ℹ️ About Codex in GitHub

\\n
\\n\\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\\n- Open a pull request for review\\n- Mark a draft as ready\\n- Comment \\\"@codex review\\\".\\n\\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\\n\\n\\n\\n\\nCodex can also answer questions or update the PR. Try commenting \\\"@codex address that feedback\\\".\\n \\n

\",\"path\":null,\"side\":null,\"line\":null}","text_elements",[],{"_384":659,"_371":372,"_386":374},{"_387":660,"_389":-5,"_41":-5,"_390":-5,"_95":303,"_91":392},[661],{"_45":655,"_91":662},"input_text","turn/started",{"_371":372,"_86":665},{"_102":-5,"_41":374,"_375":666,"_377":667},[],"inProgress",{"_377":669,"_371":372},{"_670":671,"_91":672},"activeFlags",[],"active",{"_384":674,"_371":372,"_386":675},{"_387":676,"_389":-5,"_41":-5,"_390":-5,"_95":303,"_91":392},"auto-compact-0",[677,678],{"_45":680,"_91":662},{"_45":679,"_91":662},"\n /workspace/ChainAgents\n bash\n 2026-04-20\n Etc/UTC\n","# AGENTS.md instructions for /workspace/ChainAgents\n\n\n## Skills\nA skill is a set of local instructions to follow that is stored in a `SKILL.md` file. Below is the list of skills that can be used. Each entry includes a name, description, and file path so you can open the source for full instructions when using a specific skill.\n### Available skills\n- skill-creator: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations. (file: /opt/codex/skills/.system/skill-creator/SKILL.md)\n- skill-installer: Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos). (file: /opt/codex/skills/.system/skill-installer/SKILL.md)\n### How to use skills\n- Discovery: The list above is the skills available in this session (name + description + file path). Skill bodies live on disk at the listed paths.\n- Trigger rules: If the user names a skill (with `$SkillName` or plain text) OR the task clearly matches a skill's description shown above, you must use that skill for that turn. Multiple mentions mean use them all. Do not carry skills across turns unless re-mentioned.\n- Missing/blocked: If a named skill isn't in the list or the path can't be read, say so briefly and continue with the best fallback.\n- How to use a skill (progressive disclosure):\n 1) After deciding to use a skill, open its `SKILL.md`. Read only enough to follow the workflow.\n 2) When `SKILL.md` references relative paths (e.g., `scripts/foo.py`), resolve them relative to the skill directory listed above first, and only consider other paths if needed.\n 3) If `SKILL.md` points to extra folders such as `references/`, load only the specific files needed for the request; don't bulk-load everything.\n 4) If `scripts/` exist, prefer running or patching them instead of retyping large code blocks.\n 5) If `assets/` or templates exist, reuse them instead of recreating from scratch.\n- Coordination and sequencing:\n - If multiple skills apply, choose the minimal set that covers the request and state the order you'll use them.\n - Announce which skill(s) you're using and why (one short line). If you skip an obvious skill, say why.\n- Context hygiene:\n - Keep context small: summarize long sections instead of pasting them; only load extra files when needed.\n - Avoid deep reference-chasing: prefer opening only files directly linked from `SKILL.md` unless you're blocked.\n - When variants exist (frameworks, providers, domains), pick only the relevant reference file(s) and note that choice.\n- Safety and fallback: If a skill can't be applied cleanly (missing files, unclear instructions), state the issue, pick the next-best approach, and continue.\n",{"_384":682,"_371":372,"_386":675},{"_387":683,"_389":-5,"_41":-5,"_390":-5,"_95":684,"_91":392},[685],"developer",{"_45":686,"_91":662},"\nFilesystem sandboxing defines which files can be read or written. `sandbox_mode` is `danger-full-access`: No filesystem sandboxing - all commands are permitted. Network access is enabled.\nApproval policy is currently never. Do not provide the `sandbox_permissions` for any reason, commands will be rejected.\n","thread/started",{"_689":690},"thread",{"_691":-5,"_692":-5,"_693":694,"_695":696,"_428":429,"_697":15,"_698":-5,"_699":-5,"_41":372,"_700":701,"_166":-5,"_156":702,"_703":180,"_434":704,"_377":705,"_76":706,"_707":696},"agentNickname","agentRole","cliVersion","0.114.0","createdAt",1776659398,"ephemeral","forkedFromId","gitInfo","modelProvider","openai","/opt/codex/sessions/2026/04/20/rollout-2026-04-20T04-29-58-019da926-ff32-7b82-a5ff-aba1fb1058ec.jsonl","preview","vscode",{"_91":381},[],"updatedAt",[],"messages",[711],{"_41":712,"_713":714,"_715":716,"_717":716,"_387":718,"_377":719,"_389":-5,"_720":31,"_721":722,"_723":724,"_725":-5},"c0700e78-5c02-4d2a-84d2-1e115329912a","author",{"_95":303,"_166":-5,"_721":734},"create_time",1776659397.814862,"update_time",{"_730":45,"_731":732},"finished_successfully","weight","metadata",{"_726":727},"recipient","all","channel","l1239dk1",{"_728":729},"inline_comments",[],"content_type","parts",[733],"@codex Please provide suggestions to fix this. (path=deepagent.toml line=42 side=RIGHT)\nAdd ToolUniverse research skills\n\n## Summary\n\n- Add ToolUniverse skills for literature search, clinical trials, and drug safety workflows.\n- Add per-skill tool maps covering discovery, schema inspection, execution, and domain-specific ToolUniverse tools.\n- Attach the ToolUniverse MCP server to the main agent in `deepagent.toml` so slash-invoked skills can access ToolUniverse tools when the service is running.\n\n## Validation\n\n- `.venv/bin/python -m pytest` passed on this branch: 34 passed, 2 warnings.\n- Lightweight YAML/frontmatter validation passed for all three new skills.\n\n## Notes\n\n- The ToolUniverse MCP service is expected at `http://localhost:8090/mcp`. The skills now tell the agent to report when ToolUniverse tools are unavailable rather than guessing tool names.\nComments in the same thread:\n\n**_{_{![P1 Badge](https://img.shields.io/badge/P1-orange?style=flat)}} Avoid attaching ToolUniverse MCP by default**\n\nAdding `tooluniverse` to the main agent's `mcp_servers` makes every normal chat request depend on `http://localhost:8090/mcp` being up, because `AgentRuntime._build_main_tools()` always loads all configured agent MCP tools and does not handle connection failures from `_get_mcp_tools()`. In environments where ToolUniverse is not running (the common default), this turns the whole agent unusable instead of letting it continue with repo-only tools.\n\nUseful? React with 👍 / 👎.\n\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `728e69fd63`\n \n\n

