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updating baselines for regression tests
1 parent 3143bcb commit aeb4638

10 files changed

Lines changed: 95 additions & 84 deletions

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‎CodeEntropy/levels/neighbors.py‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -95,8 +95,8 @@ def get_neighbors(self, universe, levels, groups, search_type):
9595
len(molecules) * number_frames
9696
)
9797
logger.debug(
98-
f"group: {group_id}",
99-
f"number neighbors {average_number_neighbors[group_id]}",
98+
f"group: {group_id}"
99+
f"number neighbors {average_number_neighbors[group_id]}"
100100
)
101101

102102
return average_number_neighbors
@@ -234,14 +234,13 @@ def _get_linear(self, rdkit_mol, number_heavy):
234234
Returns:
235235
linear (bool): True if molecule linear
236236
"""
237-
rdkit_heavy = Chem.RemoveHs(rdkit_mol)
238-
239237
linear = False
240238
if number_heavy == 1:
241239
linear = False
242240
elif number_heavy == 2:
243241
linear = True
244242
else:
243+
rdkit_heavy = Chem.RemoveHs(rdkit_mol)
245244
sp_count = 0
246245
for x in rdkit_heavy.GetAtoms():
247246
if x.GetHybridization() == Chem.HybridizationType.SP:

‎tests/regression/baselines/benzaldehyde.json‎

Lines changed: 13 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
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"args": {
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"top_traj_file": [
4-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/benzaldehyde/molecules.top",
5-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/benzaldehyde/trajectory.crd"
4+
"/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top",
5+
"/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
66
],
7-
"force_file": "/home/tdo96567/BioSim/CodeEntropy/tests/data/benzaldehyde/forces.frc",
7+
"force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc",
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"file_format": "MDCRD",
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"kcal_force_units": false,
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"selection_string": "all",
@@ -14,18 +14,19 @@
1414
"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
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"output_file": "/tmp/pytest-of-tdo96567/pytest-60/test_regression_matches_baseli0/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli1/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
2020
"grouping": "molecules",
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"combined_forcetorque": true,
22-
"customised_axes": true
22+
"customised_axes": true,
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"search_type": "RAD"
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},
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"provenance": {
25-
"python": "3.14.0",
26-
"platform": "Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.39",
27-
"codeentropy_version": "1.0.7",
28-
"git_sha": "226b37f7b206adba1b60253c41c7a0d467e75a58"
26+
"python": "3.13.5",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
28+
"codeentropy_version": "2.0.0",
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
@@ -35,9 +36,10 @@
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"residue:FTmat-Transvibrational": 106.71035236014967,
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"residue:FTmat-Rovibrational": 95.07735227595549,
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"united_atom:Conformational": 0.0,
38-
"residue:Conformational": 0.0
39+
"residue:Conformational": 0.0,
40+
"residue:Orientational": 25.3107189764825
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},
40-
"total": 504.56360770139844
42+
"total": 529.874326677881
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}
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}
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}

‎tests/regression/baselines/benzene.json‎

Lines changed: 13 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
22
"args": {
33
"top_traj_file": [
4-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/benzene/molecules.top",
5-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/benzene/trajectory.crd"
4+
"/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top",
5+
"/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd"
66
],
7-
"force_file": "/home/tdo96567/BioSim/CodeEntropy/tests/data/benzene/forces.frc",
7+
"force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc",
88
"file_format": "MDCRD",
99
"kcal_force_units": false,
1010
"selection_string": "all",
@@ -14,18 +14,19 @@
1414
"bin_width": 30,
1515
"temperature": 298.0,
1616
"verbose": false,
17-
"output_file": "/tmp/pytest-of-tdo96567/pytest-64/test_regression_matches_baseli0/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli2/job001/output_file.json",
1818
"force_partitioning": 0.5,
1919
"water_entropy": true,
2020
"grouping": "molecules",
2121
"combined_forcetorque": true,
22-
"customised_axes": true
22+
"customised_axes": true,
23+
"search_type": "RAD"
2324
},
2425
"provenance": {
25-
"python": "3.14.0",
26-
"platform": "Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.39",
27-
"codeentropy_version": "1.0.7",
28-
"git_sha": "226b37f7b206adba1b60253c41c7a0d467e75a58"
26+
"python": "3.13.5",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
28+
"codeentropy_version": "2.0.0",
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
@@ -35,9 +36,10 @@
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"residue:FTmat-Transvibrational": 108.34125737284016,
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"residue:FTmat-Rovibrational": 95.57598285903227,
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"united_atom:Conformational": 0.0,
38-
"residue:Conformational": 0.0
39+
"residue:Conformational": 0.0,
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"residue:Orientational": 12.282076945243183
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},
40-
"total": 441.15438565731813
42+
"total": 453.43646260256133
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}
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}
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}

