[bug] `moon docker setup` installs only the last dependency's packages in Python/uv workspaces, ignoring the focused project

[lucasmsoares96]

Describe the bug

When using moon docker setup inside a Dockerfile for a Python/uv workspace, the command runs uv venv + uv sync separately for each project in the dependency tree. Each iteration recreates the virtual environment from scratch, so only the last project's dependencies survive in the final .venv. The focused project's own dependencies are never installed.

For example, given a project python_bot that depends on a workspace package chatwoot_api:

# moon.yml (python_bot)
dependsOn:
  - chatwoot_api

The build log from moon docker setup shows:

▮▮▮▮ uv venv .venv --no-managed-python --no-python-downloads --no-progress
Using CPython 3.13.0 interpreter at: /root/.proto/tools/python/3.13.0/bin/python
Creating virtual environment at: .venv
▮▮▮▮ uv venv .venv --no-managed-python --no-python-downloads --no-progress
▮▮▮▮ uv sync --no-managed-python --no-python-downloads --no-progress
Using CPython 3.13.0 interpreter at: /root/.proto/tools/python/3.13.0/bin/python3
Creating virtual environment at: .venv          ← venv recreated, previous state lost
Resolved 220 packages in 1ms
Bytecode compiled 1 file in 318ms
Resolved 220 packages in 1ms
   Building chatwoot-api @ file:///app/backend/packages/chatwoot_api
▮▮▮▮ uv sync --no-managed-python --no-python-downloads --no-progress
Prepared 16 packages in 3.66s
Installed 16 packages in 81ms                   ← only chatwoot_api deps installed

uv sync resolves all 220 packages in the lockfile but only installs 16 — exactly chatwoot_api's dependency tree. The focused project (python_bot) has 25 dependencies (including debugpy, fastapi, uvicorn, etc.) and none of them are installed.

At runtime the container fails immediately:

/app/backend/.venv/bin/python: No module named debugpy

Steps to reproduce

1. Create a uv workspace with a root pyproject.toml:

   [project]
   name = "backend"
   requires-python = ">=3.13"
   
   [tool.uv.workspace]
   members = ["apps/*", "packages/*"]

2. Create an app (apps/my-app) with dependencies:

   [project]
   name = "my-app"
   dependencies = ["debugpy>=1.8.12", "fastapi[standard]>=0.115.5"]

3. Create a workspace package (packages/my-lib) with its own dependencies:

   [project]
   name = "my-lib"
   dependencies = ["httpx>=0.28.1"]

4. Set dependsOn: [my-lib] in apps/my-app/moon.yml.

5. Configure toolchains.yml:

   unstable_python:
     version: 3.13.0
     packageManager: "uv"
   unstable_uv:
     version: "0.9"

6. Build with this Dockerfile:

   FROM node:latest AS base
   WORKDIR /app
   RUN curl -fsSL https://moonrepo.dev/install/moon.sh | bash -s -- 2.0.1
   ENV PATH="/root/.moon/bin:/root/.proto/bin:$PATH"
   
   FROM base AS skeleton
   COPY . .
   RUN moon docker scaffold my-app-backend
   
   FROM base AS build
   COPY --from=skeleton /app/.moon/docker/configs .
   COPY --from=skeleton /app/.moon/docker/sources .
   RUN moon docker setup
   RUN moon docker prune
   
   FROM python:3.13-slim
   COPY --from=build /app /app
   CMD ["python", "-m", "my_app"]

7. Run the image — it fails with No module named ... for any of my-app's dependencies.

Expected behavior

moon docker setup should install all dependencies for the focused project and its workspace dependencies into a single virtual environment. The uv venv command should only be called once, and uv sync should install the complete dependency tree for the focused project.

