Fix to_exchange and to_coards failing on variables with second units

CHANGELOG

@@ -1,3 +1,9 @@
+v1.0.2.7 (2024-??-??)
+=====================
+* (Bug) fix to_exchange accessor failing for variables with seconds and the unit
+* (Bug) fix to_coards accessor failing for variables with seconds and the unit
+* Add status-cf-derived command that tests all all public CF files at CCHDO going from netCDF to every other supported format
+
 v1.0.2.6 (2024-03-18)
 =====================
 * Support for duplicate parameters

cchdo/hydro/accessors.py

@@ -560,7 +560,7 @@ def _make_ctd_headers(self, params) -> list[str]:
             *[f"{key} = {value}" for key, value in headers.items()],
         ]
 
-    def _make_data_block(self, params) -> list[str]:
+    def _make_data_block(self, params: dict[WHPName, xr.DataArray]) -> list[str]:
         # TODO N_PROF is guaranteed
         valid_levels = params[WHPNames["SAMPNO"]] != ""
         data_block = []
@@ -584,6 +584,10 @@ def _make_data_block(self, params) -> list[str]:
                     .tolist()
                 )
             else:
+                if da.dtype.char == "m":
+                    nat_mask = np.isnat(da)
+                    da = da.astype("timedelta64[s]").astype("float64")
+                    da[nat_mask] = np.nan
                 data = np.nditer(da[valid_levels], flags=["refs_ok"])
                 numeric_precision_override = self.cchdo_c_format_precision(
                     da.attrs.get("C_format", "")

cchdo/hydro/legacy/coards/__init__.py

@@ -281,6 +281,10 @@ def get_dataarrays(ds: xr.Dataset):
             data = variable.dt.strftime("%Y%m%d").astype(float).to_numpy()
         elif parameter_name == "BTL_TIME":
             data = variable.dt.strftime("%H%M").astype(float).to_numpy()
+        elif parameter_name == "CTDETIME":
+            nat_mask = np.isnat(variable)
+            data = variable.astype("timedelta64[s]").astype("float64").to_numpy()
+            data[nat_mask] = np.nan
         else:
             data = variable.to_numpy()
 

cchdo/hydro/tests/test_accessors.py

@@ -2,6 +2,7 @@
 from importlib.resources import read_text
 
 import pytest
+import xarray as xr
 from xarray.testing import assert_identical
 
 from ..accessors import CCHDOAccessor
@@ -90,3 +91,59 @@ def test_exchange_ctd_round_trip():
     # the magic slice removes the stamp and the newline with #
     rt = read_exchange(ds.cchdo.to_exchange()[22:])
     assert_identical(ds, rt)
+
+
+def test_nc_serialize_all_ctd(tmp_path):
+    """A crash was discovered when the ctd elapsed time param was present, and was seralized to disk then read back in"""
+    test_data = b"""CTD,test
+# some comment
+NUMBER_HEADERS = 8
+EXPOCODE = TEST
+STNNBR = 1
+CASTNO = 1
+DATE = 20200101
+TIME = 0000
+LATITUDE = 0
+LONGITUDE = 0
+CTDPRS
+DBAR
+0
+END_DATA
+"""
+    ds = read_exchange(test_data)
+    nc = tmp_path / "test.nc"
+    ds.to_netcdf(nc)
+    ds = xr.load_dataset(nc)
+    # the magic slice removes the stamp and the newline with #
+    ds.cchdo.to_exchange()
+    ds.cchdo.to_coards()
+    ds.cchdo.to_woce()
+    ds.cchdo.to_sum()
+
+
+def test_nc_serialize_all_ctdetime(tmp_path):
+    """A crash was discovered when the ctd elapsed time param was present, and was seralized to disk then read back in"""
+    test_data = b"""CTD,test
+# some comment
+NUMBER_HEADERS = 8
+EXPOCODE = TEST
+STNNBR = 1
+CASTNO = 1
+DATE = 20200101
+TIME = 0000
+LATITUDE = 0
+LONGITUDE = 0
+CTDPRS,CTDETIME
+DBAR,SECONDS
+0,-999
+END_DATA
+"""
+    ds = read_exchange(test_data)
+    nc = tmp_path / "test.nc"
+    ds.to_netcdf(nc)
+    ds = xr.load_dataset(nc)
+    # the magic slice removes the stamp and the newline with #
+    ds.cchdo.to_exchange()
+    ds.cchdo.to_coards()
+    ds.cchdo.to_woce()
+    ds.cchdo.to_sum()