@yeyuan98/opencode-bioresearcher-plugin 1.6.3 → 1.6.5

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 (189) hide show
  1. package/LICENSE +0 -0
  2. package/README.md +1 -0
  3. package/dist/agents/bioresearcher/index.d.ts +0 -0
  4. package/dist/agents/bioresearcher/index.js +0 -0
  5. package/dist/agents/bioresearcher/prompt.d.ts +0 -0
  6. package/dist/agents/bioresearcher/prompt.js +0 -0
  7. package/dist/agents/bioresearcherDR/index.d.ts +0 -0
  8. package/dist/agents/bioresearcherDR/index.js +0 -0
  9. package/dist/agents/bioresearcherDR/prompt.d.ts +0 -0
  10. package/dist/agents/bioresearcherDR/prompt.js +0 -0
  11. package/dist/agents/bioresearcherDR_worker/index.d.ts +0 -0
  12. package/dist/agents/bioresearcherDR_worker/index.js +0 -0
  13. package/dist/agents/bioresearcherDR_worker/prompt.d.ts +0 -0
  14. package/dist/agents/bioresearcherDR_worker/prompt.js +0 -0
  15. package/dist/index.d.ts +0 -0
  16. package/dist/index.js +0 -0
  17. package/dist/shared/skill-sync.d.ts +0 -0
  18. package/dist/shared/skill-sync.js +9 -2
  19. package/dist/shared/tool-restrictions.d.ts +0 -0
  20. package/dist/shared/tool-restrictions.js +0 -0
  21. package/dist/skills/bioresearcher-core/README.md +0 -0
  22. package/dist/skills/bioresearcher-core/SKILL.md +0 -0
  23. package/dist/skills/bioresearcher-core/examples/contexts.json +0 -0
  24. package/dist/skills/bioresearcher-core/examples/data-exchange-example.md +0 -0
  25. package/dist/skills/bioresearcher-core/examples/template.md +0 -0
  26. package/dist/skills/bioresearcher-core/patterns/bioresearcher/analysis-methods.md +0 -0
  27. package/dist/skills/bioresearcher-core/patterns/bioresearcher/best-practices.md +0 -0
  28. package/dist/skills/bioresearcher-core/patterns/bioresearcher/python-standards.md +0 -0
  29. package/dist/skills/bioresearcher-core/patterns/bioresearcher/report-template.md +0 -0
  30. package/dist/skills/bioresearcher-core/patterns/bioresearcher/tool-selection.md +0 -0
  31. package/dist/skills/bioresearcher-core/patterns/calculator.md +0 -0
  32. package/dist/skills/bioresearcher-core/patterns/citations.md +0 -0
  33. package/dist/skills/bioresearcher-core/patterns/data-exchange.md +0 -0
  34. package/dist/skills/bioresearcher-core/patterns/json-tools.md +0 -0
  35. package/dist/skills/bioresearcher-core/patterns/progress.md +0 -0
  36. package/dist/skills/bioresearcher-core/patterns/rate-limiting.md +0 -0
  37. package/dist/skills/bioresearcher-core/patterns/retry.md +0 -0
  38. package/dist/skills/bioresearcher-core/patterns/shell-commands.md +0 -0
  39. package/dist/skills/bioresearcher-core/patterns/subagent-waves.md +0 -0
  40. package/dist/skills/bioresearcher-core/patterns/table-tools.md +0 -0
  41. package/dist/skills/bioresearcher-core/patterns/user-confirmation.md +0 -0
  42. package/dist/skills/bioresearcher-core/python/template.md +0 -0
  43. package/dist/skills/bioresearcher-core/python/template.py +0 -0
  44. package/dist/skills/bioresearcher-tests/README.md +0 -0
  45. package/dist/skills/bioresearcher-tests/SKILL.md +0 -0
  46. package/dist/skills/bioresearcher-tests/pyproject.toml +0 -0
  47. package/dist/skills/bioresearcher-tests/resources/json_samples/in_markdown.md.gz +0 -0
  48. package/dist/skills/bioresearcher-tests/resources/json_samples/nested_object.json.gz +0 -0
  49. package/dist/skills/bioresearcher-tests/resources/json_samples/schema_draft7.json.gz +0 -0
  50. package/dist/skills/bioresearcher-tests/resources/json_samples/simple_array.json.gz +0 -0
  51. package/dist/skills/bioresearcher-tests/resources/json_samples/simple_object.json.gz +0 -0
  52. package/dist/skills/bioresearcher-tests/resources/obo_sample.obo.gz +0 -0
  53. package/dist/skills/bioresearcher-tests/resources/pubmed_sample.xml.gz +0 -0
  54. package/dist/skills/bioresearcher-tests/resources/table_sample.xlsx.gz +0 -0
