gapit 0.6.1__tar.gz → 0.6.2__tar.gz

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Files changed (464) hide show
  1. {gapit-0.6.1 → gapit-0.6.2}/CHANGELOG.md +8 -0
  2. {gapit-0.6.1 → gapit-0.6.2}/CITATION.cff +1 -1
  3. {gapit-0.6.1 → gapit-0.6.2}/PKG-INFO +1 -1
  4. {gapit-0.6.1 → gapit-0.6.2}/docs/agents.md +1 -1
  5. {gapit-0.6.1 → gapit-0.6.2}/docs/agents.zh.md +1 -1
  6. {gapit-0.6.1 → gapit-0.6.2}/docs/databases.md +1 -1
  7. {gapit-0.6.1 → gapit-0.6.2}/docs/databases.zh.md +1 -1
  8. {gapit-0.6.1 → gapit-0.6.2}/docs/datadir.md +2 -2
  9. {gapit-0.6.1 → gapit-0.6.2}/docs/datadir.zh.md +2 -2
  10. {gapit-0.6.1 → gapit-0.6.2}/docs/installation.md +2 -2
  11. {gapit-0.6.1 → gapit-0.6.2}/docs/installation.zh.md +2 -2
  12. {gapit-0.6.1 → gapit-0.6.2}/docs/mcp.md +4 -4
  13. {gapit-0.6.1 → gapit-0.6.2}/docs/mcp.zh.md +4 -4
  14. {gapit-0.6.1 → gapit-0.6.2}/docs/outputs.md +4 -4
  15. {gapit-0.6.1 → gapit-0.6.2}/docs/outputs.zh.md +4 -4
  16. {gapit-0.6.1 → gapit-0.6.2}/docs/quickstart.md +1 -1
  17. {gapit-0.6.1 → gapit-0.6.2}/docs/quickstart.zh.md +1 -1
  18. {gapit-0.6.1 → gapit-0.6.2}/docs/reads.md +6 -6
  19. {gapit-0.6.1 → gapit-0.6.2}/docs/reads.zh.md +6 -6
  20. {gapit-0.6.1 → gapit-0.6.2}/docs/screen.md +2 -2
  21. {gapit-0.6.1 → gapit-0.6.2}/docs/screen.zh.md +2 -2
  22. {gapit-0.6.1 → gapit-0.6.2}/docs/summary.md +2 -2
  23. {gapit-0.6.1 → gapit-0.6.2}/docs/summary.zh.md +2 -2
  24. {gapit-0.6.1 → gapit-0.6.2}/pixi.lock +2 -2
  25. {gapit-0.6.1 → gapit-0.6.2}/pixi.toml +1 -1
  26. {gapit-0.6.1 → gapit-0.6.2}/pyproject.toml +1 -1
  27. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/__init__.py +1 -1
  28. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster2_vp_none.json +1 -1
  29. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster2_vp_none.md +1 -1
  30. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster2_vp_o3k6.json +1 -1
  31. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster2_vp_o3k6.md +1 -1
  32. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_exact.json +1 -1
  33. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_exact.md +1 -1
  34. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_fragmented.json +1 -1
  35. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_fragmented.md +1 -1
  36. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_ambiguous.json +1 -1
  37. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_ambiguous.md +1 -1
  38. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_cm_exact.json +1 -1
  39. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_cm_exact.md +1 -1
  40. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_exact.json +1 -1
  41. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_typing_exact.md +1 -1
  42. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_vc_inaba.json +1 -1
  43. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/cluster_vc_inaba.md +1 -1
  44. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/fragments_merge.json +1 -1
  45. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/fragments_merge.md +1 -1
  46. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_dec_pic_astA.json +1 -1
  47. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_dec_pic_astA.md +1 -1
  48. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_doumith_4b.json +1 -1
  49. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_doumith_4b.md +1 -1
  50. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_l4b.json +1 -1
  51. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_l4b.md +1 -1
  52. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_mixed.json +1 -1
  53. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_mixed.md +1 -1
  54. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_vp_typed.json +1 -1
  55. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_serotyping_vp_typed.md +1 -1
  56. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_shigella_mixed.json +1 -1
  57. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_shigella_mixed.md +1 -1
  58. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_typing_exact.json +1 -1
  59. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/gene_typing_exact.md +1 -1
  60. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/reads_tinyamr.json +1 -1
  61. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/reads_tinyamr.md +1 -1
  62. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/screen_multi.json +1 -1
  63. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/screen_multi.md +1 -1
  64. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/summary_multi.json +1 -1
  65. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/summary_multi.md +1 -1
  66. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/typing_markers.json +1 -1
  67. {gapit-0.6.1 → gapit-0.6.2}/tests/golden/typing_markers.md +1 -1
  68. {gapit-0.6.1 → gapit-0.6.2}/.gitattributes +0 -0
  69. {gapit-0.6.1 → gapit-0.6.2}/.github/workflows/ci.yml +0 -0
  70. {gapit-0.6.1 → gapit-0.6.2}/.github/workflows/docs.yml +0 -0
  71. {gapit-0.6.1 → gapit-0.6.2}/.github/workflows/release.yml +0 -0
  72. {gapit-0.6.1 → gapit-0.6.2}/.gitignore +0 -0
  73. {gapit-0.6.1 → gapit-0.6.2}/AGENTS.md +0 -0
  74. {gapit-0.6.1 → gapit-0.6.2}/CODE_QUALITY_REPORT.md +0 -0
  75. {gapit-0.6.1 → gapit-0.6.2}/CONTRIBUTING.md +0 -0
  76. {gapit-0.6.1 → gapit-0.6.2}/LICENSE +0 -0
  77. {gapit-0.6.1 → gapit-0.6.2}/PLAN.md +0 -0
  78. {gapit-0.6.1 → gapit-0.6.2}/README.md +0 -0
  79. {gapit-0.6.1 → gapit-0.6.2}/SECURITY.md +0 -0
  80. {gapit-0.6.1 → gapit-0.6.2}/SPEC.md +0 -0
  81. {gapit-0.6.1 → gapit-0.6.2}/docs/custom-db.md +0 -0
  82. {gapit-0.6.1 → gapit-0.6.2}/docs/custom-db.zh.md +0 -0
  83. {gapit-0.6.1 → gapit-0.6.2}/docs/faq.md +0 -0
  84. {gapit-0.6.1 → gapit-0.6.2}/docs/faq.zh.md +0 -0
  85. {gapit-0.6.1 → gapit-0.6.2}/docs/gseek-engine.md +0 -0
  86. {gapit-0.6.1 → gapit-0.6.2}/docs/gseek-engine.zh.md +0 -0
  87. {gapit-0.6.1 → gapit-0.6.2}/docs/index.md +0 -0
  88. {gapit-0.6.1 → gapit-0.6.2}/docs/index.zh.md +0 -0
  89. {gapit-0.6.1 → gapit-0.6.2}/docs/typing.md +0 -0
  90. {gapit-0.6.1 → gapit-0.6.2}/docs/typing.zh.md +0 -0
  91. {gapit-0.6.1 → gapit-0.6.2}/mkdocs.yml +0 -0
  92. {gapit-0.6.1 → gapit-0.6.2}/scripts/cluster_calibration.py +0 -0
  93. {gapit-0.6.1 → gapit-0.6.2}/scripts/generate_vp_typing.py +0 -0
  94. {gapit-0.6.1 → gapit-0.6.2}/scripts/vp_rules_matrix.tsv +0 -0
  95. {gapit-0.6.1 → gapit-0.6.2}/scripts/vp_typing_support.py +0 -0
  96. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/blast.py +0 -0
