Merge branch 'develop'

.gitignore

@@ -171,6 +171,7 @@ test_image_save.gif
 test_image_save.jpg
 test_image_save.png
 test_image_text.png
+py_gnome/MapBounds_Island_anim.gif
 py_gnome/scripts/script_long_island/CLISShio.txt
 py_gnome/scripts/script_long_island/LI_tidesWAC.CUR
 py_gnome/scripts/script_long_island/LongIslandSoundMap.BNA

.gitlab-ci.yml

@@ -44,15 +44,16 @@ compile_pygnome:
 
     - apt-get install git g++ make libxext-dev libsm-dev libxrender-dev -y
 
-    # get the adios_db code: needed for tests and requirements
-    - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    # # get the adios_db code: needed for tests and requirements
+    # no longer needed -- pygnome is pulling adios_db from conda-forge
+    # - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
     - cd ./py_gnome
     - conda install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
-                                          --file ../oil_database/adios_db/conda_requirements.txt
+    #                                       --file ../oil_database/adios_db/conda_requirements.txt
 
-    # install adios_db
-    - pip install ../oil_database/adios_db/
+    # # install adios_db
+    # - pip install ../oil_database/adios_db/
 
     # Install pygnome
     # If you want verbose output including the compiler/linker commands,
@@ -62,6 +63,7 @@ compile_pygnome:
     # And there may be times we want to build a wheel file (.whl)
     # The following command will build a wheel in the current directory:
     #   python -m pip wheel ./
+
     - echo "compiling PyGNOME"
     - python -m pip install ./
 
@@ -169,19 +171,20 @@ test_pygnome_windows:
   script:
     - echo "Building and testing PyGNOME"
 
+    # pulled from conda-forge now
     # get the adios_db code: needed for tests and requirements
-    - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    # - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     - conda install -y python=$PYTHON_VER mamba
     - cd ./py_gnome
     - echo "Setting up conda environment"
     - mamba install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
                                           --file conda_requirements_test.txt
-                                          --file ../oil_database/adios_db/conda_requirements.txt
+                                          # --file ../oil_database/adios_db/conda_requirements.txt
 
     # install adios_db
-    - pip install ../oil_database/adios_db/
+    # - pip install ../oil_database/adios_db/
 
     # Install pygnome
     # If you want verbose output including the compiler/linker commands,
@@ -208,8 +211,8 @@ build_develop:
     - echo '' # manual override of before_script because we're on runner 12.3 and inherit options are only 12.9+
   script:
     # get the adios_db code, so we can install it in the docker image
-    # note -- is should already be there
-    - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    # note -- is should already be there from conda-forge
+    # - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     # build the py_gnome image
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -228,8 +231,8 @@ build_main:
     - echo '' # manual override of before_script because we're on runner 12.3 and inherit options are only 12.9+
   script:
     # get the adios_db code, so we can install it in the docker image
-    # note -- is should already be there
-    - git clone --depth 1 -b production https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    # note -- is should already be there -- from conda-forge
+    # - git clone --depth 1 -b production https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     # build the docs image
     - docker build -f dockerfile-docs ./py_gnome/documentation/build/html -t registry.orr.noaa.gov/gnome/pygnome/docs
@@ -253,7 +256,8 @@ build_production:
     - echo ''
   script:
     # get the adios_db code, so we can install it in the docker image
-    - git clone --depth 1 -b production https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    # should be there from conda-forge
+    # - git clone --depth 1 -b production https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
     - docker build . --build-arg PYTHON_VER=$PYTHON_VER -t registry.orr.noaa.gov/gnome/pygnome:production

Installing.rst

@@ -19,7 +19,7 @@ Create an environment for PyGNOME with all requirements:
 
 If you only need to run PyGNOME::
 
-    > conda create -n gnome --file python=3.10 conda_requirements.txt
+    > conda create -n gnome python=3.10 --file  conda_requirements.txt
 
 If you need to build, etc PyGNOME::
 

dockerfile

@@ -17,10 +17,10 @@ WORKDIR /pygnome/
 
 RUN conda install python=$PYTHON_VER \
     --file py_gnome/conda_requirements.txt \
-    --file py_gnome/conda_requirements_build.txt \
-    --file oil_database/adios_db/conda_requirements.txt
+    --file py_gnome/conda_requirements_build.txt
+#    --file oil_database/adios_db/conda_requirements.txt
 
-RUN cd oil_database/adios_db && python -m pip install ./
+# RUN cd oil_database/adios_db && python -m pip install ./
 
 RUN cd py_gnome && python -m pip install ./
 

py_gnome/conda_requirements.txt

@@ -15,18 +15,19 @@
 # if you want a full development environment,
 # you can install the whole thing at once:
 #
-# conda create -n gnome python=3.10 --file conda_requirements.txt --file conda_requirements_build.txt --file conda_requirements_test.txt --file conda_requirements_docs.txt
+# conda create -n gnome python=3.12 --file conda_requirements.txt --file conda_requirements_build.txt --file conda_requirements_test.txt --file conda_requirements_docs.txt
 
