wire docs/scripts/export_library.py, update all docstring examples refs #1

- export_library.py: BIB_DB → conf.path("db.bib")
- Update ~20 docstring usage examples across src/ to show
  config-based defaults (Store(), DuckDBContext(database=path("db.aco")))
  instead of hardcoded paths, so copy-paste stays correct

docs/scripts/export_library.py

@@ -15,7 +15,9 @@ import json
 import sys
 from pathlib import Path
 
-BIB_DB = Path("data/bib.sqlite")
+from conf import path as _conf_path
+
+BIB_DB = _conf_path("db.bib")
 OUT_PATH = Path("docs/static/library.json")
 
 

src/aco/lake/__init__.py

@@ -13,7 +13,7 @@ Four contexts, one interface::
     from aco.lake import DuckDBContext, IcebergContext
 
     # Local dev — embedded DuckDB, no Iceberg
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
 
     # Iceberg on Nessie — versioned catalog, S3 storage
     ctx = IcebergContext(

src/aco/lake/context.py

@@ -31,7 +31,7 @@ Usage::
     from aco.lake import DuckDBContext, IcebergContext
 
     # Local dev — same as today
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
     cache = readmissions.pipeline.run(ctx.load)
 
     # Iceberg on Nessie (versioned, S3-backed)
@@ -151,7 +151,7 @@ class DuckDBContext(Context):
 
         from aco.lake import DuckDBContext
 
-        ctx = DuckDBContext(database="notebooks/aco.duckdb")
+        ctx = DuckDBContext(database=path("db.aco"))  # path from conf
 
         # Load a table
         encounters = ctx.load("core.encounter")

src/aco/lake/engine.py

@@ -46,7 +46,7 @@ Usage::
     from aco.pipe import readmissions
 
     # Local dev — direct execution
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
     results = execute(readmissions.pipeline, ctx)
 
     # Iceberg on Nessie — direct execution via PyIceberg
@@ -118,7 +118,7 @@ def execute(
         from aco.lake.engine import execute
         from aco.pipe import readmissions
 
-        ctx = DuckDBContext(database="notebooks/aco.duckdb")
+        ctx = DuckDBContext(database=path("db.aco"))  # path from conf
         results = execute(readmissions.pipeline, ctx)
 
         # Access specific result

src/aco/lake/sync.py

@@ -7,7 +7,7 @@ Usage::
 
     from aco.lake import DuckDBContext, sync
 
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
 
     # Sync to Databricks (parquet + COPY INTO)
     report = sync(

src/aco/lake/transpile.py

@@ -23,7 +23,7 @@ Usage::
 
     # Or with an explicit DuckDB connection (for fidelity with real data)
     import duckdb
-    con = duckdb.connect("notebooks/aco.duckdb", read_only=True)
+    con = duckdb.connect(path("db.aco"), read_only=True)  # path from conf
     sql_map = transpile(
         readmissions.pipeline,
         con,

src/bcda/store.py

@@ -22,7 +22,7 @@ Usage::
     from bcda.client import Client
     from bcda.store import Store
 
-    store = Store("data/bcda")
+    store = Store()
 
     with Client(client_id="...", client_secret="...") as c:
         key = store.export(c, types=["Patient", "Coverage"])

src/bib/__init__.py

@@ -41,7 +41,7 @@ Usage
 
     from bib import connect, COLLECTIONS, Tag, Rule
 
-    store = connect()  # default: data/bib.sqlite
+    store = connect()  # default from stack.toml
     store.ensure_collections(COLLECTIONS)
 
     # Upsert a citation

src/bib/ingest.py

@@ -10,7 +10,7 @@ Usage::
     from bib.store import Store
     from bib import translate
 
-    store = Store("data/bib.sqlite")
+    store = Store()
     page = translate.cms_website(
         "https://www.cms.gov/.../rvu26a",
         module="pfs",

src/bib/meta.py

@@ -22,7 +22,7 @@ Usage::
     # [Tag(meta, cclf-ip-s3.1), Tag(meta, cclf-ip-s5.1.1)]
 
     # Tag all Zotero items referenced by a pipeline
-    store = Store("data/bib.sqlite")
+    store = Store()
     report = tag_items_from_pipeline(pipeline, store)
 
     # Generate a reference block for a docstring

src/bib/spider.py

@@ -15,7 +15,7 @@ Usage::
     from bib.store import Store
     from bib.spider import crawl, crawl_all
 
-    s = Store("data/bib.sqlite")
+    s = Store()
     found = crawl(s, "ABCD1234")
     # → ['KEY1', 'KEY2', ...]
 

src/bib/store.py

@@ -9,7 +9,7 @@ Usage::
     from bib.store import Store
     from bib.item import Rule
 
-    s = Store("data/bib.sqlite")
+    s = Store()
     key = s.create(Rule(title="CY 2026 PFS Final Rule", fr_volume="90"))
     item = s.get(key)
     print(s.format_citation(key))

src/bib/sync.py

@@ -10,9 +10,9 @@ Usage::
     from bib.store import Store
     from bib.sync import push_to_zotero
 
-    s = Store("data/bib.sqlite")
+    s = Store()
     items = s.list_items(tag="source:spider")
-    stats = push_to_zotero(items, zotero_db="zotero/data/zotero.sqlite")
+    stats = push_to_zotero(items)
     print(stats)
     # {'created': 5908, 'skipped': 12, 'tags': 23456, 'collections': 2}
 """

src/bib/ui/browser.py

@@ -5,7 +5,7 @@ Usage in a marimo cell::
     from bib.store import Store
     from bib.ui import library_browser
 
-    store = Store("data/bib.sqlite")
+    store = Store()
     library_browser(store)
 """
 

src/bib/ui/cite.py

@@ -5,7 +5,7 @@ Usage in a marimo cell::
     from bib.store import Store
     from bib.ui import cite, bibliography
 
-    store = Store("data/bib.sqlite")
+    store = Store()
 
     # Inline citation
     cite(store, "ABC12345")

src/pfs/pipe.py

@@ -18,9 +18,8 @@ Usage::
     from pfs.pipe import load_all
     import duckdb
 
-    con = duckdb.connect("notebooks/aco.duckdb")
+    con = duckdb.connect(path("db.aco"))  # path from conf
-    stats = load_all(con, zotero_db="zotero/data/zotero.sqlite",
+    stats = load_all(con)
-                     zotero_storage="zotero/data/storage")
     for table, info in stats.items():
         print(f"{table}: {info['rows']} rows from {info['files']} files")
 """

src/rex/__init__.py

@@ -29,7 +29,7 @@ Quick start::
 
     # Batch ingest to a lake context
     from aco.lake import DuckDBContext
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
     rex.ingest(["jan.txt", "feb.txt"], format="cms_mmr", context=ctx)
 """
 

src/rex/pipe.py

@@ -24,7 +24,7 @@ Usage::
 
     # Multiple files → lake context
     from aco.lake import DuckDBContext
-    ctx = DuckDBContext(database="notebooks/aco.duckdb")
+    ctx = DuckDBContext(database=path("db.aco"))  # path from conf
     rex.ingest(
         paths=["jan_claims.txt", "feb_claims.txt"],
         format="cms_mmr",

src/rex/store.py

@@ -26,7 +26,7 @@ Usage::
 
     from rex.store import Store
 
-    store = Store("data/rex")
+    store = Store()
 
     # Extract with state tracking
     key = store.extract_batch(