upgrade-deps

name	upgrade-deps
description	Upgrade focused runtime dependencies in AReaL. First validates and updates per-package API checklists for structural completeness, then updates pyproject files, resolves conflicts, locks, updates the Dockerfile, and audits API compatibility against the checklists.

Usage

/upgrade-deps <package==version> [<package==version> ...]

Arguments: One or more pinned package versions, e.g., /upgrade-deps megatron-core==0.17.0 sglang==0.5.10 vllm==0.18.0 transformers==4.58.0.

If a package is omitted, its current version can be preserved or upgraded, depending on the resolution of uv lock.

---

Architecture

Dual-Manifest Model

AReaL maintains two pyproject files because SGLang and vLLM pin mutually-incompatible torch / torchao versions:

File	Inference backend	Lock file
pyproject.toml	SGLang (default)	uv.lock
pyproject.vllm.toml	vLLM	uv.vllm.lock

Both share the same core dependencies, megatron extras, and dev group. They diverge only in inference backend extras and torch/torchao version constraints.

The Dockerfile builds both variants from a single file using ARG VARIANT (sglang or vllm). The base image, torch install, and flash-attn wheels are all variant-specific.

Focused Packages

The following packages are focused — their API usage in AReaL is cataloged, and any version change triggers the API compatibility audit (Step 6):

Package	Import path
megatron-core	megatron.core
megatron-bridge	megatron.bridge
mbridge	mbridge
transformers	transformers
sglang	sglang
vllm	vllm
peft	peft
torchao	torchao

torch is tracked in the Package Impact Matrix below for scope and Docker awareness, but is not a focused package — it does not receive API auditing.

Package Impact Matrix

Every entry below has a variant scope that determines which files to edit, which lock files to regenerate, and whether the Dockerfile needs review. All focused packages plus torch (tracked for Docker impact only, not API-audited) are listed.

Package	Scope	pyproject.toml locations	pyproject.vllm.toml locations	Docker impact
sglang	sglang-only	[optional-deps].sglang	—	Base image
vllm	vllm-only	—	[optional-deps].vllm	No
megatron-core	shared	[optional-deps].megatron + [tool.uv].override-dependencies	[optional-deps].megatron + [tool.uv].override-dependencies	No
megatron-bridge	shared	[optional-deps].megatron	[optional-deps].megatron	No
mbridge	shared	[optional-deps].megatron (git pin)	[optional-deps].megatron (git pin)	No
transformers	shared	[project].dependencies	[project].dependencies	No
peft	shared	[project].dependencies	[project].dependencies	No
torch	shared-divergent	[project].dependencies (≥2.9.1)	[project].dependencies (≥2.10.0)	Stage 1 torch
torchao	shared-divergent	[tool.uv].override-dependencies (==0.15.0)	[project].dependencies (==0.16.0)	No

Scope rules:

• sglang-only / vllm-only: Edit and lock only the affected variant.
• shared: Edit both files; lock both variants.
• shared-divergent: The two variants intentionally use different versions of the same package. If the user supplies a single target version, ask which variant(s) to apply it to rather than assuming convergence. If the user supplies two targets (e.g., torch==2.9.1@sglang torch==2.10.0@vllm), apply each accordingly.

Upgrade Families

Some packages are tightly coupled and should be upgraded together:

Family	Members	Reason
megatron	megatron-core, megatron-bridge	megatron-bridge wraps megatron-core; tightly coupled APIs
inference	sglang or vllm + torch + torchao	Inference backends pin specific torch/torchao versions

When the user upgrades one member, check the checklist of all family members for required co-upgrades and warn if a co-upgrade is needed but not requested.

Per-Package API Checklists

Each focused package has a dedicated markdown file under checklists/ that documents how AReaL uses that package's APIs:

.agents/skills/upgrade-deps/
├── SKILL.md
└── checklists/
    ├── megatron-core.md
    ├── megatron-bridge.md
    ├── vllm.md
    ├── sglang.md
    ├── transformers.md
    ├── peft.md
    └── torchao.md

Each checklist file MUST contain the following sections:

---
package: <pip-package-name>
github: <org/repo>                    # e.g., NVIDIA/Megatron-LM
branch_template: "v${VERSION}"        # how to construct the git branch/tag from version
upstream_paths:                        # source paths to cross-reference
  - path/to/relevant/file.py
  - path/to/relevant/module/
---

## Affected Files

### Primary (most likely to break)
| File | Imports / Usage |
| ---- | --------------- |
| ...  | ...             |

### Secondary
...

### Tertiary (tests, infra)
...

## API Usage Catalog

For each function/class, verify the call signature against the upstream source.
Focus on: removed params, renamed params, new required params, changed return types,
moved/renamed modules.

