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@vsaravind01 vsaravind01 commented Jul 10, 2025

Description

Key Changes

New Python Client Library [pyds]

  • Added pyds package as a Python SDK for DeepChem server API interactions
  • Implemented client classes for data operations, primitives (featurization, training, inference), and settings management
  • Added comprehensive test suite with code coverage report
  • Currently the code coverage for pyds is 92% with 100% coverage for the main modules such as data.py and primitives.py
  • Included proper packaging configuration with pyproject.toml and setup files

Code Quality Improvements

  • Added linting script (lint.sh) with yapf, isort, flake8, and mypy for consistent code formatting
  • Updated mypy configuration to check type hints in the pyds package
  • Improved import organization and code formatting across all modules
  • Enhanced error handling and logging throughout the codebase

Infrastructure Updates

  • Updated GitHub workflows to test the pyds library on live server
  • Modified Dockerfile to use Python 3.10 instead of slim variant
  • Added coverage configuration and CI/CD improvements

Documentation

  • Updated README files to reflect the new client library structure
  • Added packaging guide and development setup instructions

Core Module Refactoring

  • Refactored core modules (address, cards, compute, config, datastore, evaluator, feat, inference) for better maintainability
  • Improved function signatures and type hints
  • Enhanced error messages and logging
  • Updated model configurations and mappings

Type of change

Please check the option that is related to your PR.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
    • In this case, we recommend to discuss your modification on GitHub issues before creating the PR
  • Documentations (modification for documents)

Checklist

  • Run yapf -i <modified file> and check no errors
  • Run flake8 <modified file> --count and check no errors
  • Run mypy -p deepchem_server and check no errors
  • Run mypy -p py-ds and check no errors
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New unit tests pass locally with my changes
  • I have checked my code and corrected any misspellings

…e; modify Dockerfile to use full Python image
…ding version upgrades and enhanced installation verification
…tion files for cleaner repository management
…est command in CI workflow for improved clarity
…th for pyds library and enhance installation verification steps
…ettings files; update lint script to integrate isort for improved import management
… breaks for improved readability across multiple files
…breaks for enhanced readability in data, primitives, settings, and client files
…mport management, enhance formatting options, and improve documentation clarity
@vsaravind01 vsaravind01 marked this pull request as ready for review August 12, 2025 03:48
@vsaravind01 vsaravind01 changed the title Draft: Add py-ds package Feat: Add py-ds package Aug 12, 2025
@vsaravind01 vsaravind01 changed the title Feat: Add py-ds package Feat: Add pyds package Aug 12, 2025
@vsaravind01 vsaravind01 changed the title Feat: Add pyds package Feat: Add python client library [pyds] Aug 12, 2025
@vsaravind01 vsaravind01 marked this pull request as draft September 3, 2025 16:59
@vsaravind01 vsaravind01 changed the title Feat: Add python client library [pyds] Draft: Add python client library [pyds] Sep 3, 2025
@rbharath
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rbharath commented Oct 9, 2025

@vsaravind01 If this PR is obsolete, can you please close?

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3 participants