  97. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/bundled.py +0 -0
  98. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/bundled_cluster.py +0 -0
  99. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cli.py +0 -0
  100. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cluster.py +0 -0
  101. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cluster_math.py +0 -0
  102. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/clusterbuild.py +0 -0
  103. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_db.py +0 -0
  104. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_db_build.py +0 -0
  105. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_db_install.py +0 -0
  106. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_db_outdated.py +0 -0
  107. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_db_search.py +0 -0
  108. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_screen.py +0 -0
  109. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_screen_positionals.py +0 -0
  110. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_screen_reads_args.py +0 -0
  111. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_summary.py +0 -0
  112. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/cmd_typing.py +0 -0
  113. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/config.py +0 -0
  114. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoh/bundled.json +0 -0
  115. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoh/sequences +0 -0
  116. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoli_dec/bundled.json +0 -0
  117. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoli_dec/floors.json +0 -0
  118. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoli_dec/records.jsonl +0 -0
  119. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoli_dec/sequences +0 -0
  120. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ecoli_dec/typing.json +0 -0
  121. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/lm_doumith/bundled.json +0 -0
  122. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/lm_doumith/sequences +0 -0
  123. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/lm_doumith/typing.json +0 -0
  124. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ncbi/bundled.json +0 -0
  125. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/ncbi/sequences +0 -0
  126. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/resfinder/bundled.json +0 -0
  127. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/resfinder/sequences +0 -0
  128. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vc_serogroup/bundled.json +0 -0
  129. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vc_serogroup/floors.json +0 -0
  130. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vc_serogroup/records.jsonl +0 -0
  131. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vc_serogroup/sequences +0 -0
  132. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vc_serogroup/typing.json +0 -0
  133. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vp_ok/bundled.json +0 -0
  134. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vp_ok/features.json +0 -0
  135. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vp_ok/sequences +0 -0
  136. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/data/dbs/vp_ok/typing.json +0 -0
  137. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db.py +0 -0
  138. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db_build_meta.py +0 -0
  139. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db_build_ops.py +0 -0
  140. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db_ops.py +0 -0
  141. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db_query_ops.py +0 -0
  142. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/db_txn.py +0 -0
  143. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/dbbuild.py +0 -0
  144. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/dbcodec.py +0 -0
  145. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/dispatch.py +0 -0
  146. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/engines.py +0 -0
  147. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/errors.py +0 -0
  148. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/fasta.py +0 -0
  149. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/__init__.py +0 -0
  150. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/cluster.py +0 -0
  151. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/cluster2.py +0 -0
  152. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/cluster_md.py +0 -0
  153. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/csvutil.py +0 -0
  154. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/json.py +0 -0
  155. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/md.py +0 -0
  156. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/reads_json.py +0 -0
  157. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/reads_tsv.py +0 -0
  158. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/schemas.py +0 -0
  159. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/summary.py +0 -0
  160. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/tsv.py +0 -0
  161. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/formats/typing_result.py +0 -0
  162. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/fragments.py +0 -0
  163. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/gbfeatures.py +0 -0
  164. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/gene_floors.py +0 -0
  165. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/gffparse.py +0 -0
  166. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/gseek_engine.py +0 -0
  167. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/hits.py +0 -0
  168. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/mcp.py +0 -0
  169. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/mcp_schemas.py +0 -0
  170. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/mcp_tools.py +0 -0
  171. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/minimap.py +0 -0
  172. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/minimap2_run.py +0 -0
  173. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/paf.py +0 -0
  174. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/proctools.py +0 -0
  175. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/progress.py +0 -0
  176. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/__init__.py +0 -0
  177. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ab_k.py +0 -0
  178. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ab_o.py +0 -0
  179. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/argannot.py +0 -0
