Remove warnings and fixing tests

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
     "xarray (>=2025.2.0,<2027.0.0)",
     "pydantic-settings (>=2.8.1,<3.0.0)",
     "httpx (>=0.27.0,<0.29.0)",
-    "aiofiles (>=24.1.0,<25.0.0)",
+    "aiofiles (>=24.1.0,<26.0.0)",
     "cfgrib (>=0.9.15.0,<0.10.0.0)",
     "netcdf4 (>=1.7.2,<2.0.0)",
     "dask (>=2025.4.1,<2027.0.0)",
@@ -35,9 +35,9 @@ DEP002 = ["cfgrib", "dask", "netcdf4"]
 [tool.poetry.group.dev.dependencies]
 coverage = "^7.8.0"
 pre-commit = "^4.2.0"
-deptry = "^0.23.0"
+deptry = ">0.23.0"
 pytest = "^8.3.5"
-pytest-asyncio = "^0.26.0"
+pytest-asyncio = "^1.4.0"
 
 
 [tool.pytest.ini_options]

src/ogs_riverger/efas/efas_manager.py

@@ -10,12 +10,17 @@
 from tempfile import TemporaryDirectory
 from typing import Any
 from typing import Literal
+from typing import TYPE_CHECKING
 from uuid import uuid1
 from zipfile import ZipFile
 
 import dask
 import numpy as np
-import xarray as xr
+
+if TYPE_CHECKING:
+    import xarray as xr
+else:
+    import ogs_riverger.utils.lazy_xarray as xr
 
 import ogs_riverger.efas.download_tools as efas_download
 from ogs_riverger.efas.download_tools import EfasDataSource
@@ -81,7 +86,7 @@ def read_efas_data_files(
     config_content: Iterable[RiverConfigElement],
     efas_domain_file: PathLike,
     pool: None | Pool = None,
-) -> xr.Dataset:
+) -> "xr.Dataset":
     """Reads and merges the content of multiple downloaded EFAS data files.
 
     EFAS data files are distributed as GRIB or NetCDF files, optionally
@@ -149,9 +154,9 @@ def read_efas_data_files(
 def _read_raw_content_of_efas_file(
     file_path: Path,
     config_content: Iterable[RiverConfigElement],
-    efas_domain: xr.Dataset,
+    efas_domain: "xr.Dataset",
     temp_dir: Path,
-) -> xr.Dataset:
+) -> "xr.Dataset":
     """
     Reads the raw content of an EFAS file.
 
@@ -224,8 +229,8 @@ def _read_raw_content_of_efas_file(
 def _read_raw_content_of_unzipped_efas_file(
     file_path: Path,
     config_content: Iterable[RiverConfigElement],
-    efas_domain: xr.Dataset,
-) -> xr.Dataset:
+    efas_domain: "xr.Dataset",
+) -> "xr.Dataset":
     """
     Reads and processes the raw content of an unzipped EFAS file to extract
     specific river data based on given configurations and EFAS domain.
@@ -409,9 +414,9 @@ def _read_raw_content_of_unzipped_efas_file(
 def _read_single_efas_file(
     file_path: Path,
     config_content: Iterable[RiverConfigElement],
-    efas_domain: xr.Dataset,
+    efas_domain: "xr.Dataset",
     temp_dir: Path,
-) -> xr.Dataset:
+) -> "xr.Dataset":
     """Determines the type of EFAS file and processes it accordingly.
 
     This function reads the EFAS file content and examines its structure to
@@ -497,7 +502,7 @@ def _read_single_efas_file(
     )
 
 
-def _read_efas_forecast_file(dataset: xr.Dataset):
+def _read_efas_forecast_file(dataset: "xr.Dataset"):
     """Read the content of a forecast EFAS file.
 
     This function is called by `_read_single_efas_file` when the file has
@@ -550,7 +555,7 @@ def _read_efas_forecast_file(dataset: xr.Dataset):
     return dataset_sliced
 
 
-def _read_efas_operative_grib_file(dataset: xr.Dataset):
+def _read_efas_operative_grib_file(dataset: "xr.Dataset"):
     """Read the content of an operative EFAS file.
 
     This function is called by `_read_single_efas_file` when the file has

src/ogs_riverger/read_config.py

@@ -248,9 +248,14 @@ def _apply_biogeochemical_profile(
     ):
         biogeochemical = {}
         if "biogeochemical_profile" in raw_river:
-            biogeochemical = profiles[
-                raw_river["biogeochemical_profile"]
-            ].copy()
+            profile_name = raw_river["biogeochemical_profile"]
+            if profile_name not in profiles:
+                raise ValueError(
+                    f'River "{raw_river["name"]}" references a '
+                    f'biogeochemical profile "{profile_name}" that is not '
+                    f"defined in the configuration file."
+                )
+            biogeochemical = profiles[profile_name].copy()
 
         if "biogeochemical" in raw_river:
             biogeochemical.update(raw_river["biogeochemical"])

src/ogs_riverger/utils/lazy_xarray.py

@@ -0,0 +1,24 @@
+"""Lazy proxy for xarray.
+
+Importing this module does *not* import xarray. The real import happens only
+when an attribute (e.g. ``xr.Dataset``, ``xr.open_dataset``) is first
+accessed, via the module-level ``__getattr__`` hook defined in PEP 562.
+
+Usage::
+
+    import ogs_riverger.utils.lazy_xarray as xr
+
+    ds = xr.open_dataset(...)   # xarray is imported here, on first access
+"""
+
+_XARRAY = None
+
+
+def __getattr__(name: str):
+    global _XARRAY
+    if _XARRAY is None:
+        import xarray
+
+        _XARRAY = xarray
+
+    return getattr(_XARRAY, name)

tests/fixtures.py

@@ -41,6 +41,13 @@ def config_file_example(tmp_path):
         "temperature_variation": 5,
         "average_salinity": 5
       },
+      "bgc_profiles": {
+        "tyr": {
+          "B1c": 100,
+          "B1n": 10,
+          "B1p": 1
+        }
+      },
       "default_model": "stem_flux",
       "rivers": [
         {