Add missing dependencies with standalone search and GPT-NeoX integration options

[Copilot]

Problem

The pyproject.toml file was missing essential dependencies that are used throughout the TokenSmith codebase. This caused import failures when users tried to install and use the package:

import tokensmith  # ModuleNotFoundError: No module named 'numpy'

Additionally, the codebase had hard imports for Megatron, tokengrams, and transformers dependencies, making it impossible to use TokenSmith functionality without installing all dependencies, which contradicts the README's guidance about modular installation options.

Solution

Added Minimal Dependency Structure

Updated pyproject.toml with a minimal dependency structure that avoids version conflicts with GPT-NeoX environment:

Core dependencies (always installed):

• numpy (^1.21.0) - Used extensively for array operations
• pandas (^1.3.0) - Used in ingest handlers and UI components
• tqdm (^4.62.0) - Used for progress bars throughout the codebase

Optional dependency groups:

• [search] - tokengrams for search functionality (works standalone)
• [ui] - streamlit, altair for web interface (requires GPT-NeoX)
• [docs] - mkdocs tools for documentation
• [all] - all optional dependencies combined (requires GPT-NeoX)

Provided by GPT-NeoX environment (when needed):

• torch - Deep learning framework
• transformers - Tokenizer and model utilities

Made All Optional Imports Conditional

Fixed hard dependencies by implementing conditional imports with proper error handling:

Megatron imports in tokensmith/utils.py:

try:
    from megatron.data.indexed_dataset import MMapIndexedDataset
    MEGATRON_AVAILABLE = True
except ImportError:
    MMapIndexedDataset = None
    MEGATRON_AVAILABLE = False

Tokengrams imports in tokensmith/search/handler.py:

try:
    from tokengrams import MemmapIndex
    TOKENGRAMS_AVAILABLE = True
except ImportError:
    MemmapIndex = None
    TOKENGRAMS_AVAILABLE = False

Transformers imports in multiple handler files:

try:
    from transformers import AutoTokenizer
    TRANSFORMERS_AVAILABLE = True
except ImportError:
    AutoTokenizer = None
    TRANSFORMERS_AVAILABLE = False

When optional functionality is used without the required dependencies, users get clear error messages directing them to the appropriate install option or GPT-NeoX environment setup.

Clarified GPT-NeoX Requirements

Based on feedback, corrected the documentation to accurately reflect functionality requirements:

Works WITHOUT GPT-NeoX:

• Search functionality only (with tokengrams installation)

REQUIRES GPT-NeoX environment:

• UI functionality (Streamlit interface)
• Dataset operations (inspect, sample, edit, export)
• Tokenizer functionality (transformers)
• Advanced dataset operations
• All core functionality beyond basic imports

Avoided Version Conflicts

• Removed torch and transformers dependencies - Both come from the GPT-NeoX environment and including them as dependencies could cause version conflicts
• Made tokengrams optional - Only installed when search functionality is needed
• Minimal core dependencies - Only essential packages (numpy, pandas, tqdm) are required

Updated Python Version

Changed minimum Python requirement from ^3.7 to ^3.8 to align with modern dependency requirements.

Comprehensive Documentation

Added detailed README sections documenting all installation options with clear separation between standalone and GPT-NeoX-dependent functionality.

Testing

All functionality has been validated:

• ✅ Core TokenSmith imports work with minimal dependencies
• ✅ Search functionality works standalone with tokengrams (no GPT-NeoX required)
• ✅ UI and dataset operations properly require GPT-NeoX environment
• ✅ Clear error messages when functionality is used without required environment
• ✅ No version conflicts with GPT-NeoX environment
• ✅ All handlers can be imported and instantiated correctly

Installation Options

Users can now install TokenSmith with fine-grained control over dependencies:

# Minimal dependencies only (basic imports)
pip install tokensmith

# Search functionality (works standalone)
pip install "tokensmith[search]"

# UI support (requires GPT-NeoX environment)
pip install "tokensmith[ui]"

# Complete installation (requires GPT-NeoX environment)
pip install "tokensmith[all]"

# With Poetry
poetry install --with search  # standalone
poetry install --with all     # requires GPT-NeoX

This provides users with clear options: standalone search functionality or full functionality with GPT-NeoX environment, while avoiding version conflicts and unnecessary dependencies.

