Merge branch 'develop'

README.rst

@@ -56,39 +56,6 @@ and it is used in our development and testing process.
 
 `Install using Anaconda <./Installing.rst>`_
 
-Compiling PyGnome
-=================
-Move to the repository directory and activate the ``gnome`` conda environment with:
-
- (base) conda activate gnome
-
-Delete ``py3buildenv_.txt`` if re-compiling code after making software changes.  The text file `py3buildenv_.txt` is used to cache software versions to avoid repitious prompts but will cause path problems if changes have been made and needs to be deleted to avoid these erroneous path defs.  
-
-Copy ``python Py3Env.py`` to an untracked file that defines local setup, e.g. ``python Py3Env_RDM.py``, and edit  
-``places`` to point to the right directory on your local system:
-
- places = [r"put-your-VisualStudio-vcvars64.bat-directory-path-here"]
-
-This file can remain untracked in version control because it is unique to each user and easily reproducible from the tracked file ``Py3Env.py`` that will be updated with future advancements.  Once this path is corrected to local path, run the script in gnome environment:
-
- (base) conda activate gnome
-
- (gnome) python Py3Env_RDM.py
-
-A command terminal ``cmd.exe`` prompt will open.  Change directories and run ``setup.py``
-
- (gnome) cd py_gnome
-
- (gnome) python setup.py develop
-
-After many, many messages, you will see something like: 
-
- Installed c:\users\rachael.mueller\projects\pygnome\py_gnome
-
- Processing dependencies for pyGnome==1.1.7
-
- Finished processing dependencies for pyGnome==1.1.7
-
 
 The WebGNOME Interface:
 =======================

py_gnome/conda_requirements.txt

@@ -38,7 +38,7 @@ pyzmq
 # tblib
 
 ## Base numerical libs
-numpy <2
+numpy >=1.24,<2
 scipy
 
 ## Modeling libs

py_gnome/conda_requirements_build.txt

@@ -3,9 +3,10 @@
 
 cython=3.*
 setuptools>=62  # older versions uses different build dirs
-setuptools-scm>=6.2
+# setuptools-scm>=6.2
 gitpython
 python-build
 cmake
 ninja
-scikit-build-core>=0.7.*
+scikit-build-core>=0.9.9
+# hatchling

py_gnome/gnome/__init__.py

@@ -22,7 +22,7 @@
 # just so it will be in the namespace.
 from .gnomeobject import GnomeId, AddLogger
 
-__version__ = '1.1.12'
+__version__ = "1.1.13dev"
 
 
 if os.name == 'nt':

py_gnome/gnome/cy_gnome/cy_cats_mover.pyx

@@ -200,6 +200,9 @@ cdef class CyCatsMover(CyCurrentMover):
         Takes a CyShioTime object as input and sets C++ Cats mover properties
         from the Shio object.
         """
+        print("in set_shio")
+        print("CyShioTime:", CyShioTime)
+        print("cy_shio:", cy_shio)
         self.cats.SetTimeDep(cy_shio.shio)
 
         if cy_shio.station_location is not None and self.ref_point is None:

py_gnome/gnome/cy_gnome/cy_ossm_time.pyx

@@ -155,7 +155,8 @@ cdef class CyOSSMTime(object):
             wp['z'][:] = wp['z']
 
             g_wp = np.zeros((1,), dtype=basic_types.world_point)
-            g_wp[0] = (wp['long'], wp['lat'], 0)
+            g_wp[0] = (wp['long'][0], wp['lat'][0], 0)
+
 
             return tuple(g_wp[0])
 

py_gnome/gnome/cy_gnome/cy_shio_time.pyx

@@ -144,25 +144,27 @@ cdef class CyShioTime(CyOSSMTime):
                 'yeardata={0.yeardata!r}'
                 ')'.format(self))
 
-    def __str__(self):
-        """Return string representation of this object"""
-        """info = {'Long': round(g_wp[0]['long'], 2),
-                   'Lat': round( g_wp[0]['lat'], 2),
-                   'StationName': sName, 'StationType': sType,
-                   'DaylightSavingsOff': self.shio.daylight_savings_off}
-        """
-
-        info = ("CyShioTime object - Info read from file:\n"
-                "  File: {1.path_filename} \n"
-                "  StationName : {0[StationName]},"
-                "  StationType : {0[StationType]}\n"
-                "  (Long, Lat) : ({0[Long]}, {0[Lat]})\n"
-                "  DaylightSavingsOff : {0[DaylightSavingsOff]}"
-                "".format(self.get_info(), self))
-
-        return info
+    # this is broken -- no get_info method ????
+    # def __str__(self):
+    #     """Return string representation of this object"""
+    #     """info = {'Long': round(g_wp[0]['long'], 2),
+    #                'Lat': round( g_wp[0]['lat'], 2),
+    #                'StationName': sName, 'StationType': sType,
+    #                'DaylightSavingsOff': self.shio.daylight_savings_off}
+    #     """
+
+    #     info = ("CyShioTime object - Info read from file:\n"
+    #             "  File: {1.path_filename} \n"
+    #             "  StationName : {0[StationName]},"
+    #             "  StationType : {0[StationType]}\n"
+    #             "  (Long, Lat) : ({0[Long]}, {0[Lat]})\n"
+    #             "  DaylightSavingsOff : {0[DaylightSavingsOff]}"
+    #             "".format(self.get_info(), self))
+
+    #     return info
 
