Add integration testing framework with Snakemake dry-run

[Copilot]

Adds integration and unit testing capability. Tests use Snakemake dry-run mode with pre-generated TSV fixtures to validate workflow planning without CFMM server access.

Changes

• Integration tests (workflow/lib/tests/test_integration.py): 8 tests validating all workflow stages (query, filter, download, convert, fix) via dry-run mode
• Test fixtures (workflow/lib/tests/fixtures/): Mock TSV query results and test configuration
• Optional cfmm2tar import (workflow/lib/query_filter.py): Import wrapped in try/except to allow workflow parsing without external dependencies
• CI workflow (.github/workflows/test.yml): Automated testing on push/PR
• Documentation (README.md): Testing section with examples and approach explanation

Testing approach

Tests validate workflow planning correctness using pre-populated query results:

# Test fixture creates query cache to bypass actual querying
query_dir / "studies.tsv"       # Pre-generated TSV data
query_dir / "query_hash.txt"    # Hash matches config to skip re-query

# Snakemake can now parse and plan without cfmm2tar
result = subprocess.run(["snakemake", "--dry-run", "all"], ...)

Test results

• 33 tests passing (8 new integration + 25 existing unit tests)
• 2 pre-existing failures in fix_orientation_quadruped (unrelated)

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:

• pixi.sh
  • Triggering command: /usr/bin/curl curl -fsSL REDACTED (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

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This section details on the original issue you should resolve

<issue_title>No testing</issue_title>
<issue_description>No unit or integration testing in this repo yet.

First step could be dry-run integration testing (with snakemake -np), but using existing tsv query outputs so we dopnt' have to rely on cfmm2tar querying. </issue_description>

<agent_instructions>Create a testing framework </agent_instructions>

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

• Fixes No testing #49

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