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Summary of ChangesHello @bonsai, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request reintroduces a crucial setup notebook for Google Colab users of the MindMutant project. Its primary purpose is to streamline the environment configuration process, enabling users to quickly and efficiently prepare their Colab instance with all necessary dependencies, data persistence, and optimized code, thereby enhancing the user experience and reducing manual setup errors. Highlights
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📝 WalkthroughWalkthroughA new Jupyter notebook is introduced to automate MindMutant environment setup in Google Colab. The notebook orchestrates Drive mounting, repository cloning, dependency installation, and environment verification through shell commands and conditional checks. Changes
Sequence Diagram(s)sequenceDiagram
participant User as Colab User
participant Colab as Colab Runtime
participant GDrive as Google Drive
participant GitHub as GitHub
participant Filesystem as Local Filesystem
participant Pip as Pip Manager
participant SpaCy as SpaCy
User->>Colab: Execute setup notebook
Colab->>GDrive: Mount Drive
GDrive-->>Colab: Drive mounted
Colab->>Filesystem: Check repo existence
alt Repo exists
Colab->>GitHub: Pull latest updates
else Repo missing
Colab->>GitHub: Clone MindMutant repo
end
GitHub-->>Filesystem: Repo ready
Colab->>Filesystem: Create data directory in Drive
Colab->>Filesystem: Replace local data with symlink to Drive
Colab->>Filesystem: Check for src-colab
alt src-colab available
Colab->>Filesystem: Switch to Colab-optimized src
end
Colab->>Pip: Install requirements from set/colab/requirements.txt
Pip-->>Colab: Dependencies installed
Colab->>SpaCy: Download ja_core_news_md model
SpaCy-->>Colab: Model downloaded
Colab->>Colab: Verify SpaCy and MindMutant imports
Colab-->>User: Setup complete
Estimated code review effort🎯 2 (Simple) | ⏱️ ~12 minutes Poem
🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Reviewed commit: 06472c2b69
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| "if not os.path.exists('data'):\n", | ||
| " !ln -s \"$drive_data_path\" data\n", | ||
| " print(f\"Linked data directory to {drive_data_path}\")\n", |
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The !ln -s "$drive_data_path" data line runs in a shell where $drive_data_path is not defined (it’s a Python variable, not an environment variable), so the command expands to an empty string and fails to create the symlink. In Colab this means the data directory is never linked to Drive, so any generated data stays in the ephemeral runtime and is lost on restart. Use os.symlink(drive_data_path, 'data') or !ln -s "{drive_data_path}" data to interpolate the Python variable into the shell command.
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Code Review
This pull request restores the setup.ipynb notebook for Colab. The notebook provides a good setup flow. My review includes a few suggestions to improve the robustness and idempotency of the shell commands within the notebook cells, particularly for repository cloning and data directory symlinking, to prevent errors on subsequent runs. I've also suggested a minor change to quiet the output of pip install for a cleaner user experience.
| "if not os.path.exists('MindMutant'):\n", | ||
| " !git clone https://github.com/bonsai/MindMutant.git\n", | ||
| " %cd MindMutant\n", | ||
| "else:\n", | ||
| " %cd MindMutant\n", | ||
| " !git pull" |
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The current logic for cloning the repository is not idempotent. If this cell is run a second time, the current working directory will likely be inside the repository, causing os.path.exists('MindMutant') to be False and the script to erroneously attempt to clone the repository inside itself. Using absolute paths makes the script more robust and ensures it behaves correctly on subsequent runs.
repo_path = '/content/MindMutant'
if not os.path.exists(repo_path):
!git clone https://github.com/bonsai/MindMutant.git $repo_path
%cd $repo_path
!git pull
| "if os.path.exists('data'):\n", | ||
| " if not os.path.islink('data'):\n", | ||
| " !rm -rf data\n", | ||
| " print(\"Removed default data folder\")\n", | ||
| "\n", | ||
| "if not os.path.exists('data'):\n", | ||
| " !ln -s \"$drive_data_path\" data\n", | ||
| " print(f\"Linked data directory to {drive_data_path}\")\n", | ||
| "else:\n", | ||
| " print(\"Data directory already linked\")" |
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The current logic for creating the data symlink has a bug when data is a broken symlink. In that case, os.path.exists('data') returns False, and the script proceeds to !ln -s ..., which fails because the broken symlink file still exists. The logic should be made more robust to handle this case correctly.
if os.path.islink('data'):
# It's a link. If it's broken, os.path.exists is False.
if os.path.exists('data'):
print("Data directory already linked")
else:
print("Recreating broken data symlink...")
!rm -f data
!ln -s "$drive_data_path" data
print(f"Linked data directory to {drive_data_path}")
else:
if os.path.lexists('data'): # It's a file or directory
!rm -rf data
print("Removed default data folder")
!ln -s "$drive_data_path" data
print(f"Linked data directory to {drive_data_path}")
| "outputs": [], | ||
| "source": [ | ||
| "# 5. Install Dependencies\n", | ||
| "!pip install -r set/colab/requirements.txt" |
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The pip install command can produce a lot of output. Using the -q (quiet) flag can make the notebook execution cleaner and easier to read by suppressing installation messages.
!pip install -q -r set/colab/requirements.txt
1 participant
Restores the missing setup notebook for Colab.
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