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If we have a mix of ploidies in a `.vcz` file, we create sample nodes for the maximum ploidy size for each individual, that just attach to the root (because they have no data). I.e. we make a huge pol…
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### Environment Information
- spaceprime version:
- Python version: 3.11.8
- Operating System: MacOS 13.6.7
### Description
Installation seemed to go successfully, but receive an err…
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E.g.
```python
ts = msprime.sim_ancestry([msprime.SampleSet(1, time=0, ploidy=1), msprime.SampleSet(1, time=1, ploidy=1)])
d3arg = tskit_arg_visualizer.D3ARG.from_ts(ts=ts)
d3arg.draw_node(node=…
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Originally issue via slendr: https://github.com/bodkan/slendr/issues/83
To paraphrase, the user is trying to install a conda environment on an Arm64 Mac, with the following pins: pyhton=3.8 msprime…
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Hi,
I am developing a shinylive application. My app requires msprime, that in turn requires ruaml.yaml.
Both packages are included in pyodide, but I'm getting this error.
Error starting app!
T…
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Right now, installing `requirements/development.txt` gets
```
>>> import stdpopsim
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x an…
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With:
```python
import stdpopsim
sp = stdpopsim.get_species("StrAga")
contig = sp.get_contig(length=100000)
engine = stdpopsim.get_engine("msprime")
model = stdpopsim.PiecewiseConstantSize(sp.po…
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I thought it would be interesting to compare how tsinfer+tsdate do against the new "Threads" program (https://pypi.org/project/threads-arg/0.1.0/).
As a test, I have a stdpopsim model with 2 chimp …
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The need for unit tests for SLiM's popgen functions has been underlined by another discovery of a bug with them (https://groups.google.com/g/slim-discuss/c/Yacfk9EIYeU/m/bc72wVUzBAAJ). I'm not sure h…
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Would it be possible to have SINGER output the "full ARG" with marked recombination nodes (similar to that from msprime)? This would require maintaining unary nodes in the tree sequence, such as recom…