)
-        mock_log.assert_called_once()
+                                     update_person_id=True)
+        mock_log.assert_called_once_with("Cannot create an empty household")
 
     @mock.patch('logging.info')
     def test_logging_duplicates(self, mock_log):
-        # Check that the logger is called if override_person_id is False
+        # Check that the logger is called if update_person_id is False
         self.microcell.add_people(1)
         self.microcell.add_household(self.microcell.persons,
-                                     override_person_id=False)
-        mock_log.assert_called_once()
+                                     update_person_id=False)
+        person = self.microcell.persons[0]
+        household = self.microcell.households[0]
+        mock_log.assert_called_once_with(f"Person {person.id} has moved to "
+                                         f"household {household.id} but has "
+                                         f"not changed id")
 
     def test_report(self):
         self.microcell.add_people(5)
diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 0dc7e8c7..622e9c8e 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -79,7 +79,14 @@ def test___call__(self, mock_log, mock_random):
         self.assertIsNone(self.person_introduced.travel_isolation_start_time)
         self.assertEqual(len(self._microcell.households), 1)
         self.assertEqual(len(self.person_symp.household.persons), 3)
-        mock_log.assert_called()
+        mock_log.assert_has_calls([mock.call(f"Person 0.0.0.2 has moved to "
+                                             f"household 0.0.1 but has "
+                                             f"not changed id"),
+                                   mock.call(f"Person 0.0.0.2 has "
+                                             f"finished isolating and "
+                                             f"has moved to household "
+                                             f"0.0.0")])
+        self.assertEqual(mock_log.call_count, 2)
         # Introduce individual in single household
         self._microcell.add_people(
             1, status=InfectionStatus.InfectASympt, age_group=7)
@@ -87,7 +94,7 @@ def test___call__(self, mock_log, mock_random):
         person_introduced2.set_id("0.0.2.0")
         self._population.travellers.append(person_introduced2)
         self._microcell.add_household([person_introduced2],
-                                      override_person_id=False)
+                                      update_person_id=False)
         person_introduced2.travel_end_time = 40
         self.travelisolation(time=21)
         self.assertTrue(person_introduced2.household.isolation_location)

From 3edfb19f4032ddfee60a6cd7a24a89bd3e17cd45 Mon Sep 17 00:00:00 2001
From: Matthew Ghosh <matthew.ghosh88@gmail.com>
Date: Thu, 30 Nov 2023 19:04:15 +0000
Subject: [PATCH 53/53] Flake8 fix

---
 .../test_intervention/test_travel_isolation.py     | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
index 622e9c8e..6423a2ea 100644
--- a/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
+++ b/pyEpiabm/pyEpiabm/tests/test_unit/test_intervention/test_travel_isolation.py
@@ -79,13 +79,13 @@ def test___call__(self, mock_log, mock_random):
         self.assertIsNone(self.person_introduced.travel_isolation_start_time)
         self.assertEqual(len(self._microcell.households), 1)
         self.assertEqual(len(self.person_symp.household.persons), 3)
-        mock_log.assert_has_calls([mock.call(f"Person 0.0.0.2 has moved to "
-                                             f"household 0.0.1 but has "
-                                             f"not changed id"),
-                                   mock.call(f"Person 0.0.0.2 has "
-                                             f"finished isolating and "
-                                             f"has moved to household "
-                                             f"0.0.0")])
+        mock_log.assert_has_calls([mock.call("Person 0.0.0.2 has moved to " +
+                                             "household 0.0.1 but has " +
+                                             "not changed id"),
+                                   mock.call("Person 0.0.0.2 has " +
+                                             "finished isolating and " +
+                                             "has moved to household " +
+                                             "0.0.0")])
         self.assertEqual(mock_log.call_count, 2)
         # Introduce individual in single household
         self._microcell.add_people(