napistu 0.1.0__py3-none-any.whl

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Files changed (77) hide show
  1. napistu/__init__.py +12 -0
  2. napistu/__main__.py +867 -0
  3. napistu/consensus.py +1557 -0
  4. napistu/constants.py +500 -0
  5. napistu/gcs/__init__.py +10 -0
  6. napistu/gcs/constants.py +69 -0
  7. napistu/gcs/downloads.py +180 -0
  8. napistu/identifiers.py +805 -0
  9. napistu/indices.py +227 -0
  10. napistu/ingestion/__init__.py +10 -0
  11. napistu/ingestion/bigg.py +146 -0
  12. napistu/ingestion/constants.py +296 -0
  13. napistu/ingestion/cpr_edgelist.py +106 -0
  14. napistu/ingestion/identifiers_etl.py +148 -0
  15. napistu/ingestion/obo.py +268 -0
  16. napistu/ingestion/psi_mi.py +276 -0
  17. napistu/ingestion/reactome.py +218 -0
  18. napistu/ingestion/sbml.py +621 -0
  19. napistu/ingestion/string.py +356 -0
  20. napistu/ingestion/trrust.py +285 -0
  21. napistu/ingestion/yeast.py +147 -0
  22. napistu/mechanism_matching.py +597 -0
  23. napistu/modify/__init__.py +10 -0
  24. napistu/modify/constants.py +86 -0
  25. napistu/modify/curation.py +628 -0
  26. napistu/modify/gaps.py +635 -0
  27. napistu/modify/pathwayannot.py +1381 -0
  28. napistu/modify/uncompartmentalize.py +264 -0
  29. napistu/network/__init__.py +10 -0
  30. napistu/network/constants.py +117 -0
  31. napistu/network/neighborhoods.py +1594 -0
  32. napistu/network/net_create.py +1647 -0
  33. napistu/network/net_utils.py +652 -0
  34. napistu/network/paths.py +500 -0
  35. napistu/network/precompute.py +221 -0
  36. napistu/rpy2/__init__.py +127 -0
  37. napistu/rpy2/callr.py +168 -0
  38. napistu/rpy2/constants.py +101 -0
  39. napistu/rpy2/netcontextr.py +464 -0
  40. napistu/rpy2/rids.py +697 -0
  41. napistu/sbml_dfs_core.py +2216 -0
  42. napistu/sbml_dfs_utils.py +304 -0
  43. napistu/source.py +394 -0
  44. napistu/utils.py +943 -0
  45. napistu-0.1.0.dist-info/METADATA +56 -0
  46. napistu-0.1.0.dist-info/RECORD +77 -0
  47. napistu-0.1.0.dist-info/WHEEL +5 -0
  48. napistu-0.1.0.dist-info/entry_points.txt +2 -0
  49. napistu-0.1.0.dist-info/licenses/LICENSE +21 -0
  50. napistu-0.1.0.dist-info/top_level.txt +2 -0
  51. tests/__init__.py +0 -0
  52. tests/conftest.py +83 -0
  53. tests/test_consensus.py +255 -0
  54. tests/test_constants.py +20 -0
  55. tests/test_curation.py +134 -0
  56. tests/test_data/__init__.py +0 -0
  57. tests/test_edgelist.py +20 -0
  58. tests/test_gcs.py +23 -0
  59. tests/test_identifiers.py +151 -0
  60. tests/test_igraph.py +353 -0
  61. tests/test_indices.py +88 -0
  62. tests/test_mechanism_matching.py +126 -0
  63. tests/test_net_utils.py +66 -0
  64. tests/test_netcontextr.py +105 -0
  65. tests/test_obo.py +34 -0
  66. tests/test_pathwayannot.py +95 -0
  67. tests/test_precomputed_distances.py +222 -0
  68. tests/test_rpy2.py +61 -0
  69. tests/test_sbml.py +46 -0
  70. tests/test_sbml_dfs_create.py +307 -0
  71. tests/test_sbml_dfs_utils.py +22 -0
  72. tests/test_sbo.py +11 -0
  73. tests/test_set_coverage.py +50 -0
  74. tests/test_source.py +67 -0
  75. tests/test_uncompartmentalize.py +40 -0
  76. tests/test_utils.py +487 -0
  77. tests/utils.py +30 -0
napistu/__init__.py ADDED
@@ -0,0 +1,12 @@
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+ from __future__ import annotations
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+
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+ from importlib.metadata import PackageNotFoundError
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+ from importlib.metadata import version
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+
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+ __version__ = "0.2.0"
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+
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+ try:
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+ __version__ = version("calicolabs-cpr")
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+ except PackageNotFoundError:
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+ # package is not installed
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+ pass