seqforge 2026.7.1__py3-none-any.whl

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 (124) hide show
  1. seqforge/__init__.py +16 -0
  2. seqforge/cli/__init__.py +38 -0
  3. seqforge/cli/__main__.py +8 -0
  4. seqforge/cli/_common.py +105 -0
  5. seqforge/cli/compose.py +119 -0
  6. seqforge/cli/eval.py +103 -0
  7. seqforge/cli/harvest.py +417 -0
  8. seqforge/cli/hook.py +247 -0
  9. seqforge/cli/io.py +502 -0
  10. seqforge/cli/kb.py +348 -0
  11. seqforge/cli/manifest.py +536 -0
  12. seqforge/cli/probe.py +43 -0
  13. seqforge/cli/processing.py +192 -0
  14. seqforge/cli/project.py +52 -0
  15. seqforge/cli/resolve.py +55 -0
  16. seqforge/cli/root.py +66 -0
  17. seqforge/cli/run.py +463 -0
  18. seqforge/cli/schema.py +41 -0
  19. seqforge/compose/__init__.py +28 -0
  20. seqforge/compose/core.py +515 -0
  21. seqforge/compose/gates.py +113 -0
  22. seqforge/compose/params.py +447 -0
  23. seqforge/e2e.py +1926 -0
  24. seqforge/evals/__init__.py +78 -0
  25. seqforge/evals/case.py +382 -0
  26. seqforge/evals/grade.py +300 -0
  27. seqforge/evals/run.py +420 -0
  28. seqforge/harvest/__init__.py +121 -0
  29. seqforge/harvest/extract.py +319 -0
  30. seqforge/harvest/fields.py +212 -0
  31. seqforge/harvest/normalize.py +537 -0
  32. seqforge/harvest/prep.py +41 -0
  33. seqforge/harvest/providers.py +321 -0
  34. seqforge/harvest/verify.py +251 -0
  35. seqforge/hooks/__init__.py +33 -0
  36. seqforge/hooks/guards.py +214 -0
  37. seqforge/io/__init__.py +61 -0
  38. seqforge/io/archive.py +450 -0
  39. seqforge/io/attributes.py +190 -0
  40. seqforge/io/biosample/attributes.json +6341 -0
  41. seqforge/io/efo/labels.json +55 -0
  42. seqforge/io/efo.py +138 -0
  43. seqforge/io/onlist.py +661 -0
  44. seqforge/io/onlists/3M-february-2018.codes.gz +0 -0
  45. seqforge/io/onlists/737K-arc-v1.codes.gz +0 -0
  46. seqforge/io/onlists/737K-august-2016.codes.gz +0 -0
  47. seqforge/io/onlists/bd-rhapsody-cls1-384.codes.gz +0 -0
  48. seqforge/io/onlists/bd-rhapsody-cls1.codes.gz +0 -0
  49. seqforge/io/onlists/bd-rhapsody-cls2-384.codes.gz +0 -0
  50. seqforge/io/onlists/bd-rhapsody-cls2.codes.gz +0 -0
  51. seqforge/io/onlists/bd-rhapsody-cls3-384.codes.gz +0 -0
  52. seqforge/io/onlists/bd-rhapsody-cls3.codes.gz +0 -0
  53. seqforge/io/onlists/index.json +74 -0
  54. seqforge/io/remote.py +659 -0
  55. seqforge/io/taxonomy.py +194 -0
  56. seqforge/kb/__init__.py +62 -0
  57. seqforge/kb/anchor.py +169 -0
  58. seqforge/kb/generate.py +147 -0
  59. seqforge/kb/loader.py +152 -0
  60. seqforge/kb/roundtrip.py +112 -0
  61. seqforge/kb/schema.py +422 -0
  62. seqforge/kb/specs/10x-3p-gex/spec.yaml +62 -0
  63. seqforge/kb/specs/10x-3p-gex-v2/README.md +41 -0
  64. seqforge/kb/specs/10x-3p-gex-v2/spec.yaml +83 -0
  65. seqforge/kb/specs/10x-3p-gex-v3/README.md +56 -0
  66. seqforge/kb/specs/10x-3p-gex-v3/spec.yaml +118 -0
  67. seqforge/kb/specs/10x-3p-gex-v3.1/README.md +56 -0
  68. seqforge/kb/specs/10x-3p-gex-v3.1/spec.yaml +124 -0
  69. seqforge/kb/specs/bd-rhapsody-wta/README.md +103 -0
  70. seqforge/kb/specs/bd-rhapsody-wta/spec.yaml +130 -0
