CodeEntropy 2.2.1__tar.gz → 2.2.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (314) hide show
  1. {codeentropy-2.2.1 → codeentropy-2.2.2}/CITATION.cff +2 -2
  2. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/__init__.py +1 -1
  3. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/vibrational.py +2 -2
  4. {codeentropy-2.2.1 → codeentropy-2.2.2}/PKG-INFO +1 -1
  5. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/nodes/test_vibrational_node.py +1 -1
  6. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/CONTRIBUTING.md +0 -0
  7. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
  8. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  9. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/ISSUE_TEMPLATE/documentation.md +0 -0
  10. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
  11. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/ISSUE_TEMPLATE/general_report.md +0 -0
  12. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  13. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/renovate.json +0 -0
  14. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/daily.yaml +0 -0
  15. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/pr.yaml +0 -0
  16. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/release.yaml +0 -0
  17. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/update-copyright-years-in-license-file.yaml +0 -0
  18. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/update_regression_baselines.yaml +0 -0
  19. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/weekly-docs.yaml +0 -0
  20. {codeentropy-2.2.1 → codeentropy-2.2.2}/.github/workflows/weekly-regression.yaml +0 -0
  21. {codeentropy-2.2.1 → codeentropy-2.2.2}/.gitignore +0 -0
  22. {codeentropy-2.2.1 → codeentropy-2.2.2}/.pre-commit-config.yaml +0 -0
  23. {codeentropy-2.2.1 → codeentropy-2.2.2}/CODE_OF_CONDUCT.md +0 -0
  24. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/__main__.py +0 -0
  25. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/cli.py +0 -0
  26. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/config/__init__.py +0 -0
  27. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/config/argparse.py +0 -0
  28. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/config/runtime.py +0 -0
  29. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/core/__init__.py +0 -0
  30. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/core/logging.py +0 -0
  31. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/__init__.py +0 -0
  32. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/configurational.py +0 -0
  33. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/graph.py +0 -0
  34. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/__init__.py +0 -0
  35. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/aggregate.py +0 -0
  36. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/configurational.py +0 -0
  37. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/orientational.py +0 -0
  38. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/orientational.py +0 -0
  39. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/vibrational.py +0 -0
  40. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/water.py +0 -0
  41. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/workflow.py +0 -0
  42. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/__init__.py +0 -0
  43. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/axes.py +0 -0
  44. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/dihedrals.py +0 -0
  45. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/forces.py +0 -0
  46. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/frame_dag.py +0 -0
  47. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/hierarchy.py +0 -0
  48. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/level_dag.py +0 -0
  49. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/linalg.py +0 -0
  50. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/mda.py +0 -0
  51. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/neighbors.py +0 -0
  52. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/__init__.py +0 -0
  53. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/accumulators.py +0 -0
  54. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/beads.py +0 -0
  55. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/conformations.py +0 -0
  56. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/covariance.py +0 -0
  57. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/detect_levels.py +0 -0
  58. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/detect_molecules.py +0 -0
  59. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/nodes/find_neighbors.py +0 -0
  60. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/levels/search.py +0 -0
  61. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/molecules/__init__.py +0 -0
  62. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/molecules/grouping.py +0 -0
  63. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/results/__init__.py +0 -0
  64. {codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/results/reporter.py +0 -0
  65. {codeentropy-2.2.1 → codeentropy-2.2.2}/LICENSE +0 -0
  66. {codeentropy-2.2.1 → codeentropy-2.2.2}/README.md +0 -0
  67. {codeentropy-2.2.1 → codeentropy-2.2.2}/conda-recipe/meta.yaml +0 -0
  68. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/Makefile +0 -0
  69. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/README.md +0 -0
  70. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/_static/README.md +0 -0
  71. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/_static/custom.css +0 -0
  72. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/_static/logos/biosim-codeentropy_logo_dark.png +0 -0
  73. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/_static/logos/biosim-codeentropy_logo_light.png +0 -0
  74. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/_templates/README.md +0 -0
  75. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.cli.rst +0 -0
  76. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.config.argparse.rst +0 -0
  77. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.config.rst +0 -0
  78. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.config.runtime.rst +0 -0
  79. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.core.logging.rst +0 -0
  80. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.core.rst +0 -0
  81. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.configurational.rst +0 -0
  82. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.graph.rst +0 -0
  83. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.nodes.aggregate.rst +0 -0
  84. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.nodes.configurational.rst +0 -0
  85. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.nodes.rst +0 -0
