Merge branch 'master' into curvilinear-index-search

Author: CKehl

environment_py3_osx.yml

@@ -25,7 +25,7 @@ dependencies:
   - six>=1.10.0
   - xarray>=0.10.8
   - dask>=2.0
-  - cftime
+  - cftime>=1.3.1
   - pytest
   - nbval
   - scikit-learn

environment_py3_win.yml

@@ -22,7 +22,7 @@ dependencies:
   - six>=1.10.0
   - xarray>=0.5.1
   - dask>=2.0
-  - cftime
+  - cftime>=1.3.1
   - ipykernel<5.0
   - pytest
   - nbval

environment_py3p6_linux.yml

@@ -24,7 +24,7 @@ dependencies:
   - scipy>=0.16.0
   - six >=1.10.0
   - xarray>=0.10.8
-  - cftime
+  - cftime>=1.3.1
   - dask>=2.0
   - pytest
   - nbval

parcels/kernel.py

@@ -388,16 +388,15 @@ def remove_deleted_soa(self, pset, output_file, endtime):
         This deletion function is targetted to index-addressable, random-access array-collections.
         """
         # Indices marked for deletion.
-        bool_indices = np.array([p.state == OperationCode.Delete for p in pset])
+        bool_indices = pset.collection.state == OperationCode.Delete
         indices = np.where(bool_indices)[0]
         if len(indices) > 0 and output_file is not None:
             output_file.write(pset, endtime, deleted_only=bool_indices)
         pset.remove_indices(indices)
 
     def execute(self, pset, endtime, dt, recovery=None, output_file=None, execute_once=False):
         """Execute this Kernel over a ParticleSet for several timesteps"""
-        for p in pset:
-            p.set_state(StateCode.Evaluate)
+        pset.collection.state[:] = StateCode.Evaluate
 
         if abs(dt) < 1e-6 and not execute_once:
             logger.warning_once("'dt' is too small, causing numerical accuracy limit problems. Please chose a higher 'dt' and rather scale the 'time' axis of the field accordingly. (related issue #762)")

parcels/particlesets/baseparticleset.py

@@ -5,6 +5,7 @@
 from datetime import timedelta as delta
 from os import path
 import time as time_module
+import cftime
 
 import progressbar
 
@@ -350,6 +351,8 @@ def execute(self, pyfunc=AdvectionRK4, endtime=None, runtime=None, dt=1.,
             raise RuntimeError('endtime must be either a datetime or a double')
         if isinstance(endtime, datetime):
             endtime = np.datetime64(endtime)
+        elif isinstance(endtime, cftime.datetime):
+            endtime = self.time_origin.reltime(endtime)
         if isinstance(endtime, np.datetime64):
             if self.time_origin.calendar is None:
                 raise NotImplementedError('If fieldset.time_origin is not a date, execution endtime must be a double')

parcels/tools/converters.py

@@ -1,3 +1,4 @@
+# flake8: noqa: E999
 import inspect
 from datetime import timedelta as delta
 from math import cos
@@ -53,9 +54,19 @@ def reltime(self, time):
             return (time - self.time_origin) / np.timedelta64(1, 's')
         elif self.calendar in _get_cftime_calendars():
             if isinstance(time, (list, np.ndarray)):
-                return np.array([(t - self.time_origin).total_seconds() for t in time])
+                try:
+                    return np.array([(t - self.time_origin).total_seconds() for t in time])
+                except ValueError:
+                    raise ValueError("Cannot subtract 'time' (a %s object) from a %s calendar.\n"
+                                     "Provide 'time' as a %s object?"
+                                     % (type(time), self.calendar, type(self.time_origin)))
             else:
-                return (time - self.time_origin).total_seconds()
+                try:
+                    return (time - self.time_origin).total_seconds()
+                except ValueError:
+                    raise ValueError("Cannot subtract 'time' (a %s object) from a %s calendar.\n"
+                                     "Provide 'time' as a %s object?"
+                                     % (type(time), self.calendar, type(self.time_origin)))
         elif self.calendar is None:
             return time - self.time_origin
         else: