embasi 0.1.0__tar.gz

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  1. embasi-0.1.0/.gitignore +5 -0
  2. embasi-0.1.0/LICENSE +21 -0
  3. embasi-0.1.0/PKG-INFO +52 -0
  4. embasi-0.1.0/README.md +14 -0
  5. embasi-0.1.0/docs/Makefile +20 -0
  6. embasi-0.1.0/docs/_build/doctrees/ASI_Embedding.doctree +0 -0
  7. embasi-0.1.0/docs/_build/doctrees/codeintegration.doctree +0 -0
  8. embasi-0.1.0/docs/_build/doctrees/environment.pickle +0 -0
  9. embasi-0.1.0/docs/_build/doctrees/explainer.doctree +0 -0
  10. embasi-0.1.0/docs/_build/doctrees/index.doctree +0 -0
  11. embasi-0.1.0/docs/_build/doctrees/installation.doctree +0 -0
  12. embasi-0.1.0/docs/_build/doctrees/modules.doctree +0 -0
  13. embasi-0.1.0/docs/_build/doctrees/tutorials.doctree +0 -0
  14. embasi-0.1.0/docs/_build/html/.buildinfo +4 -0
  15. embasi-0.1.0/docs/_build/html/ASI_Embedding.html +893 -0
  16. embasi-0.1.0/docs/_build/html/_images/plant_asiembedding_classes.png +0 -0
  17. embasi-0.1.0/docs/_build/html/_images/plant_asiembedding_devroadmap.png +0 -0
  18. embasi-0.1.0/docs/_build/html/_images/plant_flow.png +0 -0
  19. embasi-0.1.0/docs/_build/html/_modules/ASI_Embedding/atoms_embedding_asi.html +622 -0
  20. embasi-0.1.0/docs/_build/html/_modules/ASI_Embedding/basis_info.html +197 -0
  21. embasi-0.1.0/docs/_build/html/_modules/ASI_Embedding/embedding.html +601 -0
  22. embasi-0.1.0/docs/_build/html/_modules/ASI_Embedding/parallel_utils.html +125 -0
  23. embasi-0.1.0/docs/_build/html/_modules/asiembedding/atoms_embedding_asi.html +621 -0
  24. embasi-0.1.0/docs/_build/html/_modules/asiembedding/basis_info.html +197 -0
  25. embasi-0.1.0/docs/_build/html/_modules/asiembedding/embedding.html +601 -0
  26. embasi-0.1.0/docs/_build/html/_modules/asiembedding/parallel_utils.html +172 -0
  27. embasi-0.1.0/docs/_build/html/_modules/index.html +109 -0
  28. embasi-0.1.0/docs/_build/html/_sources/ASI_Embedding.rst.txt +45 -0
  29. embasi-0.1.0/docs/_build/html/_sources/codeintegration.rst.txt +22 -0
  30. embasi-0.1.0/docs/_build/html/_sources/explainer.rst.txt +15 -0
  31. embasi-0.1.0/docs/_build/html/_sources/index.rst.txt +26 -0
  32. embasi-0.1.0/docs/_build/html/_sources/installation.rst.txt +55 -0
  33. embasi-0.1.0/docs/_build/html/_sources/modules.rst.txt +7 -0
  34. embasi-0.1.0/docs/_build/html/_sources/tutorials.rst.txt +18 -0
  35. embasi-0.1.0/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js +123 -0
  36. embasi-0.1.0/docs/_build/html/_static/basic.css +925 -0
  37. embasi-0.1.0/docs/_build/html/_static/css/badge_only.css +1 -0
  38. embasi-0.1.0/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  39. embasi-0.1.0/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  40. embasi-0.1.0/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  41. embasi-0.1.0/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  42. embasi-0.1.0/docs/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
  43. embasi-0.1.0/docs/_build/html/_static/css/fonts/fontawesome-webfont.svg +2671 -0
  44. embasi-0.1.0/docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  45. embasi-0.1.0/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
  46. embasi-0.1.0/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  47. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
  48. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  49. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-bold.woff +0 -0
  50. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
  51. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
  52. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  53. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-normal.woff +0 -0
  54. embasi-0.1.0/docs/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
  55. embasi-0.1.0/docs/_build/html/_static/css/theme.css +4 -0
  56. embasi-0.1.0/docs/_build/html/_static/doctools.js +156 -0
  57. embasi-0.1.0/docs/_build/html/_static/documentation_options.js +13 -0
  58. embasi-0.1.0/docs/_build/html/_static/file.png +0 -0
  59. embasi-0.1.0/docs/_build/html/_static/jquery.js +2 -0
  60. embasi-0.1.0/docs/_build/html/_static/js/badge_only.js +1 -0
  61. embasi-0.1.0/docs/_build/html/_static/js/html5shiv-printshiv.min.js +4 -0
  62. embasi-0.1.0/docs/_build/html/_static/js/html5shiv.min.js +4 -0
  63. embasi-0.1.0/docs/_build/html/_static/js/theme.js +1 -0
  64. embasi-0.1.0/docs/_build/html/_static/language_data.js +199 -0
  65. embasi-0.1.0/docs/_build/html/_static/minus.png +0 -0
  66. embasi-0.1.0/docs/_build/html/_static/plus.png +0 -0
  67. embasi-0.1.0/docs/_build/html/_static/pygments.css +75 -0
  68. embasi-0.1.0/docs/_build/html/_static/searchtools.js +620 -0