### 1. `module.submodule.function_or_class`

**Source:** `upstream_path/file.py`

Called in `areal/path/to/file.py:LINE`:
\```python
actual_call_site_code()
\```

**Check:** [what to verify]

### 2. ...

## Version-Guarded Code (if any)
- [file:line] description of version guard and when it can be removed

To populate a checklist, catalog AReaL's usage of the package by grepping for imports and call sites, then fill in the template sections. Each checklist should be self-contained — all API signatures, file paths, and upstream references must be recorded directly in the checklist file.

---

Workflow

Step 0: Parse Input and Record Baseline

1. Parse arguments. Each argument is <package==version> or, for shared-divergent packages, <package==version@variant> (e.g., torchao==0.16.0@vllm).
2. Validate that each package name is a recognized focused package (see Focused Packages table). If unrecognized, warn but proceed — it may be a transitive dependency the user wants to pin.
3. For shared-divergent packages (torch, torchao): if the user supplies a single version without a @variant qualifier, ask which variant(s) to apply it to before proceeding.
4. Record the current resolved versions of ALL focused packages from the applicable lock file(s) as the baseline snapshot. Use uv.lock for sglang-scoped and shared packages; uv.vllm.lock for vllm-scoped and shared packages. Packages scoped to a single variant appear only in that variant's lock file. This baseline will be used later to detect which packages actually changed — including transitive bumps caused by uv lock resolution, not just explicit pin changes.

Step 0.5: Validate and Update Checklists

Before modifying any dependencies, verify that the API checklists for the packages being upgraded are structurally complete — i.e., they document all current AReaL import sites and call patterns. Stale checklists lead to missed breaking changes in Step 6.

For each focused package explicitly requested in the command that has a checklist file under checklists/:

1. Discover all usages. Grep the AReaL codebase (areal/, tests/, examples/) for all imports matching the package's import path(s). See the Import Patterns table in CHECKLIST_MAINTENANCE.md § 2 for package-specific grep patterns. For HTTP-based integrations (sglang, vllm), also scan request-building code for endpoint paths and JSON field names.

2. Compare against the checklist. Diff the discovered files against the Affected Files tables (Primary / Secondary / Tertiary) in the checklist. Identify:

   • Missing — files that import the package but are not listed in any tier.
   • Stale — files listed in the checklist that no longer import the package.
   • Changed — files whose actual imports differ from what's documented.

3. Classify and update. For each discrepancy, follow the Structural Validation Procedure in CHECKLIST_MAINTENANCE.md § 3:

   • Add missing files to the appropriate tier (Primary / Secondary / Tertiary).
   • Add new API Usage Catalog entries for genuinely new call patterns.
   • Remove stale entries.
   • Renumber catalog entries if needed.

4. Update the Checklist File Status table at the bottom of this file if entry counts changed.

5. Report changes before proceeding:

   Checklist validation for <package>:
   - Added N files to Affected Files (P primary, S secondary, T tertiary)
   - Added M new API catalog entries: [brief list]
   - Removed K stale entries: [brief list]
   - No changes needed (if clean)
   

If a requested focused package does not have a checklist file, create one from checklists/_TEMPLATE.md using the full procedure in CHECKLIST_MAINTENANCE.md § 5.

Scope note: This step validates only the packages explicitly named in the command. Packages that are transitively bumped are identified later in Step 5; their checklists are validated at that point using the same procedure before the API audit in Step 6.

Step 1: Update Pyproject Files

For each requested package, using the Package Impact Matrix:

1. Determine the variant scope (sglang-only, vllm-only, shared, shared-divergent).
2. Edit the version pin in all declaration locations for each affected pyproject file. A single package may appear in multiple locations:
   • [project].dependencies
   • [project.optional-dependencies].<extra>
   • [tool.uv].override-dependencies
3. For upgrade families: if megatron-core is being upgraded, also check whether megatron-bridge needs a corresponding version bump. Warn if it does but was not included in the command.

Step 2: Lock Dependencies (Variant-Aware)

Regenerate lock files for each affected variant. A variant is affected if any of its pyproject file's dependencies were modified. If conflicts arise during locking, do NOT attempt to resolve them in this step — just report them and defer resolution to Step 3.

SGLang variant (if pyproject.toml was modified):

bash scripts/uv_lock.sh

vLLM variant (if pyproject.vllm.toml was modified):

bash scripts/uv_lock.sh

If uv lock fails for either variant:

1. Read the error message carefully.
2. If it's a version conflict, proceed to Step 3 to resolve, then return here to re-lock.
3. Do NOT modify dependencies without user approval to make the lock succeed.

Validation: After locking, verify both lock files exist and are non-empty.

Step 3: Resolve Dependency Conflicts

Resolve any conflicts from Step 2. After all conflicts are resolved, return to Step 2 and re-lock the affected variant(s). Classify each conflict:

Auto-resolvable — only AReaL's pin conflicts with an upstream package, and the upstream's required version is acceptable. Update AReaL's pin automatically.

