@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.
- package/LICENSE +0 -0
- package/README.md +1 -0
- package/dist/agents/bioresearcher/index.d.ts +0 -0
- package/dist/agents/bioresearcher/index.js +0 -0
- package/dist/agents/bioresearcher/prompt.d.ts +0 -0
- package/dist/agents/bioresearcher/prompt.js +0 -0
- package/dist/agents/bioresearcherDR/index.d.ts +0 -0
- package/dist/agents/bioresearcherDR/index.js +0 -0
- package/dist/agents/bioresearcherDR/prompt.d.ts +0 -0
- package/dist/agents/bioresearcherDR/prompt.js +0 -0
- package/dist/agents/bioresearcherDR_worker/index.d.ts +0 -0
- package/dist/agents/bioresearcherDR_worker/index.js +0 -0
- package/dist/agents/bioresearcherDR_worker/prompt.d.ts +0 -0
- package/dist/agents/bioresearcherDR_worker/prompt.js +0 -0
- package/dist/index.d.ts +0 -0
- package/dist/index.js +0 -0
- package/dist/shared/skill-sync.d.ts +0 -0
- package/dist/shared/skill-sync.js +9 -2
- package/dist/shared/tool-restrictions.d.ts +0 -0
- package/dist/shared/tool-restrictions.js +0 -0
- package/dist/skills/bioresearcher-core/README.md +0 -0
- package/dist/skills/bioresearcher-core/SKILL.md +0 -0
- package/dist/skills/bioresearcher-core/examples/contexts.json +0 -0
- package/dist/skills/bioresearcher-core/examples/data-exchange-example.md +0 -0
- package/dist/skills/bioresearcher-core/examples/template.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/bioresearcher/analysis-methods.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/bioresearcher/best-practices.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/bioresearcher/python-standards.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/bioresearcher/report-template.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/bioresearcher/tool-selection.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/calculator.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/citations.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/data-exchange.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/json-tools.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/progress.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/rate-limiting.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/retry.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/shell-commands.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/subagent-waves.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/table-tools.md +0 -0
- package/dist/skills/bioresearcher-core/patterns/user-confirmation.md +0 -0
- package/dist/skills/bioresearcher-core/python/template.md +0 -0
- package/dist/skills/bioresearcher-core/python/template.py +0 -0
- package/dist/skills/bioresearcher-tests/README.md +0 -0
- package/dist/skills/bioresearcher-tests/SKILL.md +0 -0
- package/dist/skills/bioresearcher-tests/pyproject.toml +0 -0
- package/dist/skills/bioresearcher-tests/resources/json_samples/in_markdown.md.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/json_samples/nested_object.json.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/json_samples/schema_draft7.json.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/json_samples/simple_array.json.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/json_samples/simple_object.json.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/obo_sample.obo.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/pubmed_sample.xml.gz +0 -0
- package/dist/skills/bioresearcher-tests/resources/table_sample.xlsx.gz +0 -0
- package/dist/skills/bioresearcher-tests/test_cases/json_tests.md +0 -0
