namdtools 0.2.3.post0.dev4__tar.gz → 0.3.0__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 (111) hide show
  1. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/MANIFEST.in +0 -1
  2. namdtools-0.3.0/PKG-INFO +18 -0
  3. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/README.md +0 -2
  4. namdtools-0.3.0/namdtools/__init__.py +12 -0
  5. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/_version.py +4 -4
  6. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/analysis/__init__.py +0 -0
  7. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/analysis/pme.py +0 -0
  8. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/io/__init__.py +0 -0
  9. namdtools-0.3.0/namdtools/io/_read_utils.c +12903 -0
  10. namdtools-0.3.0/namdtools/io/path.py +84 -0
  11. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/io/read.py +9 -17
  12. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/io/write.py +5 -5
  13. namdtools-0.3.0/namdtools.egg-info/PKG-INFO +18 -0
  14. namdtools-0.3.0/namdtools.egg-info/SOURCES.txt +22 -0
  15. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools.egg-info/requires.txt +0 -1
  16. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/requirements.txt +0 -1
  17. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/setup.cfg +1 -1
  18. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/setup.py +2 -8
  19. namdtools-0.2.3.post0.dev4/.codecov.yml +0 -0
  20. namdtools-0.2.3.post0.dev4/.gitattributes +0 -1
  21. namdtools-0.2.3.post0.dev4/.github/workflows/build.yml +0 -49
  22. namdtools-0.2.3.post0.dev4/.gitignore +0 -9
  23. namdtools-0.2.3.post0.dev4/.scripts/README +0 -4
  24. namdtools-0.2.3.post0.dev4/.scripts/get_version.sh +0 -6
  25. namdtools-0.2.3.post0.dev4/.scripts/make_docs.sh +0 -6
  26. namdtools-0.2.3.post0.dev4/.scripts/pypi.sh +0 -8
  27. namdtools-0.2.3.post0.dev4/.scripts/temp +0 -16
  28. namdtools-0.2.3.post0.dev4/.scripts/update_major.sh +0 -8
  29. namdtools-0.2.3.post0.dev4/.scripts/update_minor.sh +0 -8
  30. namdtools-0.2.3.post0.dev4/.scripts/update_patch.sh +0 -8
  31. namdtools-0.2.3.post0.dev4/PKG-INFO +0 -46
  32. namdtools-0.2.3.post0.dev4/README.rst +0 -36
  33. namdtools-0.2.3.post0.dev4/docs/.nojekyll +0 -0
  34. namdtools-0.2.3.post0.dev4/docs/Makefile +0 -20
  35. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api/core.doctree +0 -0
  36. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api/generated/namdtools.core.core.NAMD.doctree +0 -0
  37. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api/generated/namdtools.core.core.run_namd.doctree +0 -0
  38. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api/generated/namdtools.io.read_log.doctree +0 -0
  39. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api/io.doctree +0 -0
  40. namdtools-0.2.3.post0.dev4/docs/build/doctrees/api.doctree +0 -0
  41. namdtools-0.2.3.post0.dev4/docs/build/doctrees/environment.pickle +0 -0
  42. namdtools-0.2.3.post0.dev4/docs/build/doctrees/index.doctree +0 -0
  43. namdtools-0.2.3.post0.dev4/docs/build/html/.buildinfo +0 -4
  44. namdtools-0.2.3.post0.dev4/docs/build/html/.nojekyll +0 -0
  45. namdtools-0.2.3.post0.dev4/docs/build/html/_images/namdtools.svg +0 -1
  46. namdtools-0.2.3.post0.dev4/docs/build/html/_modules/index.html +0 -73
  47. namdtools-0.2.3.post0.dev4/docs/build/html/_modules/namdtools/core/core.html +0 -520
  48. namdtools-0.2.3.post0.dev4/docs/build/html/_modules/namdtools/io/read.html +0 -262
  49. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api/core.rst.txt +0 -20
  50. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api/generated/namdtools.core.core.NAMD.rst.txt +0 -11
  51. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api/generated/namdtools.core.core.run_namd.rst.txt +0 -6
  52. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api/generated/namdtools.io.read_log.rst.txt +0 -6
  53. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api/io.rst.txt +0 -12
  54. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/api.rst.txt +0 -9
  55. namdtools-0.2.3.post0.dev4/docs/build/html/_sources/index.rst.txt +0 -17
  56. namdtools-0.2.3.post0.dev4/docs/build/html/_static/basic.css +0 -903
  57. namdtools-0.2.3.post0.dev4/docs/build/html/_static/doctools.js +0 -156
  58. namdtools-0.2.3.post0.dev4/docs/build/html/_static/documentation_options.js +0 -14
  59. namdtools-0.2.3.post0.dev4/docs/build/html/_static/file.png +0 -0
