fix: evaluator.py contains hard-coded absolute paths, making it non-portable for contributors

[bhavyakeerthi3]

Problem

The src/evaluation/evaluator.py script contains two hard-coded absolute paths specific to the original author's development machine:

• Line 70: Hard-coded path to summations.csv used by the BM25 retriever
• Line 180: Hard-coded path to the Chroma embeddings directory

This causes a FileNotFoundError for every contributor except the original author, making the evaluation pipeline completely broken for community use.

Proposed Fix

Replace hard-coded paths with:

• New CLI args: --embeddings-dir and --summations-csv
• Environment variable fallbacks: REACTOME_EMBEDDINGS_DIR and REACTOME_SUMMATIONS_CSV
• A reusable resolve_path() utility with a clear error message

This makes the evaluator portable across Windows, Linux, and macOS without any code changes.

I am working on a fix and will submit a PR shortly.

[AaryanCode69]

Hi! Thanks for raising this.
A similar issue has already been reported here: #109 .

I’ve also opened a PR addressing it here: #113 .
It might be helpful to continue the discussion there to avoid duplication.

Let me know if you think something different should be handled here.

[bhavyakeerthi3]

Hi @AaryanCode69! You're right, I missed #109 and #113. My PR adds environment variable support and a reusable utility, but I'm happy to close mine to avoid duplication. Let's focus on the core system bugs!