  55. package/dist/skills/bioresearcher-tests/test_cases/json_tests.md +0 -0
  56. package/dist/skills/bioresearcher-tests/test_cases/misc_tests.md +0 -0
  57. package/dist/skills/bioresearcher-tests/test_cases/parser_tests.md +0 -0
  58. package/dist/skills/bioresearcher-tests/test_cases/skill_tests.md +0 -0
  59. package/dist/skills/bioresearcher-tests/test_cases/table_tests.md +0 -0
  60. package/dist/skills/bioresearcher-tests/test_runner.py +0 -0
  61. package/dist/skills/demo-skill/SKILL.md +0 -0
  62. package/dist/skills/demo-skill/demo_script.py +0 -0
  63. package/dist/skills/env-jsonc-setup/SKILL.md +0 -0
  64. package/dist/skills/gromacs-guides/SKILL.md +0 -0
  65. package/dist/skills/gromacs-guides/guides/create_index.md +0 -0
  66. package/dist/skills/gromacs-guides/guides/inspect_tpr.md +0 -0
  67. package/dist/skills/long-table-summary/SKILL.md +0 -0
  68. package/dist/skills/long-table-summary/combine_outputs.py +0 -0
  69. package/dist/skills/long-table-summary/generate_prompts.py +0 -0
  70. package/dist/skills/long-table-summary/pyproject.toml +0 -0
  71. package/dist/skills/pubmed-weekly/SKILL.md +0 -0
  72. package/dist/skills/pubmed-weekly/pubmed_weekly.py +0 -0
  73. package/dist/skills/pubmed-weekly/pyproject.toml +0 -0
  74. package/dist/skills/python-setup-uv/SKILL.md +0 -0
  75. package/dist/tools/db/backends/index.d.ts +0 -0
  76. package/dist/tools/db/backends/index.js +0 -0
  77. package/dist/tools/db/backends/mongodb/backend.d.ts +0 -0
  78. package/dist/tools/db/backends/mongodb/backend.js +0 -0
  79. package/dist/tools/db/backends/mongodb/connection.d.ts +0 -0
  80. package/dist/tools/db/backends/mongodb/connection.js +0 -0
  81. package/dist/tools/db/backends/mongodb/index.d.ts +0 -0
  82. package/dist/tools/db/backends/mongodb/index.js +0 -0
  83. package/dist/tools/db/backends/mongodb/translator.d.ts +0 -0
  84. package/dist/tools/db/backends/mongodb/translator.js +0 -0
  85. package/dist/tools/db/backends/mysql/backend.d.ts +0 -0
  86. package/dist/tools/db/backends/mysql/backend.js +0 -0
  87. package/dist/tools/db/backends/mysql/connection.d.ts +0 -0
  88. package/dist/tools/db/backends/mysql/connection.js +0 -0
  89. package/dist/tools/db/backends/mysql/index.d.ts +0 -0
  90. package/dist/tools/db/backends/mysql/index.js +0 -0
  91. package/dist/tools/db/backends/mysql/translator.d.ts +0 -0
  92. package/dist/tools/db/backends/mysql/translator.js +0 -0
  93. package/dist/tools/db/core/base.d.ts +0 -0
  94. package/dist/tools/db/core/base.js +0 -0
  95. package/dist/tools/db/core/config-loader.d.ts +0 -0
  96. package/dist/tools/db/core/config-loader.js +0 -0
  97. package/dist/tools/db/core/index.d.ts +0 -0
  98. package/dist/tools/db/core/index.js +0 -0
  99. package/dist/tools/db/core/jsonc-parser.d.ts +0 -0
  100. package/dist/tools/db/core/jsonc-parser.js +0 -0
  101. package/dist/tools/db/core/validator.d.ts +0 -0
  102. package/dist/tools/db/core/validator.js +0 -0
  103. package/dist/tools/db/index.d.ts +0 -0
  104. package/dist/tools/db/index.js +0 -0
  105. package/dist/tools/db/interface/backend.d.ts +0 -0
  106. package/dist/tools/db/interface/backend.js +0 -0
  107. package/dist/tools/db/interface/connection.d.ts +0 -0
  108. package/dist/tools/db/interface/connection.js +0 -0
  109. package/dist/tools/db/interface/index.d.ts +0 -0
  110. package/dist/tools/db/interface/index.js +0 -0
  111. package/dist/tools/db/interface/query.d.ts +0 -0
  112. package/dist/tools/db/interface/query.js +0 -0
  113. package/dist/tools/db/interface/schema.d.ts +0 -0
  114. package/dist/tools/db/interface/schema.js +0 -0
  115. package/dist/tools/db/tools.d.ts +0 -0
  116. package/dist/tools/db/tools.js +0 -0
  117. package/dist/tools/db/utils.d.ts +0 -0
  118. package/dist/tools/db/utils.js +0 -0
  119. package/dist/tools/misc/calculator.d.ts +0 -0
  120. package/dist/tools/misc/calculator.js +0 -0
  121. package/dist/tools/misc/index.d.ts +0 -0
