Merge pull request #270 from SABS-R3-Epidemiology/kcgallagher-bugfix-…

…default-workflows-268

Kcgallagher bugfix default workflows 268

.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

.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

.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

.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

.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

.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

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")
 

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")
 

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")
 

pyEpiabm/pyEpiabm/core/person.py

@@ -250,7 +250,7 @@ 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)")

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()

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')
 

pyEpiabm/pyEpiabm/tests/test_unit/test_routine/test_simulation.py

@@ -83,7 +83,7 @@ def test_configure(self, mock_mkdir):
             del test_sim.ih_status_writer
             del test_sim.ih_infectiousness_writer
             del test_sim.secondary_infections_writer
-        mo.assert_called_with(filename, 'w')
+        mo.assert_called_with(filename, 'w', newline='')
 
     @patch('os.makedirs')
     @patch('logging.warning')
@@ -132,7 +132,7 @@ def test_configure_ih_status(self, mock_mkdir):
             del test_sim.ih_status_writer
             del test_sim.ih_infectiousness_writer
             del test_sim.secondary_infections_writer
-        mo.assert_called_with(filename, 'w')
+        mo.assert_called_with(filename, 'w', newline='')
 
     @patch('os.makedirs')
     def test_configure_ih_infectiousness(self, mock_mkdir):
@@ -161,7 +161,7 @@ def test_configure_ih_infectiousness(self, mock_mkdir):
             del test_sim.ih_status_writer
             del test_sim.ih_infectiousness_writer
             del test_sim.secondary_infections_writer
-        mo.assert_called_with(filename, 'w')
+        mo.assert_called_with(filename, 'w', newline='')
 
     @patch('os.makedirs')
     def test_configure_secondary_infections(self, mock_mkdir):
@@ -191,7 +191,7 @@ def test_configure_secondary_infections(self, mock_mkdir):
             del test_sim.ih_status_writer
             del test_sim.ih_infectiousness_writer
             del test_sim.secondary_infections_writer
-        mo.assert_called_with(filename, 'w')
+        mo.assert_called_with(filename, 'w', newline='')
 
     @patch('logging.exception')
     @patch('os.path.join')

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()

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]
     }
 }

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]
     }
 }

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]
     }
 }

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). An [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.gif](./spatial_example/spatial_outputs/voronoi_animation.gif)
 
 ## Age Stratified Simulation
 

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]
     }
 }

python_examples/basic_simulation/simulation_flow.py

@@ -25,7 +25,7 @@
 # Pop_params are used to configure the population structure being used in this
 # simulation.
 
-pop_params = {"population_size": 100, "cell_number": 1,
+pop_params = {"population_size": 1000, "cell_number": 1,
               "microcell_number": 1, "household_number": 5,
               "place_number": 2}