pytdc

PyTDC (Therapeutics Data Commons)

Use the official PyTDC distribution (import tdc) to discover therapeutic ML tasks, load approved datasets, apply task-appropriate splits, evaluate predictions, and work with curated benchmark groups. Prefer package metadata over copied dataset lists, and plan network/storage effects before constructing any loader.

Verified snapshot

• Research date: 2026-07-23
• PyPI stable: PyTDC 1.1.15, released 2025-03-31
• Package/source repository: mims-harvard/TDC
• Code license: MIT
• PyPI supplies only a source distribution and declares no Requires-Python
• The dependency graph makes CPython 3.11 the reproducible target used here: cellxgene-census==1.15.0 excludes Python 3.12, and PyTDC's constrained RDKit release has no CPython 3.13 wheel
• PyTDC imports deprecated pkg_resources at runtime. Setuptools 82 removed that module; pin the verified compatibility release setuptools 80.9.0.
• tdc.readthedocs.io still identifies itself as TDC 0.4.1; use it as API cross-reference, not as release-version evidence
• Upstream publishes no GitHub tags/releases or maintained changelog. Treat undocumented migration claims as uncertainty and verify against the installed 1.1.15 source/metadata.

See references/sources.md for dated evidence and known documentation conflicts.

Installation

Use an isolated CPython 3.11 environment and pin the reviewed snapshot:

uv venv --python 3.11 .venv-pytdc
uv pip install --dry-run --python .venv-pytdc/bin/python \
  "setuptools==80.9.0" "PyTDC==1.1.15"
uv pip install --python .venv-pytdc/bin/python \
  "setuptools==80.9.0" "PyTDC==1.1.15"

The tested macOS ARM64 resolution installed 123 packages, including large scientific/ML dependencies, so the environment itself can transfer and occupy hundreds of megabytes before any dataset is downloaded. Review the dry run and available disk first. The direct pins identify the reviewed API snapshot; generate a platform-specific uv.lock in the user's project when every transitive version must also be frozen.