ChemVault 0.14.7__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 (80) hide show
  1. chemvault-0.14.7/.gitignore +33 -0
  2. chemvault-0.14.7/.streamlit/config.toml +6 -0
  3. chemvault-0.14.7/COPYING +674 -0
  4. chemvault-0.14.7/COPYING.LESSER +165 -0
  5. chemvault-0.14.7/LICENSE +8 -0
  6. chemvault-0.14.7/PKG-INFO +630 -0
  7. chemvault-0.14.7/README.md +597 -0
  8. chemvault-0.14.7/api/__init__.py +2 -0
  9. chemvault-0.14.7/api/job_runtime.py +33 -0
  10. chemvault-0.14.7/api/main.py +543 -0
  11. chemvault-0.14.7/api/schemas.py +185 -0
  12. chemvault-0.14.7/app.py +137 -0
  13. chemvault-0.14.7/application/__init__.py +2 -0
  14. chemvault-0.14.7/application/curation_use_cases.py +27 -0
  15. chemvault-0.14.7/application/database_use_cases.py +183 -0
  16. chemvault-0.14.7/application/harmonsmile_jobs.py +311 -0
  17. chemvault-0.14.7/application/job_contracts.py +100 -0
  18. chemvault-0.14.7/application/modelability_index.py +738 -0
  19. chemvault-0.14.7/application/modelability_jobs.py +297 -0
  20. chemvault-0.14.7/application/protein_identifiers.py +198 -0
  21. chemvault-0.14.7/application/pubchem_jobs.py +180 -0
  22. chemvault-0.14.7/application/scientific_jobs.py +132 -0
  23. chemvault-0.14.7/application/scientific_runtime.py +163 -0
  24. chemvault-0.14.7/application/structure_consolidation.py +358 -0
  25. chemvault-0.14.7/application/table_use_cases.py +95 -0
  26. chemvault-0.14.7/application/target_identity.py +195 -0
  27. chemvault-0.14.7/clients/__init__.py +1 -0
  28. chemvault-0.14.7/clients/api_client.py +354 -0
  29. chemvault-0.14.7/clients/backend_gateway.py +982 -0
  30. chemvault-0.14.7/docs/api.md +328 -0
  31. chemvault-0.14.7/docs/assets/chemvault-logo.jpeg +0 -0
  32. chemvault-0.14.7/docs/changelog.md +1 -0
  33. chemvault-0.14.7/docs/index.md +96 -0
  34. chemvault-0.14.7/docs/stylesheets/extra.css +352 -0
  35. chemvault-0.14.7/docs/usage.md +281 -0
  36. chemvault-0.14.7/pyproject.toml +115 -0
  37. chemvault-0.14.7/services/__init__.py +2 -0
  38. chemvault-0.14.7/services/activity_data.py +350 -0
  39. chemvault-0.14.7/services/activity_enrichment.py +861 -0
  40. chemvault-0.14.7/services/builders.py +85 -0
  41. chemvault-0.14.7/services/curation.py +60 -0
  42. chemvault-0.14.7/services/database.py +149 -0
  43. chemvault-0.14.7/services/database_core.py +9 -0
  44. chemvault-0.14.7/services/db_audit.py +565 -0
  45. chemvault-0.14.7/services/export.py +75 -0
  46. chemvault-0.14.7/services/harmonsmile_cache.py +605 -0
  47. chemvault-0.14.7/services/harmonsmile_ingest.py +44 -0
  48. chemvault-0.14.7/services/job_launcher.py +76 -0
  49. chemvault-0.14.7/services/job_models.py +51 -0
  50. chemvault-0.14.7/services/job_store.py +887 -0
  51. chemvault-0.14.7/services/job_worker.py +98 -0
  52. chemvault-0.14.7/services/modelability_fingerprint_artifacts.py +387 -0
  53. chemvault-0.14.7/services/modelability_index.py +242 -0
  54. chemvault-0.14.7/services/murcko_metrics.py +134 -0
  55. chemvault-0.14.7/services/murcko_nn_interface.py +191 -0
  56. chemvault-0.14.7/services/murcko_population.py +86 -0
  57. chemvault-0.14.7/services/murcko_scaffold.py +46 -0
  58. chemvault-0.14.7/services/pubchem_aid_completeness.py +352 -0
  59. chemvault-0.14.7/services/pubchem_client.py +107 -0
  60. chemvault-0.14.7/services/pubchem_job_service.py +255 -0
  61. chemvault-0.14.7/services/pubchem_models.py +54 -0
  62. chemvault-0.14.7/services/pubchem_protein_search.py +1499 -0
  63. chemvault-0.14.7/services/pubchem_repository.py +104 -0
  64. chemvault-0.14.7/services/runtime_config.py +17 -0
  65. chemvault-0.14.7/services/selection.py +41 -0
  66. chemvault-0.14.7/services/sql_utils.py +54 -0
  67. chemvault-0.14.7/services/structure_consolidation.py +521 -0
  68. chemvault-0.14.7/services/uniprot_client.py +172 -0
  69. chemvault-0.14.7/ui/__init__.py +2 -0
  70. chemvault-0.14.7/ui/dialogs.py +418 -0
  71. chemvault-0.14.7/ui/harmonsmile_state.py +188 -0
  72. chemvault-0.14.7/ui/launcher.py +57 -0
  73. chemvault-0.14.7/ui/main_page.py +1961 -0
  74. chemvault-0.14.7/ui/modelability_card.py +199 -0
  75. chemvault-0.14.7/ui/modelability_result.py +481 -0
  76. chemvault-0.14.7/ui/modelability_state.py +327 -0
  77. chemvault-0.14.7/ui/session_state.py +238 -0
  78. chemvault-0.14.7/ui/sidebar.py +677 -0
  79. chemvault-0.14.7/ui/state_keys.py +108 -0
  80. chemvault-0.14.7/ui/theme.py +89 -0
chemvault-0.14.7/.gitignore ADDED
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+ # Python cache
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+ __pycache__/
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+ *.py[cod]
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+ *$py.class
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+ .pytest_cache/
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+ .mypy_cache/
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+ .ruff_cache/
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+
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+ # SQLite databases (generated by the app)
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+ *.db
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+
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+ # Temp folder created by ChemVault at runtime
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+ tempFilesHarmonsile/
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+
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+ # Python packaging
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+ *.egg-info/
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+ dist/
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+ build/
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+
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+ # Environments
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+ .env
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+ .venv/
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+ env/
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+
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+ # OS files
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+ .DS_Store
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+ Thumbs.db
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+
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+ # VS Code
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+ .vscode/
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+
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+ # Local scientific analysis and manuscript audit artifacts
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+ analysis_artifacts/
chemvault-0.14.7/.streamlit/config.toml ADDED
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+ [theme]
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+ primaryColor = "#B45309"
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+ backgroundColor = "#FFFFFF"
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+ secondaryBackgroundColor = "#F3F4F6"
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+ textColor = "#262730"
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+ font = "sans serif"