peerreviewagents 0.5.0__tar.gz

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  1. peerreviewagents-0.5.0/LICENSE +22 -0
  2. peerreviewagents-0.5.0/PKG-INFO +744 -0
  3. peerreviewagents-0.5.0/README.md +688 -0
  4. peerreviewagents-0.5.0/peerreviewagents/__init__.py +13 -0
  5. peerreviewagents-0.5.0/peerreviewagents/agents/__init__.py +0 -0
  6. peerreviewagents-0.5.0/peerreviewagents/agents/auditors/__init__.py +37 -0
  7. peerreviewagents-0.5.0/peerreviewagents/agents/auditors/base.py +187 -0
  8. peerreviewagents-0.5.0/peerreviewagents/agents/auditors/citation_integrity.py +45 -0
  9. peerreviewagents-0.5.0/peerreviewagents/agents/auditors/methods_completeness.py +68 -0
  10. peerreviewagents-0.5.0/peerreviewagents/agents/auditors/revision_compliance.py +486 -0
  11. peerreviewagents-0.5.0/peerreviewagents/agents/author/__init__.py +12 -0
  12. peerreviewagents-0.5.0/peerreviewagents/agents/author/rebuttal.py +78 -0
  13. peerreviewagents-0.5.0/peerreviewagents/agents/author/response_verifier.py +297 -0
  14. peerreviewagents-0.5.0/peerreviewagents/agents/debate/__init__.py +0 -0
  15. peerreviewagents-0.5.0/peerreviewagents/agents/debate/advocate.py +13 -0
  16. peerreviewagents-0.5.0/peerreviewagents/agents/debate/base.py +150 -0
  17. peerreviewagents-0.5.0/peerreviewagents/agents/debate/skeptic.py +15 -0
  18. peerreviewagents-0.5.0/peerreviewagents/agents/editor/__init__.py +0 -0
  19. peerreviewagents-0.5.0/peerreviewagents/agents/editor/desk_screen.py +167 -0
  20. peerreviewagents-0.5.0/peerreviewagents/agents/editor/editor_in_chief.py +517 -0
  21. peerreviewagents-0.5.0/peerreviewagents/agents/journal_recommender/__init__.py +10 -0
  22. peerreviewagents-0.5.0/peerreviewagents/agents/journal_recommender/recommender.py +95 -0
  23. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/__init__.py +45 -0
  24. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/base.py +373 -0
  25. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/contribution_context.py +34 -0
  26. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/data_analysis.py +92 -0
  27. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/ethics.py +43 -0
  28. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/reporting_reproducibility.py +32 -0
  29. peerreviewagents-0.5.0/peerreviewagents/agents/reviewers/scientific_validity.py +31 -0
  30. peerreviewagents-0.5.0/peerreviewagents/agents/schemas.py +1184 -0
  31. peerreviewagents-0.5.0/peerreviewagents/agents/synthesis/__init__.py +0 -0
  32. peerreviewagents-0.5.0/peerreviewagents/agents/synthesis/debate_synthesizer.py +90 -0
  33. peerreviewagents-0.5.0/peerreviewagents/agents/synthesis/gap_finder.py +132 -0
  34. peerreviewagents-0.5.0/peerreviewagents/agents/utils/__init__.py +0 -0
  35. peerreviewagents-0.5.0/peerreviewagents/agents/utils/agent_states.py +207 -0
  36. peerreviewagents-0.5.0/peerreviewagents/agents/utils/agent_utils.py +924 -0
  37. peerreviewagents-0.5.0/peerreviewagents/agents/utils/llm.py +47 -0
  38. peerreviewagents-0.5.0/peerreviewagents/agents/utils/round_delta.py +381 -0
  39. peerreviewagents-0.5.0/peerreviewagents/agents/utils/structured.py +1151 -0
  40. peerreviewagents-0.5.0/peerreviewagents/article_types.py +279 -0
  41. peerreviewagents-0.5.0/peerreviewagents/checkpoints.py +84 -0