- package/dist/skills/bioresearcher-tests/test_cases/misc_tests.md +0 -0
- package/dist/skills/bioresearcher-tests/test_cases/parser_tests.md +0 -0
- package/dist/skills/bioresearcher-tests/test_cases/skill_tests.md +0 -0
- package/dist/skills/bioresearcher-tests/test_cases/table_tests.md +0 -0
- package/dist/skills/bioresearcher-tests/test_runner.py +0 -0
- package/dist/skills/demo-skill/SKILL.md +0 -0
- package/dist/skills/demo-skill/demo_script.py +0 -0
- package/dist/skills/env-jsonc-setup/SKILL.md +0 -0
- package/dist/skills/gromacs-guides/SKILL.md +0 -0
- package/dist/skills/gromacs-guides/guides/create_index.md +0 -0
- package/dist/skills/gromacs-guides/guides/inspect_tpr.md +0 -0
- package/dist/skills/long-table-summary/SKILL.md +0 -0
- package/dist/skills/long-table-summary/combine_outputs.py +0 -0
- package/dist/skills/long-table-summary/generate_prompts.py +0 -0
- package/dist/skills/long-table-summary/pyproject.toml +0 -0
- package/dist/skills/pubmed-weekly/SKILL.md +0 -0
- package/dist/skills/pubmed-weekly/pubmed_weekly.py +0 -0
- package/dist/skills/pubmed-weekly/pyproject.toml +0 -0
- package/dist/skills/python-setup-uv/SKILL.md +0 -0
- package/dist/tools/db/backends/index.d.ts +0 -0
- package/dist/tools/db/backends/index.js +0 -0
- package/dist/tools/db/backends/mongodb/backend.d.ts +0 -0
- package/dist/tools/db/backends/mongodb/backend.js +0 -0
- package/dist/tools/db/backends/mongodb/connection.d.ts +0 -0
- package/dist/tools/db/backends/mongodb/connection.js +0 -0
- package/dist/tools/db/backends/mongodb/index.d.ts +0 -0
- package/dist/tools/db/backends/mongodb/index.js +0 -0
- package/dist/tools/db/backends/mongodb/translator.d.ts +0 -0
- package/dist/tools/db/backends/mongodb/translator.js +0 -0
- package/dist/tools/db/backends/mysql/backend.d.ts +0 -0
- package/dist/tools/db/backends/mysql/backend.js +0 -0
- package/dist/tools/db/backends/mysql/connection.d.ts +0 -0
- package/dist/tools/db/backends/mysql/connection.js +0 -0
- package/dist/tools/db/backends/mysql/index.d.ts +0 -0
- package/dist/tools/db/backends/mysql/index.js +0 -0
- package/dist/tools/db/backends/mysql/translator.d.ts +0 -0
- package/dist/tools/db/backends/mysql/translator.js +0 -0
- package/dist/tools/db/core/base.d.ts +0 -0
- package/dist/tools/db/core/base.js +0 -0
- package/dist/tools/db/core/config-loader.d.ts +0 -0
- package/dist/tools/db/core/config-loader.js +0 -0
- package/dist/tools/db/core/index.d.ts +0 -0
- package/dist/tools/db/core/index.js +0 -0
- package/dist/tools/db/core/jsonc-parser.d.ts +0 -0
- package/dist/tools/db/core/jsonc-parser.js +0 -0
- package/dist/tools/db/core/validator.d.ts +0 -0
- package/dist/tools/db/core/validator.js +0 -0
- package/dist/tools/db/index.d.ts +0 -0
- package/dist/tools/db/index.js +0 -0
- package/dist/tools/db/interface/backend.d.ts +0 -0
- package/dist/tools/db/interface/backend.js +0 -0
- package/dist/tools/db/interface/connection.d.ts +0 -0
- package/dist/tools/db/interface/connection.js +0 -0
- package/dist/tools/db/interface/index.d.ts +0 -0
- package/dist/tools/db/interface/index.js +0 -0
- package/dist/tools/db/interface/query.d.ts +0 -0
- package/dist/tools/db/interface/query.js +0 -0
- package/dist/tools/db/interface/schema.d.ts +0 -0
- package/dist/tools/db/interface/schema.js +0 -0
- package/dist/tools/db/tools.d.ts +0 -0
- package/dist/tools/db/tools.js +0 -0
- package/dist/tools/db/utils.d.ts +0 -0
- package/dist/tools/db/utils.js +0 -0
- package/dist/tools/misc/calculator.d.ts +0 -0
