Package for plotting Creoptix sensograms

Installation

The following assumes installation on a NoMachine VM:

1. [only necessary first time] Install uv (a Python package and virtual environment manager):
   curl -LsSf https://astral.sh/uv/install.sh | sh

2. [only necessary first time or when code is updated] Pull the latest copy of Creoptix_Fitting from the GitHub:
   https://github.com/oxpig/Creoptix_Fitting

   • If doing this by downloading a ZIP, extract the code to the appropriate directory on the NoMachine (should be something like
     /users/<username>/Creoptix_Fitting-main/)

The following steps need to be run within the directory (folder) where Creoptix_Fitting is located, i.e. the folder containing the pyproject.toml file.

3. [only necessary first time or when code is updated] Ensure uv has synchronised (updated) any dependencies required by the Creoptix_Fitting package, which might change with a code update, by running
   uv sync
   • If uv complains about the name of the LICENCE file, copy it to LICENSE as well (e.g. cp LICENCE LICENSE or use the file browser and right-click menus to copy).
4. Run the Jupyter notebook server within this environment
   uv run --with jupyter jupyter lab
5. Within the Jupyter notebook server interface (should open in browser window after previous step), open
   Creoptix_Fitting-main/creoptix_plotting.ipynb
6. Change file paths/names within the creoptix_plotting.ipynb notebook as appropriate, remembering that NoMachine works as if a Linux host, not Windows, so does not understand the meaning of e.g. the V: drive -- e.g. if a Creoptix project file to be analysed is in V://<username>/20260202 on Windows, then the path must be given in the notebook as /users/<username>/20260202. If confused, navigate to the appropriate folder within NoMachine to confirm and copy the path from the file browser there.

Known Issues

• A Creoptix project with no data in any of the 3 active channels (FC2, FC3 or FC4) will have no valid blank cycle for blank corrections as the blank cycle for the missing channel(s) will most likely be rejected (rejecting of 3 blanks for all channels for a given cycle)