Coverage for tests/test_utils.py: 93%

1import unittest 

2 

3 

4import yaml 

5import numpy as np 

6from pathlib import Path 

7import MPP 

8import MPP.run as run_module 

9 

10 

11config_dir = "/data/evaluation/MPP/stochastic_MPP_Felix/data_production/sm/config/" 

12root = "/data/evaluation/MPP/stochastic_MPP_Felix/data_production/sm/results/" 

13 

14SYSTEMS = [ 

15 "HP35", 

16 "PDZ3_7", 

17 "aSyn_rdc_200ns", 

18 "HP35_stoch", 

19] 

20SETUPS = [ 

21 "t", 

22 "kl", 

23 "t_js", 

24 "kl_js", 

25 "gpcca", 

26] 

27 

28with open(f"{config_dir}lumpings.yaml") as f: 

29 lumpings = yaml.safe_load(f) 

30 

31 

32def get_d(system, setup, rmsd=False): 

33 d = run_module.Data( 

34 f"/data/evaluation/MPP/stochastic_MPP_Felix/data_production/sm/config/{system}.yaml" 

35 ) 

36 d.setup_mpp( 

37 lumpings[setup]["kernel similarity"], 

38 lumpings[setup]["feature kernel"], 

39 ) 

40 if setup == "gpcca": 40 ↛ 41line 40 didn't jump to line 41 because the condition on line 40 was never true

41 d.perform_gpcca("ref", f"{root}{system}/{setup}/Z.npy") 

42 else: 

43 d.perform_mpp(f"{root}{system}/{setup}/Z.npy") 

44 if rmsd: 44 ↛ 45line 44 didn't jump to line 45 because the condition on line 44 was never true

45 d.mpp.load_rmsd(f"{root}{system}/{setup}/rmsd.npy") 

46 return d 

47 

48 

49class TestProperties(unittest.TestCase): 

50 def setUp(self): 

51 self.d = get_d("HP35", "t") 

52 self.mpp = self.d.mpp 

53 

54 def test_Z_to_linkage(self): 

55 linkage = MPP.utils.Z_to_linkage(self.mpp.Z[self.mpp.n_i]) 

56 expected_linkage = np.load( 

57 Path(__file__).parent 

58 / "data" 

59 / "HP35" 

60 / "expected_output" 

61 / "t" 

62 / "linkage.npy" 

63 ) 

64 np.testing.assert_allclose(linkage, expected_linkage) 

65 

66 def test_linkage_to_Z(self): 

67 expected_linkage = np.load( 

68 Path(__file__).parent 

69 / "data" 

70 / "HP35" 

71 / "expected_output" 

72 / "t" 

73 / "linkage.npy" 

74 ) 

75 z_i, full_pop = MPP.utils.linkage_to_Z(expected_linkage, self.mpp.pop) 

76 expected_z = np.load( 

77 Path(__file__).parent / "data" / "HP35" / "expected_output" / "t" / "Z.npy" 

78 ) 

79 np.testing.assert_allclose(z_i, expected_z[0]) 

80 

81 def test_calc_full_tmat(self): 

82 expected_tmat = np.load( 

83 Path(__file__).parent 

84 / "data" 

85 / "HP35" 

86 / "expected_output" 

87 / "t" 

88 / "full_tmat.npy" 

89 ) 

90 expected_pop = np.load( 

91 Path(__file__).parent 

92 / "data" 

93 / "HP35" 

94 / "expected_output" 

95 / "t" 

96 / "full_pop.npy" 

97 ) 

98 full_tmat, full_pop = MPP.utils.calc_full_tmat( 

99 self.mpp.tmat, self.mpp.pop, self.mpp.Z 

100 ) 

101 np.testing.assert_allclose(full_tmat, expected_tmat) 

102 np.testing.assert_allclose(full_pop, expected_pop) 

103 

104 def test_Z_to_mask(self): 

105 expected_mask = np.load( 

106 Path(__file__).parent 

107 / "data" 

108 / "HP35" 

109 / "expected_output" 

110 / "t" 

111 / "full_mask.npy" 

112 ) 

113 full_mask = MPP.utils.Z_to_mask(self.mpp.Z[0]) 

114 np.testing.assert_allclose(full_mask, expected_mask) 

115 

116 

117class TestFullFeature(unittest.TestCase): 

118 def setUp(self): 

119 self.d = get_d("HP35", "t_js") 

120 

121 def test_full_feature_from_Z(self): 

122 expected_full_feature = np.load( 

123 Path(__file__).parent 

124 / "data" 

125 / "HP35" 

126 / "expected_output" 

127 / "t_js" 

128 / "full_feature.npy" 

129 ) 

130 full_feature = self.d.feature_kernel.full_feature_from_Z(self.d.mpp.Z) 

131 np.testing.assert_allclose(full_feature, expected_full_feature)