  69. embasi-0.1.0/docs/_build/html/_static/sphinx_highlight.js +154 -0
  70. embasi-0.1.0/docs/_build/html/codeintegration.html +138 -0
  71. embasi-0.1.0/docs/_build/html/explainer.html +123 -0
  72. embasi-0.1.0/docs/_build/html/genindex.html +467 -0
  73. embasi-0.1.0/docs/_build/html/index.html +144 -0
  74. embasi-0.1.0/docs/_build/html/installation.html +171 -0
  75. embasi-0.1.0/docs/_build/html/modules.html +220 -0
  76. embasi-0.1.0/docs/_build/html/objects.inv +0 -0
  77. embasi-0.1.0/docs/_build/html/py-modindex.html +145 -0
  78. embasi-0.1.0/docs/_build/html/search.html +125 -0
  79. embasi-0.1.0/docs/_build/html/searchindex.js +1 -0
  80. embasi-0.1.0/docs/_build/html/tutorials.html +117 -0
  81. embasi-0.1.0/docs/codeintegration.rst +22 -0
  82. embasi-0.1.0/docs/conf.py +35 -0
  83. embasi-0.1.0/docs/embasi.rst +45 -0
  84. embasi-0.1.0/docs/explainer.rst +15 -0
  85. embasi-0.1.0/docs/images/plant_embasi_classes.png +0 -0
  86. embasi-0.1.0/docs/images/plant_embasi_devroadmap.png +0 -0
  87. embasi-0.1.0/docs/images/plant_flow.png +0 -0
  88. embasi-0.1.0/docs/index.rst +26 -0
  89. embasi-0.1.0/docs/installation.rst +55 -0
  90. embasi-0.1.0/docs/make.bat +35 -0
  91. embasi-0.1.0/docs/modules.rst +7 -0
  92. embasi-0.1.0/docs/plant_flow.png +0 -0
  93. embasi-0.1.0/docs/tutorials.rst +18 -0
  94. embasi-0.1.0/embasi/__init__.py +4 -0
  95. embasi-0.1.0/embasi/asi_default_callbacks.py +126 -0
  96. embasi-0.1.0/embasi/atoms_embedding_asi.py +669 -0
  97. embasi-0.1.0/embasi/basis_info.py +109 -0
  98. embasi-0.1.0/embasi/embedding.py +749 -0
  99. embasi-0.1.0/embasi/parallel_utils.py +104 -0
  100. embasi-0.1.0/embasi/roothan_hall_eigensolver.py +85 -0
  101. embasi-0.1.0/embasi/roothan_hall_eigensolver_scalapack.py +288 -0
  102. embasi-0.1.0/embasi.egg-info/PKG-INFO +52 -0
  103. embasi-0.1.0/embasi.egg-info/SOURCES.txt +113 -0
  104. embasi-0.1.0/embasi.egg-info/dependency_links.txt +1 -0
  105. embasi-0.1.0/embasi.egg-info/requires.txt +2 -0
  106. embasi-0.1.0/embasi.egg-info/top_level.txt +1 -0
  107. embasi-0.1.0/examples/FHIaims/BEA_embed/bea.py +21 -0
  108. embasi-0.1.0/examples/FHIaims/BEA_embed/truncation_example.py +108 -0
  109. embasi-0.1.0/examples/FHIaims/BEA_embed/zeolite.xyz +35 -0
  110. embasi-0.1.0/examples/FHIaims/basis_truncation/decanol.xyz +35 -0
  111. embasi-0.1.0/examples/FHIaims/basis_truncation/truncation_example.py +151 -0
  112. embasi-0.1.0/examples/FHIaims/projection_embedding/dimer_meoh_example.py +118 -0
  113. embasi-0.1.0/examples/eigensolvers/test_pdsyevx.py +19 -0
  114. embasi-0.1.0/pyproject.toml +28 -0
  115. embasi-0.1.0/setup.cfg +4 -0
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+ **/__pycache__*
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+ /dist
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+ /asiembedding.egg-info
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+ /build
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+ doc/build/
embasi-0.1.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024 Gabriel A. Bramley
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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.
embasi-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: embasi
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+ Version: 0.1.0
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+ Summary: A generalised workflow for QM/QM Embedding
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+ Author-email: Gabriel Bramley <BramleyG@cardiff.ac.uk>
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+ License: MIT License
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+
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+ Copyright (c) 2024 Gabriel A. Bramley
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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.
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+ Project-URL: Homepage, https://github.com/logsdail/EmbASI
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+ Project-URL: Issues, https://github.com/logsdail/EmbASI/issues
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.9
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: ase==3.24.0
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+ Requires-Dist: asi4py>=1.4.1
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+ Dynamic: license-file
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+
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+ # EmbASI
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+
