src/core/paths.py

"""
Writable directory resolution for the agent.

These are shared infrastructure constants — an env-resolved input/output/cache
location — needed by both the ``tools`` layer (which writes analysis artifacts)
and the ``workflows`` layer (which writes combined datasets). They live in
``core`` so both layers can import them downward without violating the layering
contract (``tools`` and ``workflows`` both build on ``core``).
"""

from __future__ import annotations

import os
from pathlib import Path

# core/paths.py lives at <root>/src/core/, so two levels up is <root>/src —
# the same base directory the tool package historically resolved against.
PROJECT_ROOT = Path(__file__).parent.parent.resolve()
_DEFAULT_INPUT = PROJECT_ROOT / "tmp" / "inputs"
_DEFAULT_OUTPUT = PROJECT_ROOT / "tmp" / "outputs"
_DEFAULT_GEO_CACHE = PROJECT_ROOT / "tmp" / "geo_cache"


def _resolve_dir(env_var: str, project_default: Path, hf_fallback: Path) -> Path:
    """Return a writable directory: env var > project default > /tmp fallback."""
    env_val = os.environ.get(env_var)
    if env_val:
        p = Path(env_val)
        p.mkdir(parents=True, exist_ok=True)
        return p
    try:
        project_default.mkdir(parents=True, exist_ok=True)
        return project_default
    except PermissionError:
        hf_fallback.mkdir(parents=True, exist_ok=True)
        return hf_fallback


INPUT_DIR = _resolve_dir("RNA_INPUT_DIR", _DEFAULT_INPUT, Path("/tmp/decoupleRpy/inputs"))
OUTPUT_DIR = _resolve_dir("RNA_OUTPUT_DIR", _DEFAULT_OUTPUT, Path("/tmp/decoupleRpy/outputs"))
GEO_CACHE_DIR = _resolve_dir(
    "RNA_GEO_CACHE_DIR", _DEFAULT_GEO_CACHE, Path("/tmp/decoupleRpy/geo_cache")
)