  86. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.nodes.vibrational.rst +0 -0
  87. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.orientational.rst +0 -0
  88. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.rst +0 -0
  89. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.vibrational.rst +0 -0
  90. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.water.rst +0 -0
  91. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.entropy.workflow.rst +0 -0
  92. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.axes.rst +0 -0
  93. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.dihedrals.rst +0 -0
  94. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.forces.rst +0 -0
  95. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.frame_dag.rst +0 -0
  96. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.hierarchy.rst +0 -0
  97. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.level_dag.rst +0 -0
  98. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.linalg.rst +0 -0
  99. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.mda.rst +0 -0
  100. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.accumulators.rst +0 -0
  101. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.beads.rst +0 -0
  102. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.conformations.rst +0 -0
  103. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.covariance.rst +0 -0
  104. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.detect_levels.rst +0 -0
  105. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.detect_molecules.rst +0 -0
  106. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.nodes.rst +0 -0
  107. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.levels.rst +0 -0
  108. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.molecules.grouping.rst +0 -0
  109. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.molecules.rst +0 -0
  110. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.results.reporter.rst +0 -0
  111. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.results.rst +0 -0
  112. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/CodeEntropy.rst +0 -0
  113. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/api/modules.rst +0 -0
  114. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/conf.py +0 -0
  115. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/config.yaml +0 -0
  116. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/developer_guide.rst +0 -0
  117. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/faq.rst +0 -0
  118. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/getting_started.rst +0 -0
  119. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/index.rst +0 -0
  120. {codeentropy-2.2.1 → codeentropy-2.2.2}/docs/science.rst +0 -0
  121. {codeentropy-2.2.1 → codeentropy-2.2.2}/pyproject.toml +0 -0
  122. {codeentropy-2.2.1 → codeentropy-2.2.2}/readthedocs.yml +0 -0
  123. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/__init__.py +0 -0
  124. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/axes_off.json +0 -0
  125. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json +0 -0
  126. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/default.json +0 -0
  127. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/frame_window.json +0 -0
  128. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/grouping_each.json +0 -0
  129. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/rad.json +0 -0
  130. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzaldehyde/selection_subset.json +0 -0
  131. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/axes_off.json +0 -0
  132. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/combined_forcetorque_off.json +0 -0
  133. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/default.json +0 -0
  134. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/frame_window.json +0 -0
  135. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/grouping_each.json +0 -0
  136. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/rad.json +0 -0
  137. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/benzene/selection_subset.json +0 -0
  138. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/axes_off.json +0 -0
  139. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/combined_forcetorque_off.json +0 -0
  140. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/default.json +0 -0
  141. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/frame_window.json +0 -0
  142. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/grouping_each.json +0 -0
  143. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/rad.json +0 -0
  144. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/cyclohexane/selection_subset.json +0 -0
  145. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/axes_off.json +0 -0
  146. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/combined_forcetorque_off.json +0 -0
  147. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/default.json +0 -0
  148. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/frame_window.json +0 -0
  149. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/grouping_each.json +0 -0
  150. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/dna/selection_subset.json +0 -0
  151. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/axes_off.json +0 -0
  152. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/combined_forcetorque_off.json +0 -0
  153. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/default.json +0 -0
  154. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/frame_window.json +0 -0
  155. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/grouping_each.json +0 -0
  156. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/rad.json +0 -0
  157. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/ethyl-acetate/selection_subset.json +0 -0
  158. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/axes_off.json +0 -0
  159. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/combined_forcetorque_off.json +0 -0
  160. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/default.json +0 -0
  161. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/frame_window.json +0 -0
  162. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/grouping_each.json +0 -0
  163. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/rad.json +0 -0
  164. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methane/selection_subset.json +0 -0
  165. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/axes_off.json +0 -0
  166. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/combined_forcetorque_off.json +0 -0
  167. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/default.json +0 -0
  168. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/frame_window.json +0 -0
