Update gold files after upgrading dependencies since SeedSequence fix…

… in numpy 1.19 (numpy/numpy#16551); fix some pytest warnings

requirements_dev.txt

@@ -8,8 +8,7 @@ sphinx-rtd-theme
 twine
 pylint
 coverage
-# Upgrade pytest after fix released: https://github.com/pytest-dev/pytest/pull/6992
-pytest == 5.3.5
+pytest
 pytest-runner
 pytest-regressions
 pytest-profiling

setup.cfg

@@ -25,5 +25,7 @@ max-line-length = 160
 test = pytest
 
 [tool:pytest]
-collect_ignore = ['setup.py']
 norecursedirs = tests/condor_tests
+log_level = WARNING
+filterwarnings =
+    ignore:numpy.ufunc size changed

tests/condor_tests/test_hierarchical/test_condor_simulation_clustering_hierarchy_fdr.csv

@@ -1,60 +1,60 @@
 name,parent_name,p-value,rejected_status,adjusted_p-value
 [0-57] (size: 30),,0.0909,0,0.0909
-[25-56] (size: 17),[0-57] (size: 30),0.0909,0,1.0
-[0-23] (size: 13),[0-57] (size: 30),0.0909,0,1.0
-[32-55] (size: 13),[25-56] (size: 17),0.0909,0,1.0
-[25-30] (size: 4),[25-56] (size: 17),0.0909,0,1.0
-[17-22] (size: 4),[0-23] (size: 13),0.0909,0,1.0
-[0-15] (size: 9),[0-23] (size: 13),0.0909,0,1.0
-[51-54] (size: 3),[32-55] (size: 13),0.0909,0,1.0
-[32-49] (size: 10),[32-55] (size: 13),0.0909,0,1.0
-[25-26] (size: 2),[25-30] (size: 4),0.0909,0,1.0
-[28-29] (size: 2),[25-30] (size: 4),0.0909,0,1.0
-17,[17-22] (size: 4),0.0909,0,1.0
-[18-21] (size: 3),[17-22] (size: 4),0.0909,0,1.0
-[0-11] (size: 7),[0-15] (size: 9),0.0909,0,1.0
-[13-14] (size: 2),[0-15] (size: 9),0.0909,0,1.0
+[27-56] (size: 16),[0-57] (size: 30),0.0909,0,1.0
+[0-25] (size: 14),[0-57] (size: 30),0.0909,0,1.0
+[34-55] (size: 12),[27-56] (size: 16),0.0909,0,1.0
+[27-32] (size: 4),[27-56] (size: 16),0.0909,0,1.0
+[0-19] (size: 11),[0-25] (size: 14),0.0909,0,1.0
+[21-24] (size: 3),[0-25] (size: 14),0.0909,0,1.0
+[34-49] (size: 9),[34-55] (size: 12),0.0909,0,1.0
+[51-54] (size: 3),[34-55] (size: 12),0.0909,0,1.0
+[28-31] (size: 3),[27-32] (size: 4),0.0909,0,1.0
+27,[27-32] (size: 4),0.2727,0,1.0
+[1-18] (size: 10),[0-19] (size: 11),0.0909,0,1.0
+0,[0-19] (size: 11),0.0909,0,1.0
+21,[21-24] (size: 3),0.3636,0,1.0
+[22-23] (size: 2),[21-24] (size: 3),0.0909,0,1.0
+[34-35] (size: 2),[34-49] (size: 9),0.0909,0,1.0
+[37-48] (size: 7),[34-49] (size: 9),0.0909,0,1.0
 51,[51-54] (size: 3),0.0909,0,1.0
 [52-53] (size: 2),[51-54] (size: 3),0.0909,0,1.0
-[35-48] (size: 8),[32-49] (size: 10),0.0909,0,1.0
-[32-33] (size: 2),[32-49] (size: 10),0.0909,0,1.0
-25,[25-26] (size: 2),0.0909,0,1.0
-26,[25-26] (size: 2),0.6364,0,1.0
-29,[28-29] (size: 2),0.2727,0,1.0
-28,[28-29] (size: 2),0.0909,0,1.0
-[19-20] (size: 2),[18-21] (size: 3),0.0909,0,1.0
-18,[18-21] (size: 3),0.0909,0,1.0
-[0-3] (size: 3),[0-11] (size: 7),0.1818,0,1.0
