diff --git a/README.md b/README.md index ee444db..29011b5 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # sc2ts Infer a succinct tree sequence from SARS-COV-2 variation data -**This is an early version not intended for production use!!** +**This is an early alpha version not intended for production use!!** If you are interested in helping to develop sc2ts or would like to work with the inferred ARGS, please get in touch. @@ -109,3 +109,14 @@ metadata=$datadir/metadata.filtered.db # options+=" -b $basets" python3 -m sc2ts daily-extend $alignments $metadata $results_prefix $options ``` + +## Licensing + +The code is marked as licensed under the MIT license, +but because the current implementation is used the matching +engine from tsinfer (which is GPL licensed) this code is +therefore also GPL. + +However, we plan to switch out the matching engine for an +implementation provided by tskit, which is MIT licensed. +This will be done before the first official release. diff --git a/setup.cfg b/setup.cfg index d6c7c61..6af44ee 100644 --- a/setup.cfg +++ b/setup.cfg @@ -5,7 +5,7 @@ author_email = jerome.kelleher@bdi.ox.ac.uk license = MIT description = Infer a succinct tree sequence from SARS-CoV-2 sequence alignments long_description = file: README.md -long_description_content_type = text/x-markdown +long_description_content_type = text/markdown [options] packages = sc2ts, sc2ts.data zip_safe = False # https://mypy.readthedocs.io/en/latest/installed_packages.html