  122. package/dist/tools/misc/index.js +0 -0
  123. package/dist/tools/misc/json-extract.d.ts +0 -0
  124. package/dist/tools/misc/json-extract.js +0 -0
  125. package/dist/tools/misc/json-infer.d.ts +0 -0
  126. package/dist/tools/misc/json-infer.js +0 -0
  127. package/dist/tools/misc/json-validate.d.ts +0 -0
  128. package/dist/tools/misc/json-validate.js +0 -0
  129. package/dist/tools/misc/timer.d.ts +0 -0
  130. package/dist/tools/misc/timer.js +0 -0
  131. package/dist/tools/parser/obo/index.d.ts +0 -0
  132. package/dist/tools/parser/obo/index.js +0 -0
  133. package/dist/tools/parser/obo/obo.d.ts +0 -0
  134. package/dist/tools/parser/obo/obo.js +0 -0
  135. package/dist/tools/parser/obo/types.d.ts +0 -0
  136. package/dist/tools/parser/obo/types.js +0 -0
  137. package/dist/tools/parser/obo/utils.d.ts +0 -0
  138. package/dist/tools/parser/obo/utils.js +0 -0
  139. package/dist/tools/parser/pubmed/index.d.ts +0 -0
  140. package/dist/tools/parser/pubmed/index.js +0 -0
  141. package/dist/tools/parser/pubmed/pubmed.d.ts +0 -0
  142. package/dist/tools/parser/pubmed/pubmed.js +0 -0
  143. package/dist/tools/parser/pubmed/types.d.ts +0 -0
  144. package/dist/tools/parser/pubmed/types.js +0 -0
  145. package/dist/tools/parser/pubmed/utils.d.ts +0 -0
  146. package/dist/tools/parser/pubmed/utils.js +0 -0
  147. package/dist/tools/sandbox/bash-parser.d.ts +0 -0
  148. package/dist/tools/sandbox/bash-parser.js +0 -0
  149. package/dist/tools/sandbox/escape-scenarios.test.d.ts +0 -0
  150. package/dist/tools/sandbox/escape-scenarios.test.js +0 -0
  151. package/dist/tools/sandbox/expander.d.ts +0 -0
  152. package/dist/tools/sandbox/expander.js +0 -0
  153. package/dist/tools/sandbox/final-verification.test.d.ts +0 -0
  154. package/dist/tools/sandbox/final-verification.test.js +0 -0
  155. package/dist/tools/sandbox/hooks.d.ts +0 -0
  156. package/dist/tools/sandbox/hooks.js +0 -0
  157. package/dist/tools/sandbox/index.d.ts +0 -0
  158. package/dist/tools/sandbox/index.js +0 -0
  159. package/dist/tools/sandbox/manager.d.ts +0 -0
  160. package/dist/tools/sandbox/manager.js +0 -0
  161. package/dist/tools/sandbox/sandbox.integration.test.d.ts +0 -0
  162. package/dist/tools/sandbox/sandbox.integration.test.js +0 -0
  163. package/dist/tools/sandbox/sandbox.test.d.ts +0 -0
  164. package/dist/tools/sandbox/sandbox.test.js +0 -0
  165. package/dist/tools/sandbox/tool.d.ts +0 -0
  166. package/dist/tools/sandbox/tool.js +0 -0
  167. package/dist/tools/sandbox/types.d.ts +0 -0
  168. package/dist/tools/sandbox/types.js +0 -0
  169. package/dist/tools/sandbox/validator.d.ts +0 -0
  170. package/dist/tools/sandbox/validator.js +0 -0
  171. package/dist/tools/skill/frontmatter.d.ts +0 -0
  172. package/dist/tools/skill/frontmatter.js +0 -0
  173. package/dist/tools/skill/index.d.ts +0 -0
  174. package/dist/tools/skill/index.js +0 -0
  175. package/dist/tools/skill/registry.d.ts +0 -0
  176. package/dist/tools/skill/registry.js +0 -0
  177. package/dist/tools/skill/tool.d.ts +0 -0
  178. package/dist/tools/skill/tool.js +0 -0
  179. package/dist/tools/skill/types.d.ts +0 -0
  180. package/dist/tools/skill/types.js +0 -0
  181. package/dist/tools/table/index.d.ts +0 -0
  182. package/dist/tools/table/index.js +0 -0
  183. package/dist/tools/table/tools.d.ts +0 -0
  184. package/dist/tools/table/tools.js +0 -0
  185. package/dist/tools/table/utils.d.ts +0 -0
  186. package/dist/tools/table/utils.js +0 -0
  187. package/dist/version.d.ts +1 -1
  188. package/dist/version.js +1 -1
  189. package/package.json +1 -1
package/LICENSE CHANGED
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package/README.md CHANGED
@@ -175,6 +175,7 @@ BioMCP is absolutely required and might take time to load. You will need to have
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  | Agent not appearing | Check plugin in opencode.json is typed correctly |
