Licenses¶

A model is published under two licenses: the model and its documentation under CC BY-SA 4.0, the source code which creates and simulates it under MIT. The texts of both licenses travel with the model in its COMBINE archive, the .omex file which packs the SBML, the documentation and the figures of a model into one file. pkpdsim.licenses holds the texts as resources of the package and writes them into a directory.

The text of CC BY-SA 4.0 is the same for every model. The text of MIT starts with the copyright, which names the years and the authors of the model, e.g. Copyright (c) 2024-2025 Matthias König; it is the only part in which the MIT texts of two models differ, so it is the argument copyright of the functions, without the words Copyright (c), which the text adds.

Usage¶

from pathlib import Path

from pkpdsim.licenses import License, license_text, write_license

results = Path("results")
results.mkdir()
cc_by_sa = write_license(results, License.CC_BY_SA_4_0)
mit = write_license(results, License.MIT, copyright="2026 Matthias König")
print(cc_by_sa.name, mit.name)
print(mit.read_text(encoding="utf-8").splitlines()[0])
print(license_text(License.CC_BY_SA_4_0).splitlines()[0])

cc-by-sa-4.0.txt mit.txt
Copyright (c) 2026 Matthias König
Attribution-ShareAlike 4.0 International

The files are named after the license, cc-by-sa-4.0.txt and mit.txt, and are written in UTF-8 with line feeds as line endings on every platform, so a model creates the same files byte for byte on Linux, macOS and Windows. A license is given as a License or as its value ("mit"); MIT without a copyright, CC BY-SA 4.0 with one, and a copyright which is empty, spans several lines or starts with Copyright are errors.

The COMBINE archive of a model¶

The factory of a model writes the texts next to its models and adds them to the entries of the archive, here with pymetadata:

# not executed: a fragment of the factory of a model
from pymetadata.omex import EntryFormat, ManifestEntry

from pkpdsim.licenses import License, write_license

entries = {
    license.value: {
        "path": write_license(results_dir, license, copyright=copyright),
        "entry": ManifestEntry(
            location=f"./{license.filename}", format=EntryFormat.TXT, master=False
        ),
    }
    for license, copyright in [
        (License.CC_BY_SA_4_0, None),
        (License.MIT, "2024-2025 Matthias König"),
    ]
}