-[5-10] (size: 4),[0-11] (size: 7),0.0909,0,1.0
-14,[13-14] (size: 2),0.0909,0,1.0
-13,[13-14] (size: 2),0.0909,0,1.0
-52,[52-53] (size: 2),0.1818,0,1.0
+[29-30] (size: 2),[28-31] (size: 3),0.0909,0,1.0
+28,[28-31] (size: 3),0.0909,0,1.0
+[2-17] (size: 9),[1-18] (size: 10),0.0909,0,1.0
+1,[1-18] (size: 10),0.0909,0,1.0
+23,[22-23] (size: 2),0.2727,0,1.0
+22,[22-23] (size: 2),0.1818,0,1.0
+34,[34-35] (size: 2),0.3636,0,1.0
+35,[34-35] (size: 2),0.0909,0,1.0
+37,[37-48] (size: 7),0.0909,0,1.0
+[38-47] (size: 6),[37-48] (size: 7),0.0909,0,1.0
 53,[52-53] (size: 2),0.0909,0,1.0
-[36-47] (size: 7),[35-48] (size: 8),0.0909,0,1.0
-35,[35-48] (size: 8),0.8182,0,1.0
-33,[32-33] (size: 2),0.0909,0,1.0
-32,[32-33] (size: 2),0.0909,0,1.0
-19,[19-20] (size: 2),0.0909,0,1.0
-20,[19-20] (size: 2),0.0909,0,1.0
-0,[0-3] (size: 3),1.0,0,1.0
-[1-2] (size: 2),[0-3] (size: 3),0.6364,0,1.0
-5,[5-10] (size: 4),0.0909,0,1.0
-[6-9] (size: 3),[5-10] (size: 4),0.1818,0,1.0
-[37-46] (size: 6),[36-47] (size: 7),0.0909,0,1.0
-36,[36-47] (size: 7),0.7273,0,1.0
-2,[1-2] (size: 2),0.4545,0,1.0
-1,[1-2] (size: 2),0.4545,0,1.0
-6,[6-9] (size: 3),0.3636,0,1.0
-[7-8] (size: 2),[6-9] (size: 3),0.0909,0,1.0
-[40-45] (size: 4),[37-46] (size: 6),0.0909,0,1.0
-[37-38] (size: 2),[37-46] (size: 6),0.0909,0,1.0
-7,[7-8] (size: 2),0.1818,0,1.0
-8,[7-8] (size: 2),0.6364,0,1.0
+52,[52-53] (size: 2),0.8182,0,1.0
+29,[29-30] (size: 2),0.0909,0,1.0
+30,[29-30] (size: 2),0.4545,0,1.0
+2,[2-17] (size: 9),0.0909,0,1.0
+[3-16] (size: 8),[2-17] (size: 9),0.0909,0,1.0
+[39-46] (size: 5),[38-47] (size: 6),0.0909,0,1.0
+38,[38-47] (size: 6),0.2727,0,1.0
+[4-15] (size: 7),[3-16] (size: 8),0.0909,0,1.0
+3,[3-16] (size: 8),0.0909,0,1.0
+[40-45] (size: 4),[39-46] (size: 5),0.0909,0,1.0
+39,[39-46] (size: 5),1.0,0,1.0
+[5-14] (size: 6),[4-15] (size: 7),0.0909,0,1.0
+4,[4-15] (size: 7),0.0909,0,1.0
 [41-44] (size: 3),[40-45] (size: 4),0.0909,0,1.0
-40,[40-45] (size: 4),0.3636,0,1.0
-38,[37-38] (size: 2),0.0909,0,1.0
-37,[37-38] (size: 2),0.1818,0,1.0
-41,[41-44] (size: 3),0.3636,0,1.0
+40,[40-45] (size: 4),0.0909,0,1.0
+[6-13] (size: 5),[5-14] (size: 6),0.0909,0,1.0
+5,[5-14] (size: 6),0.5455,0,1.0
 [42-43] (size: 2),[41-44] (size: 3),0.0909,0,1.0
-43,[42-43] (size: 2),0.0909,0,1.0
+41,[41-44] (size: 3),0.0909,0,1.0
+6,[6-13] (size: 5),0.0909,0,1.0
+[7-12] (size: 4),[6-13] (size: 5),0.0909,0,1.0
 42,[42-43] (size: 2),0.0909,0,1.0
+43,[42-43] (size: 2),0.8182,0,1.0
+7,[7-12] (size: 4),0.1818,0,1.0
+[8-11] (size: 3),[7-12] (size: 4),0.0909,0,1.0
+8,[8-11] (size: 3),0.0909,0,1.0
+[9-10] (size: 2),[8-11] (size: 3),0.3636,0,1.0
+10,[9-10] (size: 2),0.1818,0,1.0
+9,[9-10] (size: 2),0.2727,0,1.0

