API changes: particlefile.py and other touchups

parcels/grid.py

@@ -279,19 +279,6 @@ class CStructuredGrid(Structure):
             )
         return self._cstruct
 
-    def lon_grid_to_target(self):
-        if self.lon_remapping:
-            self._lon = self.lon_remapping.to_target(self.lon)
-
-    def lon_grid_to_source(self):
-        if self.lon_remapping:
-            self._lon = self.lon_remapping.to_source(self.lon)
-
-    def lon_particle_to_target(self, lon):
-        if self.lon_remapping:
-            return self.lon_remapping.particle_to_target(lon)
-        return lon
-
     @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
     def check_zonal_periodic(self, *args, **kwargs):
         return self._check_zonal_periodic(*args, **kwargs)

parcels/kernel.py

@@ -367,7 +367,7 @@ def check_fieldsets_in_kernels(self, pyfunc):
                     )
             elif pyfunc is AdvectionAnalytical:
                 if self.fieldset.particlefile is not None:
-                    self.fieldset.particlefile.analytical = True
+                    self.fieldset.particlefile._is_analytical = True
                 if self._ptype.uses_jit:
                     raise NotImplementedError("Analytical Advection only works in Scipy mode")
                 if self._fieldset.U.interp_method != "cgrid_velocity":

parcels/particle.py

@@ -29,11 +29,15 @@ class Variable:
     """
 
     def __init__(self, name, dtype=np.float32, initial=0, to_write: bool | Literal["once"] = True):
-        self.name = name
+        self._name = name
         self.dtype = dtype
         self.initial = initial
         self.to_write = to_write
 
+    @property
+    def name(self):
+        return self._name
+
     def __get__(self, instance, cls):
         if instance is None:
             return self

parcels/particledata.py

@@ -5,6 +5,7 @@
 import numpy as np
 
 from parcels._compat import MPI, KMeans
+from parcels.tools._helpers import deprecated
 from parcels.tools.statuscodes import StatusCode
 
 
@@ -228,12 +229,15 @@
         """Return the length, in terms of 'number of elements, of a ParticleData instance."""
         return self._ncount
 
+    @deprecated(
+        "Use iter(...) instead, or just use the object in an iterator context (e.g. for p in particledata: ...)."
+    )  # TODO: Remove 6 months after v3.1.0 (or 9 months; doesn't contribute to code debt)
     def iterator(self):
-        return ParticleDataIterator(self)
+        return iter(self)
 
     def __iter__(self):
         """Return an Iterator that allows for forward iteration over the elements in the ParticleData (e.g. `for p in pset:`)."""
-        return self.iterator()
+        return ParticleDataIterator(self)
 
     def __getitem__(self, index):
         """Get a particle object from the ParticleData instance based on its index."""

parcels/particlefile.py

@@ -10,6 +10,7 @@
 
 import parcels
 from parcels._compat import MPI
+from parcels.tools._helpers import deprecated, deprecated_made_private
 from parcels.tools.warnings import FileWarning
 
 __all__ = ["ParticleFile"]
@@ -46,31 +47,24 @@
         ParticleFile object that can be used to write particle data to file
     """
 
-    outputdt = None
-    particleset = None
-    parcels_mesh = None
-    time_origin = None
-    lonlatdepth_dtype = None
-
     def __init__(self, name, particleset, outputdt=np.inf, chunks=None, create_new_zarrfile=True):
-        self.outputdt = outputdt.total_seconds() if isinstance(outputdt, timedelta) else outputdt
-        self.chunks = chunks
-        self.particleset = particleset
-        self.parcels_mesh = "spherical"
+        self._outputdt = outputdt.total_seconds() if isinstance(outputdt, timedelta) else outputdt
+        self._chunks = chunks
+        self._particleset = particleset
+        self._parcels_mesh = "spherical"
         if self.particleset.fieldset is not None:
-            self.parcels_mesh = self.particleset.fieldset.gridset.grids[0].mesh
-        self.time_origin = self.particleset.time_origin
+            self._parcels_mesh = self.particleset.fieldset.gridset.grids[0].mesh
         self.lonlatdepth_dtype = self.particleset.particledata.lonlatdepth_dtype
-        self.maxids = 0
-        self.pids_written = {}
-        self.create_new_zarrfile = create_new_zarrfile
-        self.vars_to_write = {}
+        self._maxids = 0
+        self._pids_written = {}
+        self._create_new_zarrfile = create_new_zarrfile
+        self._vars_to_write = {}
         for var in self.particleset.particledata.ptype.variables:
             if var.to_write:
                 self.vars_to_write[var.name] = var.dtype
-        self.mpi_rank = MPI.COMM_WORLD.Get_rank() if MPI else 0
+        self._mpi_rank = MPI.COMM_WORLD.Get_rank() if MPI else 0
         self.particleset.fieldset._particlefile = self
-        self.analytical = False  # Flag to indicate if ParticleFile is used for analytical trajectories
+        self._is_analytical = False  # Flag to indicate if ParticleFile is used for analytical trajectories
 
