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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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Stochastic unit test failures with python 3.5 #82

Closed tleonardi closed 5 years ago

tleonardi commented 5 years ago

The txComp test randomly fails with python 3.5 due to a p-value discrepancy:

============================= test session starts ==============================
platform linux -- Python 3.5.6, pytest-4.4.0, py-1.7.0, pluggy-0.9.0
rootdir: /home/travis/build/tleonardi/nanocompore
collected 45 items                                                             
tests/test_Integration.py .sssssssssssssssssss.                          [ 46%]
tests/test_SampCompDB.py ....                                            [ 55%]
tests/test_TxComp.py ...........F....                                    [ 91%]
tests/test_Whitelist.py ....                                             [100%]
=================================== FAILURES ===================================
____________________________ test_txComp_GMM_anova _____________________________
test_ref_pos_list = ([{'data': {'KD': {'KD1': {'coverage': 100, 'dwell': array([121.70757477, 129.70100881, 111.67411923, 131.1979314 ,
  ...328765287e-39, 3.3968653938213694e-40, 1.9321679678623975e-36, 8.482777798353687e-40, nan, 7.06503867181238e-40, ...]})
    def test_txComp_GMM_anova(test_ref_pos_list):
        ml = mock.Mock()
        if sys.version_info < (3, 6):
            tol = 0.0002
        else:
            tol=0.00000001
        res = txCompare(test_ref_pos_list[0], methods=['GMM'], logit=False, sequence_context=2, min_coverage=3, logger=ml, allow_warnings=False, random_state=np.random.RandomState(seed=42))
        GMM_pvalues = [pos['txComp']['GMM_anova_pvalue'] for pos in res ]
>       assert GMM_pvalues == [pytest.approx(i, abs=tol, nan_ok=True) for i in test_ref_pos_list[1]['GMM_anova']]
E       assert [0.0008574768...76768562, ...] == [0.00085747684... 2.0e-04, ...]
E         At index 3 diff: 0.0017335646468135102 != 0.0010906844025473576 ± 2.0e-04
E         Use -v to get the full diff
tests/test_TxComp.py:104: AssertionError
============== 1 failed, 25 passed, 19 skipped in 187.78 seconds ===============
The command "pytest" exited with 1.

After inspecting the results of the GMM fitting, it looks like when the test fails there's a small cluster counts discrepancy:

Passing

root@3f23411890db:/nanocompore/tests# pytest test_TxComp.py -vs                                                                                                                                                                                                                             
=================================================================================================================================== test session starts ====================================================================================================================================
platform linux -- Python 3.5.7, pytest-4.4.0, py-1.8.0, pluggy-0.9.0 -- /usr/local/bin/python                                                                                                                                                                                               
cachedir: .pytest_cache                                                                                                                                                                                                                                                                     
rootdir: /nanocompore                                                                                                                                                                                                                                                                       
collected 16 items                                                                                                                                                                                                                                                                          

