cir4mics 0.1.1

Simulating structurally variable NPCs or other ring-like structures for Microscopy

Requirements

• python, pip, git https://pip.pypa.io/en/stable/installation/

Linux, macOS

Open a terminal where you want to install the project

Windows

Recommended Windows command line shells are Windows powershell or cmd.exe. Alternatively use Windows Subsystem for Linux (WSL).

Intallation

Open a terminal of choice
Clone this repository:
Tip: Copy/paste commands to avoid typos
git clone https://github.com/MariaTheiss/cir4mics.git

Change to the directory folder:
cd cir4mics

Install poetry

pip install poetry

or following: https://python-poetry.org/docs/

Usage

From the same directory as before

Open a poetry shell

Create or start a virtual environment. Packages installed here will be isolated from the rest of the system, avoiding unfavourable crosstalk.
poetry shell
The name of the virtual environment should now be indicated in round brackets to the left of the command line prompt.

Install dependencies

Dependencies are installed according to pyproject.toml and poetry.lock
poetry install

Run the tutorial

jupyter-lab cir4mics/NPC_testlab.ipynb

Everything is properly configured if the tutorial runs to the end.
The tutorial can be modified for any specific task.

Run minimal script

• Start an IDE of your choice
• Load cir4mics/cir4mics/call_functions.py

Run without IDE

If you are already aware of what's in call_functions.py, and if it doesn't require modification.

poetry run python cir4mics/call_functions.py

To exit poetry shell

exit

Troubleshoothing

Windows: Git Bash struggles to open poetry shell
Solution: Use Powershell, cmd.exe, or WSL
see: https://github.com/python-poetry/poetry/issues/6495

Windows: poetry install is unable to install debugpy
Solution: run poetry config installer.modern-installation false
see: https://github.com/microsoft/debugpy/issues/1246

Windows: powershell does not execute poetry shell and returns <filepath> cannot be loaded because running scripts is disabled on this system error
Solution:

1. Open the powershell as administrator
2. Run Set-ExecutionPolicy RemoteSigned
   See: https://www.sharepointdiary.com/2014/03/fix-for-powershell-script-cannot-be-loaded-because-running-scripts-is-disabled-on-this-system.html

Windows: Issues with Microsoft C++ Build Tools (https://visualstudio.microsoft.com/visual-cpp-build-tools/):
Solution: Use at most version 3.10

Windows: Powershell upon running poetry shell returns Virtual environment already activated. Solution: Restart the computer See: https://visualstudio.microsoft.com/visual-cpp-build-tools/

Tutorials

Simulating NPCs:

jupyter-lab cir4mics/NPC_testlab.ipynb

Including new models into the simulator

jupyter-lab cir4mics/Include_models.ipynb

Dynamics

Dynamics do not reflect true NPC dynamics, but might be useful when hard to predict dynamics are of interest

jupyter-lab cir4mics/Dynamics.ipynb

Contact

[e-mail]