biors 0.47.3__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 (96) hide show
  1. biors-0.47.3/Cargo.lock +3286 -0
  2. biors-0.47.3/Cargo.toml +19 -0
  3. biors-0.47.3/PKG-INFO +77 -0
  4. biors-0.47.3/README.md +68 -0
  5. biors-0.47.3/packages/rust/biors-core/Cargo.toml +22 -0
  6. biors-0.47.3/packages/rust/biors-core/README.md +332 -0
  7. biors-0.47.3/packages/rust/biors-core/benches/fasta_workloads.rs +226 -0
  8. biors-0.47.3/packages/rust/biors-core/examples/benchmark_fasta.rs +108 -0
  9. biors-0.47.3/packages/rust/biors-core/examples/tokenize.rs +12 -0
  10. biors-0.47.3/packages/rust/biors-core/src/error.rs +194 -0
  11. biors-0.47.3/packages/rust/biors-core/src/fasta.rs +236 -0
  12. biors-0.47.3/packages/rust/biors-core/src/fasta_scan/tests.rs +43 -0
  13. biors-0.47.3/packages/rust/biors-core/src/fasta_scan.rs +248 -0
  14. biors-0.47.3/packages/rust/biors-core/src/hash.rs +27 -0
  15. biors-0.47.3/packages/rust/biors-core/src/lib.rs +29 -0
  16. biors-0.47.3/packages/rust/biors-core/src/model_input/tests.rs +266 -0
  17. biors-0.47.3/packages/rust/biors-core/src/model_input.rs +151 -0
  18. biors-0.47.3/packages/rust/biors-core/src/package/artifacts.rs +195 -0
  19. biors-0.47.3/packages/rust/biors-core/src/package/checksum.rs +2 -0
  20. biors-0.47.3/packages/rust/biors-core/src/package/layout.rs +147 -0
  21. biors-0.47.3/packages/rust/biors-core/src/package/manifest.rs +170 -0
  22. biors-0.47.3/packages/rust/biors-core/src/package/paths.rs +99 -0
  23. biors-0.47.3/packages/rust/biors-core/src/package/reports.rs +221 -0
  24. biors-0.47.3/packages/rust/biors-core/src/package/runtime.rs +160 -0
  25. biors-0.47.3/packages/rust/biors-core/src/package/summary.rs +82 -0
  26. biors-0.47.3/packages/rust/biors-core/src/package/tooling/tests.rs +262 -0
  27. biors-0.47.3/packages/rust/biors-core/src/package/tooling.rs +223 -0
  28. biors-0.47.3/packages/rust/biors-core/src/package/types.rs +104 -0
  29. biors-0.47.3/packages/rust/biors-core/src/package/validation.rs +223 -0
  30. biors-0.47.3/packages/rust/biors-core/src/package.rs +45 -0
  31. biors-0.47.3/packages/rust/biors-core/src/runtime/contracts.rs +213 -0
  32. biors-0.47.3/packages/rust/biors-core/src/runtime/errors.rs +133 -0
  33. biors-0.47.3/packages/rust/biors-core/src/runtime/process.rs +271 -0
  34. biors-0.47.3/packages/rust/biors-core/src/runtime/process_io.rs +97 -0
  35. biors-0.47.3/packages/rust/biors-core/src/runtime.rs +19 -0
  36. biors-0.47.3/packages/rust/biors-core/src/sequence/alphabet.rs +75 -0
  37. biors-0.47.3/packages/rust/biors-core/src/sequence/detection.rs +100 -0
  38. biors-0.47.3/packages/rust/biors-core/src/sequence/kind.rs +64 -0
  39. biors-0.47.3/packages/rust/biors-core/src/sequence/kind_validation.rs +185 -0
  40. biors-0.47.3/packages/rust/biors-core/src/sequence/normalization/tests.rs +19 -0
  41. biors-0.47.3/packages/rust/biors-core/src/sequence/normalization.rs +56 -0
  42. biors-0.47.3/packages/rust/biors-core/src/sequence/report.rs +41 -0
  43. biors-0.47.3/packages/rust/biors-core/src/sequence/residue.rs +63 -0
  44. biors-0.47.3/packages/rust/biors-core/src/sequence/types.rs +252 -0
  45. biors-0.47.3/packages/rust/biors-core/src/sequence/validation.rs +225 -0
  46. biors-0.47.3/packages/rust/biors-core/src/sequence.rs +41 -0
  47. biors-0.47.3/packages/rust/biors-core/src/service.rs +196 -0
  48. biors-0.47.3/packages/rust/biors-core/src/tokenizer/config.rs +142 -0
  49. biors-0.47.3/packages/rust/biors-core/src/tokenizer/lookup.rs +184 -0
  50. biors-0.47.3/packages/rust/biors-core/src/tokenizer/protein.rs +89 -0
