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@yczhang-nv yczhang-nv commented Oct 2, 2025

Description

Closes

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  • When the PR is ready for review, the documentation is up to date with these changes.

Summary by CodeRabbit

  • Documentation
    • Restructured and expanded the MCP section with clearer hierarchy.
    • Added a new MCP Client subsection with command usage, examples, and help summaries.
    • Enhanced Serve documentation with clearer defaults, updated examples, and a note on running workflows via the MCP front end.
    • Documented options and defaults consistently across client and serve commands, including authentication and JSON output.
    • Updated examples to reflect default host/port behavior and available endpoints.
    • Applied minor formatting tweaks for consistency and readability.

@yczhang-nv yczhang-nv self-assigned this Oct 2, 2025
@yczhang-nv yczhang-nv requested a review from a team as a code owner October 2, 2025 23:25
@yczhang-nv yczhang-nv added doc Improvements or additions to documentation non-breaking Non-breaking change labels Oct 2, 2025
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Walkthrough

Expanded and restructured CLI documentation for MCP. Added a new Client subsection with detailed help for ping and tool (list/call). Enhanced Serve subsection with updated defaults, examples, and clarified descriptions. Adjusted examples to new host/port and endpoint. Applied minor formatting consistency updates.

Changes

Cohort / File(s) Summary
Docs — MCP CLI client and serve updates
docs/source/reference/cli.md
Promoted MCP header level; added Client subsection with nat mcp client help (ping, tool list/call, options, auth); expanded Serve subsection with clarified defaults, updated example paths/ports/endpoints; standardized default descriptions and minor formatting tweaks.

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🎯 2 (Simple) | ⏱️ ~10 minutes

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Title Check ✅ Passed The title uses imperative mood with “Update,” clearly describes the change to MCP-related CLI commands in the cli.md documentation, and is concise at under 72 characters.
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@yczhang-nv yczhang-nv changed the base branch from develop to release/1.3 October 2, 2025 23:25
AnuradhaKaruppiah and others added 8 commits October 2, 2025 16:27
… match (NVIDIA#893)

Closes

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

## Summary by CodeRabbit

* Documentation
  * Clarified MCP transport configuration in client workflow docs: when using Server-Sent Events (SSE), start the MCP server with the --transport sse flag, and ensure the client and server transport types match. Documented that the default transport is streamable-http, requiring an explicit override for SSE to ensure compatibility. This guidance is now included in the MCP client documentation.

Authors:
  - Anuradha Karuppiah (https://github.com/AnuradhaKaruppiah)

Approvers:
  - Will Killian (https://github.com/willkill07)
  - David Gardner (https://github.com/dagardner-nv)

URL: NVIDIA#893
Signed-off-by: Yuchen Zhang <[email protected]>
## Description
<!-- Note: The pull request title will be included in the CHANGELOG. -->
<!-- Provide a standalone description of changes in this PR. -->
<!-- Reference any issues closed by this PR with "closes #1234". All PRs
should have an issue they close-->
Closes AIQ-1957

- Made the default workflow a react-based workflow
- Used `python_safe_workflow_name` instead for the module name
- Edited `workflow_commands.py` by replacing `workflow_name` with
`package_name`, to ensure imports work (because `package_name` doesn't
have `-`)

## By Submitting this PR I confirm:
- I am familiar with the [Contributing
Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This
certifies that the contribution is your original work, or you have
rights to submit it under the same license, or a compatible license.
- Any contribution which contains commits that are not Signed-Off will
not be accepted.
- When the PR is ready for review, new or existing tests cover these
changes.
- When the PR is ready for review, the documentation is up to date with
these changes.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Added an echo tool (configurable prefix) and a current_datetime tool
to workflows.
- Introduced a default NIM LLM using meta/llama-3.1-70b-instruct
(temperature 0.0).
- Workflows gain LangChain wrapper support and parse-agent response
retry set to 3.

- **Refactor**
- Workflow templates now use a ReAct agent type and reference the NIM
LLM and tools.
- Generated workflow names/exports now use Python-safe naming
conventions.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Daniel Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Co-authored-by: Yuchen Zhang <[email protected]>
Co-authored-by: Will Killian <[email protected]>
Signed-off-by: Yuchen Zhang <[email protected]>
This PR significantly improves OpenAI Chat Completions API compatibility by fixing response format compliance, and removing unused code. The changes ensure that NAT's OpenAI-compatible endpoints fully adhere to the OpenAI specification for both streaming and non-streaming responses.
Closes: NVIDIA#818
A follow-up issue has been created to address accurate calculation and passing of usage statistics from workflows to ChatResponse objects in OpenAI-compatible endpoints: [Issue: 891](NVIDIA#891).

