westpa 2022.13__cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl

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 (162) hide show
  1. westpa/__init__.py +14 -0
  2. westpa/_version.py +21 -0
  3. westpa/analysis/__init__.py +5 -0
  4. westpa/analysis/core.py +749 -0
  5. westpa/analysis/statistics.py +27 -0
  6. westpa/analysis/trajectories.py +369 -0
  7. westpa/cli/__init__.py +0 -0
  8. westpa/cli/core/__init__.py +0 -0
  9. westpa/cli/core/w_fork.py +152 -0
  10. westpa/cli/core/w_init.py +230 -0
  11. westpa/cli/core/w_run.py +77 -0
  12. westpa/cli/core/w_states.py +212 -0
  13. westpa/cli/core/w_succ.py +99 -0
  14. westpa/cli/core/w_truncate.py +68 -0
  15. westpa/cli/tools/__init__.py +0 -0
  16. westpa/cli/tools/ploterr.py +506 -0
  17. westpa/cli/tools/plothist.py +706 -0
  18. westpa/cli/tools/w_assign.py +597 -0
  19. westpa/cli/tools/w_bins.py +166 -0
  20. westpa/cli/tools/w_crawl.py +119 -0
  21. westpa/cli/tools/w_direct.py +557 -0
  22. westpa/cli/tools/w_dumpsegs.py +94 -0
  23. westpa/cli/tools/w_eddist.py +506 -0
  24. westpa/cli/tools/w_fluxanl.py +376 -0
  25. westpa/cli/tools/w_ipa.py +832 -0
  26. westpa/cli/tools/w_kinavg.py +127 -0
  27. westpa/cli/tools/w_kinetics.py +96 -0
  28. westpa/cli/tools/w_multi_west.py +414 -0
  29. westpa/cli/tools/w_ntop.py +213 -0
  30. westpa/cli/tools/w_pdist.py +515 -0
  31. westpa/cli/tools/w_postanalysis_matrix.py +82 -0
  32. westpa/cli/tools/w_postanalysis_reweight.py +53 -0
  33. westpa/cli/tools/w_red.py +491 -0
  34. westpa/cli/tools/w_reweight.py +780 -0
  35. westpa/cli/tools/w_select.py +226 -0
  36. westpa/cli/tools/w_stateprobs.py +111 -0
  37. westpa/cli/tools/w_timings.py +113 -0
  38. westpa/cli/tools/w_trace.py +599 -0
  39. westpa/core/__init__.py +0 -0
  40. westpa/core/_rc.py +673 -0
  41. westpa/core/binning/__init__.py +55 -0
  42. westpa/core/binning/_assign.c +36018 -0
  43. westpa/core/binning/_assign.cpython-312-aarch64-linux-gnu.so +0 -0
  44. westpa/core/binning/_assign.pyx +370 -0
  45. westpa/core/binning/assign.py +454 -0
  46. westpa/core/binning/binless.py +96 -0
  47. westpa/core/binning/binless_driver.py +54 -0
  48. westpa/core/binning/binless_manager.py +189 -0
  49. westpa/core/binning/bins.py +47 -0
  50. westpa/core/binning/mab.py +506 -0
  51. westpa/core/binning/mab_driver.py +54 -0
  52. westpa/core/binning/mab_manager.py +197 -0
  53. westpa/core/data_manager.py +1761 -0
  54. westpa/core/extloader.py +74 -0
  55. westpa/core/h5io.py +1079 -0
  56. westpa/core/kinetics/__init__.py +24 -0
  57. westpa/core/kinetics/_kinetics.c +45174 -0
  58. westpa/core/kinetics/_kinetics.cpython-312-aarch64-linux-gnu.so +0 -0
  59. westpa/core/kinetics/_kinetics.pyx +815 -0
  60. westpa/core/kinetics/events.py +147 -0
  61. westpa/core/kinetics/matrates.py +156 -0
  62. westpa/core/kinetics/rate_averaging.py +266 -0
  63. westpa/core/progress.py +218 -0
  64. westpa/core/propagators/__init__.py +54 -0
  65. westpa/core/propagators/executable.py +592 -0
  66. westpa/core/propagators/loaders.py +196 -0
  67. westpa/core/reweight/__init__.py +14 -0
  68. westpa/core/reweight/_reweight.c +36899 -0
  69. westpa/core/reweight/_reweight.cpython-312-aarch64-linux-gnu.so +0 -0
  70. westpa/core/reweight/_reweight.pyx +439 -0
  71. westpa/core/reweight/matrix.py +126 -0
  72. westpa/core/segment.py +119 -0
  73. westpa/core/sim_manager.py +839 -0
  74. westpa/core/states.py +359 -0
  75. westpa/core/systems.py +93 -0
  76. westpa/core/textio.py +74 -0
  77. westpa/core/trajectory.py +603 -0
  78. westpa/core/we_driver.py +910 -0
  79. westpa/core/wm_ops.py +43 -0
  80. westpa/core/yamlcfg.py +298 -0
  81. westpa/fasthist/__init__.py +34 -0