  169. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/grouping_each.json +0 -0
  170. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/rad.json +0 -0
  171. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/methanol/selection_subset.json +0 -0
  172. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/axes_off.json +0 -0
  173. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/combined_forcetorque_off.json +0 -0
  174. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/default.json +0 -0
  175. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/frame_window.json +0 -0
  176. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/grouping_each.json +0 -0
  177. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/rad.json +0 -0
  178. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/octonol/selection_subset.json +0 -0
  179. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/axes_off.json +0 -0
  180. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/combined_forcetorque_off.json +0 -0
  181. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/default.json +0 -0
  182. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/frame_window.json +0 -0
  183. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/grouping_each.json +0 -0
  184. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/rad.json +0 -0
  185. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/selection_subset.json +0 -0
  186. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/baselines/water/water_off.json +0 -0
  187. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/cases.py +0 -0
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  190. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/benzaldehyde/default.yaml +0 -0
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  192. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/benzaldehyde/grouping_each.yaml +0 -0
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  202. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/cyclohexane/axes_off.yaml +0 -0
  203. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml +0 -0
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  208. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/cyclohexane/selection_subset.yaml +0 -0
  209. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/dna/axes_off.yaml +0 -0
  210. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/dna/combined_forcetorque_off.yaml +0 -0
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  214. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/dna/selection_subset.yaml +0 -0
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  219. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/ethyl-acetate/grouping_each.yaml +0 -0
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  221. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/ethyl-acetate/selection_subset.yaml +0 -0
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  223. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methane/combined_forcetorque_off.yaml +0 -0
  224. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methane/default.yaml +0 -0
  225. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methane/frame_window.yaml +0 -0
  226. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methane/grouping_each.yaml +0 -0
  227. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methane/rad.yaml +0 -0
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  229. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/axes_off.yaml +0 -0
  230. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/combined_forcetorque_off.yaml +0 -0
  231. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/default.yaml +0 -0
  232. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/frame_window.yaml +0 -0
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  234. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/rad.yaml +0 -0
  235. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/methanol/selection_subset.yaml +0 -0
  236. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/axes_off.yaml +0 -0
  237. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/combined_forcetorque_off.yaml +0 -0
  238. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/default.yaml +0 -0
  239. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/frame_window.yaml +0 -0
  240. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/grouping_each.yaml +0 -0
  241. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/rad.yaml +0 -0
  242. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/octonol/selection_subset.yaml +0 -0
  243. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/axes_off.yaml +0 -0
  244. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/combined_forcetorque_off.yaml +0 -0
  245. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/default.yaml +0 -0
  246. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/frame_window.yaml +0 -0
  247. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/grouping_each.yaml +0 -0
  248. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/rad.yaml +0 -0
  249. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/selection_subset.yaml +0 -0
  250. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/configs/water/water_off.yaml +0 -0
  251. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/conftest.py +0 -0
  252. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/helpers.py +0 -0
  253. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/list_systems.py +0 -0
  254. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/regression/test_regression.py +0 -0
  255. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/cli/test___main__.py +0 -0
  256. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/cli/test_cli.py +0 -0
  257. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/conftest.py +0 -0
  258. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/test_argparse_build_parser.py +0 -0
  259. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/test_argparse_load_config.py +0 -0
  260. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/test_argparse_resolve.py +0 -0
  261. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/test_argparse_str2bool.py +0 -0
  262. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/argparse/test_argparse_validate_inputs.py +0 -0
  263. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/conftest.py +0 -0
  264. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_build_universe_branches.py +0 -0
  265. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_citation_data.py +0 -0
  266. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_create_job_folder.py +0 -0
  267. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_print_args_table.py +0 -0