‎tests/regression/baselines/cyclohexane.json‎

Lines changed: 13 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
22
"args": {
33
"top_traj_file": [
4-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/cyclohexane/molecules.top",
5-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/cyclohexane/trajectory.crd"
4+
"/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top",
5+
"/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd"
66
],
7-
"force_file": "/home/tdo96567/BioSim/CodeEntropy/tests/data/cyclohexane/forces.frc",
7+
"force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc",
88
"file_format": "MDCRD",
99
"kcal_force_units": false,
1010
"selection_string": "all",
@@ -14,18 +14,19 @@
1414
"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
17-
"output_file": "/tmp/pytest-of-tdo96567/pytest-60/test_regression_matches_baseli2/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli3/job001/output_file.json",
1818
"force_partitioning": 0.5,
1919
"water_entropy": true,
2020
"grouping": "molecules",
2121
"combined_forcetorque": true,
22-
"customised_axes": true
22+
"customised_axes": true,
23+
"search_type": "RAD"
2324
},
2425
"provenance": {
25-
"python": "3.14.0",
26-
"platform": "Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.39",
27-
"codeentropy_version": "1.0.7",
28-
"git_sha": "226b37f7b206adba1b60253c41c7a0d467e75a58"
26+
"python": "3.13.5",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
28+
"codeentropy_version": "2.0.0",
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
@@ -35,9 +36,10 @@
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"residue:FTmat-Transvibrational": 106.06698045971194,
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"residue:FTmat-Rovibrational": 99.10449330958527,
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"united_atom:Conformational": 0.0,
38-
"residue:Conformational": 0.0
39+
"residue:Conformational": 0.0,
40+
"residue:Orientational": 13.963860657362106
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},
40-
"total": 541.4879176907622
42+
"total": 555.4517783481243
4143
}
4244
}
4345
}

‎tests/regression/baselines/dna.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
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"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
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"output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli0/job001/output_file.json",
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"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli0/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
2020
"grouping": "molecules",
@@ -24,9 +24,9 @@
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},
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"provenance": {
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"python": "3.13.5",
27-
"platform": "Linux-6.17.0-1011-oem-x86_64-with-glibc2.39",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
2828
"codeentropy_version": "2.0.0",
29-
"git_sha": "44bd758498dfdd07eb391ee86e6ff2d86ea2bcb8"
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {

‎tests/regression/baselines/ethyl-acetate.json‎

Lines changed: 14 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
22
"args": {
33
"top_traj_file": [
4-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/ethyl-acetate/molecules.top",
5-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/ethyl-acetate/trajectory.crd"
4+
"/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top",
5+
"/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd"
66
],
7-
"force_file": "/home/tdo96567/BioSim/CodeEntropy/tests/data/ethyl-acetate/forces.frc",
7+
"force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc",
88
"file_format": "MDCRD",
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"kcal_force_units": false,
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"selection_string": "all",
@@ -14,30 +14,32 @@
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"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
17-
"output_file": "/tmp/pytest-of-tdo96567/pytest-60/test_regression_matches_baseli4/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli4/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
2020
"grouping": "molecules",
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"combined_forcetorque": true,
22-
"customised_axes": true
22+
"customised_axes": true,
23+
"search_type": "RAD"
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},
2425
"provenance": {
25-
"python": "3.14.0",
26-
"platform": "Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.39",
27-
"codeentropy_version": "1.0.7",
28-
"git_sha": "226b37f7b206adba1b60253c41c7a0d467e75a58"
26+
"python": "3.13.5",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
28+
"codeentropy_version": "2.0.0",
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
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"components": {
33-
"united_atom:Transvibrational": 119.77870290196522,
34+
"united_atom:Transvibrational": 124.52960172835098,
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"united_atom:Rovibrational": 144.2366436580796,
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"residue:FTmat-Transvibrational": 103.5819666889598,
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"residue:FTmat-Rovibrational": 95.68311953660015,
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"united_atom:Conformational": 8.140778318198597,
38-
"residue:Conformational": 0.0
39+
"residue:Conformational": 0.0,
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"residue:Orientational": 30.894081870911737
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},
40-
"total": 471.4212111038034
42+
"total": 507.0661918011009
4143
}
4244
}
4345
}