Needs user input — two upstream packages have mutual conflicts (e.g., sglang requires torch==2.9.1 but vllm requires torch==2.10.0). Summarize and ask the user.

Output format:

Summary

---
Auto-resolved (no action required):
- <name>: <packageA> requires <versionA>, <packageB> requires <versionB>,
  AReaL specified <oldVersion>, updated to <newVersion>
- ...

---
Conflicts (need user resolution):
- <name>: <packageA> requires <versionA>, <packageB> requires <versionB>
- ...

You may use override-dependencies in [tool.uv] to force-pin versions where needed. Remember that sglang and vllm are separate variants maintained in different pyproject files — they are never installed together in the same environment.

Step 4: Update Dockerfile (If Required)

Review the Package Impact Matrix "Docker impact" column. Only proceed with Dockerfile changes if an upgraded package has Docker impact. The most common triggers are:

Base image change (triggered by sglang upgrade):

The Dockerfile base image is lmsysorg/sglang:v{SGLANG_VERSION}-cu129-amd64-runtime. If sglang was upgraded, update line 9 of the Dockerfile:

FROM lmsysorg/sglang:v{NEW_SGLANG_VERSION}-cu129-amd64-runtime

Verify that the new base image tag exists on Docker Hub / GHCR before committing.

Torch version change (triggered by torch upgrade):

The Dockerfile Stage 1 installs torch with variant-specific versions. Update the version mapping in the RUN uv venv command:

&& if [ "$VARIANT" = "vllm" ]; then TORCH_VER="{VLLM_TORCH}"; else TORCH_VER="{SGLANG_TORCH}"; fi \

Also check flash-attn wheel compatibility — both flash-attn-2 and flash-attn-3 installs use a TORCH_TAG that must match the torch major.minor version. Update both occurrences in the Dockerfile:

# flash-attn-2 (first flash-attn RUN block)
&& if [ "$VARIANT" = "vllm" ]; then TORCH_TAG="torch{VLLM_TORCH_MAJOR_MINOR}"; else TORCH_TAG="torch{SGLANG_TORCH_MAJOR_MINOR}"; fi \

# flash-attn-3 (second flash-attn RUN block — same TORCH_TAG pattern)
&& if [ "$VARIANT" = "vllm" ]; then TORCH_TAG="torch{VLLM_TORCH_MAJOR_MINOR}"; else TORCH_TAG="torch{SGLANG_TORCH_MAJOR_MINOR}"; fi \

No Dockerfile changes needed for: megatron-core, megatron-bridge, transformers, peft, vllm, torchao. These are installed via uv pip install -r pyproject.toml in Stage 3, which reads the updated pyproject automatically.

Step 5: Identify Updated Focused Packages

Compare the baseline snapshot (Step 0) against the resolved versions in the lock files (uv.lock and/or uv.vllm.lock) produced by Step 2 (or re-locked after Step 3 conflict resolution). This catches not only explicitly requested upgrades but also transitive version bumps — e.g., upgrading sglang may pull in a newer transformers through dependency resolution.

Build a list of focused packages whose resolved version actually changed. This list determines which API checklists to audit in Step 6.

The focused packages to check are listed in the Focused Packages table (Architecture section):

• megatron-core (imports as megatron.core)
• megatron-bridge (imports as megatron.bridge)
• transformers
• sglang
• vllm
• peft
• torchao

If a package version did NOT change (even if it was in the user's input but resolved to the same version), skip its API audit.

For any newly-identified package whose checklist was NOT already validated in Step 0.5, run the same structural validation procedure (see CHECKLIST_MAINTENANCE.md § 3) on its checklist before proceeding to Step 6.

Step 6: API Compatibility Audit

For each updated focused package that has a checklist file under checklists/:

6a. Clone upstream source

Read the checklist frontmatter to get github and branch_template. Clone or checkout the target version:

REPO_ROOT=$(pwd)
PKG_DIR="${REPO_ROOT}/<package>-src"
VERSION="<target_version>"
# Validate VERSION to prevent command injection
if [[ ! "$VERSION" =~ ^[a-zA-Z0-9._/-]+$ ]]; then
  echo "Error: Invalid version format: $VERSION"; exit 1
fi
BRANCH=$(echo "<branch_template>" | sed "s/\${VERSION}/$VERSION/")
if [ ! -d "$PKG_DIR" ]; then
  git clone --depth 1 --branch "$BRANCH" "https://github.com/<github>.git" "$PKG_DIR"
else
  (cd "$PKG_DIR" && git fetch origin && git checkout "$BRANCH")
fi

If cloning fails (tag doesn't exist, etc.), report to the user immediately.

6b. Audit API signatures

For EACH entry in the checklist's API Usage Catalog:

1. Open the upstream source file at the target version (paths listed in the checklist's upstream_paths frontmatter).
2. Compare the function/class signature against the current AReaL invocation.
3. Flag any of:
   • Removed parameters still passed by AReaL → must remove from call site
   • Renamed parameters → must rename in call site
   • New required parameters (no default) → must add to call site
   • New optional parameters with useful defaults → document but skip
   • Changed return types → must update consumers
   • Removed functions/classes → must find replacement
   • Moved modules → must update import paths
   • Changed method signatures on returned objects → must update call sites
4. Record findings per-file.

6c. Check version-guarded code

If the checklist has a "Version-Guarded Code" section, check whether any guards reference versions at or below the new target. If so, verify the upstream fix is present and note the dead code for cleanup.

6d. Apply code changes (if any)

For each flagged incompatibility:

1. Update the call site in the affected AReaL file.
2. Preserve existing behavior — do NOT refactor beyond what's required.
3. If a function was removed, check the upstream migration guide or changelog.
4. Priority order: engine layer → model layer → infra layer → test files.

If there are unresolvable breaking changes, STOP and ask the user before proceeding.

6e. Update checklist file

Update the checklist file to reflect the post-upgrade state. Follow the Content Update Procedure in CHECKLIST_MAINTENANCE.md § 4:

1. Update API signatures in catalog entries where upstream changed.
2. Update call-site code snippets where Step 6d modified AReaL code.
3. Update version-guarded code entries (remove cleaned-up guards, add new ones).
4. Update frontmatter upstream_paths if source files moved.
5. Update the entry count in the Checklist File Status table (bottom of this file).

This ensures the checklist remains an accurate reference for future upgrades.

6f. Clean up cloned repositories

Remove the cloned upstream source directories to avoid cluttering the workspace:

rm -rf "${REPO_ROOT}/<package>-src"

Step 7: Run Pre-Commit

pre-commit run --all-files

Step 8: Generate Upgrade Summary

Dump a formatted markdown summary to upgrade-summary.md in the repository root (this file is gitignored and ephemeral). The summary MUST include:

## Dependency Upgrade Summary

**Date:** YYYY-MM-DD
**Requested:** <original command>

### Version Changes

| Package | Old Version | New Version | Variant(s) |
| ------- | ----------- | ----------- | ---------- |
| ...     | ...         | ...         | ...        |

### Dependency Resolution

- <auto-resolved change description>
- ...

### Dockerfile Changes

- <change description, or "No changes required">

### API Compatibility Audit

#### <package-name> (old → new)

**Breaking changes found:**
- [file:line] description of change

**Module moves / renames:**
- [old_path] → [new_path]

**Version-guarded code:**
- [file:line] status (still needed / can be removed)

**No breaking changes found** _(if clean)_

#### ...

### Unresolved Issues (if any)

- <description of issue and why it could not be >

If the upgrade failed at any step, the summary should still be generated with the failure reason clearly documented in the "Unresolved Issues" section.

Step 9: Create PR and Trigger CI (Optional)

Ask the user if they want to create a PR.

If the user agrees:

1. Load the create-pr skill to create the PR.
2. Trigger the CI workflow manually via .github/workflows/build-docker-image.yml (only if the Dockerfile was modified or inference backend versions changed).
3. The Docker build CI builds both sglang and vllm images, then automatically triggers testing on each. Debug until the overall workflow succeeds.
4. If you encounter issues that cannot be resolved, ask the user for help.

---

Checklist File Status

Package	Checklist file	Status
megatron-core	checklists/megatron-core.md	✅ 18 API entries (parallel_state, DDP, optimizer, pipeline, checkpointing, transformer config, FP8, GPTModel, tensor_parallel, layer specs, RoPE)
megatron-bridge	checklists/megatron-bridge.md	✅ 7 API entries (AutoBridge, LoRA, save/load HF, monkey-patch guard)
mbridge	checklists/mbridge.md	✅ 14 API entries (AutoBridge, Bridge properties, weight mappings, LLMBridge subclassing, register_model, monkey-patch target)
vllm	checklists/vllm.md	✅ 14 API entries (entrypoints, LoRA manager, worker V0/V1, tool parsers, CLI)
sglang	checklists/sglang.md	✅ 14 API entries (HTTP endpoints, tool/reasoning parsers, CLI flags, version guards)
transformers	checklists/transformers.md	✅ 12 API entries (Auto* classes, tokenizer, flash attention monkey-patches, Qwen VL internals, LR schedulers)
peft	checklists/peft.md	✅ 4 API entries (LoraConfig, TaskType, get_peft_model, weight key format)
torchao	checklists/torchao.md	✅ 5 API entries (fp8_blockwise_mm, enable_fp8_linear/experts, shard validation, Triton kernels)