Merge branch 'master' into update-prettier

Author: erikvansebille

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
       - id: nbqa-check-ast
       - id: nbqa-isort
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)

docs/examples/documentation_unstuck_Agrid.ipynb

@@ -155,7 +155,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note, by the way, that adding the `time_periodic=True` argument to `Field.from_netcdf()` will also mean that the climatology can be cycled for multiple years.\n"
+    "Note, by the way, that adding the `time_periodic` argument to `Field.from_netcdf()` will also mean that the climatology can be cycled for multiple years.\n"
    ]
   },
   {

docs/examples/tutorial_timestamps.ipynb

@@ -142,7 +142,7 @@ def _create_variables_attribute_dict(self):
 
         if self.time_origin.calendar is not None:
             attrs['time']['units'] = "seconds since " + str(self.time_origin)
-            attrs['time']['calendar'] = 'standard' if self.time_origin.calendar == 'np_datetime64' else self.time_origin.calendar
+            attrs['time']['calendar'] = _set_calendar(self.time_origin.calendar)
 
         for vname in self.vars_to_write:
             if vname not in ['time', 'lat', 'lon', 'depth', 'id']:
@@ -183,7 +183,7 @@ def _extend_zarr_dims(self, Z, store, dtype, axis):
             if len(obs) == Z.shape[1]:
                 obs.append(np.arange(self.chunks[1])+obs[-1]+1)
         else:
-            extra_trajs = max(self.maxids - Z.shape[0], self.chunks[0])
+            extra_trajs = self.maxids - Z.shape[0]
             if len(Z.shape) == 2:
                 a = np.full((extra_trajs, Z.shape[1]), self.fill_value_map[dtype], dtype=dtype)
             else:
@@ -233,7 +233,7 @@ def write(self, pset, time, indices=None):
                 if (self.maxids > len(ids)) or (self.maxids > self.chunks[0]):
                     arrsize = (self.maxids, self.chunks[1])
                 else:
-                    arrsize = (len(ids), 1)
+                    arrsize = (len(ids), self.chunks[1])
                 ds = xr.Dataset(attrs=self.metadata, coords={"trajectory": ("trajectory", pids),
                                                              "obs": ("obs", np.arange(arrsize[1], dtype=np.int32))})
                 attrs = self._create_variables_attribute_dict()

parcels/particlefile.py

@@ -244,6 +244,25 @@ def IncrLon(particle, fieldset, time):
     ds.close()
 
 
+@pytest.mark.parametrize('mode', ['scipy', 'jit'])
+@pytest.mark.parametrize('repeatdt', [1, 2])
+@pytest.mark.parametrize('nump', [1, 10])
+def test_pfile_chunks_repeatedrelease(fieldset, mode, repeatdt, nump, tmpdir):
+    runtime = 8
+    pset = ParticleSet(fieldset, pclass=ptype[mode], lon=np.zeros((nump, 1)),
+                       lat=np.zeros((nump, 1)), repeatdt=repeatdt)
+    outfilepath = tmpdir.join("pfile_chunks_repeatedrelease.zarr")
+    chunks = (20, 10)
+    pfile = pset.ParticleFile(outfilepath, outputdt=1, chunks=chunks)
+
+    def DoNothing(particle, fieldset, time):
+        pass
+
+    pset.execute(DoNothing, dt=1, runtime=runtime, output_file=pfile)
+    ds = xr.open_zarr(outfilepath)
+    assert ds['time'].shape == (int(nump*runtime/repeatdt), chunks[1])
+
+
 @pytest.mark.parametrize('mode', ['scipy', 'jit'])
 def test_write_timebackward(fieldset, mode, tmpdir):
     outfilepath = tmpdir.join("pfile_write_timebackward.zarr")