v0.1.2 — Development Goals & Task Tracker 🚀

[xfchen0912]

Description of feature

This issue collects and tracks development goals, planned features, compatibility updates, and known issues for scMagnify v0.1.2. The primary compatibility targets for this release are:

• Example datasets download from figshare
• Support anndata >= 0.11
• Support scanpy >= 1.11
• TF Binding Network Construction from multiple sources

📝Release metadata

• Release version: v0.1.2
• Target release date: (fill date)
• Release notes summary: (to be filled before publishing)

✅Acceptance criteria

• CI matrix includes anndata >= 0.11 and scanpy >= 1.11 and passes.
• README / examples run successfully with anndata 0.11+.
• New and updated unit/integration tests pass.
• Packaging and installation succeed in a clean environment.
• Dependency constraints updated in pyproject.toml / setup.cfg / requirements files.

✨Planned Features

• Compatibility: Ensure full compatibility with anndata >= 0.11 and scanpy >= 1.11.

  • Implementation: update calls that interact with AnnData/scanpy, run full test matrix.
  • Tests: integration example that executes common workflows under new versions.

• Feature: Support Prior Networks from database

  • Purpose: Allow users to load and use prior regulatory networks from external databases (e.g., ENCODE, JASPAR, STRING) for GRN inference.
  • Implementation notes:
    • Add an adapter/loader module that supports common formats (GMT, JSON, edge lists) and database API endpoints where feasible.
    • Add a lightweight caching layer and clear error messages for missing mappings.
  • Tests:
    • Unit tests for each format loader with mock data.
    • Integration test demonstrating using a loaded prior network in a downstream scMagnify pipeline.
  • Docs:
    • Example notebook showing how to load a prior network, perform ID mapping, and pass it to analysis functions.

• Feature: Support bulk ATAC preprocessing

  • Purpose: Ingest and preprocess bulk ATAC-seq inputs so scMagnify can operate on aggregated chromatin accessibility profiles.
  • Implementation notes:
    • Create a preprocessing pipeline to accept common bulk ATAC input formats (BED, narrowPeak, bigWig-derived counts, or matrix-like count tables).
    • Provide functions to convert bulk ATAC outputs into a form compatible with AnnData (e.g., peak x sample matrix).
    • Motif Scan.
  • Tests:
    • Unit tests for format parsing and conversion to AnnData.
    • Integration test using a synthetic bulk ATAC count matrix.
  • Docs:
    • Notebook demonstrating loading bulk ATAC data, motif scan with scMagnify.

• Feature: Support unpaired single-cell ATAC (unpaired scATAC) preprocessing

  • Purpose: Allow users to preprocess unpaired scATAC inputs (scATAC without matched scRNA) and integrate/access them in scMagnify workflows.
  • Implementation notes:
    • Add label transfer func (k-NN based) between scRNA and scATAC
  • Tests:
    • Unit tests for fragment/peak parsing and AnnData creation.
  • Docs:
    • Notebook demonstrating an end-to-end unpaired scATAC preprocessing example.

🔧Bugs to Fix

• Bug: Runtime error when interacting with anndata 0.11 objects.
  • Reproduction steps:
  • Expected behavior:
  • Notes / suspected cause:
• Bug: API return type changes in scanpy 1.11 breaking downstream code.
• Bug: CI failures/timeouts after dependency upgrades.

🧪Testing & CI

• Add CI matrix entries for:
  • Python versions supported by the project (e.g., 3.8, 3.9, 3.10)
  • anndata 0.11.x and latest
  • scanpy 1.11.x and latest
• Add unit tests and at least one small integration test using a sample AnnData object.
• Add tests and lightweight fixtures for Prior Network loaders, bulk ATAC parsing, and scATAC preprocessing modules.
• Consider using nbval or GitHub Actions to validate example notebooks.

📚Documentation & Examples

• Update README to state explicit dependency requirements (anndata >= 0.11, scanpy >= 1.11) and new feature support (prior networks, bulk ATAC, unpaired scATAC).
• Add example notebooks for:
  • Loading prior networks from database/files and using them.
  • Bulk ATAC preprocessing and conversion to AnnData.
  • Unpaired scATAC preprocessing pipeline.
• Update CHANGELOG with compatibility notes and migration guidance.