         # Reset obs_written of each particle, in case new ParticleFile created for a ParticleSet
         particleset.particledata.setallvardata("obs_written", 0)
@@ -80,11 +74,11 @@
             "Conventions": "CF-1.6/CF-1.7",
             "ncei_template_version": "NCEI_NetCDF_Trajectory_Template_v2.0",
             "parcels_version": parcels.__version__,
-            "parcels_mesh": self.parcels_mesh,
+            "parcels_mesh": self._parcels_mesh,
         }
 
         # Create dictionary to translate datatypes and fill_values
-        self.fill_value_map = {
+        self._fill_value_map = {
             np.float16: np.nan,
             np.float32: np.nan,
             np.float64: np.nan,
@@ -103,23 +97,82 @@
             # But we need to handle incompatibility with MPI mode for now:
             if MPI and MPI.COMM_WORLD.Get_size() > 1:
                 raise ValueError("Currently, MPI mode is not compatible with directly passing a Zarr store.")
-            self.fname = name
+            fname = name
         else:
             extension = os.path.splitext(str(name))[1]
             if extension in [".nc", ".nc4"]:
                 raise RuntimeError(
                     "Output in NetCDF is not supported anymore. Use .zarr extension for ParticleFile name."
                 )
             if MPI and MPI.COMM_WORLD.Get_size() > 1:
-                self.fname = os.path.join(name, f"proc{self.mpi_rank:02d}.zarr")
+                fname = os.path.join(name, f"proc{self._mpi_rank:02d}.zarr")
                 if extension in [".zarr"]:
                     warnings.warn(
-                        f"The ParticleFile name contains .zarr extension, but zarr files will be written per processor in MPI mode at {self.fname}",
+                        f"The ParticleFile name contains .zarr extension, but zarr files will be written per processor in MPI mode at {fname}",
                         FileWarning,
                         stacklevel=2,
                     )
             else:
-                self.fname = name if extension in [".zarr"] else f"{name}.zarr"
+                fname = name if extension in [".zarr"] else f"{name}.zarr"
+        self._fname = fname
+
+    @property
+    def create_new_zarrfile(self):
+        return self._create_new_zarrfile
+
+    @property
+    def outputdt(self):
+        return self._outputdt
+
+    @property
+    def chunks(self):
+        return self._chunks
+
+    @property
+    def particleset(self):
+        return self._particleset
+
+    @property
+    def fname(self):
+        return self._fname
+
+    @property
+    def vars_to_write(self):
+        return self._vars_to_write
+
+    @property
+    def time_origin(self):
+        return self.particleset.time_origin
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def parcels_mesh(self):
+        return self._parcels_mesh
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def maxids(self):
+        return self._maxids
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def pids_written(self):
+        return self._pids_written
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def mpi_rank(self):
+        return self._mpi_rank
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def fill_value_map(self):
+        return self._fill_value_map
+
+    @property
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def analytical(self):
+        return self._is_analytical
 
     def _create_variables_attribute_dict(self):
         """Creates the dictionary with variable attributes.
@@ -133,7 +186,7 @@
             "trajectory": {
                 "long_name": "Unique identifier for each particle",
                 "cf_role": "trajectory_id",
-                "_FillValue": self.fill_value_map[np.int64],
+                "_FillValue": self._fill_value_map[np.int64],
             },
             "time": {"long_name": "", "standard_name": "time", "units": "seconds", "axis": "T"},
             "lon": {"long_name": "", "standard_name": "longitude", "units": "degrees_east", "axis": "X"},
@@ -147,14 +200,17 @@
         for vname in self.vars_to_write:
             if vname not in ["time", "lat", "lon", "depth", "id"]:
                 attrs[vname] = {
-                    "_FillValue": self.fill_value_map[self.vars_to_write[vname]],
+                    "_FillValue": self._fill_value_map[self.vars_to_write[vname]],
                     "long_name": "",
                     "standard_name": vname,
                     "units": "unknown",
                 }
 
         return attrs
 
+    @deprecated(
+        "ParticleFile.metadata is a dictionary. Use `ParticleFile.metadata['key'] = ...` or other dictionary methods instead."
+    )  # TODO: Remove 6 months after v3.1.0
     def add_metadata(self, name, message):
         """Add metadata to :class:`parcels.particleset.ParticleSet`.
 
@@ -175,21 +231,25 @@
         else:
             return var
 
-    def write_once(self, var):
+    @deprecated_made_private  # TODO: Remove 6 months after v3.1.0
+    def write_once(self, *args, **kwargs):
+        return self._write_once(*args, **kwargs)
+
+    def _write_once(self, var):
         return self.particleset.particledata.ptype[var].to_write == "once"
 
     def _extend_zarr_dims(self, Z, store, dtype, axis):
         if axis == 1:
-            a = np.full((Z.shape[0], self.chunks[1]), self.fill_value_map[dtype], dtype=dtype)
+            a = np.full((Z.shape[0], self.chunks[1]), self._fill_value_map[dtype], dtype=dtype)
             obs = zarr.group(store=store, overwrite=False)["obs"]
             if len(obs) == Z.shape[1]:
                 obs.append(np.arange(self.chunks[1]) + obs[-1] + 1)
         else:
-            extra_trajs = self.maxids - Z.shape[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)
+                a = np.full((extra_trajs, Z.shape[1]), self._fill_value_map[dtype], dtype=dtype)
             else:
-                a = np.full((extra_trajs,), self.fill_value_map[dtype], dtype=dtype)
+                a = np.full((extra_trajs,), self._fill_value_map[dtype], dtype=dtype)
         Z.append(a, axis=axis)
         zarr.consolidate_metadata(store)
 
@@ -221,11 +281,11 @@
 
         if len(indices_to_write) > 0:
             pids = pset.particledata.getvardata("id", indices_to_write)
-            to_add = sorted(set(pids) - set(self.pids_written.keys()))
+            to_add = sorted(set(pids) - set(self._pids_written.keys()))
             for i, pid in enumerate(to_add):
-                self.pids_written[pid] = self.maxids + i
-            ids = np.array([self.pids_written[p] for p in pids], dtype=int)
-            self.maxids = len(self.pids_written)
+                self._pids_written[pid] = self._maxids + i
+            ids = np.array([self._pids_written[p] for p in pids], dtype=int)
+            self._maxids = len(self._pids_written)
 
             once_ids = np.where(pset.particledata.getvardata("obs_written", indices_to_write) == 0)[0]
             if len(once_ids) > 0:
@@ -234,7 +294,7 @@
 
             if self.create_new_zarrfile:
                 if self.chunks is None:
-                    self.chunks = (len(ids), 1)
+                    self._chunks = (len(ids), 1)
                 if pset._repeatpclass is not None and self.chunks[0] < 1e4:
                     warnings.warn(
                         f"ParticleFile chunks are set to {self.chunks}, but this may lead to "
@@ -243,37 +303,37 @@
                         FileWarning,
                         stacklevel=2,
                     )
-                if (self.maxids > len(ids)) or (self.maxids > self.chunks[0]):
-                    arrsize = (self.maxids, self.chunks[1])
+                if (self._maxids > len(ids)) or (self._maxids > self.chunks[0]):
+                    arrsize = (self._maxids, self.chunks[1])
                 else:
                     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()
-                obs = np.zeros((self.maxids), dtype=np.int32)
+                obs = np.zeros((self._maxids), dtype=np.int32)
                 for var in self.vars_to_write:
                     varout = self._convert_varout_name(var)
                     if varout not in ["trajectory"]:  # because 'trajectory' is written as coordinate
-                        if self.write_once(var):
+                        if self._write_once(var):
                             data = np.full(
                                 (arrsize[0],),
-                                self.fill_value_map[self.vars_to_write[var]],
+                                self._fill_value_map[self.vars_to_write[var]],
                                 dtype=self.vars_to_write[var],
                             )
                             data[ids_once] = pset.particledata.getvardata(var, indices_to_write_once)
                             dims = ["trajectory"]
                         else:
                             data = np.full(
-                                arrsize, self.fill_value_map[self.vars_to_write[var]], dtype=self.vars_to_write[var]
+                                arrsize, self._fill_value_map[self.vars_to_write[var]], dtype=self.vars_to_write[var]
                             )
                             data[ids, 0] = pset.particledata.getvardata(var, indices_to_write)
                             dims = ["trajectory", "obs"]
                         ds[varout] = xr.DataArray(data=data, dims=dims, attrs=attrs[varout])
-                        ds[varout].encoding["chunks"] = self.chunks[0] if self.write_once(var) else self.chunks
+                        ds[varout].encoding["chunks"] = self.chunks[0] if self._write_once(var) else self.chunks
                 ds.to_zarr(self.fname, mode="w")
-                self.create_new_zarrfile = False
+                self._create_new_zarrfile = False
             else:
                 # Either use the store that was provided directly or create a DirectoryStore:
                 if issubclass(type(self.fname), zarr.storage.Store):
@@ -284,9 +344,9 @@
                 obs = pset.particledata.getvardata("obs_written", indices_to_write)
                 for var in self.vars_to_write:
                     varout = self._convert_varout_name(var)
-                    if self.maxids > Z[varout].shape[0]:
+                    if self._maxids > Z[varout].shape[0]:
                         self._extend_zarr_dims(Z[varout], store, dtype=self.vars_to_write[var], axis=0)
-                    if self.write_once(var):
+                    if self._write_once(var):
                         if len(once_ids) > 0:
                             Z[varout].vindex[ids_once] = pset.particledata.getvardata(var, indices_to_write_once)
                     else: