wire remaining hardcoded paths, fix truncated quality measure docs refs #1

- bcda/client.py: output_dir default → conf.path("storage.bcda")
- bcda/express/flatten.py: store_path default → conf.path("storage.bcda")
- notebooks: eliminate all /home/kert/ absolute paths from
  bib_explorer.py and zotero_tutorial.py
- generate_quality_measure_docs.py: complete truncated f-string at
  line 561 (file was committed incomplete), add return statement
- test_client.py: update default assertion to match conf-resolved path

dev/scripts/generate_quality_measure_docs.py

@@ -560,4 +560,18 @@ def build_uamcc_passages(
     # ── Person time ───────────────────────────────────────────────────
     passages["uamcc_int_person_time"] = (
         f"Calculate at-risk person-time for each UAMCC-eligible beneficiary.\n\n"
-        f
+        f"Source: {_cite(pdf_name, '§3.11', denom_d_page)}\n\n"
+        f"UAMCC §3.11 Denominator Exclusion Details:\n"
+        f"  \"Persons are considered at risk for admission if they are alive,\n"
+        f"  enrolled in Medicare FFS, and not admitted to an acute care\n"
+        f"  hospital.  In addition to time spent in the hospital, excluded\n"
+        f"  from at-risk time are:\n"
+        f"    (1) time spent in an SNF or acute rehabilitation facility;\n"
+        f"    (2) time within 10 days following discharge from a hospital,\n"
+        f"        SNF, or acute rehabilitation facility;\n"
+        f"    (3) time after entering hospice care.\"\n\n"
+        f"Person-years = at_risk_days / 365.25\n\n"
+        f"Performance Year: {py_version}."
+    )
+
+    return passages

notebooks/bib_explorer.py

@@ -83,7 +83,7 @@ def _(ZOTERO_DB, mo, store):
         _msg = """
         ## 2. Migration
 
-        No Zotero database found at `/home/kert/zotero/zotero.sqlite`.
+        No Zotero database found at `{ZOTERO_DB}`.
         Start the Zotero container first, or add items manually below.
         """
     else:

notebooks/zotero_tutorial.py

@@ -14,7 +14,7 @@ def _():
 
     This notebook provides two modes of access:
 
-    - **Local SQLite** — reads the Zotero database directly (mounted read-only at `/home/kert/zotero`)
+    - **Local SQLite** — reads the Zotero database directly from the path configured in `stack.toml`
     - **Web API via pyzotero** — connects to `api.zotero.org` when API credentials are configured
 
     The local SQLite path works immediately with the container's library.
@@ -30,7 +30,9 @@ def _(mo):
     from pathlib import Path
     from pyzotero import zotero
 
-    ZOTERO_DB = Path("/home/kert/zotero/zotero.sqlite")
+    from conf import path as _conf_path
+
+    ZOTERO_DB = _conf_path("db.zotero")
 
     mo.md(f"""
     ## 1. Local Database Connection
@@ -586,7 +588,7 @@ def _(mo):
     | Local SQLite | Always available, read-only, fast, no credentials needed |
     | Pyzotero Web API | Read/write, sync support, requires zotero.org API key |
 
-    The local database is mounted read-only from the `zotero` container at `/home/kert/zotero/zotero.sqlite`.
+    The local database is mounted read-only from the `zotero` container at the path configured in `stack.toml` (`db.zotero`).
     Changes made through the VNC desktop app are reflected here on next Zotero save.
     """)
     return

src/bcda/client.py

@@ -82,12 +82,16 @@ class Client:
         client_secret: str,
         *,
         base_url: str = SANDBOX,
-        output_dir: str | Path = "data/bcda",
+        output_dir: str | Path | None = None,
         version: str = "v2",
         max_retries: int = MAX_RETRIES,
         retry_interval: float = RETRY_INITIAL_INTERVAL,
         timeout: float = 120.0,
     ) -> None:
+        if output_dir is None:
+            from conf import path
+
+            output_dir = path("storage.bcda")
         self.client_id = client_id
         self.client_secret = client_secret
         self.base_url = base_url.rstrip("/")

src/bcda/express/flatten.py

@@ -958,7 +958,7 @@ def _write_parquet(
 
 def flatten_export(
     ndjson_dir: str | Path,
-    store_path: str | Path = "data/bcda",
+    store_path: str | Path | None = None,
     *,
     storage_options: dict | None = None,
 ) -> dict[str, int]:
@@ -993,6 +993,10 @@ def flatten_export(
 
     from bcda.log import setup
 
+    if store_path is None:
+        from conf import path
+
+        store_path = path("storage.bcda")
     setup()
     ndjson_dir = Path(ndjson_dir)
     root = str(store_path).rstrip("/")

tests/bcda/test_client.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import gzip
-from pathlib import Path
 from unittest.mock import patch
 
 import httpx
@@ -849,7 +848,9 @@ class TestClientDefaults:
         assert c.base_url == SANDBOX
         assert c.version == "v2"
         assert c.max_retries == 3
-        assert c.output_dir == Path("data/bcda")
+        from conf import path
+
+        assert c.output_dir == path("storage.bcda")
         c.close()
 
     def test_base_url_trailing_slash(self) -> None: