Skip to main content

Biobb_Radiospineomics is a wrapped code for the extraction of conventional IVD features and radiomics from T2-weighted MRI

Project description

biobb_template

Introduction

Biobb_template is a complete code template to promote and facilitate the creation of new Biobbs by the community. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v4.1.0 2023.4

Installation

If you have no experience with anaconda, please first take a look to the New with anaconda? section of the official documentation.

Download repository

Although the biobb_template repository is available at GitHub and thus you can clone it, we strongly recommend you to download it compressed and start your new project from scratch.

Create new conda environment

Once you have the project unzipped in your computer, please follow the next steps to create a new conda environment:

cd biobb_template-master
conda env create -f conda_env/environment.yml

Update environment paths

Edit conda_env/biobb_template.pth with the paths to your biobb_template folder. Example:

/home/user_name/projects/biobb_template/
/home/user_name/projects/biobb_template/biobb_template/biobb_template

Copy the edited conda_env/biobb_template.pth file to the site-packages folder of your environment. This folder is in /[anaconda-path]/envs/biobb_template/lib/python3.7/site-packages, where /[anaconda-path] is usually /anaconda3 or /opt/conda.

cp conda_env/biobb_template.pth /[anaconda-path]/envs/biobb_template/lib/python3.7/site-packages

Activate environment

Then, activate the recently created biobb_template conda environment:

conda activate biobb_template

Create repository

This template includes some folders not standard for a biobb, such as biobb_template/adapters/, biobb_template/notebooks/ or conda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the .gitignore file before creating a new git repository:

biobb_template/adapters
biobb_template/notebooks
conda_env

Then, inialitize repository:

git init

Binary paths configuration

Additionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in the Binary path configuration section of the official documentation.

Run tests

To run tests, please execute the following instruction:

pytest /path/to/biobb_template/biobb_template/test/unitests/test_template/test_template.py

Or, if you prefer to show the BioBB output during the test process:

pytest -s /path/to/biobb_template/biobb_template/test/unitests/test_template/test_template.py

Documentation

Click here to find the API Documentation example for this template and here for Command Line documentation.

And here you can find the full documentation about how to build a new BioExcel building block from scratch.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

biobb_radiospineomics-1.1.20.tar.gz (21.7 kB view details)

Uploaded Source

Built Distribution

biobb_radiospineomics-1.1.20-py3-none-any.whl (27.4 kB view details)

Uploaded Python 3

File details

Details for the file biobb_radiospineomics-1.1.20.tar.gz.

File metadata

File hashes

Hashes for biobb_radiospineomics-1.1.20.tar.gz
Algorithm Hash digest
SHA256 1333b4fa4a9928b1b30cc3209ee5752466f966fdf7fa16f3acbd3a823c6b0e82
MD5 0a5b7ccb31e96d049cc5cc4868a4f05f
BLAKE2b-256 631854967b1da69cd0030af20cb8c4f785dfa4a1f0d584a99ec422905640e16f

See more details on using hashes here.

File details

Details for the file biobb_radiospineomics-1.1.20-py3-none-any.whl.

File metadata

File hashes

Hashes for biobb_radiospineomics-1.1.20-py3-none-any.whl
Algorithm Hash digest
SHA256 e48f42396071b0b8394de4db4d56c478cdd81971ed3498e8e13c0c2d1fc6756c
MD5 15517a4d97d6370fc5880db423e866ee
BLAKE2b-256 d2bbff45031d63e609c5471836a14569d363b7ec7d69296cd3bd0e067803c18b

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page