  42. peerreviewagents-0.5.0/peerreviewagents/cli/__init__.py +0 -0
  43. peerreviewagents-0.5.0/peerreviewagents/cli/main.py +695 -0
  44. peerreviewagents-0.5.0/peerreviewagents/cli/tui.py +510 -0
  45. peerreviewagents-0.5.0/peerreviewagents/default_config.py +625 -0
  46. peerreviewagents-0.5.0/peerreviewagents/eval/__init__.py +21 -0
  47. peerreviewagents-0.5.0/peerreviewagents/eval/__main__.py +503 -0
  48. peerreviewagents-0.5.0/peerreviewagents/eval/baseline.py +282 -0
  49. peerreviewagents-0.5.0/peerreviewagents/eval/comparison.py +187 -0
  50. peerreviewagents-0.5.0/peerreviewagents/eval/corpus.py +539 -0
  51. peerreviewagents-0.5.0/peerreviewagents/eval/figure.py +231 -0
  52. peerreviewagents-0.5.0/peerreviewagents/eval/integrity.py +126 -0
  53. peerreviewagents-0.5.0/peerreviewagents/eval/metrics.py +396 -0
  54. peerreviewagents-0.5.0/peerreviewagents/eval/runner.py +253 -0
  55. peerreviewagents-0.5.0/peerreviewagents/eval/schema.py +270 -0
  56. peerreviewagents-0.5.0/peerreviewagents/graph/__init__.py +0 -0
  57. peerreviewagents-0.5.0/peerreviewagents/graph/conditional_logic.py +40 -0
  58. peerreviewagents-0.5.0/peerreviewagents/graph/review_graph.py +607 -0
  59. peerreviewagents-0.5.0/peerreviewagents/ingest/__init__.py +0 -0
  60. peerreviewagents-0.5.0/peerreviewagents/ingest/cache.py +230 -0
  61. peerreviewagents-0.5.0/peerreviewagents/ingest/loader.py +669 -0
  62. peerreviewagents-0.5.0/peerreviewagents/ingest/prose.py +737 -0
  63. peerreviewagents-0.5.0/peerreviewagents/ingest/structured.py +316 -0
  64. peerreviewagents-0.5.0/peerreviewagents/journals/README.md +137 -0
  65. peerreviewagents-0.5.0/peerreviewagents/journals/__init__.py +215 -0
  66. peerreviewagents-0.5.0/peerreviewagents/journals/_template.toml +47 -0
  67. peerreviewagents-0.5.0/peerreviewagents/journals/analytical-chemistry.toml +39 -0
  68. peerreviewagents-0.5.0/peerreviewagents/journals/angewandte-chemie.toml +38 -0
  69. peerreviewagents-0.5.0/peerreviewagents/journals/bioinformatics.toml +46 -0
  70. peerreviewagents-0.5.0/peerreviewagents/journals/bmc-bioinformatics.toml +38 -0
  71. peerreviewagents-0.5.0/peerreviewagents/journals/briefings-in-bioinformatics.toml +38 -0
  72. peerreviewagents-0.5.0/peerreviewagents/journals/cell.toml +39 -0
  73. peerreviewagents-0.5.0/peerreviewagents/journals/elife.toml +40 -0
  74. peerreviewagents-0.5.0/peerreviewagents/journals/erc.toml +59 -0
  75. peerreviewagents-0.5.0/peerreviewagents/journals/general.toml +52 -0
  76. peerreviewagents-0.5.0/peerreviewagents/journals/genome-biology.toml +39 -0
  77. peerreviewagents-0.5.0/peerreviewagents/journals/gigascience.toml +39 -0
  78. peerreviewagents-0.5.0/peerreviewagents/journals/ieee-tpami.toml +39 -0
  79. peerreviewagents-0.5.0/peerreviewagents/journals/jacs.toml +38 -0
  80. peerreviewagents-0.5.0/peerreviewagents/journals/jmlr.toml +44 -0
  81. peerreviewagents-0.5.0/peerreviewagents/journals/journal-of-medicinal-chemistry.toml +39 -0
  82. peerreviewagents-0.5.0/peerreviewagents/journals/journal-of-proteome-research.toml +74 -0
  83. peerreviewagents-0.5.0/peerreviewagents/journals/ml-conference.toml +72 -0
  84. peerreviewagents-0.5.0/peerreviewagents/journals/molecular-cellular-proteomics.toml +39 -0
  85. peerreviewagents-0.5.0/peerreviewagents/journals/nature-biotechnology.toml +39 -0