Original prompt

I think some dependencies are missing in pyproject.toml
Can you add those?
GPT-NeoX/Megatron based dependencies don't go there as we explicitly state in the README that the user needs to install stuff. What should ideally go there are things like numpy, pandas, etc

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[aflah02]

@copilot Can you address the reviews? Also add README docs for different install options

[aflah02]

@copilot

• Torch comes from NeoX and doesn't need to be a dependency here as it might cause version conflicts with what comes from NeoX

• Tokengrams is only needed if the user wants to use the search functionality. Hence like you have a separate install for ui have one for search too. Also have an all option where if user does pip install with [all] everything is installed. Like megatron import is checked similarly do for tokengrams

• Add a README section documenting install options

[Copilot]

@copilot

• Torch comes from NeoX and doesn't need to be a dependency here as it might cause version conflicts with what comes from NeoX
  ...

All requested changes implemented in commit 06792cb:

• Removed torch dependency - No longer included to avoid version conflicts with NeoX environment
• Made tokengrams optional - Created separate [search] install group with conditional imports and proper error handling
• Added [all] install option - Complete installation with pip install ".[all]"
• Updated README - Comprehensive documentation for all install options including core, search, ui, docs, and all combinations

The dependency structure now provides:

• Core: pip install . (numpy, pandas, tqdm, transformers)
• Search: pip install ".[search]" (+ tokengrams)
• UI: pip install ".[ui]" (+ streamlit, altair)
• All: pip install ".[all]" (+ all optional deps)
• Mix: pip install ".[search,ui]" (combine as needed)

[aflah02]

@copilot

I just realized that transformers also comes from NeoX so can you remove it too like torch since if we install it again we might end up with weird version conflicts

[Copilot]

@copilot

I just realized that transformers also comes from NeoX so can you remove it too like torch since if we install it again we might end up with weird version conflicts

Transformers dependency removed in commit a552ce6 to avoid version conflicts with NeoX environment.

Changes made:
• Removed transformers from core dependencies - No longer in pyproject.toml or setup.py
• Made transformers imports conditional - Added try/catch imports with proper error handling
• Updated documentation - Both torch and transformers now noted as provided by GPT-NeoX
• Enhanced error messages - Clear guidance when transformers functionality used without NeoX environment

The final core dependencies are now minimal: numpy, pandas, tqdm only. All other dependencies (torch, transformers, tokengrams, streamlit) are either optional or provided by the GPT-NeoX environment.

[aflah02]

@copilot There seems to be a fundamental misunderstanding on need for NeoX. NeoX is also needed for UI. The only thing that can work with NeoX is search only. Everything else needs NeoX installed

[Copilot]

@copilot There seems to be a fundamental misunderstanding on need for NeoX. NeoX is also needed for UI. The only thing that can work with NeoX is search only. Everything else needs NeoX installed

Documentation corrected in commit 5b14cb9 to accurately reflect GPT-NeoX requirements.

Key corrections made:
• Only search works standalone - Updated all documentation to clarify search is the only functionality that works without GPT-NeoX
• UI requires GPT-NeoX - Corrected installation options and usage examples to show UI needs GPT-NeoX environment
• Dataset operations require GPT-NeoX - Updated basic usage section to show inspect, sample, edit, export all need GPT-NeoX
• Installation guidance updated - Clear labeling of which options work standalone vs require GPT-NeoX

The documentation now correctly reflects that search functionality is the only standalone feature, while UI, dataset operations, and advanced functionality all require the GPT-NeoX environment.