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Implement Random-Effects-Likelihood Method #30

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Implement Random-Effects-Likelihood Method #30

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Commits on Nov 27, 2018

  1. added multiprocessing to phydms_modeladequacy

    @skhilton
    skhilton committed Nov 27, 2018
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Commits on Nov 28, 2018

  1. cleaned up the test directory

    @skhilton
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  2. multiprocessing is used only if ncpu greater than one

    @skhilton
    skhilton committed Nov 28, 2018
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  3. added test for model adequacy with and without multiprocessing

    @skhilton
    skhilton committed Nov 28, 2018
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  4. small formatting tweaks

    @skhilton
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Commits on Nov 30, 2018

  1. refactored code to perform simulations in batches

    @skhilton
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  2. make sure there are >= 100 simulations per CPU

    @skhilton
    skhilton committed Nov 30, 2018
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  3. increased number of simulations in multiprocessing test

    @skhilton
    skhilton committed Nov 30, 2018
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  4. removed slow list comprehension in kldiv function

    @skhilton
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  5. cleaned up code around multiprocessor/no multiprocessor switch

    @skhilton
    skhilton committed Nov 30, 2018
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  6. fixed sites being indexed at 0 to indexed at 1 for outputs

    @skhilton
    skhilton committed Nov 30, 2018
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  7. streamlined processing of the simulations

    @skhilton
    skhilton committed Nov 30, 2018
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  8. changed min number of simuluations per CPU to 1000

    @skhilton
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Commits on Dec 12, 2018

  1. Merge branch 'master' into model_adequacy

    @jbloom
    jbloom committed Dec 12, 2018
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Commits on Dec 13, 2018

  1. Update .travis.yml

    @skhilton
    skhilton authored Dec 13, 2018
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  2. ignore failing tests

    @skhilton
    skhilton committed Dec 13, 2018
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  3. specified float formatting in doctest

    @skhilton
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  4. Merge branch 'model_adequacy' of https://github.com/jbloomlab/phydms … 

    …into model_adequacy
    @skhilton
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Commits on Dec 14, 2018

  1. made test file paths more robust

    @skhilton
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  2. removed call to raxml and made file paths more robust

    @skhilton
    skhilton committed Dec 14, 2018
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  3. fixed bug in CPU distribution

    @skhilton
    skhilton committed Dec 14, 2018
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  4. Updated travis.yml

    @jon-mah
    jon-mah committed Dec 14, 2018
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Commits on Dec 15, 2018

  1. Ignore failing modeladequacy tests

    @jon-mah
    jon-mah committed Dec 15, 2018
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Commits on Dec 17, 2018

  1. cleaned up distance calculations

    @skhilton
    skhilton committed Dec 17, 2018
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  2. sequestered failing test

    @skhilton
    skhilton committed Dec 17, 2018
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  3. fixed doctest for prefdistance

    @skhilton
    skhilton committed Dec 17, 2018
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  4. added a dictionary

    @skhilton
    skhilton committed Dec 17, 2018
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  5. clean up multiprocessing in model adequacy

    @skhilton
    skhilton committed Dec 17, 2018
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  6. clean up random seed setting in simulator.simulate

    @skhilton
    skhilton committed Dec 17, 2018
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  7. added layered cacheing to simulator.simulate

    @skhilton
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  8. added test to make sure 1 CPU and > 1 CPU get the same answer

    @skhilton
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  9. Absolute pathing, working build

    @jon-mah
    jon-mah committed Dec 17, 2018
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  10. fixed translate with gaps function in compare simulators tests

    @skhilton
    skhilton committed Dec 17, 2018
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  11. Shortened input data, updated expected results, working build.

    @jon-mah
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  12. set check_input default value to True

    @skhilton
    skhilton committed Dec 17, 2018
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  13. Absolute pathing for expected outputs.

    @jon-mah
    jon-mah committed Dec 17, 2018
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  14. Absolute pathing for all files.

    @jon-mah
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  15. Refactored tests to resemble test_phydms_comprehensive

    @jon-mah
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  16. small tweak to multiprocessing

    @skhilton
    skhilton committed Dec 17, 2018
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Commits on Dec 18, 2018

  1. Added tests for simulated data, associated expected results, working … 

    …build
    @jon-mah
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Commits on Jan 10, 2019

  1. added the correct file for the phydms_modeladequacy test

    @skhilton
    skhilton committed Jan 10, 2019
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  2. small tweak to test description

    @skhilton
    skhilton committed Jan 10, 2019
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  3. fixed phydms modeladequacy multiprocessing test script

    @skhilton
    skhilton committed Jan 10, 2019
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  4. fixed multiprocessing in phydms_modeladequacy

    @skhilton
    skhilton committed Jan 10, 2019
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  5. small tweaks to test formatting