- package/dist/tools/misc/calculator.js +0 -0
- package/dist/tools/misc/index.d.ts +0 -0
- package/dist/tools/misc/index.js +0 -0
- package/dist/tools/misc/json-extract.d.ts +0 -0
- package/dist/tools/misc/json-extract.js +0 -0
- package/dist/tools/misc/json-infer.d.ts +0 -0
- package/dist/tools/misc/json-infer.js +0 -0
- package/dist/tools/misc/json-validate.d.ts +0 -0
- package/dist/tools/misc/json-validate.js +0 -0
- package/dist/tools/misc/timer.d.ts +0 -0
- package/dist/tools/misc/timer.js +0 -0
- package/dist/tools/parser/obo/index.d.ts +0 -0
- package/dist/tools/parser/obo/index.js +0 -0
- package/dist/tools/parser/obo/obo.d.ts +0 -0
- package/dist/tools/parser/obo/obo.js +0 -0
- package/dist/tools/parser/obo/types.d.ts +0 -0
- package/dist/tools/parser/obo/types.js +0 -0
- package/dist/tools/parser/obo/utils.d.ts +0 -0
- package/dist/tools/parser/obo/utils.js +0 -0
- package/dist/tools/parser/pubmed/index.d.ts +0 -0
- package/dist/tools/parser/pubmed/index.js +0 -0
- package/dist/tools/parser/pubmed/pubmed.d.ts +0 -0
- package/dist/tools/parser/pubmed/pubmed.js +0 -0
- package/dist/tools/parser/pubmed/types.d.ts +0 -0
- package/dist/tools/parser/pubmed/types.js +0 -0
- package/dist/tools/parser/pubmed/utils.d.ts +0 -0
- package/dist/tools/parser/pubmed/utils.js +0 -0
- package/dist/tools/sandbox/bash-parser.d.ts +0 -0
- package/dist/tools/sandbox/bash-parser.js +0 -0
- package/dist/tools/sandbox/escape-scenarios.test.d.ts +0 -0
- package/dist/tools/sandbox/escape-scenarios.test.js +0 -0
- package/dist/tools/sandbox/expander.d.ts +0 -0
- package/dist/tools/sandbox/expander.js +0 -0
- package/dist/tools/sandbox/final-verification.test.d.ts +0 -0
- package/dist/tools/sandbox/final-verification.test.js +0 -0
- package/dist/tools/sandbox/hooks.d.ts +0 -0
- package/dist/tools/sandbox/hooks.js +0 -0
- package/dist/tools/sandbox/index.d.ts +0 -0
- package/dist/tools/sandbox/index.js +0 -0
- package/dist/tools/sandbox/manager.d.ts +0 -0
- package/dist/tools/sandbox/manager.js +0 -0
- package/dist/tools/sandbox/sandbox.integration.test.d.ts +0 -0
- package/dist/tools/sandbox/sandbox.integration.test.js +0 -0
- package/dist/tools/sandbox/sandbox.test.d.ts +0 -0
- package/dist/tools/sandbox/sandbox.test.js +0 -0
- package/dist/tools/sandbox/tool.d.ts +0 -0
- package/dist/tools/sandbox/tool.js +0 -0
- package/dist/tools/sandbox/types.d.ts +0 -0
- package/dist/tools/sandbox/types.js +0 -0
- package/dist/tools/sandbox/validator.d.ts +0 -0
- package/dist/tools/sandbox/validator.js +0 -0
- package/dist/tools/skill/frontmatter.d.ts +0 -0
- package/dist/tools/skill/frontmatter.js +0 -0
- package/dist/tools/skill/index.d.ts +0 -0
- package/dist/tools/skill/index.js +0 -0
- package/dist/tools/skill/registry.d.ts +0 -0
- package/dist/tools/skill/registry.js +0 -0
- package/dist/tools/skill/tool.d.ts +0 -0
- package/dist/tools/skill/tool.js +0 -0
- package/dist/tools/skill/types.d.ts +0 -0
- package/dist/tools/skill/types.js +0 -0
- package/dist/tools/table/index.d.ts +0 -0
- package/dist/tools/table/index.js +0 -0
- package/dist/tools/table/tools.d.ts +0 -0
- package/dist/tools/table/tools.js +0 -0
- package/dist/tools/table/utils.d.ts +0 -0
- package/dist/tools/table/utils.js +0 -0
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +1 -1
package/LICENSE
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@@ -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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export const PLUGIN_VERSION = "1.6.4";
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