Ideally the setup step should run something equivalent to:

uv venv .venv --no-managed-python --no-python-downloads
uv sync --package my-app --no-managed-python --no-python-downloads

Environment

➜  python_bot git:(moon) ✗ pnpm dlx envinfo

  System:
    OS: Linux 6.17 Ubuntu 24.04.4 LTS 24.04.4 LTS (Noble Numbat)
    CPU: (8) x64 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
    Memory: 5.91 GB / 15.35 GB
    Container: Yes
    Shell: 5.9 - /usr/bin/zsh
  Binaries:
    Node: 22.22.0 - /home/lucas/.proto/tools/node/22.22.0/bin/node
    npm: 10.9.4 - /home/lucas/.proto/tools/node/22.22.0/bin/npm
    pnpm: 10.28.1 - /home/lucas/.proto/tools/pnpm/10.28.1/shims/pnpm
    Watchman: 20251124.015248.0 - /usr/local/bin/watchman
  Managers:
    Apt: 2.8.3 - /usr/bin/apt
  Utilities:
    Git: 2.43.0 - /usr/bin/git
    FFmpeg: 6.1.1 - /usr/bin/ffmpeg
    Curl: 8.5.0 - /usr/bin/curl
    OpenSSL: 3.0.13 - /usr/bin/openssl
  Virtualization:
    Docker: 29.2.1 - /usr/bin/docker
  IDEs:
    Nano: 7.2 - /usr/bin/nano
    Claude Code: 2.1.39 - /home/lucas/.local/bin/claude
    opencode: 1.1.53 - /home/lucas/.opencode/bin/opencode
    Vim: 0.9.5 - /usr/bin/vim
  Languages:
    Bash: 5.2.21 - /usr/bin/bash
    Java: 21.0.10 - /usr/bin/javac
    Perl: 5.38.2 - /usr/bin/perl
    Python: 3.13.0 - /home/lucas/.proto/shims/python
    Python3: 3.12.3 - /usr/bin/python3
  Databases:
    SQLite: 3.44.4 - /home/lucas/Android/Sdk/platform-tools/sqlite3
  Browsers:
    Chrome: 145.0.7632.75
    Firefox: 147.0.4
    Firefox Developer Edition: 147.0.4

Additional context

• This bug also occurs on moon 1.41.8 (pre-2.0 migration) — it is not a regression from the v2 upgrade.
• The moon docker prune step (which runs in 0.6s and does nothing visible for Python) does not mitigate or worsen the issue. The packages are already missing after moon docker setup.
• The root cause appears to be that moon iterates over each project in the dependency graph and runs uv venv + uv sync independently for each one, with each uv venv call wiping the previous environment.
• Current workaround: add a manual uv sync step in the Dockerfile after moon docker setup:

  RUN moon docker setup
  WORKDIR /app/backend
  RUN /root/.proto/tools/uv/0.9.30/uv sync --package my-app --no-managed-python --no-python-downloads
  WORKDIR /app
  RUN moon docker prune

[milesj]

The fact that multiple venv's are running means the workspace detection is failing. The way it's designed should be 1 venv per uv workspace. https://github.com/moonrepo/plugins/blob/master/toolchains/python/src/tier2.rs#L69

Can you paste the logs? I want to see where locate_dependencies_root is failing.

[lucasmsoares96]

Here are the trace logs from MOON_LOG=trace docker build.

moon-docker-build-logs.txt

[milesj]

Ok yeah, something weird is going on.

For backend/apps/python_bot it returns:

{"members":["apps/*","packages/*"],"root":"/workspace/backend"}

For backend/packages/chatwoot_api it returns:

{"root":"/workspace/backend/packages/chatwoot_api"}

What's in chatwoot_api's pyproject.toml? Is there something in that dir (like a lockfile) that is causing it to act like a root?

[lucasmsoares96]

Below are some information about the chatwoot_api package:

pwd

/home/user/moon/backend/packages/chatwoot_api

tree

.
├── moon.yml
├── pyproject.toml
├── README.md
└── src
    └── chatwoot_api
        ├── __init__.py
        ├── py.typed
        ├── settings.py
        └── sql
            ├── check_tag.sql
            ├── get_campaign_contacts.sql
            ├── get_google_calendar_credentials.sql
            ├── get_user_token.sql
            ├── insert_ai_request_log.sql
            ├── update_attachment_transcription.sql
            └── verify_campaign_tag.sql