tests/condor_tests/test_hierarchical/test_condor_simulation_random_hierarchy_fdr.csv

@@ -2,60 +2,60 @@ name,parent_name,p-value,rejected_status,adjusted_p-value
 [0-58] (size: 30),,0.0909,0,0.0909
 [31-57] (size: 14),[0-58] (size: 30),0.0909,0,1.0
 [0-29] (size: 16),[0-58] (size: 30),0.0909,0,1.0
-[31-44] (size: 8),[31-57] (size: 14),0.5455,0,1.0
+[31-44] (size: 8),[31-57] (size: 14),0.0909,0,1.0
 [46-56] (size: 6),[31-57] (size: 14),0.0909,0,1.0
 [0-13] (size: 8),[0-29] (size: 16),0.0909,0,1.0
 [15-28] (size: 8),[0-29] (size: 16),0.0909,0,1.0
-[31-36] (size: 4),[31-44] (size: 8),0.3636,0,1.0
-[38-43] (size: 4),[31-44] (size: 8),0.9091,0,1.0
+[31-36] (size: 4),[31-44] (size: 8),0.6364,0,1.0
+[38-43] (size: 4),[31-44] (size: 8),0.0909,0,1.0
 [46-51] (size: 4),[46-56] (size: 6),0.0909,0,1.0
-[53-55] (size: 2),[46-56] (size: 6),0.1818,0,1.0
+[53-55] (size: 2),[46-56] (size: 6),0.2727,0,1.0
 [7-12] (size: 4),[0-13] (size: 8),0.0909,0,1.0
 [0-5] (size: 4),[0-13] (size: 8),0.0909,0,1.0
 [15-20] (size: 4),[15-28] (size: 8),0.0909,0,1.0
 [22-27] (size: 4),[15-28] (size: 8),0.0909,0,1.0
-[31-32] (size: 2),[31-36] (size: 4),0.5455,0,1.0
-[34-35] (size: 2),[31-36] (size: 4),0.6364,0,1.0
-[38-39] (size: 2),[38-43] (size: 4),1.0,0,1.0
-[41-42] (size: 2),[38-43] (size: 4),0.8182,0,1.0
+[31-32] (size: 2),[31-36] (size: 4),0.3636,0,1.0
+[34-35] (size: 2),[31-36] (size: 4),0.3636,0,1.0
+[38-39] (size: 2),[38-43] (size: 4),0.1818,0,1.0
+[41-42] (size: 2),[38-43] (size: 4),0.0909,0,1.0
 [46-47] (size: 2),[46-51] (size: 4),0.0909,0,1.0
-[49-50] (size: 2),[46-51] (size: 4),0.9091,0,1.0
-[53-54] (size: 2),[53-55] (size: 2),0.2727,0,1.0
-[10-11] (size: 2),[7-12] (size: 4),0.1818,0,1.0
+[49-50] (size: 2),[46-51] (size: 4),0.2727,0,1.0
+[53-54] (size: 2),[53-55] (size: 2),0.4545,0,1.0
+[10-11] (size: 2),[7-12] (size: 4),0.0909,0,1.0
 [7-8] (size: 2),[7-12] (size: 4),0.0909,0,1.0
 [0-1] (size: 2),[0-5] (size: 4),0.0909,0,1.0
 [3-4] (size: 2),[0-5] (size: 4),0.0909,0,1.0
