napistu 0.2.5.dev3__tar.gz → 0.2.5.dev4__tar.gz

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Files changed (103) hide show
  1. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/PKG-INFO +1 -1
  2. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/setup.cfg +1 -1
  3. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/server.py +17 -2
  4. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/PKG-INFO +1 -1
  5. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/LICENSE +0 -0
  6. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/README.md +0 -0
  7. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/pyproject.toml +0 -0
  8. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/setup.py +0 -0
  9. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/__init__.py +0 -0
  10. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/__main__.py +0 -0
  11. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/consensus.py +0 -0
  12. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/constants.py +0 -0
  13. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/gcs/__init__.py +0 -0
  14. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/gcs/constants.py +0 -0
  15. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/gcs/downloads.py +0 -0
  16. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/gcs/utils.py +0 -0
  17. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/identifiers.py +0 -0
  18. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/indices.py +0 -0
  19. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/__init__.py +0 -0
  20. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/bigg.py +0 -0
  21. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/constants.py +0 -0
  22. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/cpr_edgelist.py +0 -0
  23. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/identifiers_etl.py +0 -0
  24. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/obo.py +0 -0
  25. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/psi_mi.py +0 -0
  26. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/reactome.py +0 -0
  27. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/sbml.py +0 -0
  28. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/string.py +0 -0
  29. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/trrust.py +0 -0
  30. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/ingestion/yeast.py +0 -0
  31. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/__init__.py +0 -0
  32. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/__main__.py +0 -0
  33. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/client.py +0 -0
  34. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/codebase.py +0 -0
  35. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/codebase_utils.py +0 -0
  36. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/constants.py +0 -0
  37. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/documentation.py +0 -0
  38. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/documentation_utils.py +0 -0
  39. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/execution.py +0 -0
  40. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/health.py +0 -0
  41. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/profiles.py +0 -0
  42. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/tutorials.py +0 -0
  43. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/tutorials_utils.py +0 -0
  44. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/utils.py +0 -0
  45. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mechanism_matching.py +0 -0
  46. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/__init__.py +0 -0
  47. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/constants.py +0 -0
  48. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/curation.py +0 -0
  49. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/gaps.py +0 -0
  50. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/pathwayannot.py +0 -0
  51. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/modify/uncompartmentalize.py +0 -0
  52. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/__init__.py +0 -0
  53. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/constants.py +0 -0
  54. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/neighborhoods.py +0 -0
  55. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/net_create.py +0 -0
  56. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/net_propagation.py +0 -0
  57. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/net_utils.py +0 -0
  58. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/paths.py +0 -0
  59. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/network/precompute.py +0 -0
  60. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/rpy2/__init__.py +0 -0
  61. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/rpy2/callr.py +0 -0
  62. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/rpy2/constants.py +0 -0
  63. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/rpy2/netcontextr.py +0 -0
  64. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/rpy2/rids.py +0 -0
  65. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/sbml_dfs_core.py +0 -0
  66. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/sbml_dfs_utils.py +0 -0
  67. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/source.py +0 -0
  68. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/utils.py +0 -0
  69. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/SOURCES.txt +0 -0
  70. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/dependency_links.txt +0 -0
  71. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/entry_points.txt +0 -0
  72. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/requires.txt +0 -0
  73. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/top_level.txt +0 -0
  74. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/__init__.py +0 -0
  75. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/conftest.py +0 -0
  76. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_consensus.py +0 -0
  77. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_constants.py +0 -0
  78. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_curation.py +0 -0
  79. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_data/__init__.py +0 -0
  80. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_edgelist.py +0 -0
  81. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_gaps.py +0 -0
  82. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_gcs.py +0 -0
  83. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_identifiers.py +0 -0
  84. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_igraph.py +0 -0
  85. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_indices.py +0 -0
  86. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_mcp_documentation_utils.py +0 -0
  87. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_mechanism_matching.py +0 -0
  88. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_net_propagation.py +0 -0
  89. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_net_utils.py +0 -0
  90. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_netcontextr.py +0 -0
  91. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_obo.py +0 -0
  92. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_pathwayannot.py +0 -0
  93. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_precomputed_distances.py +0 -0
  94. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_rpy2.py +0 -0
  95. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_sbml.py +0 -0
  96. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_sbml_dfs_core.py +0 -0
  97. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_sbml_dfs_utils.py +0 -0
  98. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_sbo.py +0 -0
  99. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_set_coverage.py +0 -0
  100. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_source.py +0 -0
  101. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_uncompartmentalize.py +0 -0
  102. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/test_utils.py +0 -0
  103. {napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/tests/utils.py +0 -0
{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: napistu
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- Version: 0.2.5.dev3
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+ Version: 0.2.5.dev4
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  Summary: Connecting high-dimensional data to curated pathways
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  Home-page: https://github.com/napistu/napistu-py
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  Author: Sean Hackett
{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
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  [metadata]
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  name = napistu
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- version = 0.2.5.dev3
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+ version = 0.2.5.dev4
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  description = Connecting high-dimensional data to curated pathways
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  long_description = file: README.md
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  long_description_content_type = text/markdown
{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu/mcp/server.py RENAMED
@@ -170,7 +170,7 @@ def start_mcp_server(
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  server_name=env_server_name,
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  )
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- # Create server
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+ # Create server with Cloud Run proxy settings
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  mcp = create_server(profile, host=env_host, port=env_port)
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  # Initialize components first (separate async call)
@@ -187,4 +187,19 @@ def start_mcp_server(
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  logger.info("🚀 Starting MCP server...")
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  logger.info(f"Using HTTP transport on http://{env_host}:{env_port}")
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- mcp.run(transport="streamable-http")
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+
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+ # Configure for Cloud Run proxy environment
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+ if os.getenv("K_SERVICE"): # Cloud Run environment
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+ logger.info("Detected Cloud Run environment")
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+ # Run with proxy-friendly settings
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+ mcp.run(
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+ transport="streamable-http",
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+ host=env_host,
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+ port=env_port,
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+ # Add proxy headers support
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+ forwarded_allow_ips="*",
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+ proxy_headers=True,
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+ )
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+ else:
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+ # Local development
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+ mcp.run(transport="streamable-http", host=env_host, port=env_port)
{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/src/napistu.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: napistu
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- Version: 0.2.5.dev3
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+ Version: 0.2.5.dev4
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  Summary: Connecting high-dimensional data to curated pathways
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  Home-page: https://github.com/napistu/napistu-py
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  Author: Sean Hackett
{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/LICENSE RENAMED
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{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/README.md RENAMED
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{napistu-0.2.5.dev3 → napistu-0.2.5.dev4}/setup.py RENAMED
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