feat: initial project scaffold

pyproject.toml (Python 3.12, uv), codex/ package (config, db, models),
infra/ (docker-compose + schema), .env.example, .gitignore, README.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

codex/config.py

@@ -0,0 +1,85 @@
+"""Application configuration via environment variables / .env file.
+
+All settings are read from the environment (or a .env file in the project
+root).  Import :func:`get_settings` wherever you need configuration; the
+returned object is cached after the first call.
+"""
+
+from __future__ import annotations
+
+from functools import lru_cache
+
+from pydantic import Field
+from pydantic_settings import BaseSettings, SettingsConfigDict
+
+
+class Settings(BaseSettings):
+    """Centralised, env-driven configuration for the codex application."""
+
+    model_config = SettingsConfigDict(
+        env_file=".env",
+        env_file_encoding="utf-8",
+        case_sensitive=False,
+        extra="ignore",
+    )
+
+    # ------------------------------------------------------------------
+    # Database
+    # ------------------------------------------------------------------
+    database_url: str = Field(
+        default="postgresql://researcher:change_me@localhost:5432/papers",
+        description=(
+            "libpq-compatible connection string consumed by psycopg. "
+            "Example: postgresql://user:pass@host:5432/dbname"
+        ),
+    )
+
+    # ------------------------------------------------------------------
+    # External services
+    # ------------------------------------------------------------------
+    grobid_url: str = Field(
+        default="http://localhost:8070",
+        description="Base URL of the GROBID HTTP API (containerised).",
+    )
+
+    ollama_base_url: str = Field(
+        default="http://localhost:11434",
+        description="Base URL of the local Ollama endpoint (optional Q&A layer).",
+    )
+
+    # ------------------------------------------------------------------
+    # Embeddings
+    # ------------------------------------------------------------------
+    embedding_model: str = Field(
+        default="BAAI/bge-m3",
+        description=(
+            "sentence-transformers model identifier. "
+            "Must match EMBEDDING_DIM. Default: BAAI/bge-m3 (1024 dims)."
+        ),
+    )
+
+    embedding_dim: int = Field(
+        default=1024,
+        gt=0,
+        description=(
+            "Dimension of the dense embedding vectors. "
+            "Must match the output dimension of EMBEDDING_MODEL."
+        ),
+    )
+
+    # ------------------------------------------------------------------
+    # API etiquette
+    # ------------------------------------------------------------------
+    openalex_mailto: str = Field(
+        default="",
+        description=(
+            "E-mail address for the OpenAlex Polite Pool (faster rate limits). "
+            "Required by OpenAlex ToS for automated access."
+        ),
+    )
+
+
+@lru_cache(maxsize=1)
+def get_settings() -> Settings:
+    """Return the cached application settings singleton."""
+    return Settings()