Plot population level from lineage data - #988
Merged
Merged
Conversation
figure0.py used the pre-refactor get_leaves_idx() helper, which no longer exists after the CSR sparse array rework; switch to the lin.leaves_idx attribute instead. The taxol loading code (import_taxol* / assign_observs_Taxol / sep_lineages in import_lineage.py, and the taxol block in Lineage_collections.py) depended on lineage/data/taxol/, which is gitignored and not available, breaking every import of Lineage_collections. Remove it along with figureS18.py/figureS19.py, the only figures that depended on it. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XBehA2a1Zp2n2ce8Vr1ATa
actions/checkout@v4 and astral-sh/setup-uv@v5 both target Node 20, which GitHub Actions runners are deprecating; bump to actions/checkout@v7 and astral-sh/setup-uv@v10, which target Node 24. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XBehA2a1Zp2n2ce8Vr1ATa
astral-sh/setup-uv only publishes exact version tags for v8+ (no v10 alias), unlike actions/checkout; pin to v10.0.1 explicitly. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XBehA2a1Zp2n2ce8Vr1ATa
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
figure 0 for lapatinib and gemcitabine.
Randomly choosing leaf cells and traversing back to root cells and **2 at each transition/division.