 
 # These packages should all be in one of the following channels:
 # defaults
 # conda-forge
 
-# it'll probably work with 3.9 -- 3.12, but CI is testing with 3.10
+# it'll probably work with 3.9 -- 3.13, but CI is testing with 3.10
 
-python>=3.9,<3.12
+python>=3.9,<=3.12
 
 ## System libs
+awesome-slugify
 colander <2
 progressbar
 psutil
@@ -55,7 +56,7 @@ pyproj
 shapely>=2.0.6 # older one broken with numpy2
 
 # NOAA maintained packages
-gridded>=0.6.9
+gridded>=0.6.10
 pynucos>=3.3.0
 cell_tree2d
 py_gd>=2.3

py_gnome/conda_requirements_build.txt

@@ -2,11 +2,12 @@
 # NOTE: you also need a compiler set up to build Python extensions
 
 cython=3.*
+pip
 setuptools>=62  # older versions uses different build dirs
 # setuptools-scm>=6.2
+pip
 gitpython
 python-build
 cmake
 ninja
 scikit-build-core>=0.9.9
-# hatchling

create_conda_env.py → py_gnome/create_conda_env.py

@@ -13,7 +13,7 @@
 
 default is "all" -- full dev environment
 
-"run" will only give you wnat you need to run the code
+"run" will only give you what you need to run the code
 
 "build" will add what's needed to build PYGNOME
 
@@ -28,10 +28,10 @@
 Will create and environment called "gnome" with everything needed to
 build, run and test PyGNOME
 
-NOTE: currently hard-coded for Python 3.10
+NOTE: currently hard-coded for Python 3.12
 """
 
-PYTHON="3.10"
+PYTHON="3.12"
 
 if __name__ == "__main__":
     try:
@@ -57,6 +57,7 @@
     for req in reqs:
         cmd.extend(["--file", req])
     print("running\n", cmd)
+    # subprocess.run(cmd, shell=True)
     subprocess.run(cmd)
 
 

py_gnome/documentation/source/scripting/model.rst

@@ -30,7 +30,7 @@ Wind, currents, and diffusion all have uncertainty parameters with default value
 You can set the coefficients that control the size and distribution of the uncertainty on the individual movers.
 The uncertainty only applies to the model transport. Uncertainty for weathering is under development.
 
-To run the model backwards, set both the time_step and the duration to negative values
+To run the model backwards, include run_backwards=True. The model will start at the start_time and step backwards through the duration.
 
 
 Configuring the Model

py_gnome/documentation/source/scripting/sample_scripts.rst

@@ -44,6 +44,12 @@ A script that demonstrates how to use gridded currents and winds from netcdf fil
 Demonstration of adding uncertainty to a model, and adjusting the uncertainty parameters of a current mover.
 
 
+``polygon_release_script.py``
+---------------------
+
+A script that demonstrates how to create a spill from a shape file or list of polygons.
+
+
 Testing Scripts
 ===============
 

py_gnome/documentation/source/scripting/scripting_intro.rst

@@ -46,8 +46,8 @@ This example does not load any external data, but creates a simple map and mover
 The "spill" is a conservative substance, i.e. a "passive tracer."
 
 This example is in the PyGNOME source under "scripts/example_scripts", or can be downloaded here:
-.. this download link is getting rendered oddly -- and why do I need so many ../?
-:download:`simple_script.py <../../../../../scripts/example_scripts/simple_script.py`
+
+:download:`simple_script.py <../../../../../scripts/example_scripts/simple_script.py>`
 
 Initialize the Model
 --------------------

py_gnome/documentation/source/scripting/spills.rst

@@ -86,6 +86,29 @@ Polygon Releases
 The :class:`gnome.spills.release.PolygonRelease` Object releases particles distributed over a polygon or set
 of polygons. The particles are distributed randomly over the polygons with a simple weighting by polygon area (i.e., geographically larger polygons will be seeded with more particles). The subclass :class:`gnome.spills.release.NESDISRelease` can be used specifically with the |nesdis_reports| operationally produced by NOAA's Office of Satellite and Product Operations.
 
+Here's an example setting up a spill from a polygon. The polygon file used in the example can be accessed :download:`here <spatial_example.zip>`. A list of polygons can be used instead of a shapefile:
+
+.. code-block:: python
+
+    import gnome.scripting as gs
+    start_time = "2024-10-01T00:00"
+    model = gs.Model(start_time=start_time,
+                     duration=gs.days(2),
+                     time_step=60 * 60  # 1 hour in seconds
+                     )
+    release = gs.PolygonRelease(filename='spatial_example.zip',
+                                  release_time=start_time
+                                  )
+    spill = gs.Spill(release=release)
+    model.spills += spill
+
+You can find a complete script using a PolygonRelease in:
+
+``pygnome/py_gnome/scripts/example_scripts/polygon_release_script.py``
+
+Or download it here:
+:download:`polygon_release_script.py <../../../scripts/example_scripts/polygon_release_script.py>`
+
 
 Using Helper Functions
 ----------------------
@@ -126,6 +149,32 @@ The helper function creates both the ``Release`` and the ``Substance`` objects a
 
     model.full_run()
 