-[18-19] (size: 2),[15-20] (size: 4),0.7273,0,1.0
+[18-19] (size: 2),[15-20] (size: 4),0.6364,0,1.0
 [15-16] (size: 2),[15-20] (size: 4),0.0909,0,1.0
 [22-23] (size: 2),[22-27] (size: 4),0.0909,0,1.0
 [25-26] (size: 2),[22-27] (size: 4),0.0909,0,1.0
-32,[31-32] (size: 2),0.8182,0,1.0
-31,[31-32] (size: 2),0.7273,0,1.0
-35,[34-35] (size: 2),0.6364,0,1.0
+32,[31-32] (size: 2),0.4545,0,1.0
+31,[31-32] (size: 2),0.5455,0,1.0
+35,[34-35] (size: 2),0.5455,0,1.0
 34,[34-35] (size: 2),0.2727,0,1.0
 38,[38-39] (size: 2),0.7273,0,1.0
-39,[38-39] (size: 2),1.0,0,1.0
-41,[41-42] (size: 2),0.8182,0,1.0
-42,[41-42] (size: 2),1.0,0,1.0
+39,[38-39] (size: 2),0.3636,0,1.0
+41,[41-42] (size: 2),0.9091,0,1.0
+42,[41-42] (size: 2),0.0909,0,1.0
 47,[46-47] (size: 2),0.0909,0,1.0
 46,[46-47] (size: 2),0.0909,0,1.0
-50,[49-50] (size: 2),0.9091,0,1.0
-49,[49-50] (size: 2),1.0,0,1.0
-54,[53-54] (size: 2),0.0909,0,1.0
-53,[53-54] (size: 2),0.4545,0,1.0
+50,[49-50] (size: 2),0.7273,0,1.0
+49,[49-50] (size: 2),0.0909,0,1.0
+54,[53-54] (size: 2),0.2727,0,1.0
+53,[53-54] (size: 2),0.8182,0,1.0
 11,[10-11] (size: 2),0.0909,0,1.0
-10,[10-11] (size: 2),0.1818,0,1.0
+10,[10-11] (size: 2),0.7273,0,1.0
 7,[7-8] (size: 2),0.0909,0,1.0
-8,[7-8] (size: 2),0.4545,0,1.0
+8,[7-8] (size: 2),0.6364,0,1.0
 0,[0-1] (size: 2),0.0909,0,1.0
 1,[0-1] (size: 2),0.0909,0,1.0
-4,[3-4] (size: 2),0.7273,0,1.0
+4,[3-4] (size: 2),0.9091,0,1.0
 3,[3-4] (size: 2),0.0909,0,1.0
-18,[18-19] (size: 2),0.9091,0,1.0
-19,[18-19] (size: 2),0.5455,0,1.0
-15,[15-16] (size: 2),0.8182,0,1.0
+18,[18-19] (size: 2),0.7273,0,1.0
+19,[18-19] (size: 2),0.7273,0,1.0
+15,[15-16] (size: 2),0.7273,0,1.0
 16,[15-16] (size: 2),0.0909,0,1.0
 23,[22-23] (size: 2),0.0909,0,1.0
-22,[22-23] (size: 2),0.0909,0,1.0
+22,[22-23] (size: 2),1.0,0,1.0
 26,[25-26] (size: 2),0.0909,0,1.0
 25,[25-26] (size: 2),0.0909,0,1.0

tests/condor_tests/test_hierarchical/test_condor_simulation_shuffling_perturbation_fdr.csv

