Repository navigation
Remove copied GPL code and make GPL dependencies optional - #223
Merged
Merged
Conversation
Scarf's Harmony (harmony.py) and LISI (metrics.py) were copied from harmonypy, which is GPL-3.0-or-later. Both now call harmonypy 0.0.10 through a new `harmony` extra. New tests pin outputs recorded from the code they replace, so results are unchanged. make_graph checks for harmonypy before doing any work, and stored harmonized data loads without it. leidenalg (GPL-3.0-or-later), and with it igraph, moves from the required dependencies to a new `leiden` extra, so `pip install scarf` no longer installs them. plot_cluster_tree draws its pies as matplotlib paths, ported from CyteArc, replacing a StackOverflow snippet under CC BY-SA 4.0. Add THIRD_PARTY_NOTICES.md and the GPL-3.0 text for the bundled sgtsne binary, and declare BSD-3-Clause AND MIT AND GPL-3.0-only. The install docs, README, CI and Docker image install the new extras.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Scarf's Harmony (harmony.py) and LISI (metrics.py) were copied from harmonypy, which is GPL-3.0-or-later. Both now call harmonypy 0.0.10 through a new
harmonyextra. New tests pin outputs recorded from the code they replace, so results are unchanged. make_graph checks for harmonypy before doing any work, and stored harmonized data loads without it.leidenalg (GPL-3.0-or-later), and with it igraph, moves from the required dependencies to a new
leidenextra, sopip install scarfno longer installs them.plot_cluster_tree draws its pies as matplotlib paths, ported from CyteArc, replacing a StackOverflow snippet under CC BY-SA 4.0.
Add THIRD_PARTY_NOTICES.md and the GPL-3.0 text for the bundled sgtsne binary, and declare BSD-3-Clause AND MIT AND GPL-3.0-only. The install docs, README, CI and Docker image install the new extras.