     def __eq(self, CyShioTime other):
+        # used by __richcmp__
         attrs = ('filename', 'daylight_savings_off', 'scale_factor',
                  'station', 'station_type', 'station_location',
                  'yeardata')

py_gnome/gnome/environment/environment.py

@@ -56,7 +56,7 @@ def __init__(self, make_default_refs=True, **kwargs):
         self.array_types = {}
         super().__init__(**kwargs)
 
-    def at(self, points, time, *, units=None, extrapolate=False, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, **kwargs):
         """
         Find the value of the property at positions P at time T
 

py_gnome/gnome/environment/environment_objects.py

@@ -119,7 +119,7 @@ def v(self):
         return self._v
 
 
-    def at(self, points, time, *, units=None, extrapolate=False, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, **kwargs):
         """
         Find the value of the property at positions of points at time T
 
@@ -486,7 +486,7 @@ class GridCurrent(VelocityGrid, Environment):
 #                      'surface_northward_sea_water_velocity'],
 #                'w': ['upward_sea_water_velocity']}
 
-    def at(self, points, time, *, units=None, extrapolate=False, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, **kwargs):
         '''
         Find the value of the property at positions P at time T
 
@@ -516,7 +516,9 @@ def at(self, points, time, *, units=None, extrapolate=False, **kwargs):
             if res is not None:
                 return res
 
-        extrapolate = self.extrapolation_is_allowed or extrapolate
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
+
 
         value = super(GridCurrent, self).at(points, time,
                                             units=units,
@@ -580,7 +582,7 @@ def __init__(self,
 
         self.wet_dry_mask = wet_dry_mask
 
-    def at(self, points, time, *, units=None, extrapolate=False, coord_sys='uv', _auto_align=True, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, coord_sys='uv', _auto_align=True, **kwargs):
         '''
         Find the value of the property at positions P at time T
 
@@ -628,7 +630,8 @@ def at(self, points, time, *, units=None, extrapolate=False, coord_sys='uv', _au
                 return self.transform_result(value, coord_sys)
 
         if value is None:
-            extrapolate = self.extrapolation_is_allowed or extrapolate
+            if extrapolate is None:
+                extrapolate = self.extrapolation_is_allowed
             value = super(GridWind, self).at(pts, time,
                                              units=units,
                                              extrapolate=extrapolate,
@@ -711,7 +714,7 @@ def __init__(self, *args, **kwargs):
 
         kwargs['data'] = data
 
-    def at(self, points, time, *, units=None, extrapolate=False,
+    def at(self, points, time, *, units=None, extrapolate=None,
            _hash=None, _mem=True, **kwargs):
 
         if _hash is None:
@@ -728,6 +731,9 @@ def at(self, points, time, *, units=None, extrapolate=False,
         _time_idx = self.time.index_of(time)
         order = self.dimension_ordering
 
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
+
         if order[0] == 'time':
             value = self._time_interp(points, time, units=units, extrapolate=extrapolate,
                                       _mem=_mem, _hash=_hash, **kwargs)
@@ -840,8 +846,9 @@ def init_from_netCDF(self,
             **kwargs
         )
 
-    def at(self, points, time, *, units=None, extrapolate=False, **kwargs):
-        extrapolate = self.extrapolation_is_allowed or extrapolate
+    def at(self, points, time, *, units=None, extrapolate=None, **kwargs):
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
         cctn = (self.ice_concentration.at(points, time,
                                             extrapolate=extrapolate, **kwargs)
                   .copy())
@@ -907,13 +914,14 @@ def from_netCDF(cls,
                              ice_velocity=ice_velocity,
                              **kwargs))
 