4 directories, 13 files

moon.yml

stack: backend
layer: library
language: python

pyproject.toml

[project]
name = "chatwoot-api"
version = "0.0.5"
description = "Chatwoot API"
readme = "README.md"
authors = [{ name = "****", email = "*****" }]
requires-python = ">=3.13"
dependencies = [
    "asyncpg>=0.30.0",
    "httpx>=0.28.1",
    "pydantic>=2.10.6",
    "pydantic-settings>=2.7.1",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatchling.build.targets.wheel]
packages = ["src/chatwoot_api"]

[tool.hatchling.build.targets.wheel.force-include]
"src/chatwoot_api/sql" = "chatwoot_api/sql"

[dependency-groups]
dev = ["ruff>=0.9.4"]

[tool.ruff.lint]
select = ["ALL"]
ignore = ["E501"]

[milesj]

Interesting. It must be hitting this branch: https://github.com/moonrepo/plugins/blob/master/toolchains/python/src/tier2.rs#L118

But why? I'm assuming uv.lock and workspace stuff is in a parent somewhere?

[lucasmsoares96]

git ls-files | tree --fromfile

.
├── backend
│   ├── apps
│   │   ├── python_bot
│   │   │   ├── docker-compose.yml
│   │   │   ├── Dockerfile
│   │   │   ├── moon.yml
│   │   │   ├── pyproject.toml
│   │   │   ├── python_bot
│   │   │   │   ├── main.py
│   │   │   └── sql
│   │   │       └── clean_messages.sql
│   ├── packages
│   │   ├── chatwoot_api
│   │   │   ├── moon.yml
│   │   │   ├── pyproject.toml
│   │   │   └── src
│   │   │       └── chatwoot_api
│   │   │           ├── __init__.py
│   │   │           ├── py.typed
│   │   │           └── sql
│   │   │               └── check_tag.sql
│   ├── pyproject.toml
│   └── uv.lock
├── .moon
│   ├── tasks
│   │   ├── backend-application.yml
│   ├── toolchains.yml
│   └── workspace.yml
└── .prototools

backend/pyproject.toml

[project]
name = "backend"
version = "0.1.0"
description = "Add your description here"
readme = "README.md"
requires-python = ">=3.13"

[tool.uv.workspace]
members = ["apps/*", "packages/*"]

[tool.uv.sources]
chatwoot_api = { workspace = true }

[tool.pyright]
typeCheckingMode = "strict"

Do you want me to create a sample repository for you to clone and try to reproduce the problem more easily?

[milesj]

This is very weird. Is the repo public by chance?

[lucasmsoares96]

You can reproduce this problem on the moon-v2 branch. The main branch was used to report another issue.

https://github.com/lucasmsoares96/moon-bug/tree/moon-v2

[milesj]

This is weird, when I test it locally (not in Docker), it resolves the root correctly:

[DEBUG 11:25:32.744] moon_project_expander::project_expander  Expanding project chatwoot_api  project_id="chatwoot_api"

[TRACE 11:25:32.745] warpgate::plugin  Calling guest function locate_dependencies_root  id="python" plugin="a125a3dd-363b-4583-8351-2b5bed3d526c" input={"context":{"working_dir":{"path":"/workspace/","virtual_prefix":"/workspace","real_prefix":"/Users/miles/Projects/3rd-party/moon-bug-python/.moon/docker/configs"},"workspace_root":{"path":"/workspace/","virtual_prefix":"/workspace","real_prefix":"/Users/miles/Projects/3rd-party/moon-bug-python/.moon/docker/configs"}},"starting_dir":{"path":"/workspace/backend/packages/chatwoot_api","virtual_prefix":"/workspace","real_prefix":"/Users/miles/Projects/3rd-party/moon-bug-python/.moon/docker/configs"},"toolchain_config":{"packageManager":"uv","version":"3.13.0"}}

[TRACE 11:25:32.745] warpgate::plugin  Called guest function locate_dependencies_root  id="python" plugin="a125a3dd-363b-4583-8351-2b5bed3d526c" output={"members":["apps/*","packages/*"],"root":"/workspace/backend"} elapsed=205.25µs

I have a feeling that a file is missing/invalid/etc in Docker. But not entirely sure which.