Fixed custom output command not rendering correctly. Convert config a…

…nd output paths to absolute paths. (#360)

HISTORY.rst

@@ -7,6 +7,8 @@ History
 * Upgraded `owslib` to `>=0.29.1`. (PR #358)
 * All operations that open NetCDF files or DAP links accept an `engine` argument. The default for all of these is `h5netcdf`. (PR #358)
 * Added `pydap` as an alternate backend for opening DAP links. (PR #358)
+* Fixed buggy CustomOutput command
+* Make sure config and output paths are absolute
 
 Internal changes
 ^^^^^^^^^^^^^^^^

docs/notebooks/time_series_analysis.ipynb

@@ -59,7 +59,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The base flow index needs as input arguments the link to a NetCDF file storing the stream flow time series, the name of the stream flow variable, and the frequency at which the index is computed (`YS`: yearly, `QS-DEC`: seasonally)."
+    "The base flow index needs as input arguments a DataArray storing the stream flow time series, and the frequency at which the index is computed (`YS`: yearly, `QS-DEC`: seasonally)."
    ]
   },
   {

ravenpy/config/commands.py

@@ -163,7 +163,7 @@ class EvaluationPeriod(LineCommand):
     end: dt.date
 
 
-class CustomOutput(FlatCommand):
+class CustomOutput(LineCommand):
     """
     Create custom output file to track a single variable, parameter or forcing function over time at a number of
     basins, HRUs, or across the watershed.
@@ -796,7 +796,10 @@ def from_nc(
             forcings.difference_update(data)
 
         if len(data) == 0:
-            raise ValueError("No data found in netCDF files.")
+            raise ValueError(
+                "No data found in netCDF files. Check that variable names follow CF conventions, "
+                "or if not, provide `alt_names` mapping Raven data types to variable names."
+            )
 
         # Default Gauge name
         attrs["name"] = attrs.get("name", f"Gauge_{idx}")

ravenpy/config/utils.py

@@ -60,7 +60,9 @@ def nc_specs(
     else:
         raise ValueError("NetCDF file not found.")
 
-    if isinstance(alt_names, str):
+    if alt_names is None:
+        alt_names = ()
+    elif isinstance(alt_names, str):
         alt_names = (alt_names,)
 
     attrs = {

ravenpy/ravenpy.py

@@ -283,14 +283,14 @@ def run(
         )
 
     # Confirm configdir exists
-    configdir = Path(configdir)
+    configdir = Path(configdir).absolute()
     if not configdir.exists():
         raise OSError("Workdir should include configuration files.")
 
     # Create outputdir
     outputdir = Path(outputdir or "output")
     if not outputdir.is_absolute():
-        outputdir = configdir / outputdir
+        outputdir = (configdir / outputdir).absolute()
 
     if overwrite and outputdir.exists():
         shutil.rmtree(str(outputdir))

ravenpy/utilities/coords.py

@@ -120,7 +120,7 @@ def units_transform(source, target, context="hydro"):
     context : str, optional
         Context of unit conversion. Default: "hydro".
     """
-    from xclim.core.units import convert_units_to, units
+    from xclim.core.units import convert_units_to
 
     b = convert_units_to(0 * source, target, context)
     a = convert_units_to(1 * source, target, context) - b

tests/test_commands.py

@@ -9,13 +9,29 @@
 
 from ravenpy.config import commands as rc
 from ravenpy.config import options as o
-from ravenpy.config.base import RV
+from ravenpy.config.base import RV, optfield
 
 salmon_land_hru_1 = dict(
     area=4250.6, elevation=843.0, latitude=54.4848, longitude=-123.3659, hru_type="land"
 )
 
 
+def test_custom_ouputs():
+    class Test(RV):
+        co: Sequence[rc.CustomOutput] = optfield(alias="CustomOutput")
+
+    co = rc.CustomOutput(
+        time_per="YEARLY",
+        stat="AVERAGE",
+        variable="PRECIP",
+        space_agg="ENTIRE_WATERSHED",
+    )
+    assert (
+        Test(co=[co]).to_rv().strip()
+        == ":CustomOutput         YEARLY AVERAGE PRECIP ENTIRE_WATERSHED"
+    )
+
+
 def test_evaluation_metrics():
     class Test(RV):
         em: Sequence[o.EvaluationMetrics] = Field(