test_TxComp.py::test_combine_pvalues_hou[pvalues0] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues1] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues2] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues3] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues0] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues1] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues2] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_nonparametric_test[v10-v20-expected0] PASSED                                                                                                                                                                                                                           
test_TxComp.py::test_sum_of_squares[x0-1243] PASSED                                                                                                                                                                                                                                         
test_TxComp.py::test_sum_of_squares[2-4] PASSED                                                                                                                                                                                                                                             
test_TxComp.py::test_sum_of_squares[x2-201] PASSED                                                                                                                                                                                                                                          
test_TxComp.py::test_txComp_GMM_anova {'GMM_anova_model': {'delta_logit': -5.154130973499999, 'table': F_onewayResult(statistic=915.3557790180453, pvalue=0.0010906844025473576), 'pvalue': 0.0010906844025473576, 'log_ratios': array([ 2.77258872, -2.60796674, -2.46385324,  2.46385324])
}, 'shift_stats': OrderedDict([('c1_mean_intensity', 101.25371018948026), ('c2_mean_intensity', 120.1690563433108), ('c1_median_intensity', 101.27532194257512), ('c2_median_intensity', 120.70768400991767), ('c1_sd_intensity', 9.976570066976405), ('c2_sd_intensity', 9.138834592954336)
, ('c1_mean_dwell', 99.53689876631836), ('c2_mean_dwell', 121.33193242927064), ('c1_median_dwell', 99.33218082115548), ('c2_median_dwell', 121.12071127421946), ('c1_sd_dwell', 10.25957982066471), ('c2_sd_dwell', 9.296922575493252)]), 'GMM_model': {'cluster_counts': 'KD1:95/5__WT1:6/9
4__WT2:7/93__KD2:93/7', 'model': GaussianMixture(covariance_type='full', init_params='kmeans', max_iter=1000,                                                                                                                                                                               
        means_init=None, n_components=2, n_init=1, precisions_init=None,                                                                                                                                                                                                                    
        random_state=<mtrand.RandomState object at 0x7f47adf82438>,                                                                                                                                                                                                                         
        reg_covar=1e-06, tol=0.001, verbose=0, verbose_interval=10,                                                                                                                                                                                                                         
        warm_start=False, weights_init=None)}, 'GMM_anova_pvalue_context_2': 4.706324386384477e-14, 'GMM_anova_pvalue': 0.0010906844025473576}                                                                                                                                              
PASSED                                                                                                                                                                                                                                                                                      
test_TxComp.py::test_txComp_GMM_logit [1.2742453287653416e-39, 3.3968653938213694e-40, 1.9321679678623975e-36, 6.01195032712085e-40, nan, 7.06503867181238e-40, 1.8392720921153275e-40, 9.162002495725215e-32, 5.92288489163853e-34, 3.1972432623453856e-40]                                
[1.274245328765287e-39, 3.3968653938213694e-40, 1.9321679678623975e-36, 8.482777798353687e-40, nan, 7.06503867181238e-40, 1.839272092115274e-40, 9.162002495725215e-32, 5.922884891638699e-34, 3.1972432623454785e-40]                                                                      
['KD1:94/6__WT1:7/93__WT2:9/91__KD2:95/5', 'KD1:92/8__WT1:12/88__WT2:7/93__KD2:93/7', 'KD1:82/18__WT1:5/95__WT2:10/90__KD2:85/15', 'KD1:95/5__WT1:6/94__WT2:7/93__KD2:93/7', 'NC', 'KD1:9/91__WT1:96/4__WT2:92/8__KD2:8/92', 'KD1:8/92__WT1:95/5__WT2:90/10__KD2:8/92', 'KD1:15/85__WT1:96/4
__WT2:98/2__KD2:14/86', 'KD1:3/97__WT1:86/14__WT2:84/16__KD2:5/95', 'KD1:7/93__WT1:94/6__WT2:93/7__KD2:7/93']                                                                                                                                                                               
PASSED                                                                                                                                                                                                                                                                                      
test_TxComp.py::test_txComp_GMM_anova_0_var PASSED                                                                                                                                                                                                                                          
test_TxComp.py::test_txComp_GMM_dup_lab PASSED                                                                                                                                                                                                                                              
test_TxComp.py::test_txComp_lowCov PASSED                                                                                                                                                                                                                                                   

================================================================================================================================ 16 passed in 1.13 seconds ================================================================================================================================$

Failing

root@3f23411890db:/nanocompore/tests# pytest test_TxComp.py -vs                                                                                                                                                                                                                             
=================================================================================================================================== test session starts ====================================================================================================================================
platform linux -- Python 3.5.7, pytest-4.4.0, py-1.8.0, pluggy-0.9.0 -- /usr/local/bin/python                                                                                                                                                                                               
cachedir: .pytest_cache                                                                                                                                                                                                                                                                     
rootdir: /nanocompore                                                                                                                                                                                                                                                                       
collected 16 items                                                                                                                                                                                                                                                                          

