UNMAINTAINED

READ THE COMPLETE FILE BEFORE INSTALLATION. AT LEAST READ THE CAUTION SECTION THOROUGHLY

Installation:

INSTALLATION SHOULD HAPPEN LOCALLY FOR THE USER. DO NOT PROVIDE ROOT/ADMINISTRATIVE PRIVILEGES (OTHER THAN PYTHON INSTALLATION)

Windows 10

Recommended:

Use pip method as described below.

Else, if you really insist on a Windows EXE,

Download and extract git repository. Navigate to working directory

Run file PathPandem.exe.

This executable file cannot be copied to any another location, as its dependencies are packed in the same folder.

Linux

Recommended:

Use pip method as described below.

Else,

Use generic method

Generic: From the source-code

1. Download and unzip the git repository.
   • Using git.

git clone https://github.com/pradyparanjpe/PathPandem

2. Confirm pre-requisites.
3. In Command Line/Shell, navigate to the repository folder and run

python bin/PathPandem

Pre-requisites for running from the source-code:

1. Python3.6 or higher
2. Numpy >= 1.18
3. Matplotlib >= 3.2.1
4. Gooey >= 1.0.3

1 can be installed from official source; further, 2, 3, 4 can be installed by command pip install <module>.

pip

1. Install python3 from official website
   • For Windows, enable "Add to PATH environment variable" during installation. (Recommended) install from Windows Store.
   • This may require Root/Administrative privileges.
2. Install PathPandem by typing in CommandPrompt/ Shell:

pip install --user PathPandem

3. Run by typing in CommandPrompt/ Shell:

python -m "PathPandem"

On Unix-like systems, the file bin/PathPandem is executable.

Uninstallation

If installed by pip

1. In CommandPrompt/Shell, type

pip uninstall PathPandem

2. If not needed, remove python [like any regular program]

If installed by cloning git repo:

1. Delete repository folder
2. If not needed, remove python [like any regular program]

If Windows 10 folder was downloaded

1. Delete folder

Updates:

If installed by pip

1. In CommandPrompt/Shell, type

pip install --upgrade PathPandem

If installed by cloning git repo:

1. In CommandPrompt/Shell, navigate inside the repo folder
2. Type

git pull

If Windows 10 folder was downloaded

1. Consider the option of deleting the folder and installation via pip or git
2. If you still insist on EXE, delete the previous folder and download updated folder from git repository.

Back-up files before deleting the previous version. Recurrent downloads may consume a lot of Internet-Data.

Known Issues:

1. Python2's end-of-life was 2019-12-31.
   • If python means python2 on an operating system, most commonly due to an earlier-installed python2, try migrating to python3 (recommended), or if you understand what you are doing, install python3 alongside and run all commands with explicit mention of python3: python3, pip3, etc.
2. wxPython currently fails installation via pip, [at least] on Linux.
   • Install it using a package-manager (dnf, pacman, apt[, brew, chocolate,] etc) or manually before pip tries to install Gooey`.

Plot Legend:

Background Colour:

Movements

• Green: No restrictions on movement.
• Red: Lockdown Imposed.

Medical Progress

• Blue: Drug discovered.
• Cyan: Vaccine discovered.

Combinations

• Grey: Red + Cyan.
• Magenta: Red + Blue.
• (Any other standard RGB combinations).

Caution:

1. Population more than 10000 may stall the system.
2. Tested only on Linux running from source-code.
3. True numbers are plotted. However in reality, infection manifests symptoms after an initial lag of 1-3 days and test results appear further later by 1-2 days. Hence, graph trends need be imagined as having shifted suitably.
4. Visualization is recommended only with very small population size.
5. Although Infection may appear to exhaust in small sized, limited population; in reality, due to birth of new individuals, and in a very large population, the pathogen persists around at extemely low density.
6. With small population size, random fluctuations become impactful. Multiple runs with same parameters are recommended.

Composition of scenario:

• The GUI only edits the blanket population behaviour.
• A heterogenous population can be composed using basic Python scripting in the spread_simul.py to construct heterogenously behaving population.

TODO:

• Replace unimodal movement of people around their home to bimodal movement between home and workplace.
• Parallelize numpy matrix ufuncs if possible.
• Include asymptomatic patients/carriers. Limit movement of serious cases [although this won't have a visible effect for diseases with majority of cases being mild].
• Animation, saved as mp4 for review

Brief epidemiological explanation:

• Herd immunity starts reducing viral presence in community after viral steady state. i.e. plot of Active patients flattens. This happens when [1 - (1/R_{0})] fraction of the community becomes resistant. (Through vaccination or exposure)
• Medicine development is fairly a rare event given the rightful stringency involved in testing.