+Similarly we can use the :func:`gnome.scripting.polygon_release_spill` helper function to initialize a polygon spill.
+The oil type is specified using the sample oil file provided above with a spill volume of 1000 barrels. The polygon shapefile used is the sample file provided above.
+
+.. code-block:: python
+
+    import gnome.scripting as gs
+    start_time = gs.asdatetime("2024-10-01T00:00")
+    model = gs.Model(start_time=start_time,
+                     duration=gs.days(2),
+                     time_step=60 * 60, # 1 hour in seconds
+                     )
+
+    spill = gs.polygon_release_spill(filename='spatial_example.zip',
+                                        release_time=start_time,
+                                        amount=1000,
+                                        substance=gs.GnomeOil(filename='alaska-north-slope_AD00020.json'),
+                                        units='bbl',
+                                        windage_range=(0.01, 0.02),
+                                        windage_persist=-1,
+                                        name='polygon spill')
+    model.spills += spill
+
+    # ... add movers/weatherers
+
+    model.full_run()
+
 .. _subsurface_plume:
 
 Subsurface plume

py_gnome/gnome/__init__.py

@@ -66,7 +66,7 @@ def ver_check(required, installed):
         else:
             return True
 
-    libs = [('gridded', '0.6.9', ''),
+    libs = [('gridded', '0.6.10', ''),
             ('nucos', '3.3.0', ''),
             ('py_gd', '2.3.0', ''),
             ('adios_db', '1.2.4', 'Only required to use the ADIOS Database '

py_gnome/gnome/cy_gnome/cy_cats_mover.pyx

@@ -261,12 +261,17 @@ cdef class CyCatsMover(CyCurrentMover):
         cdef OSErr err
 
         err = self.cats.InitMover()
-        if err is not False:
-            raise ValueError('CATSMover.compute_velocity_scale(..) '
-                             'returned an error. Reference point not valid. OSErr: {0}'
-                             .format(err))
+        if err:
+            return err
 
-        return True
+# Make this a runtime error or warning, let calling function decide
+#         if err is not False:
+#             raise ValueError('CATSMover.compute_velocity_scale(..) '
+#                              'returned an error. Reference point not valid. OSErr: {0}'
+#                              .format(err))
+
+        #return True
+        return 0
 
     def get_move(self,
                  model_time,

py_gnome/gnome/environment/environment_objects.py

@@ -246,9 +246,13 @@ def get_data_vectors(self):
             if 'degree' in self.angle.units:
                 raw_ang = raw_ang * np.pi/180.
 
-            ctr_mask = gridded.utilities.gen_celltree_mask_from_center_mask(self.grid.center_mask, angle_padding_slice)
+            if self.grid.center_mask is not None:
+                ctr_mask = gridded.utilities.gen_celltree_mask_from_center_mask(self.grid.center_mask, angle_padding_slice)
+                ctr_mask = ctr_mask.reshape(-1)
+            else:
+                ctr_mask = False
             ang = raw_ang.reshape(-1)
-            ang = np.ma.MaskedArray(ang, mask = ctr_mask.reshape(-1))
+            ang = np.ma.MaskedArray(ang, mask = ctr_mask)
             ang = ang.compressed()
 
             x = lin_u[:] * np.cos(ang) - lin_v[:] * np.sin(ang)

py_gnome/gnome/environment/gridded_objects_base.py

@@ -257,7 +257,7 @@ def get_centers(self):
             lats = (self.node_lat[0:-1, 0:-1] + self.node_lat[1:, 1:]) / 2
             return np.stack((lons, lats), axis=-1).reshape(-1, 2)
         else:
-            if self._get_geo_mask('center'):
+            if self._get_geo_mask('center') is not None:
                 if not self._cell_tree:
                     self.build_celltree(use_mask=True)
                 ctr_padding_slice = self.get_padding_slices(self.center_padding)

py_gnome/gnome/environment/names.py

@@ -16,13 +16,13 @@
 
 **nc_names:**
 
-These are common variable names used for the variables PyGNOME uses. If you set the variable names in
-a netcdf files to one these names, PYGNOME should be able to load the file.
+These are common variable names used for the variables PyGNOME uses.
+If you set the variable names in a netcdf files to one these names,
+PyGNOME should be able to load the file.
 
 **Name Mapping:**
 
 
-
 **grid_temperature**
 
   Default Names: temp, water_t, TEMP, WATER_T
@@ -175,15 +175,17 @@ def capitalize_name_mapping(name_map):
     for variable, data in name_map.items():
         def_names = data['default_names']
         try:
-            for name in def_names[:]:
-                def_names.append(name.upper())
-            def_names[:] = list(set(def_names))
-        except TypeError:  # it's nested
             for sub_var in def_names.values():
                 for name in sub_var[:]:
                     sub_var.append(name.upper())
                     # eliminate the duplicates
                 sub_var[:] = list(set(sub_var))
+        except AttributeError:  # it's not nested
+            for name in def_names[:]:
+                def_names.append(name.upper())
+            def_names[:] = list(set(def_names))
+
+
 capitalize_name_mapping(nc_names)
 
 def insert_names_table(table_text):