@yeyuan98/opencode-bioresearcher-plugin 1.6.3 → 1.6.4

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 +0 -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 +6 -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
File without changes
package/README.md CHANGED
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
package/dist/index.d.ts CHANGED
File without changes
package/dist/index.js CHANGED
File without changes
File without changes
@@ -10,10 +10,14 @@ function getPluginSkillsDir() {
10
10
  const isDist = currentDir.includes(`${pathSep}dist${pathSep}`);
11
11
  const isSrc = currentDir.includes(`${pathSep}src${pathSep}`);
12
12
  if (isDist) {
13
- return path.join(currentDir, "..", "..", "skills");
13
+ const candidate = path.join(currentDir, "..", "..", "skills");
14
+ if (existsSync(candidate))
15
+ return candidate;
14
16
  }
15
17
  else if (isSrc) {
16
- return path.join(currentDir, "..", "..", "..", "skills");
18
+ const candidate = path.join(currentDir, "..", "..", "..", "skills");
19
+ if (existsSync(candidate))
20
+ return candidate;
17
21
  }
18
22
  let searchDir = currentDir;
19
23
  for (let i = 0; i < 6; i++) {
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
package/dist/version.d.ts CHANGED
@@ -1 +1 @@
1
- export declare const PLUGIN_VERSION = "1.6.3";
1
+ export declare const PLUGIN_VERSION = "1.6.4";
package/dist/version.js CHANGED
@@ -1 +1 @@
1
- export const PLUGIN_VERSION = "1.6.3";
1
+ export const PLUGIN_VERSION = "1.6.4";
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@yeyuan98/opencode-bioresearcher-plugin",
3
- "version": "1.6.3",
3
+ "version": "1.6.4",
4
4
  "description": "OpenCode plugin that adds a bioresearcher agent",
5
5
  "main": "dist/index.js",
6
6
  "types": "dist/index.d.ts",