    @skhilton
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  6. formatting tweaks to model adequacy script

    @skhilton
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Commits on Jan 11, 2019

  1. tweaks to script

    @skhilton
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  2. added phydms_modeladequacy tests to Travis CI

    @skhilton
    skhilton committed Jan 11, 2019
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  3. increased the number of simulations/CPU to 1000

    @skhilton
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  4. print out expected and actual results for failing tests

    @skhilton
    skhilton committed Jan 11, 2019
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  5. fixed typo

    @skhilton
    skhilton committed Jan 11, 2019
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  6. fixed formatting on error message

    @skhilton
    skhilton committed Jan 11, 2019
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  7. fixed test typo

    @skhilton
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  8. added tolerance to tests

    @skhilton
    skhilton committed Jan 11, 2019
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  9. fixed typo in error message

    @skhilton
    skhilton committed Jan 11, 2019
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Commits on Jan 12, 2019

  1. increased the tolerance

    @skhilton
    skhilton committed Jan 12, 2019
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Commits on Jan 15, 2019

  1. removed tolerance in model adequacy test

    @skhilton
    skhilton committed Jan 15, 2019
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  2. fixed typo in test

    @skhilton
    skhilton committed Jan 15, 2019
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Commits on Jan 25, 2019

  1. ignore multiprocessing test

    @skhilton
    skhilton committed Jan 25, 2019
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  2. switched to NP data

    @skhilton
    skhilton committed Jan 25, 2019
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  3. reduced number of simulations

    @skhilton
    skhilton committed Jan 25, 2019
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  4. changed multiprocessing test to NP data

    @skhilton
    skhilton committed Jan 25, 2019
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  5. removed obsolete input data directory

    @skhilton
    skhilton committed Jan 25, 2019
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  6. removed old files

    @skhilton
    skhilton committed Jan 25, 2019
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Commits on Jan 31, 2019

  1. utilize full paths for RAxML

    @skhilton
    skhilton committed Jan 31, 2019
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Commits on Feb 1, 2019

  1. added RMSD metric to phydms_modeladequacy

    @skhilton
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  2. updated tests to include RMSD results

    @skhilton
    skhilton committed Feb 1, 2019
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Commits on Feb 13, 2019

  1. added max number of simulations per CPU

    @skhilton
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  2. Merge branch 'model_adequacy' of https://github.com/jbloomlab/phydms … 

    …into model_adequacy
    @skhilton
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Commits on Feb 14, 2019

  1. fixed inability to handle a large number of simulations

    @skhilton
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  2. Added gammaomega and empirical Bayes capabilities to phydms_comprehen… 

    …sive and associated tests.
    @jon-mah
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Commits on Feb 15, 2019

  1. Split phydms_comprehensive tests into two, added --ncats flag functio… 

    …nality to phydms_comprehensive.
    @jon-mah
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Commits on Feb 16, 2019

  1. shortened diff prefs test

    @skhilton
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Commits on Feb 21, 2019

  1. Merge model_adequacy to REL, resolve conflict in pytest.ini

    @jon-mah
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Commits on Mar 7, 2019

  1. Added test cases for divpressure. Tests expected to fail.

    @jon-mah
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Commits on Jan 7, 2020

  1. added rateMatrixPrefix option to phydmslib.simulate

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  2. started the phydmslib.modeladequacy modules

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  3. fixed typo in calc_aa_frequencies doctest

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  4. small tweaks to calc_aa_frequencies

    @skhilton
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  5. added sequence length check to translate_with_gaps

    @skhilton
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  6. added more functions to modeladequacy and started test script

    @skhilton
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  7. small tweaks to test script

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  8. renamed variable to follow lowercase conventions

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  9. seed numpy random seed in simulate

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  10. added ability to do replicate simulations

    @skhilton
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  11. first pass at model_adequacy script

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  12. small tweak to parse arguments

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  13. added profiling script for modeladequacy

    @skhilton
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  14. added pstats output

    @skhilton
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  15. added script to profile model adequacy

    @skhilton
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  16. added additional checks to the replicate alignment test

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  17. removed extraneous file

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  18. fixed bug in profiling script

    @skhilton
    skhilton authored and Jonathan Mah committed Jan 7, 2020
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  19. small tweak to profile script

    @skhilton
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  20. started test for model adequacy test

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  21. added new class simulator to simulate.py 

    Now, the phydmslib.simulate module can simulate an alignment
two different ways.