  180. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/bacmet2.py +0 -0
  181. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/card.py +0 -0
  182. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/cluster_common.py +0 -0
  183. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/common.py +0 -0
  184. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ecoh.py +0 -0
  185. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ecoli_kps.py +0 -0
  186. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ecoli_vf.py +0 -0
  187. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/kosc_k.py +0 -0
  188. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/kosc_o.py +0 -0
  189. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/kpsc_k.py +0 -0
  190. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/kpsc_o.py +0 -0
  191. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/megares.py +0 -0
  192. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/ncbi.py +0 -0
  193. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/plasmidfinder.py +0 -0
  194. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/resfinder.py +0 -0
  195. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/upec_expec_vf.py +0 -0
  196. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/vfdb.py +0 -0
  197. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/providers/victors.py +0 -0
  198. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/py.typed +0 -0
  199. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/readpairs.py +0 -0
  200. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/reads.py +0 -0
  201. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/records.py +0 -0
  202. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/report.py +0 -0
  203. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/screening.py +0 -0
  204. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/screening_cluster.py +0 -0
  205. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/screening_reads.py +0 -0
  206. {gapit-0.6.1 → gapit-0.6.2}/src/gapit/screening_reads_positional.py +0 -0
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  406. {gapit-0.6.1 → gapit-0.6.2}/tests/test_gffparse.py +0 -0
  407. {gapit-0.6.1 → gapit-0.6.2}/tests/test_gseek_engine.py +0 -0
  408. {gapit-0.6.1 → gapit-0.6.2}/tests/test_gseek_parity.py +0 -0
  409. {gapit-0.6.1 → gapit-0.6.2}/tests/test_hits.py +0 -0
  410. {gapit-0.6.1 → gapit-0.6.2}/tests/test_json_format.py +0 -0
  411. {gapit-0.6.1 → gapit-0.6.2}/tests/test_lm_doumith.py +0 -0
  412. {gapit-0.6.1 → gapit-0.6.2}/tests/test_mcp.py +0 -0
  413. {gapit-0.6.1 → gapit-0.6.2}/tests/test_mcp_db_tools.py +0 -0
  414. {gapit-0.6.1 → gapit-0.6.2}/tests/test_mcp_protocol.py +0 -0
  415. {gapit-0.6.1 → gapit-0.6.2}/tests/test_mcp_reads.py +0 -0
  416. {gapit-0.6.1 → gapit-0.6.2}/tests/test_md_format.py +0 -0
  417. {gapit-0.6.1 → gapit-0.6.2}/tests/test_minimap.py +0 -0
  418. {gapit-0.6.1 → gapit-0.6.2}/tests/test_mol_type.py +0 -0
  419. {gapit-0.6.1 → gapit-0.6.2}/tests/test_oversubscription.py +0 -0
  420. {gapit-0.6.1 → gapit-0.6.2}/tests/test_paf.py +0 -0
  421. {gapit-0.6.1 → gapit-0.6.2}/tests/test_paf_identity.py +0 -0
  422. {gapit-0.6.1 → gapit-0.6.2}/tests/test_parser_fuzz.py +0 -0
  423. {gapit-0.6.1 → gapit-0.6.2}/tests/test_progress.py +0 -0
  424. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_argannot.py +0 -0
  425. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_bacmet2.py +0 -0
  426. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_card.py +0 -0
  427. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_ecoh.py +0 -0
  428. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_ecoli_vf.py +0 -0
  429. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_kaptive.py +0 -0
  430. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_megares.py +0 -0
  431. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_ncbi.py +0 -0
  432. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_plasmidfinder.py +0 -0
  433. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_resfinder.py +0 -0
  434. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_upec_expec_vf.py +0 -0
  435. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_vfdb.py +0 -0
  436. {gapit-0.6.1 → gapit-0.6.2}/tests/test_provider_victors.py +0 -0
  437. {gapit-0.6.1 → gapit-0.6.2}/tests/test_providers_common.py +0 -0
  438. {gapit-0.6.1 → gapit-0.6.2}/tests/test_readpairs.py +0 -0
  439. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads2_homologs.py +0 -0
  440. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads2_model.py +0 -0
  441. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads_aggregate.py +0 -0
  442. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads_integration.py +0 -0
  443. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads_interval_union.py +0 -0
  444. {gapit-0.6.1 → gapit-0.6.2}/tests/test_reads_streaming.py +0 -0
  445. {gapit-0.6.1 → gapit-0.6.2}/tests/test_records.py +0 -0
  446. {gapit-0.6.1 → gapit-0.6.2}/tests/test_report.py +0 -0
  447. {gapit-0.6.1 → gapit-0.6.2}/tests/test_screen_integration.py +0 -0
  448. {gapit-0.6.1 → gapit-0.6.2}/tests/test_screening_reads_unit.py +0 -0
  449. {gapit-0.6.1 → gapit-0.6.2}/tests/test_seqconvert.py +0 -0
  450. {gapit-0.6.1 → gapit-0.6.2}/tests/test_seqconvert_differential.py +0 -0
  451. {gapit-0.6.1 → gapit-0.6.2}/tests/test_streaming_chunks.py +0 -0
  452. {gapit-0.6.1 → gapit-0.6.2}/tests/test_summary.py +0 -0
  453. {gapit-0.6.1 → gapit-0.6.2}/tests/test_summary_formats.py +0 -0
  454. {gapit-0.6.1 → gapit-0.6.2}/tests/test_tsv.py +0 -0
  455. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_command.py +0 -0
  456. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_engine.py +0 -0
  457. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_models.py +0 -0
  458. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_schemes.py +0 -0
  459. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_schemes_cluster.py +0 -0
  460. {gapit-0.6.1 → gapit-0.6.2}/tests/test_typing_stage2.py +0 -0
  461. {gapit-0.6.1 → gapit-0.6.2}/tests/test_vc_serogroup.py +0 -0
  462. {gapit-0.6.1 → gapit-0.6.2}/tests/test_version.py +0 -0
  463. {gapit-0.6.1 → gapit-0.6.2}/tests/test_vp_ok.py +0 -0
  464. {gapit-0.6.1 → gapit-0.6.2}/tests/test_vp_ok_acceptance.py +0 -0
@@ -5,6 +5,14 @@ All notable changes to gapit are documented in this file.
5
5
  The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this
6
6
  project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
7
7
 
