Fix/config

examples/em_deposition.py

@@ -22,6 +22,8 @@
 from rich.panel import Panel
 from rich.text import Text
 
+from onedep_lib.config import DepositConfig
+
 logging.disable(logging.ERROR)
 
 _console = Console(stderr=True)
@@ -60,6 +62,8 @@ def print_report(label: str, report: dsp.CheckReport) -> None:
 
 
 def main() -> None:
+    config = DepositConfig.load()
+
     # ── 0. Validate configuration ─────────────────────────────────────────────
     _unset = [
         name
@@ -80,7 +84,7 @@ def main() -> None:
 
     with _console.status("[cyan]Initializing deposit…[/cyan]", spinner="dots") as spin:
         # ── 1. Initialization ────────────────────────────────────────────────
-        dep = dsp.deposit_init(email=EMAIL, users=USERS, country=dsp.Country.USA)
+        dep = dsp.deposit_init(email=EMAIL, users=USERS, country=dsp.Country.USA, config=config)
         ok(f"Deposit initialized  session_id={dep.session_id}")
 
         # ── 2. Set experiment type and EM-specific params ─────────────────────
@@ -91,7 +95,7 @@ def main() -> None:
 
         # ── 3. Check auth key ─────────────────────────────────────────────────
         spin.update("[cyan]Checking auth key…[/cyan]")
-        auth_ok = dsp.check_auth_key()
+        auth_ok = dsp.check_auth_key(config=config)
         if auth_ok:
             ok("Auth key valid")
         else:

examples/xray_deposition.py

@@ -22,17 +22,19 @@
 from rich.panel import Panel
 from rich.text import Text
 
+from onedep_lib.config import DepositConfig
+
 logging.disable(logging.ERROR)
 
 _console = Console(stderr=True)
 
 # ── Configuration ─────────────────────────────────────────────────────────────
 # Change all values marked with  <<<< CHANGE THIS  before running.
 
-EMAIL = os.getenv("WWPDB_EMAIL") or "your.email@example.com"  # <<<< CHANGE THIS
-USERS = os.getenv("WWPDB_USERS") and os.getenv("WWPDB_USERS").split(",") or ["0000-0000-0000-0000"]  # <<<< CHANGE THIS  (ORCID iD)
-COORD_FILE = os.getenv("WWPDB_COORD_FILE") or "/path/to/your/coord.cif"  # <<<< CHANGE THIS
-SF_FILE = os.getenv("WWPDB_SF_FILE") or "/path/to/your/sf.cif"  # <<<< CHANGE THIS
+EMAIL = os.getenv("WWPDB_EMAIL") or "your.email@example.com"
+USERS = os.getenv("WWPDB_USERS") and os.getenv("WWPDB_USERS").split(",") or ["0000-0000-0000-0000"]
+COORD_FILE = os.getenv("WWPDB_COORD_FILE") or "/path/to/your/coord.cif"
+SF_FILE = os.getenv("WWPDB_SF_FILE") or "/path/to/your/sf.cif"
 
 
 def ok(msg: str) -> None:
@@ -53,6 +55,8 @@ def print_report(label: str, report: dsp.CheckReport) -> None:
 
 
 def main() -> None:
+    config = DepositConfig.load()
+
     # ── 0. Validate configuration ─────────────────────────────────────────────
     _unset = [
         name
@@ -74,7 +78,7 @@ def main() -> None:
 
     with _console.status("[cyan]Initializing deposit…[/cyan]", spinner="dots") as spin:
         # ── 1. Initialization ────────────────────────────────────────────────
-        dep = dsp.deposit_init(email=EMAIL, users=USERS, country=dsp.Country.USA)
+        dep = dsp.deposit_init(email=EMAIL, users=USERS, country=dsp.Country.USA, config=config)
         ok(f"Deposit initialized  session_id={dep.session_id}")
 
         # ── 2. Set experiment type ────────────────────────────────────────────
@@ -84,7 +88,7 @@ def main() -> None:
 
         # ── 3. Check auth key ─────────────────────────────────────────────────
         spin.update("[cyan]Checking auth key…[/cyan]")
-        auth_ok = dsp.check_auth_key()
+        auth_ok = dsp.check_auth_key(config=config)
         if auth_ok:
             ok("Auth key valid")
         else:
@@ -162,3 +166,4 @@ def main() -> None:
 
 if __name__ == "__main__":
     main()
+

src/onedep_lib/dsp.py

@@ -58,10 +58,8 @@ def list_sessions(base_dir: Path | None = None) -> list[tuple[LocalSession, list
     return results
 
 
-def check_auth_key(config: DepositConfig = None) -> bool:
+def check_auth_key(config: DepositConfig) -> bool:
     """Return True if the configured credentials are valid, False otherwise."""
-    config = config or DepositConfig.load()
-
     try:
         api_client = HttpApiClient(config, auth_provider=TokenStore(config))
         api_client.get_all_depositions()
@@ -74,10 +72,10 @@ def deposit_init(
     email: str,
     users: list[str],
     country: Country,
+    config: DepositConfig,
     experiment_type: ExperimentType | None = None,
     em_subtype: EMSubType | None = None,
     coordinates: bool | None = None,
-    config: DepositConfig | None = None,
     _base_dir: Path | None = None,
     _api_client: ApiClient | None = None,
     _check_runner: CheckRunnerProtocol | None = None,
@@ -99,7 +97,6 @@ def deposit_init(
     Returns:
         A Deposition object representing the local session.
     """
-    config = config or DepositConfig.load()
     session_id = str(uuid.uuid4())
     base_dir = _base_dir or config.session_dir
     store: SessionStore = JsonSessionStore(session_id, base_dir=base_dir)
@@ -125,7 +122,7 @@ def deposit_init(
 
 def deposit_resume(
     session_id: str,
-    config: DepositConfig | None = None,
+    config: DepositConfig,
     _base_dir: Path | None = None,
     _api_client: ApiClient | None = None,
     _check_runner: CheckRunnerProtocol | None = None,
@@ -145,7 +142,6 @@ def deposit_resume(
     Raises:
         KeyError: If no session with the given session_id exists.
     """
-    config = config or DepositConfig.load()
     base_dir = _base_dir or config.session_dir
     store: SessionStore = JsonSessionStore(session_id, base_dir=base_dir)
     store.get_session()  # raises KeyError if not found