feat: output netCDF4 files for all geocenter runs

.github/workflows/auto-update-files.yml

@@ -24,7 +24,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:
@@ -64,7 +64,7 @@ jobs:
         fi
     - name: Create pull request
       if: steps.changes.outputs.DETECTED == 'true'
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v5
       with:
         assignees: ${{ github.actor }}
         title: "data: automatic time updates"

.github/workflows/python-publish.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/python-request.yml

@@ -22,7 +22,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:

gravity_toolkit/geocenter.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 geocenter.py
-Written by Tyler Sutterley (05/2023)
+Written by Tyler Sutterley (09/2023)
 Data class for reading and processing geocenter data
 
 PYTHON DEPENDENCIES:
@@ -15,6 +15,8 @@
         https://github.com/yaml/pyyaml
 
 UPDATE HISTORY:
+    Updated 09/2023: add group option to netCDF read function
+        add functions to return variables or class attributes
     Updated 05/2023: use pathlib to define and operate on paths
     Updated 03/2023: convert shape and ndim to harmonic class properties
         improve typing for variables in docstrings
@@ -54,10 +56,7 @@
 try:
     import netCDF4
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("netCDF4 not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 class geocenter(object):
     """
@@ -788,7 +787,7 @@ def from_tellus(self, geocenter_file, **kwargs):
         # return the geocenter harmonics
         return self
 
-    def from_netCDF4(self, geocenter_file, **kwargs):
+    def from_netCDF4(self, geocenter_file, group=None, **kwargs):
         """
         Reads geocenter file and extracts dates and spherical harmonic data
         from a netCDF4 file
@@ -797,6 +796,8 @@ def from_netCDF4(self, geocenter_file, **kwargs):
         ----------
         geocenter_file: str
             degree 1 netCDF4 file
+        group: str or NoneType, default None
+            netCDF4 group name
         compression: str or NoneType, default None
             file compression type
 
@@ -807,7 +808,7 @@ def from_netCDF4(self, geocenter_file, **kwargs):
             and ocean model outputs", *Remote Sensing*, 11(18), 2108, (2019).
             `doi: 10.3390/rs11182108 <https://doi.org/10.3390/rs11182108>`_
         """
-        kwargs.setdefault('compression',None)
+        kwargs.setdefault('compression', None)
         # set filename
         self.case_insensitive_filename(geocenter_file)
         # Open the netCDF4 file for reading
@@ -822,10 +823,12 @@ def from_netCDF4(self, geocenter_file, **kwargs):
                 memory=self.filename.read())
         else:
             fileID = netCDF4.Dataset(self.filename, mode='r')
+        # check if reading from root group or sub-group
+        ncf = fileID.groups[group] if group else fileID
         # Getting the data from each netCDF4 variable
         DEG1 = {}
         # converting netCDF4 objects into numpy arrays
-        for key,val in fileID.variables.items():
+        for key, val in ncf.variables.items():
             DEG1[key] = val[:].copy()
         # close the netCDF4 file
         fileID.close()
@@ -1241,6 +1244,36 @@ def power(self, power):
         temp.S11 = np.power(self.S11,power)
         return temp
 
+    def get(self, field: str):
+        """
+        Get a field from the ``geocenter`` object
+
+        Parameters
+        ----------
+        field: str
+            field name
+
+        Returns
+        -------
+        var: np.ndarray
+            variable for field
+        """
+        var = getattr(self, field)
+        return copy.copy(var)
+
+    @property
+    def fields(self):
+        return ['C10', 'C11', 'S11']
+
+    def __str__(self):
+        """String representation of the ``geocenter`` object
+        """
+        properties = ['gravity_toolkit.geocenter']
+        if self.month:
+            properties.append(f"    start_month: {min(self.month)}")
+            properties.append(f"    end_month: {max(self.month)}")
+        return '\n'.join(properties)
+
     def __len__(self):
         """Number of months
         """

gravity_toolkit/harmonics.py

@@ -111,20 +111,15 @@
 try:
     from geoid_toolkit.read_ICGEM_harmonics import read_ICGEM_harmonics
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("geoid_toolkit not available", ImportWarning)
 try:
     import h5py
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     import netCDF4
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("netCDF4 not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 class harmonics(object):
     """

gravity_toolkit/read_gfc_harmonics.py

@@ -77,10 +77,7 @@
 try:
     from geoid_toolkit.read_ICGEM_harmonics import read_ICGEM_harmonics
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("geoid_toolkit not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read spherical harmonic coefficients of a gravity model
 def read_gfc_harmonics(input_file, TIDE=None, FLAG='gfc'):

gravity_toolkit/spatial.py

@@ -87,15 +87,11 @@
 try:
     import h5py
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     import netCDF4
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("netCDF4 not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 class spatial(object):
     """

gravity_toolkit/tools.py

@@ -54,24 +54,20 @@
 try:
     import ipywidgets
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("ipywidgets not available", ImportWarning)
 try:
     import matplotlib.cm as cm
     import matplotlib.colors as colors
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("matplotlib not available", ImportWarning)
 try:
     from tkinter import Tk, filedialog
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("tkinter not available", ImportWarning)
     filedialog = None
 try:
     import IPython.display
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("IPython.display not available", ImportWarning)
 # ignore warnings
 warnings.filterwarnings('ignore')

gravity_toolkit/utilities.py

@@ -85,10 +85,7 @@
 try:
     import boto3
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("boto3 not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: get absolute path within a package from a relative path
 def get_data_path(relpath: list | str | pathlib.Path):