‎tests/regression/baselines/methane.json‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
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"bin_width": 30,
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"temperature": 112.0,
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"verbose": false,
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"output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli1/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli5/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
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"grouping": "molecules",
@@ -24,19 +24,19 @@
2424
},
2525
"provenance": {
2626
"python": "3.13.5",
27-
"platform": "Linux-6.17.0-1011-oem-x86_64-with-glibc2.39",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
2828
"codeentropy_version": "2.0.0",
29-
"git_sha": "44bd758498dfdd07eb391ee86e6ff2d86ea2bcb8"
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"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
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"components": {
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"united_atom:Transvibrational": 75.73291215434239,
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"united_atom:Rovibrational": 68.80103728327107,
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"united_atom:Conformational": 0.0,
37-
"united_atom:Orientational": 5.499485304173264
37+
"united_atom:Orientational": 6.742734054179628
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},
39-
"total": 150.03343474178672
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"total": 151.27668349179308
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}
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}
4242
}

‎tests/regression/baselines/methanol.json‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
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"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
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"output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli2/job001/output_file.json",
17+
"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli6/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
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"grouping": "molecules",
@@ -24,9 +24,9 @@
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},
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"provenance": {
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"python": "3.13.5",
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"platform": "Linux-6.17.0-1011-oem-x86_64-with-glibc2.39",
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"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
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"codeentropy_version": "2.0.0",
29-
"git_sha": "44bd758498dfdd07eb391ee86e6ff2d86ea2bcb8"
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"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
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"0": {
@@ -37,9 +37,9 @@
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"residue:FTmat-Rovibrational": 59.61417719536213,
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"residue:Conformational": 0.0,
40-
"residue:Orientational": 16.370329454731248
40+
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"total": 255.32937360755813
42+
"total": 256.0586060738593
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}
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}
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}

‎tests/regression/baselines/octonol.json‎

Lines changed: 14 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
22
"args": {
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"top_traj_file": [
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"/home/tdo96567/BioSim/CodeEntropy/tests/data/octonol/molecules.top",
5-
"/home/tdo96567/BioSim/CodeEntropy/tests/data/octonol/trajectory.crd"
4+
"/home/ogo12949/CodeEntropy/.testdata/octonol/molecules.top",
5+
"/home/ogo12949/CodeEntropy/.testdata/octonol/trajectory.crd"
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],
7-
"force_file": "/home/tdo96567/BioSim/CodeEntropy/tests/data/octonol/forces.frc",
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"force_file": "/home/ogo12949/CodeEntropy/.testdata/octonol/forces.frc",
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"file_format": "MDCRD",
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"kcal_force_units": false,
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"selection_string": "all",
@@ -14,30 +14,32 @@
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"bin_width": 30,
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"temperature": 298.0,
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"verbose": false,
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"output_file": "/tmp/pytest-of-tdo96567/pytest-65/test_regression_matches_baseli0/job001/output_file.json",
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"output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli7/job001/output_file.json",
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"force_partitioning": 0.5,
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"water_entropy": true,
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"grouping": "molecules",
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"combined_forcetorque": true,
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"customised_axes": true
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"customised_axes": true,
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"search_type": "RAD"
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},
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"provenance": {
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"python": "3.14.0",
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"platform": "Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.39",
27-
"codeentropy_version": "1.0.7",
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"git_sha": "226b37f7b206adba1b60253c41c7a0d467e75a58"
26+
"python": "3.13.5",
27+
"platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
28+
"codeentropy_version": "2.0.0",
29+
"git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f"
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},
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"groups": {
3132
"0": {
3233
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33-
"united_atom:Transvibrational": 222.4800037654818,
34+
"united_atom:Transvibrational": 254.7961136639108,
3435
"united_atom:Rovibrational": 345.86413400118744,
3536
"residue:FTmat-Transvibrational": 101.79847675768119,
3637
"residue:FTmat-Rovibrational": 92.71423842383722,
3738
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38-
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39+
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40+
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3941
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40-
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42+
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4143
}
4244
}
4345
}

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