  268. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_required_args.py +0 -0
  269. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_run_entropy_workflow_branches.py +0 -0
  270. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_runtime_properties.py +0 -0
  271. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_show_splash.py +0 -0
  272. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_unit_conversions.py +0 -0
  273. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/config/runtime/test_universe_io.py +0 -0
  274. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/conftest.py +0 -0
  275. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_configure_loggers.py +0 -0
  276. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_error_filter.py +0 -0
  277. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_export_console.py +0 -0
  278. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_get_console_singleton.py +0 -0
  279. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_handlers_setup.py +0 -0
  280. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/core/logging/test_set_level.py +0 -0
  281. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/conftest.py +0 -0
  282. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/nodes/test_aggregate_node.py +0 -0
  283. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/nodes/test_configurational_node.py +0 -0
  284. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/nodes/test_orientational_node.py +0 -0
  285. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_configurational_edges.py +0 -0
  286. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_configurational_entropy_math.py +0 -0
  287. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_graph.py +0 -0
  288. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_orientational_entropy.py +0 -0
  289. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_vibrational_entropy_math.py +0 -0
  290. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_water_entropy.py +0 -0
  291. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/test_workflow.py +0 -0
  292. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/conftest.py +0 -0
  293. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_build_beads_node.py +0 -0
  294. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_conformations_node.py +0 -0
  295. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_detect_levels_node.py +0 -0
  296. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_detect_molecules_node.py +0 -0
  297. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py +0 -0
  298. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_frame_covariance_node.py +0 -0
  299. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/nodes/test_init_covariance_accumulators_node.py +0 -0
  300. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_axes.py +0 -0
  301. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_dihedrals.py +0 -0
  302. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_forces_force_torque_calculator.py +0 -0
  303. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_frame_graph.py +0 -0
  304. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_hierarchy_builder.py +0 -0
  305. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_level_dag_orchestration.py +0 -0
  306. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_level_dag_reduce.py +0 -0
  307. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_level_dag_reduction.py +0 -0
  308. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_linalg_matrix_utils.py +0 -0
  309. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_mda_universe_operations.py +0 -0
  310. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_neighbors.py +0 -0
  311. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/levels/test_search.py +0 -0
  312. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/molecules/test_grouping.py +0 -0
  313. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/results/test_reporter.py +0 -0
  314. {codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/conftest.py +0 -0
{codeentropy-2.2.1 → codeentropy-2.2.2}/CITATION.cff RENAMED
@@ -76,5 +76,5 @@ keywords:
76
76
  - biomolecular simulations
77
77
  - protein flexibility
78
78
  license: MIT
79
- version: 2.2.1
80
- date-released: '2026-04-30'
79
+ version: 2.2.2
80
+ date-released: '2026-05-01'
{codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/__init__.py RENAMED
@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
8
8
  and statistical mechanics.
9
9
  """
10
10
 
11
- __version__ = "2.2.1"
11
+ __version__ = "2.2.2"
{codeentropy-2.2.1 → codeentropy-2.2.2}/CodeEntropy/entropy/nodes/vibrational.py RENAMED
@@ -323,7 +323,7 @@ class VibrationalEntropyNode:
323
323
  EntropyPair containing translational entropy (from force covariance) and
324
324
  rotational entropy (from torque covariance).
325
325
  """
326
- if fmat is None or tmat is None:
326
+ if fmat is None and tmat is None:
327
327
  return EntropyPair(trans=0.0, rot=0.0)
328
328
 
329
329
  f = self._mat_ops.filter_zero_rows_columns(
@@ -333,7 +333,7 @@ class VibrationalEntropyNode:
333
333
  np.asarray(tmat), atol=self._zero_atol
334
334
  )
335
335
 
336
- if f.size == 0 or t.size == 0:
336
+ if f.size == 0 and t.size == 0:
337
337
  return EntropyPair(trans=0.0, rot=0.0)
338
338
 
339
339
  s_trans = ve.vibrational_entropy_calculation(
{codeentropy-2.2.1 → codeentropy-2.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: CodeEntropy
3
- Version: 2.2.1
3
+ Version: 2.2.2
4
4
  Summary: CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
5
5
  Keywords: entropy,macromolecular systems,MD simulation
6
6
  Author-email: Arghya 'Argo' Chakravorty <arghyac@umich.edu>, Donald Chung-HK <donald.chung@stfc.ac.uk>, Sarah Fegan <sarah.fegan@stfc.ac.uk>, James Gebbie-Rayet <james.gebbie@stfc.ac.uk>, Sarah Harris <sarah.harris@sheffield.ac.uk>, Richard Henchman <rhen7213@uni.sydney.edu.au>, Jonathan Higham <j.higham4@lancaster.ac.uk>, Jas Kalayan <jas.kalayan@stfc.ac.uk>, Ioana Papa <iapapa1@sheffield.ac.uk>
{codeentropy-2.2.1 → codeentropy-2.2.2}/tests/unit/CodeEntropy/entropy/nodes/test_vibrational_node.py RENAMED
@@ -321,7 +321,7 @@ def test_compute_force_torque_entropy_returns_zero_when_missing_matrix(shared_gr
321
321
  node = VibrationalEntropyNode()
322
322
  ve = MagicMock()
323
323
  pair = node._compute_force_torque_entropy(
324
- ve=ve, temp=298.0, fmat=None, tmat=np.eye(3), flexible=0, highest=True
324
+ ve=ve, temp=298.0, fmat=None, tmat=None, flexible=0, highest=True
325
325
  )
326
326
  assert pair == EntropyPair(trans=0.0, rot=0.0)
327
327
 
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{codeentropy-2.2.1 → codeentropy-2.2.2}/docs/Makefile RENAMED
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