upgrade-packages

name	upgrade-packages
description	Upgrade all dependencies/packages to their latest versions for C#/.NET and Python. Use when the user says "upgrade packages", "update dependencies", "bump versions", "update packages", or "upgrade deps".
argument-hint	[--check-only] [--major] [package-name]

Upgrade Packages

Upgrade all project dependencies to their latest compatible (or latest major, if --major) versions for HealthcareSamples (C#/.NET primary, Python embedding service + scripts).

Arguments

• --check-only — List outdated packages without upgrading. Stop after Step 2.
• --major — Include major version bumps (breaking changes). Without this flag, stay within semver-compatible ranges.
• Any other argument is treated as a specific package name to upgrade (instead of all packages).

Step 1 — Detect language and package manager

Inspect the repo for these manifest files:

Manifest file	Language	Package manager
*.csproj / *.sln	C# / .NET	NuGet (dotnet)
Directory.Build.props	C# / .NET	NuGet (dotnet) — central version pinning
requirements.txt	Python (ICD10/embedding-service, ICD10/scripts/CreateDb)	pip
package.json	TypeScript (Dashboard/dashboard-ts)	pnpm (check lockfile)

This repo uses all three. Process .NET first, then Python, then TypeScript.

If you cannot detect any manifest file, stop and tell the user.

Step 2 — List outdated packages

Run the appropriate command to list what's outdated BEFORE upgrading anything. Show the user what will change.

C# / .NET (NuGet)

dotnet list HealthcareSamples.sln package --outdated

For transitive dependencies too: dotnet list HealthcareSamples.sln package --outdated --include-transitive

Read the docs: https://learn.microsoft.com/en-us/dotnet/core/tools/dotnet-list-package

Python (pip)

The Python pieces use plain requirements.txt files. Install each in a venv and run pip list --outdated:

# embedding service
python -m venv /tmp/embedding-venv
/tmp/embedding-venv/bin/pip install -r ICD10/embedding-service/requirements.txt
/tmp/embedding-venv/bin/pip list --outdated

# DB scripts
python -m venv /tmp/scripts-venv
/tmp/scripts-venv/bin/pip install -r ICD10/scripts/CreateDb/requirements.txt
/tmp/scripts-venv/bin/pip list --outdated

Read the docs: https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-U

TypeScript (pnpm)

cd Dashboard/dashboard-ts && pnpm outdated

Read the docs: https://pnpm.io/cli/update

If --check-only was passed, stop here and report the outdated list.

Step 3 — Read the official upgrade docs

Before running any upgrade command, you MUST fetch and read the official documentation URL listed above for the detected package manager. Use WebFetch to retrieve the page. This ensures you use the correct flags and understand the behavior. Do not guess at flags or options from memory.

Step 4 — Upgrade packages

Run the upgrade. If a specific package name was given as an argument, upgrade only that package.

C# / .NET (NuGet)

There is NO single dotnet upgrade-all command. You must upgrade each package individually:

# For each outdated package from Step 2:
dotnet add <project.csproj> package <PackageName>    # upgrades to latest
# Or with specific version:
dotnet add <project.csproj> package <PackageName> --version <version>

For Directory.Build.props, edit the version numbers directly in the XML.

Read the docs: https://learn.microsoft.com/en-us/dotnet/core/tools/dotnet-add-package

Alternatively, use the dotnet-outdated global tool:

dotnet tool install --global dotnet-outdated-tool
dotnet outdated --upgrade

Read the docs: https://github.com/dotnet-outdated/dotnet-outdated

Python (pip)

For requirements.txt:

/tmp/embedding-venv/bin/pip install --upgrade -r ICD10/embedding-service/requirements.txt
/tmp/embedding-venv/bin/pip freeze > ICD10/embedding-service/requirements.txt

/tmp/scripts-venv/bin/pip install --upgrade -r ICD10/scripts/CreateDb/requirements.txt
/tmp/scripts-venv/bin/pip freeze > ICD10/scripts/CreateDb/requirements.txt

TypeScript (pnpm)

cd Dashboard/dashboard-ts && pnpm update
# --major flag:
cd Dashboard/dashboard-ts && pnpm update --latest

Step 5 — Verify the upgrade

After upgrading, run the project's build and test suite to confirm nothing broke:

make ci

If tests fail:

1. Read the failure output carefully
2. Check the changelog / migration guide for the upgraded packages (fetch the release notes URL if available)
3. Fix breaking changes in the code
4. Re-run tests
5. If stuck after 3 attempts on the same failure, report it to the user with the error details and the package that caused it

Step 6 — Report

Provide a summary:

• Packages upgraded (old version -> new version)
• Packages skipped (and why, e.g., major version bump without --major flag)
• Build/test result after upgrade
• Any breaking changes that were fixed
• Any packages that could not be upgraded (with error details)

Rules

• Always list outdated packages first before upgrading anything
• Always read the official docs for the package manager before running upgrade commands
• Always run tests after upgrading to catch breakage immediately
• Never remove packages unless they were explicitly deprecated and replaced
• Never downgrade packages unless rolling back a broken upgrade
• Never modify lockfiles manually (pnpm-lock.yaml, etc.) — let the package manager regenerate them
• Commit nothing — leave changes in the working tree for the user to review

Success criteria

• All outdated packages upgraded to latest compatible (or latest major if --major)
• Build passes
• Tests pass
• User has a clear summary of what changed