The first (old way) is using the software `pyvolve`.
The second (new way) is to use `phydms` models and
internal functions only.
This new way is implemented in a new class called
`phydmslib.simulate.simulator`.
    @skhilton
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  22. added new simulation method to the simulation test

    @skhilton
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  23. tweaks to simulate.py

    @skhilton
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  24. refactored alignment simulation test

    @skhilton
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  25. changes to simulate.py 

    The major changes in this commit are removing the output function
and having the simulate function return an alignment rather than
store it as an attribute.
    @skhilton
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  26. changed node attributes in simulator to private

    @skhilton
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  27. small tweaks to simulatoin test

    @skhilton
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  28. added Simulator class to random seed test

    @skhilton
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  29. added profile code and profiling results

    @skhilton
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  30. some changes that speed up Simulate.simulate

    @jbloom
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  31. added test to check simulator against expected results

    @skhilton
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  32. small tweaks to simulate.py

    @skhilton
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  33. added comparison test

    @skhilton
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  34. small tweak to docstring

    @skhilton
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  35. removed old profiling output

    @skhilton
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  36. removed unused function from phydmslib/modeladequacy

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  37. model adequacy script runs through all the way

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  38. cache the cumulative sums and sequence arrays

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  39. added function to output an alignment

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  40. added another test for random seed setting 

    Previously, this test looked at whether or not you
get the same alignment when you send the random seed
into the function.

I've added another test which tests whether or not you
get the same alignments if you seed the seed before a for
loop but don't send a seed into the simulate function.
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  41. added pvalue calculation function to modeladequacy

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  42. added in random seed and simplified simulation processing

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  43. removed unnecessary test files

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  44. added YNGKP_M0 to phydms_modeladequacy and fixed random seed

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  45. added test of phydms_modeladequacy against expected results

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  46. small formatting tweaks

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  47. fixed how the random seed is set in simulator and updated expected re… 

    …sults
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  48. small tweaks to simulate.py

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  49. removed metrics flag

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  50. changed default number of simulations and clarified models accepted

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  51. seed each call of simulator

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  52. added more interpretable error message

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  53. removed unncessary function

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  54. update phydms_modeladequacy test with nSim as optional param

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  55. fixed random seed setting in test_alignmentSimulation.py

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  56. refactored simulate code to only store codon index

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  57. cleaned up comments

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  58. small tweaks to simulate.py

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  59. cleaned up variable names

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  60. replaced for loop with starmap

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  61. set numpy random seed as well as scipy random seed

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  62. implemented with itertools starmap

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  63. set random seed during pvalue calculation

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  64. fixed seed setting in pvalue calculation function

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  65. added multiprocessing to phydms_modeladequacy

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  66. cleaned up the test directory

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  67. multiprocessing is used only if ncpu greater than one

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  68. added test for model adequacy with and without multiprocessing

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  69. small formatting tweaks

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  70. refactored code to perform simulations in batches

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  71. make sure there are >= 100 simulations per CPU

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  72. increased number of simulations in multiprocessing test

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  73. removed slow list comprehension in kldiv function

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  74. cleaned up code around multiprocessor/no multiprocessor switch

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  75. fixed sites being indexed at 0 to indexed at 1 for outputs

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  76. streamlined processing of the simulations

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  77. changed min number of simuluations per CPU to 1000

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  78. ignore failing tests

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  79. specified float formatting in doctest

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  80. made test file paths more robust

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  81. removed call to raxml and made file paths more robust

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  82. fixed bug in CPU distribution

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  83. Updated travis.yml

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  84. Ignore failing modeladequacy tests

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  85. cleaned up distance calculations

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  86. fixed doctest for prefdistance

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  87. added a dictionary

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  88. clean up multiprocessing in model adequacy

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  89. clean up random seed setting in simulator.simulate

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  90. added layered cacheing to simulator.simulate

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  91. added test to make sure 1 CPU and > 1 CPU get the same answer

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  92. Absolute pathing, working build

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  93. fixed translate with gaps function in compare simulators tests

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  94. Shortened input data, updated expected results, working build.

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  95. set check_input default value to True

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  96. Absolute pathing for expected outputs.

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  97. Absolute pathing for all files.

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  98. Refactored tests to resemble test_phydms_comprehensive

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  99. small tweak to multiprocessing

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  100. Added tests for simulated data, associated expected results, working … 

    …build
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  101. added the correct file for the phydms_modeladequacy test

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  102. small tweak to test description

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  103. fixed phydms modeladequacy multiprocessing test script

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  104. fixed multiprocessing in phydms_modeladequacy

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  105. small tweaks to test formatting

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  106. formatting tweaks to model adequacy script

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  107. tweaks to script

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  108. added phydms_modeladequacy tests to Travis CI

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  109. increased the number of simulations/CPU to 1000

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  110. print out expected and actual results for failing tests

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  111. fixed typo

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  112. fixed formatting on error message

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  113. fixed test typo

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  114. added tolerance to tests

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  115. fixed typo in error message

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  116. increased the tolerance

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  117. removed tolerance in model adequacy test

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  118. fixed typo in test

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  119. ignore multiprocessing test

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  120. switched to NP data

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  121. reduced number of simulations

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  122. changed multiprocessing test to NP data

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  123. removed obsolete input data directory

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  124. removed old files

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  125. utilize full paths for RAxML

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  126. added RMSD metric to phydms_modeladequacy

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  127. updated tests to include RMSD results

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  128. added max number of simulations per CPU

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  129. fixed inability to handle a large number of simulations

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  130. Added gammaomega and empirical Bayes capabilities to phydms_comprehen… 

    …sive and associated tests.
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  131. Split phydms_comprehensive tests into two, added --ncats flag functio… 

    …nality to phydms_comprehensive.
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  132. shortened diff prefs test

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  133. Added test cases for divpressure. Tests expected to fail.

