Merge branch 'main' into secondary-infections

SABS-R3-Epidemiology · Nov 26, 2024 · bd91057 · bd91057
2 parents 939c9a6 + 1cc1fb9
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diff --git a/.github/workflows/coverage-test.yml b/.github/workflows/coverage-test.yml
@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.11'
           architecture: x64
 
       - name: install pyEpiabm

diff --git a/.github/workflows/doc-tests.yml b/.github/workflows/doc-tests.yml
@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python '3.11'
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.11'
           architecture: x64
 
       - name: install pyEpiabm
@@ -33,3 +33,14 @@ jobs:
         run: |
           cd pyEpiabm
           python run_tests.py --docs
+
+  Validate-CITATION-cff:
+    name: Validate CITATION.cff
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3
diff --git a/.github/workflows/func-tests.yml b/.github/workflows/func-tests.yml
@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.11'
           architecture: x64
 
       - name: install pyEpiabm

diff --git a/.github/workflows/os-tests.yml b/.github/workflows/os-tests.yml
@@ -17,12 +17,12 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.11'
           architecture: x64
 
       - name: install pyEpiabm

diff --git a/.github/workflows/style-test.yml b/.github/workflows/style-test.yml
@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.11'
           architecture: x64
 
       - name: install pyEpiabm

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -14,13 +14,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           architecture: x64

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,13 +1,11 @@
-# CITATION.cff file for Epiabm, generated with cffinit.
+# This CITATION.cff file was generated with cffinit.
 
-cff-version: 1.1.0
+cff-version: 1.2.0
 title: Epiabm
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
+message: "Please cite this software using the metadata from 'preferred-citation'."
 type: software
 authors:
-  - given-names: 'Kit '
+  - given-names: Kit
     family-names: Gallagher
     email: [email protected]
     affiliation: 'Mathematical Institute, University of Oxford'
@@ -21,6 +19,9 @@ authors:
   - given-names: Nathan
     family-names: Schofield
     affiliation: 'Mathematical Institute, University of Oxford'
+  - given-names: Matthew
+    family-names: Ghosh
+    affiliation: 'Doctoral Training Centre, University of Oxford'
   - given-names: Henriette
     family-names: Capel
     affiliation: 'Department of Statistics, University of Oxford'
@@ -33,6 +34,9 @@ authors:
   - given-names: Jiayuan
     family-names: Zhu
     affiliation: 'Department of Engineering, University of Oxford'
+  - given-names: Abbie
+    family-names: Evans
+    affiliation: 'Doctoral Training Centre, University of Oxford'
   - given-names: Patricia
     family-names: Lamirande
     affiliation: 'Mathematical Institute, University of Oxford'
@@ -41,13 +45,13 @@ authors:
     affiliation: 'Department of Computer Science, University of Oxford'
   - given-names: Richard
     family-names: Creswell
-    affiliation: 'Department of Engineering, University of Oxford'
+    affiliation: 'Department of Computer Science, University of Oxford'
   - given-names: Isaac
     family-names: Ellmen
     affiliation: 'Department of Statistics, University of Oxford'
   - given-names: Pietro
     family-names: Monticone
-    affiliation: 'University of Turin'
+    affiliation: University of Turin
 identifiers:
   - type: doi
     value: 10.5281/zenodo.7327443
@@ -63,5 +67,37 @@ keywords:
   - Agent-Based Modelling
   - Epidemiology
 license: BSD-3-Clause
-version: 1.1.0
-date-released: '2023-10-17'
+version: 1.2.0
+date-released: '2024-08-06'
+
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Kit
+    family-names: Gallagher
+    orcid: 'https://orcid.org/0000-0003-1401-115X'
+  - given-names: Ioana
+    family-names: Bouros
+  - given-names: Nicholas
+    family-names: Fan
+  - given-names: Elizabeth
+    family-names: Hayman
+  - given-names: Luke
+    family-names: Heirene
+  - given-names: Patricia
+    family-names: Lamirande
+  - given-names: Annabelle
+    family-names: "Lemenuel-Diot"
+  - given-names: Ben
+    family-names: Lambert
+  - given-names: David
+    family-names: Gavaghan    
+  - given-names: Richard
+    family-names: Creswell
+  doi: "10.5334/jors.449"
+  journal: "Journal of Open Research Software"
+  month: 3
+  title: "Epidemiological Agent-Based Modelling Software (Epiabm)"
+  issue: 1
+  volume: 12
+  year: 2024
diff --git a/pyEpiabm/pyEpiabm/core/cell.py b/pyEpiabm/pyEpiabm/core/cell.py
@@ -87,7 +87,7 @@ def set_id(self, id: str, cells: typing.List):
             raise TypeError("Provided id must be a string")
 
