Flora's comments on first changes

Tree Inference Benchmark Notes

Flora: I should divide this into specific issues to address when I'll have time

Add parallel into the environment.yaml for install
Sort leaves before simplifying the slim tree so that the subsampled slim tree, the vcf, and the inferred tree have the same leaf indexes and order. It will ease downstream tree comparisons

Decide if we should raise the error and stop the program if (i) all job failed (ii) some jobs failed but not all
Sample file created for 4 samples (4 individuals) with 78013 variable sites. /miniconda3/envs/ctrs/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype,
if the folder already exists we should remove all previous files? or at least ask? otherwise it's source of potential bug/mix of simulations with different parameters? at least the tsv seems overwritten so based on it one see the last simulated pool and its param

/miniconda3/envs/ctrs/lib/python3.8/site-packages/pyslim/slim_tree_sequence.py:30: FutureWarning: The SlimTreeSequence class is being phased out, as most important functionality is provided by tskit. Please see the documentation <https://tskit.dev/pyslim/latest/previous_versions.html>_. Please use pyslim.recapitate( ) instead.

save parameters into a csv table inside the simulation directory? it's already save together with the summary statistics in the upper directory. It might be better to save the table within the simu dir, in case people move the directory somewhere else?
add logging system?

I added parallel into the environment.yaml for install. But I also commented libzlma and xz because it was preventing the conda install to work properly. There are likely many unused packages because they were extracted automatically from Ferdinand laptop. We should
scan file for PEP8
add tests

Edited Apr 28, 2025 by Fanny Pouyet