Add Copilot instructions for repository

[Copilot]

Configures GitHub Copilot coding agent instructions as per best practices documentation.

Changes

• Created .github/copilot-instructions.md with:
  • Tech stack: Python 3.12, Conda + pip dual management, pinned dependencies (numpy 1.26.4, hnswlib 0.7.0)
  • Build flow: conda env setup → C++ kmer_searcher submodule build → pip install
  • Code conventions: type hints (typing + numpy.typing), custom logger over print, @njit for hot paths, sparse matrix patterns
  • Architecture: feature extraction → dimensionality reduction → approximate kNN pipeline
  • Constraints: memory efficiency for large-scale sequencing data, thread-safe parallelization, seed-based reproducibility

Enables Copilot to generate context-aware suggestions aligned with bioinformatics pipeline patterns and project conventions.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• gh.io
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>✨ Set up Copilot instructions</issue_title>
<issue_description>Configure instructions for this repository as documented in Best practices for Copilot coding agent in your repository.

</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes ✨ Set up Copilot instructions #7

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.