More unit tests fixed now that decode_cf works

Author: erikvansebille

tests/test_particlefile.py

@@ -107,11 +107,8 @@ def test_pfile_array_remove_all_particles(fieldset, chunks_obs, tmp_zarrfile):
     pfile.write(pset, fieldset.time_interval.left + np.timedelta64(1, "D"))
     pfile.write(pset, fieldset.time_interval.left + np.timedelta64(2, "D"))
 
-    ds = xr.open_zarr(tmp_zarrfile, decode_cf=False).load()
-    pytest.skip(
-        "TODO v4: Set decode_cf=True, which will mean that missing values get decoded to NaT rather than fill value"
-    )
-    assert np.allclose(ds["time"][:, 0], np.timedelta64(0, "s"), atol=np.timedelta64(1, "ms"))
+    ds = xr.open_zarr(tmp_zarrfile)
+    np.testing.assert_allclose(ds["time"][:, 0] - fieldset.time_interval.left, np.timedelta64(0, "s"))
     if chunks_obs is not None:
         assert ds["time"][:].shape == chunks
     else:
@@ -200,7 +197,7 @@ def IncrLon(particles, fieldset):  # pragma: no cover
     for _ in range(npart):
         pset.execute(IncrLon, dt=dt, runtime=np.timedelta64(1, "s"), output_file=pfile)
 
-    ds = xr.open_zarr(tmp_zarrfile, decode_cf=False)
+    ds = xr.open_zarr(tmp_zarrfile)
     samplevar = ds["sample_var"][:]
     assert samplevar.shape == (npart, min(maxvar, npart + 1))
     # test whether samplevar[:, k] = k
@@ -216,12 +213,10 @@ def test_write_timebackward(fieldset, tmp_zarrfile):
     pfile = ParticleFile(tmp_zarrfile, outputdt=np.timedelta64(1, "s"))
     pset.execute(DoNothing, runtime=np.timedelta64(3, "s"), dt=-np.timedelta64(1, "s"), output_file=pfile)
 
-    # TODO v4: Fix decode_cf and remove the following lines
-    ds = xr.open_zarr(tmp_zarrfile, decode_cf=False)
+    ds = xr.open_zarr(tmp_zarrfile)
     trajs = ds["trajectory"][:]
 
     output_time = ds["time"][:].values
-    output_time = np.where(output_time > 100.0, np.nan, output_time)  # ignore fill values
 
     assert trajs.values.dtype == "int64"
     assert np.all(np.diff(trajs.values) < 0)  # all particles written in order of release
@@ -298,13 +293,12 @@ def IncreaseAge(particles, fieldset):  # pragma: no cover
 
     pset.execute(IncreaseAge, runtime=np.timedelta64(npart * 2, "s"), dt=np.timedelta64(1, "s"), output_file=ofile)
 
-    # TODO v4: Fix metadata and re-enable decode_cf
-    ds = xr.open_zarr(tmp_zarrfile, decode_cf=False)
+    ds = xr.open_zarr(tmp_zarrfile)
     age = ds["age"][:].values
-    ds_time = np.zeros_like(age)
+    ds_timediff = np.zeros_like(age)
     for i in range(npart):
-        ds_time[i, :] = ds.time.values[i, :] - (time[i] - fieldset.time_interval.left) / np.timedelta64(1, "s")
-    assert np.allclose(age[~np.isnan(age)], ds_time[~np.isnan(age)])
+        ds_timediff[i, :] = (ds.time.values[i, :] - time[i]) / np.timedelta64(1, "s")
+    np.testing.assert_equal(age, ds_timediff)
 
 
 def test_reset_dt(fieldset, tmp_zarrfile):