@@ -11,51 +11,51 @@ name,parent_name,p-value,rejected_status,adjusted_p-value
 [7-12] (size: 4),[0-13] (size: 8),0.0909,0,1.0
 [0-5] (size: 4),[0-13] (size: 8),0.0909,0,1.0
 [38-43] (size: 4),[31-44] (size: 8),0.0909,0,1.0
-[31-36] (size: 4),[31-44] (size: 8),0.8182,0,1.0
+[31-36] (size: 4),[31-44] (size: 8),0.0909,0,1.0
 [53-55] (size: 2),[46-56] (size: 6),0.0909,0,1.0
 [46-51] (size: 4),[46-56] (size: 6),0.0909,0,1.0
-[18-19] (size: 2),[15-20] (size: 4),0.4545,0,1.0
+[18-19] (size: 2),[15-20] (size: 4),0.0909,0,1.0
 [15-16] (size: 2),[15-20] (size: 4),0.0909,0,1.0
-[25-26] (size: 2),[22-27] (size: 4),1.0,0,1.0
+[25-26] (size: 2),[22-27] (size: 4),0.2727,0,1.0
 [22-23] (size: 2),[22-27] (size: 4),0.0909,0,1.0
 [10-11] (size: 2),[7-12] (size: 4),0.0909,0,1.0
 [7-8] (size: 2),[7-12] (size: 4),0.0909,0,1.0
 [3-4] (size: 2),[0-5] (size: 4),0.0909,0,1.0
 [0-1] (size: 2),[0-5] (size: 4),0.0909,0,1.0
 [38-39] (size: 2),[38-43] (size: 4),0.0909,0,1.0
 [41-42] (size: 2),[38-43] (size: 4),0.0909,0,1.0
-[34-35] (size: 2),[31-36] (size: 4),0.5455,0,1.0
-[31-32] (size: 2),[31-36] (size: 4),0.9091,0,1.0
+[34-35] (size: 2),[31-36] (size: 4),0.9091,0,1.0
+[31-32] (size: 2),[31-36] (size: 4),0.0909,0,1.0
 [53-54] (size: 2),[53-55] (size: 2),0.0909,0,1.0
 [46-47] (size: 2),[46-51] (size: 4),0.0909,0,1.0
 [49-50] (size: 2),[46-51] (size: 4),0.0909,0,1.0
-18,[18-19] (size: 2),0.2727,0,1.0
-19,[18-19] (size: 2),0.6364,0,1.0
+18,[18-19] (size: 2),0.4545,0,1.0
+19,[18-19] (size: 2),0.2727,0,1.0
 15,[15-16] (size: 2),0.0909,0,1.0
 16,[15-16] (size: 2),0.0909,0,1.0
-26,[25-26] (size: 2),0.9091,0,1.0
-25,[25-26] (size: 2),0.8182,0,1.0
-22,[22-23] (size: 2),1.0,0,1.0
+26,[25-26] (size: 2),0.4545,0,1.0
+25,[25-26] (size: 2),0.2727,0,1.0
+22,[22-23] (size: 2),0.7273,0,1.0
 23,[22-23] (size: 2),0.0909,0,1.0
-11,[10-11] (size: 2),0.7273,0,1.0
+11,[10-11] (size: 2),0.2727,0,1.0
 10,[10-11] (size: 2),0.0909,0,1.0
-7,[7-8] (size: 2),0.6364,0,1.0
+7,[7-8] (size: 2),0.2727,0,1.0
 8,[7-8] (size: 2),0.0909,0,1.0
 3,[3-4] (size: 2),0.0909,0,1.0
 4,[3-4] (size: 2),0.0909,0,1.0
 0,[0-1] (size: 2),0.0909,0,1.0
-1,[0-1] (size: 2),0.7273,0,1.0
-38,[38-39] (size: 2),0.5455,0,1.0
+1,[0-1] (size: 2),0.1818,0,1.0
+38,[38-39] (size: 2),0.6364,0,1.0
 39,[38-39] (size: 2),0.0909,0,1.0
-42,[41-42] (size: 2),0.4545,0,1.0
+42,[41-42] (size: 2),0.5455,0,1.0
 41,[41-42] (size: 2),0.0909,0,1.0
 34,[34-35] (size: 2),0.6364,0,1.0
-35,[34-35] (size: 2),0.3636,0,1.0
-31,[31-32] (size: 2),1.0,0,1.0
-32,[31-32] (size: 2),0.8182,0,1.0
+35,[34-35] (size: 2),1.0,0,1.0
+31,[31-32] (size: 2),0.0909,0,1.0
+32,[31-32] (size: 2),0.3636,0,1.0
 54,[53-54] (size: 2),0.0909,0,1.0
 53,[53-54] (size: 2),0.0909,0,1.0
-46,[46-47] (size: 2),0.3636,0,1.0
+46,[46-47] (size: 2),0.9091,0,1.0
 47,[46-47] (size: 2),0.0909,0,1.0
-50,[49-50] (size: 2),0.3636,0,1.0
+50,[49-50] (size: 2),0.0909,0,1.0
 49,[49-50] (size: 2),0.0909,0,1.0