ℹ️ About Codex in GitHub

\n
\n\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\n- Open a pull request for review\n- Mark a draft as ready\n- Comment \"@codex review\".\n\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\n\n\n\n\nCodex can also answer questions or update the PR. Try commenting \"@codex address that feedback\".\n \n

",{},"created",1776659487.1916122,"Completing the task","event_type","info",{"_91":392,"_95":92,"_387":850},{"_91":767,"_768":769},{"_91":743,"_744":745,"_746":747,"_748":749,"_750":-5},"pr","pr_title","Make ToolUniverse MCP optional in main agent config","pr_message","### Motivation\n- Avoid making normal chat startup depend on the ToolUniverse MCP server so the agent remains usable when `http://localhost:8090/mcp` is not running.\n\n### Description\n- Removed `tooluniverse` from the main-agent `mcp_servers` list in `deepagent.toml` and added a commented opt-in example showing how to re-enable it (`mcp_servers = [\"repo\", \"tooluniverse\"]`).\n\n### Testing\n- Ran the automated test suite with `.venv/bin/python -m pytest -q`, which completed successfully: `34 passed, 2 warnings`.","output_diff",{"_91":748,"_751":177,"_127":128,"_752":-5,"_302":753,"_754":755,"_756":306,"_757":758,"_759":306,"_760":761,"_762":763},"pre_apply_patch","repo_id","preapply_patch_base_commit_sha","diff --git a/deepagent.toml b/deepagent.toml\nindex 550491fbcad9d0da06b3409eca121696753819e6..fae0c60eeec7a4e45b3336c913beeded4a419100 100644\n--- a/deepagent.toml\n+++ b/deepagent.toml\n@@ -17,51 +17,54 @@ reasoning_effort = \"medium\"\n #provider = \"openai_compatible\"\n #base_url = \"http://127.0.0.1:1234/v1\"\n #temperature = 0\n #name = \"google/gemma-4-26b-a4b\"\n #reasoning_effort = \"medium\"\n # api_key = \"optional\"\n \n \n \n [mcp]\n tool_name_prefix = false\n stateful = true\n \n [mcp.servers.repo]\n transport = \"stdio\"\n command = \"npx\"\n args = [\"-y\", \"@modelcontextprotocol/server-filesystem@2025.8.21\", \".\"]\n cwd = \".\"\n \n [mcp.servers.tooluniverse]\n transport = \"http\"\n url = \"http://localhost:8090/mcp\"\n \n [agent]\n skills = [\"skills\"]\n-mcp_servers = [\"repo\", \"tooluniverse\"]\n+mcp_servers = [\"repo\"]\n+# Keep ToolUniverse optional for slash-invoked skills in environments where the\n+# MCP service is available by adding it to mcp_servers when needed:\n+# mcp_servers = [\"repo\", \"tooluniverse\"]\n \n [rag]\n enabled = true\n persist_directory = \".rag\"\n include_globs = [\"README.md\", \"chainlit.md\", \"prompts/**/*.md\", \"skills/**/*.md\"]\n exclude_globs = [\"AGENTS.md\", \"AGENT.md\"]\n chunk_size = 1200\n chunk_overlap = 200\n top_k = 4\n \n [rag.embedding]\n provider = \"auto\"\n # For Ollama, the default embedding model is \"nomic-embed-text\".\n # model = \"nomic-embed-text\"\n # base_url = \"http://127.0.0.1:11434\"\n \n # Async subagent backed by the local LangGraph Agent Protocol server.\n [[async_subagents]]\n name = \"async-researcher\"\n description = \"Runs longer research jobs in the background, such as reading documentation or running code analysis tools.\"\n graph_id = \"async-researcher\"\n url = \"http://127.0.0.1:2024\"\n \n # If you run only the co-deployed langgraph.json setup, omit url for ASGI transport.