8
+ ## [0.6.2] - 2026-10-26
9
+
10
+ ### Changed
11
+
12
+ - **Version-only release.** No functional changes since 0.6.1; this release aligns
13
+ the package, pixi lock, docs examples, goldens, CITATION, and conda recipe on the
14
+ requested 0.6.2 version and republishes the 0.6.1 hardening set.
15
+
8
16
  ## [0.6.1] - 2026-10-26
9
17
 
10
18
  ### Fixed
@@ -7,7 +7,7 @@ authors:
7
7
  repository-code: "https://github.com/indexofire/gapit"
8
8
  url: "https://indexofire.github.io/gapit/"
9
9
  license: MIT
10
- version: "0.6.1"
10
+ version: "0.6.2"
11
11
  date-released: "2026-10-26"
12
12
  keywords:
13
13
  - bioinformatics
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.5
2
2
  Name: gapit
3
- Version: 0.6.1
3
+ Version: 0.6.2
4
4
  Summary: Mass screening of contigs and reads for known genes — agent-first Python reimplementation of abricate
5
5
  Project-URL: Homepage, https://github.com/indexofire/gapit
6
6
  Project-URL: Documentation, https://indexofire.github.io/gapit/
@@ -13,7 +13,7 @@ Version, as one JSON line:
13
13
 
14
14
  ```console
15
15
  $ gapit --version --json
16
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
16
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
17
17
  ```
18
18
 
19
19
  Output schemas. Twelve documents are introspectable: `report`, `typing_result`, `reads`,
@@ -12,7 +12,7 @@ gapit 生来就是被程序驱动的。每个输出都以机器可读为设计
12
12
 
13
13
  ```console
14
14
  $ gapit --version --json
15
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
15
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
16
16
  ```
17
17
 
18
18
  输出 schema。十二个文档可自省:`report`、`typing_result`、`reads`、`reads2`、`cluster`、`cluster2`、
@@ -564,7 +564,7 @@ versions. A real one, from the plasmidfinder database:
564
564
  "upstream_version": "",
565
565
  "tool": {
566
566
  "name": "gapit",
567
- "version": "0.6.1"
567
+ "version": "0.6.2"
568
568
  },
569
569
  "makeblastdb_version": "blastn: 2.17.0+",
570
570
  "minimap2_version": "2.31-r1302"
@@ -527,7 +527,7 @@ manifest,来自 plasmidfinder 数据库:
527
527
  "upstream_version": "",
528
528
  "tool": {
529
529
  "name": "gapit",
530
- "version": "0.6.1"
530
+ "version": "0.6.2"
531
531
  },
532
532
  "makeblastdb_version": "blastn: 2.17.0+",
533
533
  "minimap2_version": "2.31-r1302"
@@ -180,7 +180,7 @@ docker run --rm -it \
180
180
  --user "$(id -u):$(id -g)" \
181
181
  -v gapit-data:/data/gapit \
182
182
  -e GAPIT_DATADIR=/data/gapit \
183
- gapit:0.6.1 gapit db list
183
+ gapit:0.6.2 gapit db list
184
184
  ```
185
185
 
186
186
  For CI, mount or cache a workspace directory and pin versions:
@@ -189,7 +189,7 @@ For CI, mount or cache a workspace directory and pin versions:
189
189
  docker run --rm \
190
190
  -v "$PWD/.gapit-db:/data/gapit" \
191
191
  -e GAPIT_DATADIR=/data/gapit \
192
- gapit:0.6.1 gapit screen sample.fna --db ecoli_dec
192
+ gapit:0.6.2 gapit screen sample.fna --db ecoli_dec
193
193
  ```
194
194
 
