theislab / theislab/moscot

BirthDeathProblem.solve Error: tp1[8, 9].set_graph_xy(dfs[8, 9].astype("float"), t=100.0)

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Python
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Description

Dear contributors,

Thank you for providing such an excellent tool!
However, I’ve recently encountered some issues while using it. When following the code from the section “Disentangling lineage relationships of delta and epsilon cells in pancreatic development with the TemporalProblem,” I was able to successfully run the previous steps. However, after running .set_graph_xy(), an error occurs when I run .solve(). Interestingly, if I skip set_graph_xy, .solve() runs without any problem. Could you please help me understand what might be causing this issue?

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tp1[8,9].xy is the result after running .set_graph_xy(),while tp0[8,9].xy is not.

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I’m looking forward to your response. Below is my Python ipykernel version, which should not be the issue.

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Contributor guide

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the documented pancreatic-development example with TemporalProblem, comparing BirthDeathProblem.solve() with and without set_graph_xy(). Start by inspecting the traceback and the state produced by tp1[8, 9].xy versus tp0[8, 9].xy; done means the reported workflow solves successfully after set_graph_xy() or the incompatibility is documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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