\n # In Chainlit, set url here or use CHAINLIT_ASYNC_SUBAGENT_URL for HTTP transport.\n","external_storage_diff",{"_764":765,"_766":-5},"files_modified","lines_added",4,"lines_removed","commit_message","Make ToolUniverse MCP optional for main agent","additional_parent_commit_shas",[],"file_id","file_00000000bfec720ca97ddd8ca501bd39","ttl","partial_repo_snapshot","files",[770],{"_156":439,"_771":-5,"_772":773,"_774":-5},"contents","line_range_contents",[775],"missing_reason",{"_776":306,"_777":778,"_387":779,"_780":57},"line_range_start","line_range_end",86,[781,782,783,784,785,786,787,180,788,789,790,791,792,180,180,793,794,795,796,797,798,799,180,180,180,800,801,802,180,803,804,805,806,807,180,808,809,810,180,811,812,813,814,815,816,180,817,818,819,820,821,822,823,824,180,825,826,827,828,829,180,830,831,832,833,834,835,180,836,837,838,839,180,840,841,842,843,812,813,180,844,845,846,847,848,849],"contains_end_of_file","[model]","provider = \"ollama\"","base_url = \"http://127.0.0.1:11434\"","temperature = 0","name = \"gemma4:26b\"","#name = \"gpt-oss:20b\"","reasoning_effort = \"medium\"","# For LM Studio or another OpenAI-compatible server, switch to:","# provider = \"openai_compatible\"","# base_url = \"http://127.0.0.1:1234/v1\"","# name = \"your-loaded-model-id\"","# api_key = \"\"","#[model]","#provider = \"openai_compatible\"","#base_url = \"http://127.0.0.1:1234/v1\"","#temperature = 0","#name = \"google/gemma-4-26b-a4b\"","#reasoning_effort = \"medium\"","# api_key = \"optional\"","[mcp]","tool_name_prefix = false","stateful = true","[mcp.servers.repo]","transport = \"stdio\"","command = \"npx\"","args = [\"-y\", \"@modelcontextprotocol/server-filesystem@2025.8.21\", \".\"]","cwd = \".\"","[mcp.servers.tooluniverse]","transport = \"http\"","url = \"http://localhost:8090/mcp\"","[agent]","skills = [\"skills\"]","mcp_servers = [\"repo\"]","# Keep ToolUniverse optional for slash-invoked skills in environments where the","# MCP service is available by adding it to mcp_servers when needed:","# mcp_servers = [\"repo\", \"tooluniverse\"]","[rag]","enabled = true","persist_directory = \".rag\"","include_globs = [\"README.md\", \"chainlit.md\", \"prompts/**/*.md\", \"skills/**/*.md\"]","exclude_globs = [\"AGENTS.md\", \"AGENT.md\"]","chunk_size = 1200","chunk_overlap = 200","top_k = 4","[rag.embedding]","provider = \"auto\"","# For Ollama, the default embedding model is \"nomic-embed-text\".","# model = \"nomic-embed-text\"","# base_url = \"http://127.0.0.1:11434\"","# Async subagent backed by the local LangGraph Agent Protocol server.","[[async_subagents]]","name = \"async-researcher\"","description = \"Runs longer research jobs in the background, such as reading documentation or running code analysis tools.\"","graph_id = \"async-researcher\"","url = \"http://127.0.0.1:2024\"","# If you run only the co-deployed langgraph.json setup, omit url for ASGI transport.","# In Chainlit, set url here or use CHAINLIT_ASYNC_SUBAGENT_URL for HTTP transport.","#url = \"https://researcher-deployment.langsmith.dev\"","#headers = { Authorization = \"Bearer ${RESEARCHER_TOKEN}\" }","[[subagents]]","name = \"repo-researcher\"","description = \"Researches the current repository, explains architecture, and identifies the right files to change.