195
195
  You can bake reference databases into an image for **read-only** screening:
@@ -164,7 +164,7 @@ docker run --rm -it \
164
164
  --user "$(id -u):$(id -g)" \
165
165
  -v gapit-data:/data/gapit \
166
166
  -e GAPIT_DATADIR=/data/gapit \
167
- gapit:0.6.1 gapit db list
167
+ gapit:0.6.2 gapit db list
168
168
  ```
169
169
 
170
170
  CI 中挂载或缓存 workspace 目录,并固定版本:
@@ -173,7 +173,7 @@ CI 中挂载或缓存 workspace 目录,并固定版本:
173
173
  docker run --rm \
174
174
  -v "$PWD/.gapit-db:/data/gapit" \
175
175
  -e GAPIT_DATADIR=/data/gapit \
176
- gapit:0.6.1 gapit screen sample.fna --db ecoli_dec
176
+ gapit:0.6.2 gapit screen sample.fna --db ecoli_dec
177
177
  ```
178
178
 
179
179
  可以为**只读**筛查把参考库烤进镜像:
@@ -48,9 +48,9 @@ gapit --version
48
48
 
49
49
  ```console
50
50
  $ gapit --version
51
- gapit 0.6.1
51
+ gapit 0.6.2
52
52
  $ gapit --version --json
53
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
53
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
54
54
  ```
55
55
 
56
56
  ## Optional gseek engine
@@ -46,9 +46,9 @@ gapit --version
46
46
 
47
47
  ```console
48
48
  $ gapit --version
49
- gapit 0.6.1
49
+ gapit 0.6.2
50
50
  $ gapit --version --json
51
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
51
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
52
52
  ```
53
53
 
54
54
  ## 可选 gseek 引擎
@@ -98,7 +98,7 @@ EOF
98
98
  Response line 1, verbatim:
99
99
 
100
100
  ```text
101
- {"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.1"}}}
101
+ {"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.2"}}}
102
102
  ```
103
103
 
104
104
  Response line 2 (real output, elided in the middle; each tool carries its full
@@ -121,7 +121,7 @@ the same run):
121
121
  ```json
122
122
  {
123
123
  "schema": "gapit.report/1",
124
- "tool": {"name": "gapit", "version": "0.6.1"},
124
+ "tool": {"name": "gapit", "version": "0.6.2"},
125
125
  "created_at": "2026-09-19T01:15:44Z",
126
126
  "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
127
127
  "files": [
@@ -177,7 +177,7 @@ the same run):
177
177
  ```json
178
178
  {
179
179
  "schema": "gapit.reads/1",
180
- "tool": {"name": "gapit", "version": "0.6.1"},
180
+ "tool": {"name": "gapit", "version": "0.6.2"},
181
181
  "created_at": "2026-09-22T00:07:35Z",
182
182
  "params": {
183
183
  "db": "tinyreads",
@@ -252,7 +252,7 @@ hit is the gene the agent just built the database from (real output):
252
252
  ```json
253
253
  {
254
254
  "schema": "gapit.report/1",
255
- "tool": {"name": "gapit", "version": "0.6.1"},
255
+ "tool": {"name": "gapit", "version": "0.6.2"},
256
256
  "created_at": "2026-09-20T13:38:39Z",
257
257
  "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
258
258
  "files": [
@@ -94,7 +94,7 @@ EOF
94
94
  响应第 1 行,原样:
95
95
 
96
96
  ```text
97
- {"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.1"}}}
97
+ {"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.2"}}}
98
98
  ```
99
99
 
100
100
  响应第 2 行(真实输出,中段省略;每个工具携带完整的 `inputSchema`):
@@ -115,7 +115,7 @@ EOF
115
115
  ```json
116
116
  {
117
117
  "schema": "gapit.report/1",
118
- "tool": {"name": "gapit", "version": "0.6.1"},
118
+ "tool": {"name": "gapit", "version": "0.6.2"},
119
119
  "created_at": "2026-09-19T01:15:44Z",
120
120
  "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
121
121
  "files": [
@@ -169,7 +169,7 @@ EOF
169
169
  ```json
170
170
  {
171
171
  "schema": "gapit.reads/1",
172
- "tool": {"name": "gapit", "version": "0.6.1"},
172
+ "tool": {"name": "gapit", "version": "0.6.2"},
173
173
  "created_at": "2026-09-22T00:07:35Z",
174
174
  "params": {
175
175
  "db": "tinyreads",
@@ -242,7 +242,7 @@ export GAPIT_DATADIR=/tmp/gapit-mcp-demo/datadir
242
242
  ```json
243
243
  {
244
244
  "schema": "gapit.report/1",
245
- "tool": {"name": "gapit", "version": "0.6.1"},
245
+ "tool": {"name": "gapit", "version": "0.6.2"},
246
246
  "created_at": "2026-09-20T13:38:39Z",
247
247
  "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
248
248
  "files": [
@@ -141,7 +141,7 @@ Real document, same run as the TSV above:
141
141
  "schema": "gapit.report/1",
142
142
  "tool": {
143
143
  "name": "gapit",
144
- "version": "0.6.1"
144
+ "version": "0.6.2"
145
145
  },
146
146
  "created_at": "2026-09-19T01:12:20Z",
147
147
  "params": {
@@ -232,7 +232,7 @@ row by `(%IDENTITY, %COVERAGE)`. Real document (trimmed):
232
232
  ```json
233
233
  {
234
234
  "schema": "gapit.typing_result/1",
235
- "tool": {"name": "gapit", "version": "0.6.1"},
235
+ "tool": {"name": "gapit", "version": "0.6.2"},
236
236
  "created_at": "2026-10-02T10:04:55Z",
237
237
  "source": ["dec.tsv"],
238
238
  "db": "ecoli_dec",
@@ -419,7 +419,7 @@ summarizing two report files, one with a `tetA` hit and one with none:
419
419
  "schema": "gapit.summary/1",
420
420
  "tool": {
421
421
  "name": "gapit",
422
- "version": "0.6.1"
422
+ "version": "0.6.2"
423
423
  },
424
424
  "created_at": "2026-09-19T01:11:09Z",
425
425
  "params": {
@@ -543,7 +543,7 @@ An agent can discover the whole contract from the binary alone.
543
543
 
544
544
  ```console
545
545
  $ gapit --version --json
546
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
546
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
547
547
  ```
548
548
 
549
549
  `gapit schema <name>` prints the JSON Schema for each document. The eleven names: `report`,
@@ -130,7 +130,7 @@ non-DEC。零命中文件不产生筛查行,因此不会出现在判定输出
130
130
  "schema": "gapit.report/1",
131
131
  "tool": {
132
132
  "name": "gapit",
133
- "version": "0.6.1"
133
+ "version": "0.6.2"
134
134
  },
135
135
  "created_at": "2026-09-19T01:12:20Z",
136
136
  "params": {
@@ -219,7 +219,7 @@ non-DEC。零命中文件不产生筛查行,因此不会出现在判定输出
219
219
  ```json
220
220
  {
221
221
  "schema": "gapit.typing_result/1",
222
- "tool": {"name": "gapit", "version": "0.6.1"},
222
+ "tool": {"name": "gapit", "version": "0.6.2"},
223
223
  "created_at": "2026-10-02T10:04:55Z",
224
224
  "source": ["dec.tsv"],
225
225
  "db": "ecoli_dec",
@@ -402,7 +402,7 @@ typing 的数据库是同一个表头去掉 `PHENOTYPE`。没有位点判定的
402
402
  "schema": "gapit.summary/1",
403
403
  "tool": {
404
404
  "name": "gapit",
405
- "version": "0.6.1"
405
+ "version": "0.6.2"
406
406
  },
407
407
  "created_at": "2026-09-19T01:11:09Z",
408
408
  "params": {
@@ -525,7 +525,7 @@ agent 只凭二进制就能发现整个契约。
525
525
 