         # This regex will match on any string which has 1 or more digits
-        if not re.match("^\\d+$", id):
+        if not re.match("^-?\\d+$", id):
             raise ValueError(f"Invalid id: {id}. id must be of the form 'i' "
                              f"where i is an integer")
 

diff --git a/pyEpiabm/pyEpiabm/core/household.py b/pyEpiabm/pyEpiabm/core/household.py
@@ -126,7 +126,7 @@ def set_id(self, id: str):
 
         # 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+$", id):
+        if not re.match("^-?\\d+\\.-?\\d+\\.-?\\d+$", id):
             raise ValueError(f"Invalid id: {id}. id must be of the form "
                              f"'i.j.k' where i, j, k are integers")
 

diff --git a/pyEpiabm/pyEpiabm/core/microcell.py b/pyEpiabm/pyEpiabm/core/microcell.py
@@ -72,7 +72,7 @@ def set_id(self, id):
 
         # 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+$", id):
+        if not re.match("^-?\\d+\\.-?\\d+$", id):
             raise ValueError(f"Invalid id: {id}. id must be of the form 'i.j' "
                              f"where i, j are integers")
 

diff --git a/pyEpiabm/pyEpiabm/core/person.py b/pyEpiabm/pyEpiabm/core/person.py
@@ -252,7 +252,7 @@ def set_id(self, id: str):
 
         # 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+$", id):
+        if not re.match("^-?\\d+\\.-?\\d+\\.-?\\d*\\.-?\\d+$", 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)")

diff --git a/pyEpiabm/pyEpiabm/output/_csv_dict_writer.py b/pyEpiabm/pyEpiabm/output/_csv_dict_writer.py
@@ -36,7 +36,7 @@ def __init__(self, folder: str, filename: str, fieldnames: typing.List,
             folder, os.path.splitext(filename)[0])
         self.fieldnames = fieldnames
 
-        self.f = open(os.path.join(folder, filename), 'w')
+        self.f = open(os.path.join(folder, filename), 'w', newline='')
         self.writer = csv.DictWriter(
             self.f, fieldnames=fieldnames, delimiter=',')
         self.writer.writeheader()

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_output/test_csv_dict_writer.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_output/test_csv_dict_writer.py
@@ -20,7 +20,7 @@ def test_init(self, mock_mkdir):
                                          mock_categories)
             del m
         mo.assert_called_once_with(
-            os.path.join('mock_folder', 'mock_filename'), 'w')
+            os.path.join('mock_folder', 'mock_filename'), 'w', newline='')
         mo().write.assert_called_once_with('Cat1,Cat2,Cat3\r\n')
         mock_mkdir.assert_called_with('mock_folder')
 

diff --git a/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_demographics_sweep.py b/pyEpiabm/pyEpiabm/tests/test_unit/test_sweep/test_initial_demographics_sweep.py
@@ -1,4 +1,5 @@
 import os
+import unittest
 from unittest.mock import patch, mock_open, call
 
 import pyEpiabm as pe
@@ -87,8 +88,8 @@ def test_construct(self, mock_mkdir):
                                                       "Age group 0"])
             del dem_sweep.writer
             del dem_sweep.counts_writer
-        mo.assert_has_calls([call(file_name, 'w'),
-                             call(counts_file_name, 'w')],
+        mo.assert_has_calls([call(file_name, 'w', newline=''),
+                             call(counts_file_name, 'w', newline='')],
                             any_order=True)
 
     @patch('os.makedirs')
@@ -115,8 +116,8 @@ def test_construct_age_spatial(self, mock_mkdir):
                              [f"Age group {i}" for i in range(17)])
             del dem_sweep.writer
             del dem_sweep.counts_writer
-        mo.assert_has_calls([call(file_name, 'w'),
-                             call(counts_file_name, 'w')],
+        mo.assert_has_calls([call(file_name, 'w', newline=''),
+                             call(counts_file_name, 'w', newline='')],
                             any_order=True)
 