tests/condor_tests/test_temporal/test_condor_simulation_classifier1.json

@@ -11,16 +11,16 @@
   },
   "model": {
     "windows": [
-      "(14, 17)",
-      "(3, 14)",
-      "(2, 11)",
-      "(15, 16)",
+      "(3, 18)",
+      "(5, 10)",
+      "(1, 10)",
       "(7, 19)",
-      "(1, 16)",
-      "(12, 19)",
-      "(10, 15)",
-      "(14, 16)",
-      "(2, 10)"
+      "(3, 11)",
+      "(7, 17)",
+      "(1, 10)",
+      "(0, 11)",
+      "(1, 10)",
+      "(7, 17)"
     ],
     "aggregation_fns": [
       "Slope",
@@ -40,9 +40,9 @@
     "FDR": 0.0,
     "Power": 0.8,
     "Ordering_All_Important_FDR": 0.0,
-    "Ordering_All_Important_Power": 0.6,
+    "Ordering_All_Important_Power": 0.8,
     "Ordering_Identified_Important_FDR": 0.0,
-    "Ordering_Identified_Important_Power": 0.75,
+    "Ordering_Identified_Important_Power": 1.0,
     "Average_Window_FDR": 0.0,
     "Average_Window_Power": 1.0,
     "Window_Overlap": {
@@ -52,9 +52,9 @@
       "6": 1.0
     },
     "Window_Important_FDR": 0.0,
-    "Window_Important_Power": 1.0,
+    "Window_Important_Power": 0.75,
     "Window_Ordering_Important_FDR": 0.0,
-    "Window_Ordering_Important_Power": 0.5,
+    "Window_Ordering_Important_Power": 1.0,
     "overall_scores_corr": 1.0,
     "window_scores_corr": 1.0,
     "overall_relevant_scores_corr": 1.0,

tests/condor_tests/test_temporal/test_condor_simulation_classifier2.json

@@ -11,16 +11,16 @@
   },
   "model": {
     "windows": [
-      "(14, 17)",
-      "(3, 14)",
-      "(2, 11)",
-      "(15, 16)",
+      "(3, 18)",
+      "(5, 10)",
+      "(1, 10)",
       "(7, 19)",
-      "(1, 16)",
-      "(12, 19)",
-      "(10, 15)",
-      "(14, 16)",
-      "(2, 10)"
+      "(3, 11)",
+      "(7, 17)",
+      "(1, 10)",
+      "(0, 11)",
+      "(1, 10)",
+      "(7, 17)"
     ],
     "aggregation_fns": [
       "Slope",
@@ -40,17 +40,17 @@
     "FDR": 0.0,
     "Power": 1.0,
     "Ordering_All_Important_FDR": 0.0,
-    "Ordering_All_Important_Power": 0.8,
+    "Ordering_All_Important_Power": 1.0,
     "Ordering_Identified_Important_FDR": 0.0,
-    "Ordering_Identified_Important_Power": 0.8,
+    "Ordering_Identified_Important_Power": 1.0,
     "Average_Window_FDR": 0.0,
-    "Average_Window_Power": 1.0,
+    "Average_Window_Power": 0.9246153846,
     "Window_Overlap": {
       "1": 1.0,
-      "3": 1.0,
+      "3": 0.9615384615384616,
       "5": 1.0,
       "6": 1.0,
-      "8": 1.0
+      "8": 0.85
     },
     "Window_Important_FDR": 0.0,
     "Window_Important_Power": 1.0,