526
526
  ```console
527
527
  $ gapit --version --json
528
- {"schema":"gapit.version/1","name":"gapit","version":"0.6.1"}
528
+ {"schema":"gapit.version/1","name":"gapit","version":"0.6.2"}
529
529
  ```
530
530
 
531
531
  `gapit schema <name>` 打印每个文档的 JSON Schema。十二个名字:`report`、
@@ -94,7 +94,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
94
94
  "schema": "gapit.report/1",
95
95
  "tool": {
96
96
  "name": "gapit",
97
- "version": "0.6.1"
97
+ "version": "0.6.2"
98
98
  },
99
99
  "created_at": "2026-09-19T01:11:06Z",
100
100
  "params": {
@@ -89,7 +89,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
89
89
  "schema": "gapit.report/1",
90
90
  "tool": {
91
91
  "name": "gapit",
92
- "version": "0.6.1"
92
+ "version": "0.6.2"
93
93
  },
94
94
  "created_at": "2026-09-19T01:11:06Z",
95
95
  "params": {
@@ -123,7 +123,7 @@ table, one chunk for the one sample).
123
123
  ## Options
124
124
 
125
125
  Reads mode runs through the same `gapit screen` command; these are the flags that apply
126
- (transcribed from `gapit screen --help`, gapit 0.6.1). Contig-mode flags not listed here
126
+ (transcribed from `gapit screen --help`, gapit 0.6.2). Contig-mode flags not listed here
127
127
  (`--minid`, `--mincov`, `--fofn`, `--noheader`, `--nopath`) do not apply; `--jobs` applies
128
128
  to the wildcard path only.
129
129
 