  82. westpa/fasthist/_fasthist.c +38755 -0
  83. westpa/fasthist/_fasthist.cpython-312-aarch64-linux-gnu.so +0 -0
  84. westpa/fasthist/_fasthist.pyx +222 -0
  85. westpa/mclib/__init__.py +271 -0
  86. westpa/mclib/__main__.py +28 -0
  87. westpa/mclib/_mclib.c +34610 -0
  88. westpa/mclib/_mclib.cpython-312-aarch64-linux-gnu.so +0 -0
  89. westpa/mclib/_mclib.pyx +226 -0
  90. westpa/oldtools/__init__.py +4 -0
  91. westpa/oldtools/aframe/__init__.py +35 -0
  92. westpa/oldtools/aframe/atool.py +75 -0
  93. westpa/oldtools/aframe/base_mixin.py +26 -0
  94. westpa/oldtools/aframe/binning.py +178 -0
  95. westpa/oldtools/aframe/data_reader.py +560 -0
  96. westpa/oldtools/aframe/iter_range.py +200 -0
  97. westpa/oldtools/aframe/kinetics.py +117 -0
  98. westpa/oldtools/aframe/mcbs.py +153 -0
  99. westpa/oldtools/aframe/output.py +39 -0
  100. westpa/oldtools/aframe/plotting.py +88 -0
  101. westpa/oldtools/aframe/trajwalker.py +126 -0
  102. westpa/oldtools/aframe/transitions.py +469 -0
  103. westpa/oldtools/cmds/__init__.py +0 -0
  104. westpa/oldtools/cmds/w_ttimes.py +361 -0
  105. westpa/oldtools/files.py +34 -0
  106. westpa/oldtools/miscfn.py +23 -0
  107. westpa/oldtools/stats/__init__.py +4 -0
  108. westpa/oldtools/stats/accumulator.py +35 -0
  109. westpa/oldtools/stats/edfs.py +129 -0
  110. westpa/oldtools/stats/mcbs.py +96 -0
  111. westpa/tools/__init__.py +33 -0
  112. westpa/tools/binning.py +472 -0
  113. westpa/tools/core.py +340 -0
  114. westpa/tools/data_reader.py +159 -0
  115. westpa/tools/dtypes.py +31 -0
  116. westpa/tools/iter_range.py +198 -0
  117. westpa/tools/kinetics_tool.py +343 -0
  118. westpa/tools/plot.py +283 -0
  119. westpa/tools/progress.py +17 -0
  120. westpa/tools/selected_segs.py +154 -0
  121. westpa/tools/wipi.py +751 -0
  122. westpa/trajtree/__init__.py +4 -0
  123. westpa/trajtree/_trajtree.c +17829 -0
  124. westpa/trajtree/_trajtree.cpython-312-aarch64-linux-gnu.so +0 -0
  125. westpa/trajtree/_trajtree.pyx +130 -0
  126. westpa/trajtree/trajtree.py +117 -0
  127. westpa/westext/__init__.py +0 -0
  128. westpa/westext/adaptvoronoi/__init__.py +3 -0
  129. westpa/westext/adaptvoronoi/adaptVor_driver.py +214 -0
  130. westpa/westext/hamsm_restarting/__init__.py +3 -0
  131. westpa/westext/hamsm_restarting/example_overrides.py +35 -0
  132. westpa/westext/hamsm_restarting/restart_driver.py +1165 -0
  133. westpa/westext/stringmethod/__init__.py +11 -0
  134. westpa/westext/stringmethod/fourier_fitting.py +69 -0
  135. westpa/westext/stringmethod/string_driver.py +253 -0
  136. westpa/westext/stringmethod/string_method.py +306 -0
  137. westpa/westext/weed/BinCluster.py +180 -0
  138. westpa/westext/weed/ProbAdjustEquil.py +100 -0
  139. westpa/westext/weed/UncertMath.py +247 -0
  140. westpa/westext/weed/__init__.py +10 -0
  141. westpa/westext/weed/weed_driver.py +192 -0
  142. westpa/westext/wess/ProbAdjust.py +101 -0
  143. westpa/westext/wess/__init__.py +6 -0
  144. westpa/westext/wess/wess_driver.py +217 -0
  145. westpa/work_managers/__init__.py +57 -0
  146. westpa/work_managers/core.py +396 -0
  147. westpa/work_managers/environment.py +134 -0
  148. westpa/work_managers/mpi.py +318 -0
  149. westpa/work_managers/processes.py +201 -0
  150. westpa/work_managers/serial.py +28 -0
  151. westpa/work_managers/threads.py +79 -0
  152. westpa/work_managers/zeromq/__init__.py +20 -0
  153. westpa/work_managers/zeromq/core.py +635 -0
  154. westpa/work_managers/zeromq/node.py +131 -0
  155. westpa/work_managers/zeromq/work_manager.py +526 -0
  156. westpa/work_managers/zeromq/worker.py +320 -0
  157. westpa-2022.13.dist-info/METADATA +179 -0