  71. seqforge/kb/specs/bd-rhapsody-wta-enhanced/spec.yaml +99 -0
  72. seqforge/kb/specs/bd-rhapsody-wta-enhanced-v1/spec.yaml +93 -0
  73. seqforge/kb/specs/bd-rhapsody-wta-enhanced-v2/spec.yaml +81 -0
  74. seqforge/kb/specs/bulk-rnaseq-pe/README.md +35 -0
  75. seqforge/kb/specs/bulk-rnaseq-pe/spec.yaml +97 -0
  76. seqforge/kb/specs/splitseq/README.md +51 -0
  77. seqforge/kb/specs/splitseq/spec.yaml +157 -0
  78. seqforge/manifest/__init__.py +61 -0
  79. seqforge/manifest/fill.py +531 -0
  80. seqforge/manifest/hash.py +77 -0
  81. seqforge/manifest/instruct.py +114 -0
  82. seqforge/manifest/policy.py +409 -0
  83. seqforge/manifest/validate.py +274 -0
  84. seqforge/models/__init__.py +268 -0
  85. seqforge/models/assertion.py +68 -0
  86. seqforge/models/base.py +100 -0
  87. seqforge/models/blocker.py +71 -0
  88. seqforge/models/conflict.py +47 -0
  89. seqforge/models/dataset.py +320 -0
  90. seqforge/models/evidenced.py +54 -0
  91. seqforge/models/observation.py +157 -0
  92. seqforge/models/processing.py +231 -0
  93. seqforge/models/records.py +145 -0
  94. seqforge/models/resolve.py +216 -0
  95. seqforge/probe/__init__.py +46 -0
  96. seqforge/probe/core.py +232 -0
  97. seqforge/probe/signals.py +250 -0
  98. seqforge/probe/streaming.py +118 -0
  99. seqforge/project.py +177 -0
  100. seqforge/py.typed +0 -0
  101. seqforge/resolve/__init__.py +98 -0
  102. seqforge/resolve/assign.py +204 -0
  103. seqforge/resolve/cache.py +119 -0
  104. seqforge/resolve/confuse.py +215 -0
  105. seqforge/resolve/engine.py +646 -0
  106. seqforge/resolve/escalate.py +668 -0
  107. seqforge/resolve/evaluators.py +306 -0
  108. seqforge/resolve/geometry.py +89 -0
  109. seqforge/resolve/group.py +85 -0
  110. seqforge/resolve/records.py +550 -0
  111. seqforge/resolve/scoring.py +373 -0
  112. seqforge/resolve/window.py +206 -0
  113. seqforge/workflows/__init__.py +234 -0
  114. seqforge/workflows/cram.py +117 -0
  115. seqforge/workflows/h5ad.py +368 -0
  116. seqforge/workflows/map/star.smk +101 -0
  117. seqforge/workflows/map/starsolo.smk +360 -0
  118. seqforge/workflows/qc.py +157 -0
  119. seqforge/workspace.py +125 -0
  120. seqforge-2026.7.1.dist-info/METADATA +125 -0
  121. seqforge-2026.7.1.dist-info/RECORD +124 -0
  122. seqforge-2026.7.1.dist-info/WHEEL +4 -0
  123. seqforge-2026.7.1.dist-info/entry_points.txt +2 -0
  124. seqforge-2026.7.1.dist-info/licenses/LICENSE +21 -0
seqforge/io/onlists/index.json ADDED
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+ "uri": "https://teichlab.github.io/scg_lib_structs/data/BD/BD_CLS1.txt",
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+ "width": 9
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+ "bd-rhapsody-cls2": {
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+ "n_entries": 97,
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+ "bd-rhapsody-cls3": {
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+ "uri": "https://teichlab.github.io/scg_lib_structs/data/BD/BD_CLS3.txt",
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+ "bd-rhapsody-cls3-384": {
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+ }