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

## Summary by CodeRabbit

- New Features
  - All responses — including error replies — now include usage statistics (prompt, completion, total tokens).

- Refactor
  - OpenAI-compatible non‑streaming path simplified to return a single JSON response; Content-Type set explicitly for JSON and streaming.
  - Default model identifier standardized to "unknown-model" in responses.

- Compatibility
  - Streaming chunk roles standardized to an enum-style role; response payloads and tests now include and expect usage metadata.

Authors:
  - Eric Evans II (https://github.com/ericevans-nv)

Approvers:
  - Will Killian (https://github.com/willkill07)

URL: NVIDIA#889
Signed-off-by: Yuchen Zhang <[email protected]>
Enable optional token storage for MCP OAuth2 with in-memory or external object-store backends (e.g., S3/MinIO), which are persistent and also more secure. Also enabled users to implement their own external object-store interface.

Closes AIQ-1965

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

## Summary by CodeRabbit

- New Features
  - Secure token storage for MCP OAuth2: in-memory default with optional external object-store backing, persistent across restarts, multi-user isolation, automatic refresh, and graceful fallback.

- Documentation
  - Added “Secure Token Storage” guide with examples and deployment guidance; MCP auth docs and index updated to reference it.

- Tests
  - Extensive tests covering token storage backends, key hashing/serialization, provider integration, lazy object-store resolution, and persistence.

Authors:
  - Yuchen Zhang (https://github.com/yczhang-nv)

Approvers:
  - Eric Evans II (https://github.com/ericevans-nv)

URL: NVIDIA#883
Signed-off-by: Yuchen Zhang <[email protected]>
Cleans up the default configuration + workflow template a little more

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

## Summary by CodeRabbit

- New Features
  - None
- Refactor
  - Simplified generated workflow configuration by removing redundant logging and frontend blocks and a deprecated retry option.
  - Aligned workflow registration naming to a consistent convention.
- Documentation
  - Added comprehensive docstrings to the workflow and helper to improve clarity and editor hints.
- Chores
  - Cleaned up default config output to reduce noise and simplify generated templates.

Authors:
  - Will Killian (https://github.com/willkill07)

Approvers:
  - Eric Evans II (https://github.com/ericevans-nv)

URL: NVIDIA#899
Signed-off-by: Yuchen Zhang <[email protected]>
Update the CLI tree based on features since 1.2 release
Closes

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

## Summary by CodeRabbit

* **Documentation**
  * Expanded CLI reference with new top-level groups: mcp (client, serve), object-store (mysql, redis, s3), and sizing (calc).
  * Reorganized structure: promoted sizing to top-level; removed nested serve/client subtree from Start workflow.
  * Adjusted Workflow ordering: “delete” now precedes “reinstall” under Reinstall/Delete.
  * Updated navigation and anchors for clarity and discoverability.
  * Content-only changes; no impact on command behavior.

Authors:
  - Will Killian (https://github.com/willkill07)

Approvers:
  - Eric Evans II (https://github.com/ericevans-nv)

URL: NVIDIA#900
Signed-off-by: Yuchen Zhang <[email protected]>
## Description
<!-- Note: The pull request title will be included in the CHANGELOG. -->
<!-- Provide a standalone description of changes in this PR. -->
<!-- Reference any issues closed by this PR with "closes #1234". All PRs
should have an issue they close-->
Closes 1897

**Added**:
- `ContextState` fields: `workflow_run_id`, `workflow_trace_id`
(`src/nat/builder/context.py`)
- Non-zero ID generators & validators for OpenTelemetry-sized IDs
(`src/nat/data_models/span.py`)
- Workflow start/end event emission with metadata: `workflow_run_id`,
`workflow_trace_id`, `conversation_id` (`src/nat/runtime/runner.py`)
- Span attributes for correlation: `.workflow.run_id`,
`.workflow.trace_id`, `.conversation.id`
(`src/nat/observability/exporter/span_exporter.py`)
- Tests: `tests/nat/opentelemetry/test_otel_span_ids.py`,
`tests/nat/runtime/test_runner_trace_ids.py`,
`tests/nat/runtime/test_session_traceparent.py`, updates to
`tests/nat/runtime/test_runner.py`