     @patch('os.makedirs')
@@ -253,3 +254,7 @@ def test_write_to_file_age_spatial(self, mock_mkdir):
         mock_mkdir.assert_called_with(os.path.join(os.getcwd(),
                                                    self.dem_file_params[
                                                        "output_dir"]))
+
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/python_examples/NZ_example/NewZealand_noInt_parameters.json b/python_examples/NZ_example/NewZealand_noInt_parameters.json
@@ -448,5 +448,14 @@
         "constant_introduce_cases": [0],
         "duration_travel_stay": [2, 14],
         "prob_existing_household": 0.8
+    },
+    "use_waning_immunity": 0,
+    "rate_multiplier_params": {
+        "gp_to_hosp": [0, 1],
+        "gp_to_death": [0, 1],
+        "exposed_to_infect": [0, 1],
+        "hosp_to_death": [0, 1],
+        "hosp_to_icu": [0, 1],
+        "icu_to_death": [0, 1]
     }
 }
diff --git a/python_examples/NZ_example/NewZealand_parameters.json b/python_examples/NZ_example/NewZealand_parameters.json
@@ -511,5 +511,14 @@
             "isolation_effectiveness": 0.1,
             "isolation_house_effectiveness": 0.5
         }
+    },
+    "use_waning_immunity": 0,
+    "rate_multiplier_params": {
+        "gp_to_hosp": [0, 1],
+        "gp_to_death": [0, 1],
+        "exposed_to_infect": [0, 1],
+        "hosp_to_death": [0, 1],
+        "hosp_to_icu": [0, 1],
+        "icu_to_death": [0, 1]
     }
 }
diff --git a/python_examples/NZ_example/NewZealand_parameters_relaxed.json b/python_examples/NZ_example/NewZealand_parameters_relaxed.json
@@ -511,5 +511,14 @@
             "isolation_effectiveness": 0.1,
             "isolation_house_effectiveness": 0.5
         }
+    },
+    "use_waning_immunity": 0,
+    "rate_multiplier_params": {
+        "gp_to_hosp": [0, 1],
+        "gp_to_death": [0, 1],
+        "exposed_to_infect": [0, 1],
+        "hosp_to_death": [0, 1],
+        "hosp_to_icu": [0, 1],
+        "icu_to_death": [0, 1]
     }
 }
diff --git a/python_examples/README.md b/python_examples/README.md
@@ -8,7 +8,7 @@ This script outlines all commands necessary to run a basic simulation. It models
 
 It subsequently saves the results to a .csv file, and plots a basic SIR plot of the simulation output, depicted below:
 
-![SIR plot from simulation_flow.pt](./basic_example/simulation_outputs/simulation_flow_SIR_plot.png)
+![SIR plot from simulation_flow.pt](./basic_simulation/simulation_outputs/simulation_flow_SIR_plot.png)
 
 ## Basic Infection History Simulation
 
@@ -20,15 +20,15 @@ These .csv files are then used in the repository https://github.com/SABS-R3-Epid
 
 ## Spatial Simulations
 
-Contained within the `spatial_example/` directory, this script runs a basic simulation with spatial dependance. It considers a population of 1000 individuals, spread across 40 households in 20 cells, each with a single microcell.
+Contained within the `spatial_example/` directory, this script runs a basic simulation with spatial dependance. It considers a population of 10000 individuals, spread across 225 cells, each with a two microcells.
 
-It subsequently saves the results to a .csv file, and plots the infection curve for each region. There is currently no differentiation between cells, and so any variation is due to random fluctuations. Any null curves are because there were no infectious individuals seeded in that cell, and no inter-cellular infection mechanisms are currently implemented.
+It subsequently saves the results to a .csv file, and plots the infection curve for each region. There is currently no differentiation between cells, and so any variation is due to random fluctuations. 
 
 ![Infection curves for multiple cells.pt](./spatial_example/spatial_outputs/spatial_flow_Icurve_plot.png)
 
-We also provide a script (`voronoi_plotting_example.py`) for visualising the spatial distribution of the epidemic, generating cells based on a single location coordinate using [Voronoi Tesselation](https://en.wikipedia.org/wiki/Voronoi_diagram).
+We also provide a script (`voronoi_plotting_example.py`) for visualising the spatial distribution of the epidemic, generating cells based on a single location coordinate using [Voronoi Tesselation](https://en.wikipedia.org/wiki/Voronoi_diagram). A [grid version](./spatial_example/spatial_outputs/voronoi_grid_img.png) of this plot is also generated.
 
-![Voronoi_grid.pt](./spatial_example/spatial_outputs/voronoi_grid_img.png)
+![Voronoi grid](./spatial_example/spatial_outputs/voronoi_animation.gif)
 
 ## Age Stratified Simulation
 

diff --git a/python_examples/basic_simulation/simple_parameters.json b/python_examples/basic_simulation/simple_parameters.json
@@ -21,6 +21,7 @@
     "false_positive_rate": 0,
     "place_transmission": 0.1,
     "use_ages": 0,
+    "use_waning_immunity": 0,
     "note1": "Mainly change values above this",
     "age_contact": [0.6, 0.7, 0.75, 1, 1, 1, 1, 1,
         1, 1, 1, 1, 1, 1, 1, 0.75, 0.5],
@@ -403,5 +404,13 @@
                                 0.47651, 0.47651, 0.47651, 0.47651,
                                 0.47651, 0.47651, 0.47651, 0.47651,
                                 0.47651]
+    },
+    "rate_multiplier_params": {
+        "gp_to_hosp": [0, 1],
+        "gp_to_death": [0, 1],
+        "exposed_to_infect": [0, 1],
+        "hosp_to_death": [0, 1],
+        "hosp_to_icu": [0, 1],
+        "icu_to_death": [0, 1]
     }
 }