@@ -337,7 +337,7 @@ The short-read fixture behaves the same with one calibration: `sr` soft-clipping
337
337
  $ gapit screen --r1 ont_homologs.fq --db homologs --read-type map-ont --min-identity 95 --format md --quiet
338
338
  ---
339
339
  schema: gapit.reads/2
340
- tool: gapit 0.6.1
340
+ tool: gapit 0.6.2
341
341
  created_at: 2026-09-20T14:23:33Z
342
342
  db: homologs
343
343
  read_type: map-ont
@@ -433,7 +433,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
433
433
  "schema": "gapit.reads/1",
434
434
  "tool": {
435
435
  "name": "gapit",
436
- "version": "0.6.1"
436
+ "version": "0.6.2"
437
437
  },
438
438
  "created_at": "2026-09-19T01:12:25Z",
439
439
  "params": {
@@ -528,7 +528,7 @@ $ gapit screen --r1 tetx_lane1.fq,tetx_lane2.fq --db tinyreads --format json --q
528
528
  $ gapit screen --r1 tetx_full.fq --db tinyreads --format md
529
529
  ---
530
530
  schema: gapit.reads/1
531
- tool: gapit 0.6.1
531
+ tool: gapit 0.6.2
532
532
  created_at: 2026-09-19T01:12:25Z
533
533
  db: tinyreads
534
534
  read_type: sr
@@ -630,7 +630,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
630
630
  "schema": "gapit.reads/1",
631
631
  "tool": {
632
632
  "name": "gapit",
633
- "version": "0.6.1"
633
+ "version": "0.6.2"
634
634
  },
635
635
  "created_at": "2026-09-19T14:23:00Z",
636
636
  "params": {
@@ -689,7 +689,7 @@ cost of allele-level precision. That trade suggests a two-stage workflow over ma
689
689
  pipeline, which applies the identity and coverage floors at abricate parity.
690
690
 
691
691
  Real numbers, one K. pneumoniae RefSeq assembly (GCF_000240185.1, 5.3 Mb, `--db ncbi`,
692
- single-threaded, gapit 0.6.1):
692
+ single-threaded, gapit 0.6.2):
693
693
 
694
694
  ```console
695
695
  $ # Stage 1: survey, ~0.9 s
@@ -113,7 +113,7 @@ frontmatter 保留 `files:`/`genes_found:` 运行总计(它的 tsv 默认渲
113
113
  ## 选项
114
114
 
115
115
  reads 模式走同一条 `gapit screen` 命令;以下是适用的参数(转写自 `gapit screen
116
- --help`,gapit 0.6.1)。这里未列出的 contig 模式参数(`--minid`、`--mincov`、
116
+ --help`,gapit 0.6.2)。这里未列出的 contig 模式参数(`--minid`、`--mincov`、
117
117
  `--fofn`、`--noheader`、`--nopath`)不适用;`--jobs` 只适用于通配符路径(见上文)。
118
118
 
119
119
  | 参数 | 类型 | 默认值 | 说明 |
@@ -318,7 +318,7 @@ Markdown 形式:
318
318
  $ gapit screen --r1 ont_homologs.fq --db homologs --read-type map-ont --min-identity 95 --format md --quiet
319
319
  ---
320
320
  schema: gapit.reads/2
321
- tool: gapit 0.6.1
321
+ tool: gapit 0.6.2
322
322
  created_at: 2026-09-20T14:23:33Z
323
323
  db: homologs
324
324
  read_type: map-ont
@@ -410,7 +410,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
410
410
  "schema": "gapit.reads/1",
411
411
  "tool": {
412
412
  "name": "gapit",
413
- "version": "0.6.1"
413
+ "version": "0.6.2"
414
414
  },
415
415
  "created_at": "2026-09-19T01:12:25Z",
416
416
  "params": {
@@ -505,7 +505,7 @@ $ gapit screen --r1 tetx_lane1.fq,tetx_lane2.fq --db tinyreads --format json --q
505
505
  $ gapit screen --r1 tetx_full.fq --db tinyreads --format md
506
506
  ---
507
507
  schema: gapit.reads/1
508
- tool: gapit 0.6.1
508
+ tool: gapit 0.6.2
509
509
  created_at: 2026-09-19T01:12:25Z
510
510
  db: tinyreads
511
511
  read_type: sr
@@ -605,7 +605,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
605
605
  "schema": "gapit.reads/1",
606
606
  "tool": {
607
607
  "name": "gapit",
608
- "version": "0.6.1"
608
+ "version": "0.6.2"
609
609
  },
610
610
  "created_at": "2026-09-19T14:23:00Z",
611
611
  "params": {
@@ -663,7 +663,7 @@ minimap2 一段完全跳过 BLAST 索引,把 assembly 送进 minimap2 引擎
663
663
  性应用一致性与覆盖度下限。
664
664
 
665
665
  真实数字,一株 K. pneumoniae RefSeq assembly(GCF_000240185.1,5.3 Mb,`--db ncbi`,
666
- 单线程,gapit 0.6.1):
666
+ 单线程,gapit 0.6.2):
667
667
 
668
668
  ```console
669
669
  $ # Stage 1: survey, ~0.9 s
@@ -9,7 +9,7 @@ Database setup is covered in [./databases.md](./databases.md); a full walk-throu
9
9
 
10
10
  ## Options
11
11
 
12
- Transcribed from `gapit screen --help` (gapit 0.6.1). Flags marked *reads mode* apply only when
12
+ Transcribed from `gapit screen --help` (gapit 0.6.2). Flags marked *reads mode* apply only when
13
13
  you pass `--r1`/`--r2`; they are documented in [./reads.md](./reads.md).
14
14
 
15
15
  Every option also accepts the single-dash short form listed in the **Short** column (e.g.
@@ -107,7 +107,7 @@ $ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
107
107
  "schema": "gapit.report/1",
108
108
  "tool": {
109
109
  "name": "gapit",
110
- "version": "0.6.1"
110
+ "version": "0.6.2"
111
111
  },
112
112
  "created_at": "2026-09-19T01:12:04Z",
113
113
  "params": {
@@ -9,7 +9,7 @@
9
9
 