  86. peerreviewagents-0.5.0/peerreviewagents/journals/nature-communications.toml +38 -0
  87. peerreviewagents-0.5.0/peerreviewagents/journals/nature-machine-intelligence.toml +38 -0
  88. peerreviewagents-0.5.0/peerreviewagents/journals/nature-methods.toml +46 -0
  89. peerreviewagents-0.5.0/peerreviewagents/journals/nature.toml +40 -0
  90. peerreviewagents-0.5.0/peerreviewagents/journals/nejm.toml +40 -0
  91. peerreviewagents-0.5.0/peerreviewagents/journals/nih-r01.toml +70 -0
  92. peerreviewagents-0.5.0/peerreviewagents/journals/nih-r21.toml +57 -0
  93. peerreviewagents-0.5.0/peerreviewagents/journals/nsf.toml +59 -0
  94. peerreviewagents-0.5.0/peerreviewagents/journals/nucleic-acids-research.toml +38 -0
  95. peerreviewagents-0.5.0/peerreviewagents/journals/plos-biology.toml +41 -0
  96. peerreviewagents-0.5.0/peerreviewagents/journals/plos-computational-biology.toml +39 -0
  97. peerreviewagents-0.5.0/peerreviewagents/journals/plos-genetics.toml +41 -0
  98. peerreviewagents-0.5.0/peerreviewagents/journals/plos-ntds.toml +42 -0
  99. peerreviewagents-0.5.0/peerreviewagents/journals/plos-one.toml +41 -0
  100. peerreviewagents-0.5.0/peerreviewagents/journals/pnas.toml +38 -0
  101. peerreviewagents-0.5.0/peerreviewagents/journals/science.toml +37 -0
  102. peerreviewagents-0.5.0/peerreviewagents/journals/scientific-reports.toml +39 -0
  103. peerreviewagents-0.5.0/peerreviewagents/journals/tmlr.toml +41 -0
  104. peerreviewagents-0.5.0/peerreviewagents/mcp/__init__.py +5 -0
  105. peerreviewagents-0.5.0/peerreviewagents/mcp/__main__.py +4 -0
  106. peerreviewagents-0.5.0/peerreviewagents/mcp/server.py +267 -0
  107. peerreviewagents-0.5.0/peerreviewagents/observability.py +594 -0
  108. peerreviewagents-0.5.0/peerreviewagents/panel.py +61 -0
  109. peerreviewagents-0.5.0/peerreviewagents/reports.py +493 -0
  110. peerreviewagents-0.5.0/peerreviewagents/research/__init__.py +47 -0
  111. peerreviewagents-0.5.0/peerreviewagents/research/arxiv.py +75 -0
  112. peerreviewagents-0.5.0/peerreviewagents/research/biorxiv.py +73 -0
  113. peerreviewagents-0.5.0/peerreviewagents/research/interface.py +182 -0
  114. peerreviewagents-0.5.0/peerreviewagents/research/pubmed.py +94 -0
  115. peerreviewagents-0.5.0/peerreviewagents/research/semantic_scholar.py +70 -0
  116. peerreviewagents-0.5.0/peerreviewagents/research/tools.py +104 -0
  117. peerreviewagents-0.5.0/peerreviewagents/rounds.py +432 -0
  118. peerreviewagents-0.5.0/peerreviewagents/runtime/__init__.py +3 -0
  119. peerreviewagents-0.5.0/peerreviewagents/runtime/providers.py +779 -0
  120. peerreviewagents-0.5.0/peerreviewagents/runtime/subscriptions.py +610 -0
  121. peerreviewagents-0.5.0/peerreviewagents/strictness.py +115 -0
  122. peerreviewagents-0.5.0/peerreviewagents/web/__init__.py +12 -0
  123. peerreviewagents-0.5.0/peerreviewagents/web/bus.py +107 -0
  124. peerreviewagents-0.5.0/peerreviewagents/web/jobs.py +177 -0
  125. peerreviewagents-0.5.0/peerreviewagents/web/runner.py +398 -0
  126. peerreviewagents-0.5.0/peerreviewagents/web/server.py +521 -0
  127. peerreviewagents-0.5.0/peerreviewagents/web/static/app.js +780 -0
  128. peerreviewagents-0.5.0/peerreviewagents/web/static/index.html +215 -0
  129. peerreviewagents-0.5.0/peerreviewagents/web/static/job.html +92 -0
  130. peerreviewagents-0.5.0/peerreviewagents/web/static/review.html +152 -0