\"","system_prompt_file = \"prompts/repo-researcher.md\"","[chainlit]","commands = ["," { name = \"ask-researcher\", description = \"Delegate to repo-researcher.\", target = \"subagent\", value = \"repo-researcher\", template = \"{input}\" },"," { name = \"repo-readme\", description = \"Run an MCP tool directly.\", target = \"mcp_tool\", value = \"repo_read_file\", mcp_server = \"repo\", template = \"{\\\"path\\\":\\\"README.md\\\"}\" },"," { name = \"summarize\", description = \"Apply a prompt template.\", target = \"prompt\", value = \"Summarize the input\", template = \"Summarize this:\\n{input}\" }","]",[851,852,853,854,855],{"_730":45,"_45":862},{"_730":857,"_156":439,"_776":861,"_777":858},{"_730":45,"_45":860},{"_730":857,"_156":439,"_776":858,"_777":859},{"_730":45,"_45":856},"\n* Committed the change on the current branch (`f64cee3`) and created a follow-up PR entry via the `make_pr` tool.\n\n**Testing**\n* ✅ `git status --short && .venv/bin/python -m pytest -q` (34 passed, 2 warnings)\n* ✅ `git add deepagent.toml && git commit -m \"Make ToolUniverse MCP optional for main agent\"`","repo_file_citation",43,45,"\n* Added a commented opt-in example showing how to re-enable ToolUniverse when `http://localhost:8090/mcp` is available, preserving discoverability for that workflow.",40,"### Summary\n* Updated the main agent configuration to **not require ToolUniverse by default** by changing `mcp_servers` from `[\"repo\", \"tooluniverse\"]` to `[\"repo\"]`, so normal chat remains usable when ToolUniverse is offline.",{"_91":303,"_41":83,"_95":303,"_865":866,"_867":868,"_869":870,"_131":-5,"_118":871},[82],"input_items",[887,888,889,890],"external_post_config",{"_872":873,"_242":177,"_874":283,"_253":-5,"_751":236,"_875":-5,"_876":877,"_878":743,"_879":-5,"_880":-5,"_881":882,"_883":15,"_884":57,"_885":52,"_886":15},"user_model_slug","slug",1776659313.971171,"installation_id",102429218,"pr_number","review_trigger","comment_id",3108235579,"comment_type","pr_write_guard_token","pending_pr_reaction_id","pending_comment_reaction_id",382549210,"comment_if_no_findings","comment_on_error","share_url","is_parallel_review",{"_91":392,"_95":303,"_387":901},{"_290":291,"_292":293,"_898":297,"_899":128,"_299":-5,"_91":900},{"_91":891,"_292":895,"_156":439,"_893":896,"_894":897},{"_91":891,"_292":892,"_156":-5,"_893":-5,"_894":-5},"pull_request_comment","\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `728e69fd63`\n \n\n

ℹ️ About Codex in GitHub

","side","line","Comments in the same thread:\n\n**_{_{![P1 Badge](https://img.shields.io/badge/P1-orange?style=flat)}} Avoid attaching ToolUniverse MCP by default**\n\nAdding `tooluniverse` to the main agent's `mcp_servers` makes every normal chat request depend on `http://localhost:8090/mcp` being up, because `AgentRuntime._build_main_tools()` always loads all configured agent MCP tools and does not handle connection failures from `_get_mcp_tools()`. In environments where ToolUniverse is not running (the common default), this turns the whole agent unusable instead of letting it continue with repo-only tools.\n\nUseful? React with 👍 / 👎.","RIGHT",42,"base_ref","head_ref","pull_request_info",[902],{"_730":45,"_45":903},"@codex Please provide suggestions to fix this. 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