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  | BioMCP tool failures | Make sure you have BioMCP [installed and enabled](https://opencode.ai/docs/mcp-servers/#enable). The `mcp.biomcp` config in opencode.json is **required** — without it, biomcp tools will not exist regardless of agent permissions. |
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  | biomcp tools not available to agents | Ensure the `mcp` section is present in your `opencode.json`. Agent permission config only controls access to tools that already exist — it cannot create tools that the MCP server hasn't registered. |
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+ | Skills not copying after update | Clear stale plugin cache: `rm -rf ~/.cache/opencode/packages/@yeyuan98/opencode-bioresearcher-plugin@latest` |
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  | Research taking a long time | Check whether subagents are generating outputs; could be slow model / API throttle / overcomplicated query / etc. |
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  ## License
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@@ -10,10 +10,17 @@ function getPluginSkillsDir() {
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  const isDist = currentDir.includes(`${pathSep}dist${pathSep}`);
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  const isSrc = currentDir.includes(`${pathSep}src${pathSep}`);
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  if (isDist) {
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- return path.join(currentDir, "..", "..", "skills");
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+ const distSkills = path.join(currentDir, "..", "skills");
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+ if (existsSync(distSkills))
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+ return distSkills;
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+ const rootSkills = path.join(currentDir, "..", "..", "skills");
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+ if (existsSync(rootSkills))
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+ return rootSkills;
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  }
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  else if (isSrc) {
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- return path.join(currentDir, "..", "..", "..", "skills");
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+ const candidate = path.join(currentDir, "..", "..", "..", "skills");
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+ if (existsSync(candidate))
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+ return candidate;
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  }
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  let searchDir = currentDir;
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  for (let i = 0; i < 6; i++) {
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package/dist/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const PLUGIN_VERSION = "1.6.3";
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+ export declare const PLUGIN_VERSION = "1.6.4";
package/dist/version.js CHANGED
@@ -1 +1 @@
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- export const PLUGIN_VERSION = "1.6.3";
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+ export const PLUGIN_VERSION = "1.6.4";
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@yeyuan98/opencode-bioresearcher-plugin",
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- "version": "1.6.3",
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+ "version": "1.6.5",
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  "description": "OpenCode plugin that adds a bioresearcher agent",
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  "main": "dist/index.js",
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  "types": "dist/index.d.ts",