cellpy cookies

Cookiecutter templates that set up the folder structure and the Jupyter notebooks for a cellpy session, so you do not have to build them from scratch every time.

Templates

Template	Requires cellpy	Purpose
standard	>= 2.1	The main template: a batch experiment split over notebooks for loading, life, cycles, ICA and plots. Start here.
single	>= 2.1	One cell, one notebook, written for quarto rendering (html / docx).
ife	>= 2.1	standard plus IFE extras: an interactive panel app for tweaking dQ/dV parameters and a HoloViews pickle workflow in the plots notebook. Needs panel, holoviews and hvplot in addition to cellpy.
standard_1_x	1.x only	The standard template frozen at its cellpy 1.x state. Use it if you cannot upgrade yet.
ife_1_x	1.x only	The ife template frozen at its cellpy 1.x state.
standard_1_0_0	1.0.0 only	Older frozen variant, kept for reproducing old sessions.

The templates check your installed cellpy version in a pre_gen_project hook and refuse to generate if it does not match, so you cannot accidentally create 1.x notebooks against cellpy 2 (or the other way around). The hook can only abort - it cannot redirect you - so pick the right template yourself.

Creating a session

Through cellpy (it fetches the templates from GitHub for you):

cellpy new --list                 # see the available templates
cellpy new --template standard

Or with cookiecutter directly:

cookiecutter gh:jepegit/cellpy_cookies --directory standard

Both ask for the project name, session id, author and so on.

cellpy new only knows the three live templates (standard, ife, single) - they are the ones registered in cellpy.utils.template_registry. The frozen 1.x templates are reachable through cookiecutter only:

cookiecutter gh:jepegit/cellpy_cookies --directory standard_1_x
cookiecutter gh:jepegit/cellpy_cookies --directory ife_1_x
cookiecutter gh:jepegit/cellpy_cookies --directory standard_1_0_0

What you get

cellpy_project/
└── 2026_01_01_experiment_001
    ├── cellpy_batch_experiment_001.json   (written when you run the loader notebook)
    ├── data
    │   ├── external
    │   ├── interim
    │   ├── processed
    │   └── raw
    ├── out
    │   └── note.md
    ├── 00_experiment_001_notes.ipynb
    ├── 01_experiment_001_loader.ipynb
    ├── 02_experiment_001_life.ipynb
    ├── 03_experiment_001_cycles.ipynb
    ├── 04_experiment_001_ica.ipynb
    └── 05_experiment_001_plots.ipynb

Run the notebooks in order. 01_..._loader builds the journal (batch.load) and saves it in the experiment folder; the other notebooks pick it up from there with allow_from_journal=True. The single template gives you one notebook instead.

Notes

• Remember to save your notebooks.
• The 02 - 04 notebooks use cellpy.collect (summary_collector, cycles_collector, ica_collector); collection.save("out") writes the collected frames, collection.plot() draws them.
• Loading from a lab database (the batch_col / Batch.from_db path) only works where that database is reachable; everything else runs off the journal and the cellpy-files.