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+ EmbASI is a python-based wrapper for QM/QM embedding simulations using the ASI (Atomic Simulation Interface). The wrapper handles communication between QM code library calls through C-based callbacks, and imports/exports relevant matices such as density matrices and hamiltonians required for embedding schemes such as Projection-Based Embedding (PbE). Atomic information is communicated through Atomic Simulation Environment (ASE) atoms objects.
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+
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+ # Supported QM Pakage(s)
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+
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+ - FHI-aims
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+
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+ # Requires
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+
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+ - Python >=3.8
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+ - ASE <=2.3.1
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+ - asi4py (Bespoke version currently)
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+ - Shared-object library for relevant QM driver
embasi-0.1.0/README.md ADDED
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+ # EmbASI
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+
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+ EmbASI is a python-based wrapper for QM/QM embedding simulations using the ASI (Atomic Simulation Interface). The wrapper handles communication between QM code library calls through C-based callbacks, and imports/exports relevant matices such as density matrices and hamiltonians required for embedding schemes such as Projection-Based Embedding (PbE). Atomic information is communicated through Atomic Simulation Environment (ASE) atoms objects.
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+
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+ # Supported QM Pakage(s)
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+
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+ - FHI-aims
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+
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+ # Requires
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+
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+ - Python >=3.8
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+ - ASE <=2.3.1
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+ - asi4py (Bespoke version currently)
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+ - Shared-object library for relevant QM driver
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+ # Minimal makefile for Sphinx documentation
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+ #
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+
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+ # You can set these variables from the command line, and also
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+ # from the environment for the first two.
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+ SPHINXOPTS ?=
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+ SPHINXBUILD ?= sphinx-build
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+ SOURCEDIR = .
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+ BUILDDIR = _build
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+
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+ # Put it first so that "make" without argument is like "make help".
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+ help:
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+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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+
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+ .PHONY: help Makefile
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+
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+ # Catch-all target: route all unknown targets to Sphinx using the new
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+ # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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+ %: Makefile
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+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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+ # Sphinx build info version 1
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+ # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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+ config: e2a322a3219f408affe635deab923b0b
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+ tags: 645f666f9bcd5a90fca523b33c5a78b7