  60. namdtools-0.2.3.post0.dev4/docs/build/html/_static/language_data.js +0 -199
  61. namdtools-0.2.3.post0.dev4/docs/build/html/_static/minus.png +0 -0
  62. namdtools-0.2.3.post0.dev4/docs/build/html/_static/nature.css +0 -248
  63. namdtools-0.2.3.post0.dev4/docs/build/html/_static/plus.png +0 -0
  64. namdtools-0.2.3.post0.dev4/docs/build/html/_static/pygments.css +0 -83
  65. namdtools-0.2.3.post0.dev4/docs/build/html/_static/searchtools.js +0 -566
  66. namdtools-0.2.3.post0.dev4/docs/build/html/_static/sphinx_highlight.js +0 -144
  67. namdtools-0.2.3.post0.dev4/docs/build/html/api/core.html +0 -138
  68. namdtools-0.2.3.post0.dev4/docs/build/html/api/generated/namdtools.core.core.NAMD.html +0 -204
  69. namdtools-0.2.3.post0.dev4/docs/build/html/api/generated/namdtools.core.core.run_namd.html +0 -140
  70. namdtools-0.2.3.post0.dev4/docs/build/html/api/generated/namdtools.io.read_log.html +0 -126
  71. namdtools-0.2.3.post0.dev4/docs/build/html/api/io.html +0 -127
  72. namdtools-0.2.3.post0.dev4/docs/build/html/api.html +0 -111
  73. namdtools-0.2.3.post0.dev4/docs/build/html/genindex.html +0 -152
  74. namdtools-0.2.3.post0.dev4/docs/build/html/index.html +0 -114
  75. namdtools-0.2.3.post0.dev4/docs/build/html/objects.inv +0 -0
  76. namdtools-0.2.3.post0.dev4/docs/build/html/search.html +0 -95
  77. namdtools-0.2.3.post0.dev4/docs/build/html/searchindex.js +0 -1
  78. namdtools-0.2.3.post0.dev4/docs/index.html +0 -11
  79. namdtools-0.2.3.post0.dev4/docs/make.bat +0 -35
  80. namdtools-0.2.3.post0.dev4/docs/source/_templates/autosummary/base.rst +0 -5
  81. namdtools-0.2.3.post0.dev4/docs/source/_templates/autosummary/class.rst +0 -10
  82. namdtools-0.2.3.post0.dev4/docs/source/_templates/autosummary/module.rst +0 -30
  83. namdtools-0.2.3.post0.dev4/docs/source/api/core.rst +0 -20
  84. namdtools-0.2.3.post0.dev4/docs/source/api/generated/namdtools.core.core.NAMD.rst +0 -11
  85. namdtools-0.2.3.post0.dev4/docs/source/api/generated/namdtools.core.core.run_namd.rst +0 -6
  86. namdtools-0.2.3.post0.dev4/docs/source/api/generated/namdtools.io.read_log.rst +0 -6
  87. namdtools-0.2.3.post0.dev4/docs/source/api/io.rst +0 -12
  88. namdtools-0.2.3.post0.dev4/docs/source/api.rst +0 -9
  89. namdtools-0.2.3.post0.dev4/docs/source/conf.py +0 -65
  90. namdtools-0.2.3.post0.dev4/docs/source/index.rst +0 -17
  91. namdtools-0.2.3.post0.dev4/namdtools/__init__.py +0 -29
  92. namdtools-0.2.3.post0.dev4/namdtools/analysis/compare.py +0 -5
  93. namdtools-0.2.3.post0.dev4/namdtools/core/__init__.py +0 -9
  94. namdtools-0.2.3.post0.dev4/namdtools/core/core.py +0 -447
  95. namdtools-0.2.3.post0.dev4/namdtools/exceptions.py +0 -13
  96. namdtools-0.2.3.post0.dev4/namdtools/io/_read_utils.c +0 -7189
  97. namdtools-0.2.3.post0.dev4/namdtools/io/_read_utils.cpython-38-x86_64-linux-gnu.so +0 -0
  98. namdtools-0.2.3.post0.dev4/namdtools/io/_read_utils.cpython-39-darwin.so +0 -0
  99. namdtools-0.2.3.post0.dev4/namdtools/options.py +0 -40
  100. namdtools-0.2.3.post0.dev4/namdtools/protocols/__init__.py +0 -0
  101. namdtools-0.2.3.post0.dev4/namdtools/protocols/replica_exchange.py +0 -121
  102. namdtools-0.2.3.post0.dev4/namdtools.egg-info/PKG-INFO +0 -46
  103. namdtools-0.2.3.post0.dev4/namdtools.egg-info/SOURCES.txt +0 -104
  104. namdtools-0.2.3.post0.dev4/namdtools.svg +0 -1
  105. namdtools-0.2.3.post0.dev4/requirements_dev.txt +0 -7
  106. namdtools-0.2.3.post0.dev4/version.yml +0 -3
  107. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/io/_read_utils.pyx +0 -0
  108. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools.egg-info/dependency_links.txt +0 -0
  109. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools.egg-info/top_level.txt +0 -0
  110. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools.egg-info/zip-safe +0 -0
  111. {namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/versioneer.py +0 -0
{namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/MANIFEST.in RENAMED
@@ -1,3 +1,2 @@
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  recursive-include namdtools *.c *.pyf *.f90 *.pyx *.yml
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  include requirements.txt
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- include version.yml
namdtools-0.3.0/PKG-INFO ADDED
@@ -0,0 +1,18 @@
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+ Metadata-Version: 2.2
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+ Name: namdtools