-    def at(self, points, time, *, units=None, extrapolate=False, min_val=0, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, min_val=0, **kwargs):
         """
         :param min_val: Minimum value for wind speed. If computed wind speed is less than this
                         value, it will be set to this value.
         :type min_val: float
         """
-        extrapolate = self.extrapolation_is_allowed or extrapolate
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
 
         cctn = self.ice_concentration.at(points, time, extrapolate=extrapolate, **kwargs)
         wind_v = super(IceAwareWind, self).at(points, time,

py_gnome/gnome/environment/gridded_objects_base.py

@@ -589,7 +589,10 @@ def from_netCDF(cls, *args, **kwargs):
         return var
 
     @combine_signatures
-    def at(self, points, time, *, units=None, extrapolate=False, unmask=True, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, unmask=True, **kwargs):
+
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
 
         value = super(Variable, self).at(points, time,
                                          units=units,
@@ -744,7 +747,7 @@ def __init__(self,
                  **kwargs):
         super(VectorVariable, self).__init__(*args, **kwargs)
         self.extrapolation_is_allowed = extrapolation_is_allowed
-        
+
         #Adding this so unit conversion happens properly in the components
         #I really don't think we will be doing mixed units in one of these
         #anytime soon.
@@ -755,8 +758,8 @@ def __init__(self,
                         warnings.warn("Variable {0} has units {1} which are not the same as the VectorVariable {2} units {3}.".format(var.name, var._gnome_unit, self.name, self._gnome_unit))
                 else:
                     var._gnome_unit = self._gnome_unit
-                
-            
+
+
 
     def __repr__(self):
         try:
@@ -939,7 +942,7 @@ def constant(cls,
         :param values: vector of values
         :type values: array-like
         '''
-        
+
         Grid = Grid_S
         Time = cls._default_component_types['time']
         _node_lon = np.array(([-360, 0, 360], [-360, 0, 360], [-360, 0, 360]))
@@ -952,9 +955,11 @@ def constant(cls,
         _vars = [Variable(grid=_grid, units=units[i], time=_time, data=d) for i, d in enumerate(_datas)]
         return cls(name=name, grid=_grid, time=_time, variables=_vars)
 
-    def at(self, points, time, *, units=None, extrapolate=False, unmask=True, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, unmask=True, **kwargs):
         units = units if units else self._gnome_unit #no need to convert here, its handled in the subcomponents
-        value = super(VectorVariable, self).at(points, time, 
+        if extrapolate is None:
+            extrapolate = self.extrapolation_is_allowed
+        value = super(VectorVariable, self).at(points, time,
                                                units=units,
                                                extrapolate=extrapolate,
                                                unmask=unmask,
@@ -1013,7 +1018,7 @@ def get_data_vectors(self):
             xt = x.shape[0]
             y = raw_v[:]
             yt = y.shape[0]
-            if raw_u.shape[-2:] == raw_v.shape[-2:] and raw_u.shape[-2:] == self.grid.center_mask.shape: 
+            if raw_u.shape[-2:] == raw_v.shape[-2:] and raw_u.shape[-2:] == self.grid.center_mask.shape:
                 #raw u/v are same shape and on center
                 #need to padding_slice the variable since they are not interpolated from u/v
                 x = x[(np.s_[:],) + ctr_padding_slice]

py_gnome/gnome/environment/wind.py

@@ -509,7 +509,7 @@ def get_value(self, time):
 
         return tuple(data[0]['value'])
 
-    def at(self, points, time, *, units=None, extrapolate=False, coord_sys='uv',_auto_align=True, **kwargs):
+    def at(self, points, time, *, units=None, extrapolate=None, coord_sys='uv',_auto_align=True, **kwargs):
         # fixme: this isn't quite aligned with the Environment base class signature.
         # it should be:
         # def at(self, points, time, units=None, extrapolate=False, coord_sys='uv', _auto_align=True):
@@ -553,17 +553,24 @@ def at(self, points, time, *, units=None, extrapolate=False, coord_sys='uv',_aut
         else:
             raise ValueError('invalid coordinate system {0}'.format(coord_sys))
 
-        if extrapolate:
-            self.extrapolation_is_allowed = True
-        else:
-            self.extrapolation_is_allowed = False
+        # since extrapolation_is_allowed is not passed into the C code we need
+        # to temporarily set it if extrapolate is passed in, and then change it back
+        original_extrapolation =  self.extrapolation_is_allowed # save value
+        if extrapolate is not None: # passed in a value, assume this is what we want
+            self.extrapolation_is_allowed = extrapolate
+        else: # otherwise probably set on the wind_mover
+            if self.extrapolation_is_allowed is None: # shouldn't happen
+                self.extrapolation_is_allowed = False
         #print(f"{self.extrapolation_is_allowed=}")
         try:
             data = self.get_wind_data(time, 'm/s', cs)[0]['value']
         except IndexError:
             # CyTimeseries is raising an IndexError
             raise ValueError(f'time specified ({time}) is not within the bounds of the time: '
                              f'({self.data_start} to {self.data_stop})')
+        finally: # make sure it gets restored even if there's an error
+            self.extrapolation_is_allowed = original_extrapolation # put it back the way it was
+
         if idx is None:
             ret_data[:, 0] = data[0]
             ret_data[:, 1] = data[1]