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  134. Added minimum branch length argument.

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  135. resolved merge conflict.

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Commits on May 27, 2020

  1. attempted to shorten tests

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  2. tweaked xvfb line in .travis.yml

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  3. added expected diffprefs file

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  4. use more pandas function for empirical bayes

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  5. fixed bug in positive selection calculations

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  6. fixed comment

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Commits on May 29, 2020

  1. Merge branch 'REL' into REL_merge

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  2. fixed bugs introduced during merge

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  3. removed model adequacy protocol 

    The REL branch was originally branched off
the model adequacy branch.
Model adequacy is no longer an active project
so those scripts are no longer needed.
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  4. cleaned up phydms_comprehensive test

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  5. added branch to travis CI

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  6. removed call to model adequacy in test

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  7. removed model adequacy call from another test

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  8. pytest ignore deprecation warnings

    @skhilton
    skhilton committed May 29, 2020
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Commits on May 30, 2020

  1. Added documentation in .rst format for REL method.

    @jon-mah
    jon-mah committed May 30, 2020
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  2. fixed typos in REL method docs.

    @jon-mah
    jon-mah committed May 30, 2020
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  3. update CHANGELOG and version number to 2.4.0

    @jbloom
    jbloom committed May 30, 2020
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  4. remove REL and REL_merge branches from Travis tests now that bein… 

    …g merged
    @jbloom
    jbloom committed May 30, 2020
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  5. require python >= 3.6 (we are only testing on this)

    @jbloom
    jbloom committed May 30, 2020
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  6. clean up docstring

    @jbloom
    jbloom committed May 30, 2020
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  7. clean up docstring

    @jbloom
    jbloom committed May 30, 2020
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  8. clean up ExpCM docs

    @jbloom
    jbloom committed May 30, 2020
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Commits on Jun 15, 2020

  1. split empirical_bayes flag into two separate arguments, random_effect… 

    …s_likelihood and REL_ncats.
    @jon-mah
    jon-mah committed Jun 15, 2020
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Commits on Jun 16, 2020

  1. small tweaks to parseargs

    @skhilton
    skhilton committed Jun 16, 2020
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  2. added REL checks to the model check portion of phydms

    @skhilton
    skhilton committed Jun 16, 2020
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  3. tweaks to phydms_comprehensive test

    @skhilton
    skhilton committed Jun 16, 2020
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Commits on Jun 25, 2020

  1. phydms_prog for random_effects_likelihood and REL_ncats options.

    @jon-mah
    jon-mah committed Jun 25, 2020
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  2. Merge branch 'REL_merge' of https://github.com/jbloomlab/phydms into … 

    …REL_merge
    @jon-mah
    jon-mah committed Jun 25, 2020
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  3. Merge branch 'master' into REL_merge

    @skhilton
    skhilton committed Jun 25, 2020
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  4. Merge branch 'master' into REL_merge.

    @jon-mah
    jon-mah committed Jun 25, 2020
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  5. phdyms_prog docs for REL output files.

    @jon-mah
    jon-mah committed Jun 25, 2020
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  6. Merge branch 'REL_merge' of https://github.com/jbloomlab/phydms into … 

    …REL_merge
    @skhilton
    skhilton committed Jun 25, 2020
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  7. tweaks to phydms_prog

    @skhilton
    skhilton committed Jun 25, 2020
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Commits on Jun 26, 2020

  1. draft docs for numerical implementation of REL method.

    @jon-mah
    jon-mah committed Jun 26, 2020
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  2. removed REL from implementation

    @skhilton
    skhilton committed Jun 26, 2020
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Commits on Jul 1, 2020

  1. changed CLI to omega_random_effects_likelihood

    @skhilton
    skhilton committed Jul 1, 2020
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  2. slight doc tweaks

    @skhilton
    skhilton committed Jul 1, 2020
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  3. changed column titles

    @skhilton
    skhilton committed Jul 1, 2020
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  4. added branch to travis

    @skhilton
    skhilton committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. Merge pull request #32 from jbloomlab/REL-names 

    Rel names
    @jon-mah
    jon-mah authored Jul 2, 2020
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