Modernize template: pixi environment + copilot instructions #7
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…d config - Add pixi.toml with GPU-ready single-cell stack (torch, jax, cellrank, scvi-tools) - Add .github/copilot-instructions.md with project context placeholders - Simplify pyproject.toml to metadata + tool configs only (deps in pixi.toml) - Update workflows to use pixi instead of hatch - Rename package: fancypackage -> myanalysis - Update README with comprehensive setup instructions - Add pixi artifacts to .gitignore
…copilot instructions
- Add analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb demonstrating: - Local vs GPU/Euler workflow for scRNA-seq analysis - Using custom plotting functions from local package - Git sync workflow between local and cluster - scVI model training, rapids-singlecell usage - Add src/myanalysis/plotting.py with: - qc_violin(): QC metrics visualization - styled_umap(): Clean UMAP plots with consistent styling - embedding_density(): Cell density visualization - Update __init__.py to export plotting functions - Update pixi.toml: - Add shapely from conda (for spatial dependencies) - Comment out decoupler (optional, pygeos conflict with rapids-singlecell)
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Summary
Modernizes the analysis template to use pixi for environment management and adds GitHub Copilot instructions.
Changes
Testing
pixi install✓ resolves all dependenciespixi run test✓ passesWorkflows will run on this PR to verify CI works.