Description

Uniovi Simur WearablePerMed Pipeline.

Schaffolding

Execute PyScaffold command to create the project:

$ putup --markdown uniovi-simur-wearablepermed-pipeline -p wearablepermed_pipeline \
     -d "Uniovi Simur WearablePerMed Pipeline." \
     -u https://github.com/SiMuR-UO/uniovi-simur-wearablepermed-pipeline.git 

Create a virtual environment inside for your project and active it:

$ python3 -m venv .venv
$ source .venv/bin/activate

Install and upgrade tox automation project manager:

$ pip install --upgrade tox

Install and upgrade project modules:

$ pip install -U pandas uniovi-simur-wearablepermed-utils

Code and Debugging

Install library modules:

$ pip install -r requirements.txt

Install module locally for debugg

$ pip install -e .

Update project requirements:

$ pip freeze > requirements.txt

If you want upgrade the pipeline library to the last uniovi-simur-wearablepermed-utils you must execute this command (two times):

$ pip install uniovi-simur-wearablepermed-utils --upgrade

Project management

Project commands for: test, clean, build, generate documentation or publish your library in pypi repository. Don't forget update the version library from setup.cfg project build file

$ tox
$ tox -e clean
$ tox -e build
$ tox -e docs
$ tox -e publish -- --repository pypi

Testing

Execute one pipeline from this command:

python3 main.py \
    --verbose \
    --execute-steps 2,3,4,5,6 \
    --dataset-folder /home/miguel/git/uniovi/simur/uniovi-simur-wearablepermed-utils/data/input \
    --participants-missing-file /home/miguel/temp/wearablepermed_pipeline/missing_end_datetimes.csv \
    --crop-columns 1:7 \
    --window-size 250 \
    --window-overlapping-percent 50 \
    --ml-models ESANN,RandomForest \
    --ml-sensors thigh,hip,wrist \
    --output-case-folder /home/miguel/git/uniovi/simur/uniovi-simur-wearablepermed-utils/data/output \
    --case-id case_sample

Note

This project has been set up using PyScaffold 4.6. For details and usage information on PyScaffold see https://pyscaffold.org/.