Add cursor rule to run pre-commit, update devcontainer for recipes to install cursor-agent (#1311)

Signed-off-by: Peter St. John <[email protected]>

Author: pstjohn

.cursorrules

@@ -0,0 +1,40 @@
+# Cursor Rules for BioNeMo Framework
+
+## Pre-commit and Linting
+
+1. **Always run pre-commit hooks after making changes:**
+   - After editing any file, run `pre-commit run --all-files` or `pre-commit run` to check modified files
+   - If pre-commit hooks fail, fix the issues before considering the task complete
+   - Pre-commit hooks include:
+     - Ruff linting and formatting (with auto-fix)
+     - Markdown formatting
+     - License header checks
+     - Trailing whitespace and end-of-file fixes
+     - YAML validation
+     - Secret detection
+
+2. **Fix linter errors immediately:**
+   - When making code changes, check for linter errors using `read_lints` tool
+   - Fix all linter errors before completing the task
+   - The project uses:
+     - Ruff for Python linting and formatting (configured in pyproject.toml)
+     - Pyright for type checking (configured in pyproject.toml)
+   - Ruff will auto-fix many issues, but you should verify all fixes are appropriate
+
+3. **Code quality standards:**
+   - Follow the project's ruff configuration (line-length: 119, specific ignores)
+   - Ensure all Python files follow Google-style docstrings (pydocstyle convention)
+   - Import sorting follows isort configuration (2 lines after imports)
+   - Test files and `__init__.py` files have relaxed linting rules as configured
+
+4. **Workflow:**
+   - Make code changes
+   - Check for linter errors with `read_lints`
+   - Fix any linter errors
+   - Run pre-commit: `pre-commit run --all-files` or `pre-commit run` for changed files
+   - If pre-commit fails, fix the issues and re-run until all checks pass
+   - Only mark a task as complete when all linter errors are resolved and pre-commit passes
+
+5. **Exceptions:**
+   - If a linting rule genuinely conflicts with the required change or is a false positive, document why in comments
+   - Some files may have per-file ignores configured in pyproject.toml - respect those configurations

.devcontainer/recipes/Dockerfile

@@ -4,3 +4,6 @@ RUN --mount=type=cache,target=/root/.cache/pip \
     PIP_CONSTRAINT= pip install -r /workspace/requirements.txt
 
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/
+USER ubuntu
+RUN curl https://cursor.com/install -fsS | bash  # Install cursor-agent CLI tool
+RUN uv tool install pre-commit --with pre-commit-uv --force-reinstall

.devcontainer/recipes/devcontainer.json

@@ -10,7 +10,9 @@
         "source=${localEnv:HOME}/.netrc,target=/home/ubuntu/.netrc,type=bind,consistency=cached",
         "source=${localEnv:HOME}/.bash_history_devcontainer,target=/home/ubuntu/.bash_history,type=bind,consistency=cached",
         "source=${localEnv:HOME}/.ssh,target=/home/ubuntu/.ssh,readonly,type=bind,consistency=cached",
-        "source=${localEnv:HOME}/.gnupg,target=/home/ubuntu/.gnupg,type=bind,consistency=cached"
+        "source=${localEnv:HOME}/.gnupg,target=/home/ubuntu/.gnupg,type=bind,consistency=cached",
+        "source=${localEnv:HOME}/.config,target=/home/ubuntu/.config,type=bind,consistency=cached",
+        "source=${localEnv:HOME}/.cursor,target=/home/ubuntu/.cursor,type=bind,consistency=cached"
     ],
     "postCreateCommand": ".devcontainer/recipes/postCreateCommand.sh",
     "initializeCommand": ".devcontainer/recipes/initializeCommand.sh",
@@ -20,7 +22,7 @@
         "--shm-size=4g"
     ],
     "containerEnv": {
-        "PRE_COMMIT_HOME": "/home/ubuntu/.cache/pre-commit-devcontainer"
+        "PRE_COMMIT_HOME": "/home/ubuntu/.cache/pre-commit-devcontainer",
     },
     "customizations": {
         "vscode": {

.devcontainer/recipes/initializeCommand.sh

@@ -5,6 +5,8 @@ mkdir -p ~/.devcontainer_cache
 mkdir -p ~/.ssh
 mkdir -p ~/.cache/pre-commit-devcontainer
 mkdir -p ~/.gnupg
+mkdir -p ~/.config
+mkdir -p ~/.cursor
 [ ! -f ~/.netrc ] && touch ~/.netrc
 
 # Create the ~/.bash_history_devcontainer file if it doesn't exist

.devcontainer/recipes/postCreateCommand.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 set -euo pipefail
-uv tool install pre-commit --with pre-commit-uv --force-reinstall
 # Run via uv to avoid relying on updated PATH in this shell
 if git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
   uvx pre-commit install