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+ Version: 0.3.0
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+ Summary: A Python interface to NAMD
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+ Home-page: https://www.lockhartlab.org
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+ Author: C. Lockhart
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+ Author-email: clockha2@gmu.edu
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+ Requires-Dist: Cython
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+ Requires-Dist: numpy
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+ Requires-Dist: pandas
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+ Requires-Dist: pyyaml>=5.3
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+ Requires-Dist: scipy
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+ Requires-Dist: sympy
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: home-page
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+ Dynamic: requires-dist
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+ Dynamic: summary
{namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/README.md RENAMED
@@ -1,4 +1,3 @@
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- <img src="namdtools.svg" alt="namdtools" height="200px">
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  a Python interface to NAMD
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  http://www.ks.uiuc.edu/Research/namd/
@@ -7,7 +6,6 @@ http://www.ks.uiuc.edu/Research/namd/
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  <span style="white-space: nowrap;">
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  <a href="https://pypi.org/project/namdtools/"><img src="https://img.shields.io/pypi/v/namdtools" /></a>
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  <a href="https://travis-ci.com/github/LockhartLab/namdtools"><img src="https://img.shields.io/travis/com/lockhartlab/namdtools/master" /></a>
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- <a href="https://codecov.io/gh/LockhartLab/namdtools"><img src="https://img.shields.io/codecov/c/github/lockhartlab/namdtools/master" /></a>
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  </span>
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  <hr>
namdtools-0.3.0/namdtools/__init__.py ADDED
@@ -0,0 +1,12 @@
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+
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+ from . import analysis
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+ from .analysis import *
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+
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+ from . import io
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+ from .io import *
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+
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+ __all__ = analysis.__all__
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+ __all__.extend(io.__all__)
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+
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+ from . import _version
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+ __version__ = _version.get_versions()['version']
{namdtools-0.2.3.post0.dev4 → namdtools-0.3.0}/namdtools/_version.py RENAMED
@@ -8,11 +8,11 @@ import json
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  version_json = '''
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  {
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- "date": "2022-12-30T19:31:30-0500",
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- "dirty": false,
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+ "date": "2025-11-01T21:25:41-0400",
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+ "dirty": true,
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  "error": null,
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- "full-revisionid": "7734c79da634b2dd5873fb690843e903be99cd0a",
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- "version": "0.2.3.post0.dev4"
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+ "full-revisionid": "fa78589176a151b6ce51f902af0b460842c08776",
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+ "version": "0.3.0"
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  }
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  ''' # END VERSION_JSON
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