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meyer-lab / tHMM

A general Python framework for using hidden Markov models on binary trees or cell lineage trees.
https://asmlab.org
MIT License
10 stars 1 forks source link

set up random seed for reproducible results #981

Closed Farnazmdi closed 1 year ago

Farnazmdi commented 1 year ago

In this PR:

codecov[bot] commented 1 year ago

Codecov Report

Merging #981 (b81713b) into master (3364cd2) will increase coverage by 0.06%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #981      +/-   ##
==========================================
+ Coverage   73.84%   73.91%   +0.06%     
==========================================
  Files          26       26              
  Lines        2065     2070       +5     
==========================================
+ Hits         1525     1530       +5     
  Misses        540      540
Flag Coverage Δ
unittests 73.91% <100.00%> (+0.06%) :arrow_up:

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Impacted Files Coverage Δ
lineage/Analyze.py 93.00% <100.00%> (+0.21%) :arrow_up:
lineage/CellVar.py 100.00% <100.00%> (ø)
lineage/LineageTree.py 97.85% <100.00%> (-0.06%) :arrow_down:
lineage/states/StateDistributionGaPhs.py 100.00% <100.00%> (ø)
lineage/states/StateDistributionGamma.py 94.01% <100.00%> (+0.05%) :arrow_up:
lineage/tHMM.py 96.62% <100.00%> (ø)
lineage/tests/test_BaumWelch.py 100.00% <100.00%> (ø)
lineage/tests/test_StateEstimation.py 100.00% <100.00%> (ø)
lineage/tests/test_tHMM.py 100.00% <100.00%> (ø)

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aarmey commented 1 year ago

The test needs to initialize and then pass in the rng to ensure it is set to the same state. I am not seeing anything set within the tests that are failing...

aarmey commented 1 year ago

@Farnazmdi this should now be working. Please look this over then I can merge.

Farnazmdi commented 1 year ago

Thank you so much.. Just one question. Does it matter that we use the same random seed number in all files? Or it just matters that those numbers, in any function, stay the same when we run the functions at different times?

aarmey commented 1 year ago

I would suggest you read through the numpy documentation, and think about how this works within the context of the analysis. This is something you should be able to answer at this point.