emrad_analysis
│ README.md
├── emrad_analysis # The core library folder. All project-wide helper and algorithms go here
|
├── experiments # The main folder for all experiements. Each experiment has its own subfolder
| ├── experiment_1 # A single experiment (can be created with `poe experiment experiment_name`)
| | ├── notebooks # All narrative notebooks belonging to the experiment.
| | ├── scripts # Python scripts for this experiment
| | ├── helper # A Python module with experiment specific helper functions
| |
| ├── experiment_2
| ├── ...
|
├── tests # Unit tests for the `emrad_analysis` library
|
├── data # The main data folder. This is ignored in the `.gitignore` by default.
|
| pyproject.toml # The required python dependencies for the project
| poetry.lock # The frozen python dependencies to reproduce exact results
|
This project was created using the mad-cookiecutter ds-base template.
To work with the project you need to install:
- poetry
- poethepoet in your global python env (
pip install poethepoet)
Afterwards run:
poetry install
Then you can create a new experiment using:
poe experiment experiment_name
All dependencies are manged using poetry.
Poetry will automatically create a new venv for the project, when you run poetry install.
Check out the documentation on how to add and remove dependencies.
To use jupyter notebooks with the project you need to add a jupyter kernel pointing to the venv of the project. This can be done by running:
poe conf_jupyter
Afterwards a new kernel called emrad_analysis should be available in the jupyter lab / jupyter notebook interface.
Use that kernel for all notebooks related to this project.
All jupyter notebooks should go into the notebooks subfolder of the respective experiment.
To make best use of the folder structure, the parent folder of each notebook should be added to the import path.
This can be done by adding the following lines to your first notebook cell:
# Optional: Auto reloads the helper and the main emrad_analysis module
%load_ext autoreload
%autoreload 2
from emrad_analysis import conf_rel_path
conf_rel_path()This allows to then import the helper and the script module belonging to a specific experiment as follows:
import helper
# or
from helper import ...
To ensure consistent code structure this project uses prospector, black, and ruff to automatically check (and fix) the code format.
poe format # runs black and ruff with the autofix flag
poe lint # runs ruff without autofix (will show issues that can not automatically be fixed)
If you want to check if all code follows the code guidelines, run poe ci_check.
This can be useful in the CI context
All tests are located in the tests folder and can be executed by using poe test.