  51. biors-0.47.3/packages/rust/biors-core/src/tokenizer/sinks/tests.rs +121 -0
  52. biors-0.47.3/packages/rust/biors-core/src/tokenizer/sinks.rs +199 -0
  53. biors-0.47.3/packages/rust/biors-core/src/tokenizer/types.rs +54 -0
  54. biors-0.47.3/packages/rust/biors-core/src/tokenizer/vocab.rs +168 -0
  55. biors-0.47.3/packages/rust/biors-core/src/tokenizer.rs +262 -0
  56. biors-0.47.3/packages/rust/biors-core/src/verification/diff.rs +82 -0
  57. biors-0.47.3/packages/rust/biors-core/src/verification/fixtures.rs +211 -0
  58. biors-0.47.3/packages/rust/biors-core/src/verification/hash.rs +40 -0
  59. biors-0.47.3/packages/rust/biors-core/src/verification/types.rs +177 -0
  60. biors-0.47.3/packages/rust/biors-core/src/verification.rs +14 -0
  61. biors-0.47.3/packages/rust/biors-core/src/versioning.rs +201 -0
  62. biors-0.47.3/packages/rust/biors-core/src/workflow/reproducibility.rs +83 -0
  63. biors-0.47.3/packages/rust/biors-core/src/workflow.rs +246 -0
  64. biors-0.47.3/packages/rust/biors-core/tests/api_parity.rs +32 -0
  65. biors-0.47.3/packages/rust/biors-core/tests/fasta_parsing.rs +110 -0
  66. biors-0.47.3/packages/rust/biors-core/tests/fasta_phase3.rs +81 -0
  67. biors-0.47.3/packages/rust/biors-core/tests/fasta_validation.rs +70 -0
  68. biors-0.47.3/packages/rust/biors-core/tests/fixture_contract.rs +75 -0
  69. biors-0.47.3/packages/rust/biors-core/tests/fixtures/fasta/invalid/empty_identifier.fasta +2 -0
  70. biors-0.47.3/packages/rust/biors-core/tests/fixtures/fasta/invalid/missing_header.fasta +1 -0
  71. biors-0.47.3/packages/rust/biors-core/tests/fixtures/fasta/invalid/missing_sequence.fasta +1 -0
  72. biors-0.47.3/packages/rust/biors-core/tests/fixtures/fasta/valid/mixed_case_whitespace.fasta +4 -0
  73. biors-0.47.3/packages/rust/biors-core/tests/fixtures/manifest/invalid_manifest.json +19 -0
  74. biors-0.47.3/packages/rust/biors-core/tests/fixtures/runtime_process.py +64 -0
  75. biors-0.47.3/packages/rust/biors-core/tests/fixtures/tokenizer/protein_20_expected.json +41 -0
  76. biors-0.47.3/packages/rust/biors-core/tests/model_input_build.rs +100 -0
  77. biors-0.47.3/packages/rust/biors-core/tests/model_input_contract.rs +79 -0
  78. biors-0.47.3/packages/rust/biors-core/tests/module_boundaries.rs +111 -0
  79. biors-0.47.3/packages/rust/biors-core/tests/package.rs +629 -0
  80. biors-0.47.3/packages/rust/biors-core/tests/package_validation.rs +167 -0
  81. biors-0.47.3/packages/rust/biors-core/tests/runtime.rs +397 -0
  82. biors-0.47.3/packages/rust/biors-core/tests/schema_versioning.rs +72 -0
  83. biors-0.47.3/packages/rust/biors-core/tests/sequence_phase3.rs +86 -0
  84. biors-0.47.3/packages/rust/biors-core/tests/service_interface.rs +49 -0
  85. biors-0.47.3/packages/rust/biors-core/tests/tokenizer_contract.rs +150 -0
  86. biors-0.47.3/packages/rust/biors-core/tests/tokenizer_profiles.rs +59 -0
  87. biors-0.47.3/packages/rust/biors-core/tests/verification.rs +171 -0
  88. biors-0.47.3/packages/rust/biors-core/tests/wasm_readiness.rs +33 -0
  89. biors-0.47.3/packages/rust/biors-python/.gitignore +18 -0
  90. biors-0.47.3/packages/rust/biors-python/Cargo.toml +20 -0
  91. biors-0.47.3/packages/rust/biors-python/README.md +68 -0
  92. biors-0.47.3/packages/rust/biors-python/src/lib.rs +258 -0
  93. biors-0.47.3/packages/rust/biors-python/tests/test_python_api.py +50 -0
  94. biors-0.47.3/pyproject.toml +16 -0
  95. biors-0.47.3/python/biors/__init__.py +33 -0
  96. biors-0.47.3/python/biors/py.typed +0 -0
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