data-PAM50

Part of spinalcordtoolbox.

How to update this dataset

1. Edit and commit the files in src/spinalcordtoolbox/data/

2. Go to https://github.com/spinalcordtoolbox/data-PAM50/releases

3. Click "Draft Release"

4. Fill in a version tag. We recommend using date-based releases (e.g. 2020.1.1, 2022.5.18, etc.).

   Note: The version must be formatted in a way that complies with PEP 440. The easiest way to do this is to use a numerical version number in the form of X.Y.Z, but there is some flexibility here.

5. Click "Publish Release"

6. Wait a few minutes;

7. Monitor the progress at https://github.com/spinalcordtoolbox/data-PAM50/actions/workflows/release.yml

8. The release should appear on https://github.com/spinalcordtoolbox/data-PAM50/releases with the .tar.gz (sdist) and .whl (wheel) formats attached momentarily.

How to test this repo locally

If you've encountered an error during the GitHub Actions workflow, you can use the following steps to test the repo locally:

# Create a virtual environment
python -m venv venv
source venv/bin/activate

# Install the `build` package (which is necessary to build pip packages)
pip install build

# Build the pip package, which will generate:
#   1. A build folder (containing a copy of the files to be packaged)
#   2. A packaged wheel (stored in ./dist/${package-name}.whl)
#   3. A packaged source distribution (stored in ./dist/${package-name}.tar.gz)
#   4. Package metadata (stored in ./src/${package-name}.egg-info
python -m build --wheel --sdist

# Install the generated wheel. 
# As a result, the contents of ./src/ will be installed to:
#   ./venv/lib/python3.7/site-packages/spinalcordtoolbox/data/PAM50
# This means that the installed data package will coexist alongside the
# installed `spinalcordtoolbox` pip package.
pip install dist/*.whl

This should give you enough clues to hopefully to track down any problems.