**Changed**:
- Ensure non-zero 128-bit trace IDs and 64-bit span IDs in OTEL plugin
(`packages/nvidia_nat_opentelemetry/src/nat/plugins/opentelemetry/otel_span.py`)
- Runner establishes workflow-scoped run/trace IDs and resets them on
exit (`src/nat/runtime/runner.py`)
- Exporter prefers parent/context trace ID; falls back to workflow trace
ID and sets correlated attributes
(`src/nat/observability/exporter/span_exporter.py`)
- `SpanContext` defaults & field validators enforce size/range and
non-zero invariants (`src/nat/data_models/span.py`)
- Parse/propagate incoming W3C `traceparent` and workflow headers to
session/runner (`src/nat/runtime/session.py`,
`tests/nat/runtime/test_session_traceparent.py`)

**Removed**:
- None

**Why it matters**:
- Consistent cross-span correlation and easier log/trace joins across
agents and sub-spans
- Fewer broken traces: eliminates zero/invalid IDs, aligns with
OpenTelemetry sizing
- Improves debugging and fleet-wide reporting via explicit `.workflow.*`
and `.conversation.id` attributes
- Safer header handling for external callers; preserves upstream traces

**Breaking changes / Migrations**:
- None

**Docs**:
- None

## By Submitting this PR I confirm:
- I am familiar with the [Contributing
Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This
certifies that the contribution is your original work, or you have
rights to submit it under the same license, or a compatible license.
- Any contribution which contains commits that are not Signed-Off will
not be accepted.
- When the PR is ready for review, new or existing tests cover these
changes.
- When the PR is ready for review, the documentation is up to date with
these changes.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Workflow-level run and trace IDs are created, stored in context,
propagated, and emitted with WORKFLOW_START/WORKFLOW_END events.
* Incoming HTTP tracing headers (traceparent, workflow-trace-id,
workflow-run-id) are parsed into context.

* **Improvements**
* Span metadata now includes workflow IDs and richer attributes (event
type, function info, timestamps, conversation/run IDs).
* ID generation and validation tightened to ensure non-zero, correctly
sized trace and span IDs; span context ID generation approach updated.

* **Tests**
* Added tests validating span ID formats, runner trace/run ID behavior,
and header parsing.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Daniel Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Signed-off-by: Yuchen Zhang <[email protected]>
Signed-off-by: Yuchen Zhang <[email protected]>
@yczhang-nv yczhang-nv force-pushed the yuchen-update-mcp-cli-doc branch from ce04ab2 to c1aa472 Compare October 2, 2025 23:28
zhongxuanwang-nv and others added 6 commits October 2, 2025 16:29
<!-- Note: The pull request title will be included in the CHANGELOG. -->
<!-- Provide a standalone description of changes in this PR. -->
<!-- Reference any issues closed by this PR with "closes #1234". All PRs
should have an issue they close-->
Closes AIQ-1957

- Made the default workflow a react-based workflow
- Used `python_safe_workflow_name` instead for the module name
- Edited `workflow_commands.py` by replacing `workflow_name` with
`package_name`, to ensure imports work (because `package_name` doesn't
have `-`)

- I am familiar with the [Contributing
Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This
certifies that the contribution is your original work, or you have
rights to submit it under the same license, or a compatible license.
- Any contribution which contains commits that are not Signed-Off will
not be accepted.
- When the PR is ready for review, new or existing tests cover these
changes.
- When the PR is ready for review, the documentation is up to date with
these changes.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

- **New Features**
- Added an echo tool (configurable prefix) and a current_datetime tool
to workflows.
- Introduced a default NIM LLM using meta/llama-3.1-70b-instruct
(temperature 0.0).
- Workflows gain LangChain wrapper support and parse-agent response
retry set to 3.

- **Refactor**
- Workflow templates now use a ReAct agent type and reference the NIM
LLM and tools.
- Generated workflow names/exports now use Python-safe naming
conventions.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Daniel Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Co-authored-by: Yuchen Zhang <[email protected]>
Co-authored-by: Will Killian <[email protected]>
Cleans up the default configuration + workflow template a little more

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.



