First Time Program and Python Setup on Windows:

Open Windows terminal

Type "python" to open up the microsoft store and click the "Get" button on the Python page to install Python for terminal usage

Go to the directory that contains the OURE simulation (Refer to the Windows section of the startup guide if you do not know the commands for navigating directories inside of terminal)

Type "python3 wormpop.py --parameters=constants.json" to attempt to run the program

You should then be told by the terminal that you lack some of the modules used in the simulation

Use the command "pip3 install NameOfTheModule" to install the module needed through terminal. Repeat this process until the terminal stops telling you that you are missing a module

Once all of the modules it asks for are installed using the above method, the program should be able to run on your profile

---

How to install and use the sqlitebrowser to make the database easily viewable:

    Go to the url "https://sqlitebrowser.org/dl/"

    Click on the download link under the Windows portion called "DB Browser for SQLite - Standard installer for 64-bit Windows"

    Go through the installation process

    Open the program once it is installed and click the "Open Database" option on the interface

    Navigate to the file that contains the database for the simulation and open it

    The database should now be viewable in an organized fashion

---

Windows:

Press the Windows key.

Type "cmd" or "PowerShell" and press Enter to open the Command Prompt or PowerShell.

Use the ‘cd’ command to navigate to the directory where your wormpop.py script is located. For example, if your script is in C:\Example\Directory\Path, you can use the following commands in Command Prompt:

    To move through all directory paths at once:

        cd Example\Directory\Path

    To move through one directory at a time:

        cd Example

        cd Directory

        cd Path

   (You can also look inside the directory you are currently in to see what is inside it and what the next directory path you have to navigate to is called with the "ls" or "dir" command)

   If you wish to go back a directory:

       cd ..

You can use a text editor like Notepad or a code editor like Visual Studio Code to open wormpop.py. For example, to open it with Notepad, you can run the following command in Command Prompt:

        notepad wormpop.py  

        (Remember: you cannot run a simulation on notepad)

To run the simulation on a python file, you need to run the following command in Command prompt:

        python3 wormpop.py 

        or

        py wormpop.py

End the simulation:

    Press “Ctrl + C” to stop the simulation

---

Linux:

Open the Linux terminal

To move through all directory paths at once: 

    cd Example\Directory\Path

To move through one directory at a time:

    cd Example

    cd Directory

    cd Path

(You can also look inside the directory you are currently in to see what is inside it and what the next directory path you have to navigate to is called with the "ls" command)

If you wish to go back a directory

    cd ..

Open wormpop.py

    nano wormpop.py

Please refer to the "How to use the constants.json commandline argument for the simulation" section of the guide for simulation constant modification.

    Make sure to note the original values of the constants before changing them so that they can be changed back later.

Exit the code and save any changes.

    Ctrl + X | When asked "Save modified buffer" hit Y for yes or N for no

Run the simulation

    python3 wormpop.py

If you wish to cancel the simulation early

    Ctrl + Z

---

How to use the constants.json commandline argument for the simulation:

python3 wormpop.py --parameters=constants.json

OR

python3 wormpop.py < constants.json

    All simulation parameters are set to the defaults in constants.json

Full commandline argument

    python3 wormpop.py [--parameters=<string>] [--database=<string>] [--name=<string>] [--directory=<string>]

        --database specifies the name of the SQLITE database to use. By default, this is :memory:, so it writes to a in memory sqlite3 database

        --name allows you to store the name of the simulation run. By default the value is "Simulation". The name is stored in the sqlite3 database. This is used mostly for metadata purposes

        --directory specifies the output of the TSV file

To modify constant values in the constants.json file (Take note of which constants you modify and their original values so that you can change them back after you are finished running the modified simulation):

    Windows:

        notepad constants.json

        Modify any constant values you wish to have ran differently in the simulation

        Ctrl + S to save the modified code

    Linux:

        nano constants.json

        Modify any constant values you wish to have ran differently in the simulation

        Close the modified file with Ctrl + X | When asked "Save modified buffer" hit Y for yes or N for no