  131. peerreviewagents-0.5.0/peerreviewagents/web/static/style.css +973 -0
  132. peerreviewagents-0.5.0/peerreviewagents.egg-info/PKG-INFO +744 -0
  133. peerreviewagents-0.5.0/peerreviewagents.egg-info/SOURCES.txt +174 -0
  134. peerreviewagents-0.5.0/peerreviewagents.egg-info/dependency_links.txt +1 -0
  135. peerreviewagents-0.5.0/peerreviewagents.egg-info/entry_points.txt +3 -0
  136. peerreviewagents-0.5.0/peerreviewagents.egg-info/requires.txt +35 -0
  137. peerreviewagents-0.5.0/peerreviewagents.egg-info/top_level.txt +1 -0
  138. peerreviewagents-0.5.0/pyproject.toml +104 -0
  139. peerreviewagents-0.5.0/setup.cfg +4 -0
  140. peerreviewagents-0.5.0/tests/test_article_types.py +205 -0
  141. peerreviewagents-0.5.0/tests/test_checkpoints.py +70 -0
  142. peerreviewagents-0.5.0/tests/test_cli_panel.py +123 -0
  143. peerreviewagents-0.5.0/tests/test_config_validation.py +253 -0
  144. peerreviewagents-0.5.0/tests/test_correction_mode.py +203 -0
  145. peerreviewagents-0.5.0/tests/test_decision_chain.py +524 -0
  146. peerreviewagents-0.5.0/tests/test_desk_screen.py +105 -0
  147. peerreviewagents-0.5.0/tests/test_downstream_compat.py +282 -0
  148. peerreviewagents-0.5.0/tests/test_eval.py +761 -0
  149. peerreviewagents-0.5.0/tests/test_gap_finder.py +110 -0
  150. peerreviewagents-0.5.0/tests/test_incomplete_panel.py +149 -0
  151. peerreviewagents-0.5.0/tests/test_ingest_backend.py +722 -0
  152. peerreviewagents-0.5.0/tests/test_journals.py +158 -0
  153. peerreviewagents-0.5.0/tests/test_mcp_server.py +121 -0
  154. peerreviewagents-0.5.0/tests/test_metadata.py +65 -0
  155. peerreviewagents-0.5.0/tests/test_observability.py +128 -0
  156. peerreviewagents-0.5.0/tests/test_pipeline.py +491 -0
  157. peerreviewagents-0.5.0/tests/test_pricing.py +297 -0
  158. peerreviewagents-0.5.0/tests/test_prompt_cache_prefix.py +195 -0
  159. peerreviewagents-0.5.0/tests/test_prose.py +680 -0
  160. peerreviewagents-0.5.0/tests/test_providers.py +499 -0
  161. peerreviewagents-0.5.0/tests/test_real_pdf_ingest.py +124 -0
  162. peerreviewagents-0.5.0/tests/test_reasoning_effort.py +117 -0
  163. peerreviewagents-0.5.0/tests/test_reference_list.py +250 -0
  164. peerreviewagents-0.5.0/tests/test_research_routing.py +279 -0
  165. peerreviewagents-0.5.0/tests/test_response_verifier.py +380 -0
  166. peerreviewagents-0.5.0/tests/test_revision_adversarial.py +606 -0
  167. peerreviewagents-0.5.0/tests/test_revision_compliance.py +714 -0
  168. peerreviewagents-0.5.0/tests/test_revision_reviewers.py +313 -0
  169. peerreviewagents-0.5.0/tests/test_round_delta.py +518 -0
  170. peerreviewagents-0.5.0/tests/test_rounds.py +602 -0
  171. peerreviewagents-0.5.0/tests/test_strictness.py +104 -0
  172. peerreviewagents-0.5.0/tests/test_structured.py +938 -0
  173. peerreviewagents-0.5.0/tests/test_subscriptions.py +229 -0
  174. peerreviewagents-0.5.0/tests/test_usage_table.py +250 -0
  175. peerreviewagents-0.5.0/tests/test_verdict_calibration.py +66 -0
  176. peerreviewagents-0.5.0/tests/test_web.py +569 -0
peerreviewagents-0.5.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2026 Patrick Garrett, Aleix Navarro Garrido,
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+ Ricard Garcia-Carbonell, and John R. Yates III
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.