## Summary by CodeRabbit

- New Features
  - None
- Refactor
  - Simplified generated workflow configuration by removing redundant logging and frontend blocks and a deprecated retry option.
  - Aligned workflow registration naming to a consistent convention.
- Documentation
  - Added comprehensive docstrings to the workflow and helper to improve clarity and editor hints.
- Chores
  - Cleaned up default config output to reduce noise and simplify generated templates.

Authors:
  - Will Killian (https://github.com/willkill07)

Approvers:
  - Eric Evans II (https://github.com/ericevans-nv)

URL: NVIDIA#899
Signed-off-by: Yuchen Zhang <[email protected]>
<!-- Note: The pull request title will be included in the CHANGELOG. -->
<!-- Provide a standalone description of changes in this PR. -->
<!-- Reference any issues closed by this PR with "closes #1234". All PRs
should have an issue they close-->
Closes AIQ-1957

- Made the default workflow a react-based workflow
- Used `python_safe_workflow_name` instead for the module name
- Edited `workflow_commands.py` by replacing `workflow_name` with
`package_name`, to ensure imports work (because `package_name` doesn't
have `-`)

- I am familiar with the [Contributing
Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This
certifies that the contribution is your original work, or you have
rights to submit it under the same license, or a compatible license.
- Any contribution which contains commits that are not Signed-Off will
not be accepted.
- When the PR is ready for review, new or existing tests cover these
changes.
- When the PR is ready for review, the documentation is up to date with
these changes.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

- **New Features**
- Added an echo tool (configurable prefix) and a current_datetime tool
to workflows.
- Introduced a default NIM LLM using meta/llama-3.1-70b-instruct
(temperature 0.0).
- Workflows gain LangChain wrapper support and parse-agent response
retry set to 3.

- **Refactor**
- Workflow templates now use a ReAct agent type and reference the NIM
LLM and tools.
- Generated workflow names/exports now use Python-safe naming
conventions.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Daniel Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Signed-off-by: Zhongxuan (Daniel) Wang <[email protected]>
Co-authored-by: Yuchen Zhang <[email protected]>
Co-authored-by: Will Killian <[email protected]>
Cleans up the default configuration + workflow template a little more

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.



## Summary by CodeRabbit

- New Features
  - None
- Refactor
  - Simplified generated workflow configuration by removing redundant logging and frontend blocks and a deprecated retry option.
  - Aligned workflow registration naming to a consistent convention.
- Documentation
  - Added comprehensive docstrings to the workflow and helper to improve clarity and editor hints.
- Chores
  - Cleaned up default config output to reduce noise and simplify generated templates.

Authors:
  - Will Killian (https://github.com/willkill07)

Approvers:
  - Eric Evans II (https://github.com/ericevans-nv)

URL: NVIDIA#899
Signed-off-by: Yuchen Zhang <[email protected]>
In the last PR NVIDIA#885 I forgot to add this file to the commit, resulting in the bug still persisting.

Closes

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/NeMo-Agent-Toolkit/blob/develop/docs/source/resources/contributing.md).
- We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
  - Any contribution which contains commits that are not Signed-Off will not be accepted.
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.




## Summary by CodeRabbit

- Chores
  - Updated demo module linting configuration to reduce false-positive warnings and streamline code maintenance.
  - Adjusted imports to align with available tool integrations, preparing the demo for time and weather-related capabilities.
  - No changes to existing user workflows or features; behavior remains unchanged.

- Tests
  - No test impact identified.

- Documentation
  - No user-facing documentation changes.

Authors:
  - Will Killian (https://github.com/willkill07)

Approvers:
  - Zhongxuan (Daniel) Wang (https://github.com/zhongxuanwang-nv)

URL: NVIDIA#901
Signed-off-by: Yuchen Zhang <[email protected]>
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docs/source/**/*

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This directory contains the source code for the documentation. All documentation should be written in Markdown format. Any image files should be placed in the docs/source/_static directory.

Files:

  • docs/source/reference/cli.md
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@rapids-bot rapids-bot bot merged commit 1910117 into NVIDIA:release/1.3 Oct 2, 2025
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@yczhang-nv yczhang-nv deleted the yuchen-update-mcp-cli-doc branch October 2, 2025 23:58
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