10
10
  ## 选项
11
11
 
12
- 转写自 `gapit screen --help`(gapit 0.6.1)。标记为 *reads 模式* 的参数只在传入
12
+ 转写自 `gapit screen --help`(gapit 0.6.2)。标记为 *reads 模式* 的参数只在传入
13
13
  `--r1`/`--r2` 时生效,记录在 [./reads.md](./reads.md)。
14
14
 
15
15
  每个选项都接受 **短** 列给出的单横线短形式(例如 `--db` 的 `-d`);长形式仍是规范写法,
@@ -104,7 +104,7 @@ $ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
104
104
  "schema": "gapit.report/1",
105
105
  "tool": {
106
106
  "name": "gapit",
107
- "version": "0.6.1"
107
+ "version": "0.6.2"
108
108
  },
109
109
  "created_at": "2026-09-19T01:12:04Z",
110
110
  "params": {
@@ -10,7 +10,7 @@ exactly what `gapit screen` writes. See [./screen.md](./screen.md) for producing
10
10
 
11
11
  ## Options
12
12
 
13
- Transcribed from `gapit summary --help` (gapit 0.6.1):
13
+ Transcribed from `gapit summary --help` (gapit 0.6.2):
14
14
 
15
15
  | Flag | Type | Default | Description |
16
16
  |---|---|---|---|
@@ -150,7 +150,7 @@ $ gapit summary tests/data/summary/sample_a.tsv tests/data/summary/sample_b.tsv
150
150
  "schema": "gapit.summary/1",
151
151
  "tool": {
152
152
  "name": "gapit",
153
- "version": "0.6.1"
153
+ "version": "0.6.2"
154
154
  },
155
155
  "created_at": "2026-09-19T01:12:48Z",
156
156
  "params": {
@@ -10,7 +10,7 @@ screen` 写出的格式。如何产生报告见 [./screen.md](./screen.md);输
10
10
 
11
11
  ## 选项
12
12
 
13
- 转写自 `gapit summary --help`(gapit 0.6.1):
13
+ 转写自 `gapit summary --help`(gapit 0.6.2):
14
14
 
15
15
  | 参数 | 类型 | 默认值 | 说明 |
16
16
  |---|---|---|---|
@@ -143,7 +143,7 @@ $ gapit summary tests/data/summary/sample_a.tsv tests/data/summary/sample_b.tsv
143
143
  "schema": "gapit.summary/1",
144
144
  "tool": {
145
145
  "name": "gapit",
146
- "version": "0.6.1"
146
+ "version": "0.6.2"
147
147
  },
148
148
  "created_at": "2026-09-19T01:12:48Z",
149
149
  "params": {
@@ -923,8 +923,8 @@ packages:
923
923
  timestamp: 1694615932610
924
924
  - pypi: ./
925
925
  name: gapit
926
- version: 0.6.1
927
- sha256: 4a479d05ee4b26aa6a17ab54bd6f95c079aa038af5c501f14770e2a90615ca2e
926
+ version: 0.6.2
927
+ sha256: 9b658132fb916ff93a1e2530c4935a13aa52eca5059026558025a5f7c814d2e5
928
928
  requires_dist:
929
929
  - click>=8.2
930
930
  - pydantic>=2.7
@@ -3,7 +3,7 @@ authors = ["indexofire <indexofire@gmail.com>"]
3
3
  channels = ["conda-forge", "bioconda"]
4
4
  name = "gapit"
5
5
  platforms = ["linux-64"]
6
- version = "0.6.1"
6
+ version = "0.6.2"
7
7
 
8
8
  [tasks]
9
9
  lint = "ruff check"
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
4
4
 
5
5
  [project]
6
6
  name = "gapit"
7
- version = "0.6.1"
7
+ version = "0.6.2"
8
8
  description = "Mass screening of contigs and reads for known genes — agent-first Python reimplementation of abricate"
9
9
  readme = "README.md"
10
10
  authors = [{ name = "indexofire", email = "indexofire@gmail.com" }]
@@ -1,3 +1,3 @@
1
1
  """gapit — agent-first Python reimplementation of abricate."""
2
2
 
3
- __version__ = "0.6.1"
3
+ __version__ = "0.6.2"
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/2",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-10-01T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/2
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-10-01T12:00:00Z
5
5
  db: vp_ok
6
6
  preset: asm20
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/2",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-10-01T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/2
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-10-01T12:00:00Z
5
5
  db: vp_ok
6
6
  preset: asm20
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/1",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-09-30T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/1
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-09-30T12:00:00Z
5
5
  db: cps
6
6
  preset: asm20
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/1",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-09-30T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/1
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-09-30T12:00:00Z
5
5
  db: cps
6
6
  preset: asm20
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/1",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-09-30T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/1
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-09-30T12:00:00Z
5
5
  db: cps
6
6
  preset: asm20
@@ -2,7 +2,7 @@
2
2
  "schema": "gapit.cluster/1",
3
3
  "tool": {
4
4
  "name": "gapit",
5
- "version": "0.6.1"
5
+ "version": "0.6.2"
6
6
  },
7
7
  "created_at": "2026-09-30T12:00:00Z",
8
8
  "params": {
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  schema: gapit.cluster/1
3
- tool: gapit 0.6.1
3
+ tool: gapit 0.6.2
4
4
  created_at: 2026-09-30T12:00:00Z
5
5
  db: cps
6
6
  preset: asm20