  158. westpa-2022.13.dist-info/RECORD +162 -0
  159. westpa-2022.13.dist-info/WHEEL +7 -0
  160. westpa-2022.13.dist-info/entry_points.txt +30 -0
  161. westpa-2022.13.dist-info/licenses/LICENSE +21 -0
  162. westpa-2022.13.dist-info/top_level.txt +1 -0
westpa-2022.13.dist-info/entry_points.txt ADDED
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+ [console_scripts]
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+ ploterr = westpa.cli.tools.ploterr:entry_point
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+ plothist = westpa.cli.tools.plothist:entry_point
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+ w_assign = westpa.cli.tools.w_assign:entry_point
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+ w_bins = westpa.cli.tools.w_bins:entry_point
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+ w_crawl = westpa.cli.tools.w_crawl:entry_point
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+ w_direct = westpa.cli.tools.w_direct:entry_point
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+ w_dumpsegs = westpa.cli.tools.w_dumpsegs:entry_point
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+ w_eddist = westpa.cli.tools.w_eddist:entry_point
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+ w_fluxanl = westpa.cli.tools.w_fluxanl:entry_point
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+ w_fork = westpa.cli.core.w_fork:entry_point
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+ w_init = westpa.cli.core.w_init:entry_point
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+ w_ipa = westpa.cli.tools.w_ipa:entry_point
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+ w_kinavg = westpa.cli.tools.w_kinavg:entry_point
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+ w_kinetics = westpa.cli.tools.w_kinetics:entry_point
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+ w_multi_west = westpa.cli.tools.w_multi_west:entry_point
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+ w_ntop = westpa.cli.tools.w_ntop:entry_point
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+ w_pdist = westpa.cli.tools.w_pdist:entry_point
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+ w_postanalysis_matrix = westpa.cli.tools.w_postanalysis_matrix:entry_point
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+ w_postanalysis_reweight = westpa.cli.tools.w_postanalysis_reweight:entry_point
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+ w_red = westpa.cli.tools.w_red:entry_point
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+ w_reweight = westpa.cli.tools.w_reweight:entry_point
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+ w_run = westpa.cli.core.w_run:entry_point
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+ w_select = westpa.cli.tools.w_select:entry_point
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+ w_stateprobs = westpa.cli.tools.w_stateprobs:entry_point
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+ w_states = westpa.cli.core.w_states:entry_point
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+ w_succ = westpa.cli.core.w_succ:entry_point
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+ w_timings = westpa.cli.tools.w_timings:entry_point
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+ w_trace = westpa.cli.tools.w_trace:entry_point
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+ w_truncate = westpa.cli.core.w_truncate:entry_point
westpa-2022.13.dist-info/licenses/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2013 WESTPA Developers
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
westpa-2022.13.dist-info/top_level.txt ADDED
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+ westpa