test_TxComp.py::test_combine_pvalues_hou[pvalues0] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues1] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues2] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_hou[pvalues3] PASSED                                                                                                                                                                                                                                   
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues0] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues1] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_combine_pvalues_raises_exception_with_invalid_pvalues[pvalues2] PASSED                                                                                                                                                                                                 
test_TxComp.py::test_nonparametric_test[v10-v20-expected0] PASSED                                                                                                                                                                                                                           
test_TxComp.py::test_sum_of_squares[x0-1243] PASSED                                                                                                                                                                                                                                         
test_TxComp.py::test_sum_of_squares[2-4] PASSED                                                                                                                                                                                                                                             
test_TxComp.py::test_sum_of_squares[x2-201] PASSED                                                                                                                                                                                                                                          
test_TxComp.py::test_txComp_GMM_anova {'GMM_anova_pvalue': 0.0017335646468135102, 'GMM_anova_model': {'log_ratios': array([ 2.77258872, -2.46385324,  2.46385324, -2.77258872]), 'table': F_onewayResult(statistic=575.3465305297385, pvalue=0.0017335646468135102), 'pvalue': 0.00173356464
68135102, 'delta_logit': -5.236441963}, 'GMM_model': {'cluster_counts': 'KD1:95/5__WT2:7/93__KD2:93/7__WT1:5/95', 'model': GaussianMixture(covariance_type='full', init_params='kmeans', max_iter=1000,                                                                                     
        means_init=None, n_components=2, n_init=1, precisions_init=None,                                                                                                                                                                                                                    
        random_state=<mtrand.RandomState object at 0x7fd59152e708>,                                                                                                                                                                                                                         
        reg_covar=1e-06, tol=0.001, verbose=0, verbose_interval=10,                                                                                                                                                                                                                         
        warm_start=False, weights_init=None)}, 'GMM_anova_pvalue_context_2': 1.2760955364845727e-13, 'shift_stats': OrderedDict([('c1_mean_intensity', 101.25371018948026), ('c2_mean_intensity', 120.16905634331079), ('c1_median_intensity', 101.27532194257512), ('c2_median_intensity', 
120.70768400991767), ('c1_sd_intensity', 9.976570066976405), ('c2_sd_intensity', 9.138834592954336), ('c1_mean_dwell', 99.53689876631836), ('c2_mean_dwell', 121.33193242927064), ('c1_median_dwell', 99.33218082115548), ('c2_median_dwell', 121.12071127421946), ('c1_sd_dwell', 10.259579
82066471), ('c2_sd_dwell', 9.296922575493252)])}
FAILED
test_TxComp.py::test_txComp_GMM_logit [1.2742453287653416e-39, 3.396865393821225e-40, 1.9321679678623975e-36, 8.482777798354296e-40, nan, 7.0650386718125795e-40, 1.8392720921153275e-40, 4.6826664356268694e-32, 5.922884891638699e-34, 3.197243262345706e-40]
[1.274245328765287e-39, 3.3968653938213694e-40, 1.9321679678623975e-36, 8.482777798353687e-40, nan, 7.06503867181238e-40, 1.839272092115274e-40, 9.162002495725215e-32, 5.922884891638699e-34, 3.1972432623454785e-40]
['KD1:94/6__WT2:9/91__KD2:95/5__WT1:7/93', 'KD1:92/8__WT2:7/93__KD2:93/7__WT1:12/88', 'KD1:82/18__WT2:10/90__KD2:85/15__WT1:5/95', 'KD1:95/5__WT2:7/93__KD2:93/7__WT1:5/95', 'NC', 'KD1:9/91__WT2:92/8__KD2:8/92__WT1:96/4', 'KD1:8/92__WT2:90/10__KD2:8/92__WT1:95/5', 'KD1:14/86__WT2:98/2
__KD2:14/86__WT1:96/4', 'KD1:3/97__WT2:84/16__KD2:5/95__WT1:86/14', 'KD1:7/93__WT2:93/7__KD2:7/93__WT1:94/6']
PASSED
test_TxComp.py::test_txComp_GMM_anova_0_var PASSED
test_TxComp.py::test_txComp_GMM_dup_lab PASSED
test_TxComp.py::test_txComp_lowCov PASSED

========================================================================================================================================= FAILURES =========================================================================================================================================
__________________________________________________________________________________________________________________________________ test_txComp_GMM_anova ___________________________________________________________________________________________________________________________________

test_ref_pos_list = ([{'data': {'KD': {'KD1': {'coverage': 100, 'dwell': array([121.70757477, 129.70100881, 111.67411923, 131.1979314 ,
  ...328765287e-39, 3.3968653938213694e-40, 1.9321679678623975e-36, 8.482777798353687e-40, nan, 7.06503867181238e-40, ...]})

    def test_txComp_GMM_anova(test_ref_pos_list):
        ml = mock.Mock()
        if sys.version_info < (3, 6):
            tol = 0.0002
        else:
            tol=0.00000001
        res = txCompare(test_ref_pos_list[0], methods=['GMM'], logit=False, sequence_context=2, min_coverage=3, logger=ml, allow_warnings=False, random_state=np.random.RandomState(seed=42))
        GMM_pvalues = [pos['txComp']['GMM_anova_pvalue'] for pos in res ]
        print(res[3]['txComp'])
>       assert GMM_pvalues == [pytest.approx(i, abs=tol, nan_ok=True) for i in test_ref_pos_list[1]['GMM_anova']]
E       AssertionError: assert [0.0008574768...76768562, ...] == [0.00085747684... 2.0e-04, ...]
E         At index 3 diff: 0.0017335646468135102 != 0.0010906844025473576 ± 2.0e-04
E         Full diff:
E         - [0.0008574768473501677,
E         + [0.0008574768473501677 ± 2.0e-04,
E         ?                       ++++++++++
E         -  0.0036329291397528157,
E         +  0.0036329291397528157 ± 2.0e-04,...
E         
E         ...Full output truncated (24 lines hidden), use '-vv' to show

test_TxComp.py:105: AssertionError
=========================================================================================================================== 1 failed, 15 passed in 1.34 seconds ============================================================================================================================
tleonardi commented 5 years ago

As a temporary workaround I'm lowering the tol for python 3.5

a-slide commented 5 years ago

At the moment it would be advisable to use Python3.6+ instead