refactor: use wrapper to importlib for optional dependencies (#146)

feat: make classes subscriptable and allow item assignment
feat: add lomb scargle wrapper program
refactor: remove timescale class and leap second calculations

doc/source/api_reference/time.rst

@@ -82,12 +82,3 @@ General Methods
 .. autofunction:: gravity_toolkit.time.convert_calendar_decimal
 
 .. autofunction:: gravity_toolkit.time.convert_julian
-
-.. autoclass:: gravity_toolkit.time.timescale
-   :members:
-
-.. autofunction:: gravity_toolkit.time.count_leap_seconds
-
-.. autofunction:: gravity_toolkit.time.get_leap_seconds
-
-.. autofunction:: gravity_toolkit.time.update_leap_seconds

doc/source/api_reference/time_series/lomb_scargle.rst

@@ -0,0 +1,11 @@
+========================
+time_series.lomb_scargle
+========================
+
+- Wrapper function for computing Lomb-Scargle periodograms using ``scipy.signal.lombscargle``
+
+`Source code`__
+
+.. __: https://github.com/tsutterley/gravity-toolkit/blob/main/gravity_toolkit/time_series/lomb_scargle.py
+
+.. autofunction:: gravity_toolkit.time_series.lomb_scargle

doc/source/api_reference/time_series/regress.rst

@@ -10,7 +10,7 @@ Calling Sequence
 .. code-block:: python
 
     import gravity_toolkit.time_series
-   tsbeta = gravity_toolkit.time_series.regress(t_in, d_in, ORDER=1, CYCLES=[0.5,1.0], CONF=0.95)
+    tsbeta = gravity_toolkit.time_series.regress(t_in, d_in, ORDER=1, CYCLES=[0.5,1.0], CONF=0.95)
 
 `Source code`__
 

doc/source/index.rst

@@ -74,6 +74,7 @@ missions
     api_reference/time.rst
     api_reference/time_series/amplitude.rst
     api_reference/time_series/fit.rst
+    api_reference/time_series/lomb_scargle.rst
     api_reference/time_series/piecewise.rst
     api_reference/time_series/regress.rst
     api_reference/time_series/savitzky_golay.rst

gravity_toolkit/geocenter.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 geocenter.py
-Written by Tyler Sutterley (09/2023)
+Written by Tyler Sutterley (06/2024)
 Data class for reading and processing geocenter data
 
 PYTHON DEPENDENCIES:
@@ -15,6 +15,8 @@
         https://github.com/yaml/pyyaml
 
 UPDATE HISTORY:
+    Updated 06/2024: use wrapper to importlib for optional dependencies
+    Updated 05/2024: make subscriptable and allow item assignment
     Updated 09/2023: add group option to netCDF read function
         add functions to return variables or class attributes
         prevent double printing of filenames when using debug
@@ -47,17 +49,13 @@
 import time
 import uuid
 import yaml
-import logging
 import pathlib
-import warnings
 import numpy as np
 import gravity_toolkit.time
+from gravity_toolkit.utilities import import_dependency
 
 # attempt imports
-try:
-    import netCDF4
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("netCDF4 not available", ImportWarning)
+netCDF4 = import_dependency('netCDF4')
 
 class geocenter(object):
     """
@@ -1300,3 +1298,9 @@ def __next__(self):
         # add to index
         self.__index__ += 1
         return temp
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)

gravity_toolkit/harmonics.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 harmonics.py
-Written by Tyler Sutterley (10/2023)
+Written by Tyler Sutterley (06/2024)
 Contributions by Hugo Lecomte
 
 Spherical harmonic data class for processing GRACE/GRACE-FO Level-2 data
@@ -25,6 +25,8 @@
     destripe_harmonics.py: filters spherical harmonics for correlated errors
 
 UPDATE HISTORY:
+    Updated 06/2024: use wrapper to importlib for optional dependencies
+    Updated 05/2024: make subscriptable and allow item assignment
     Updated 10/2023: place time and month variables in try/except block
     Updated 09/2023: prevent double printing of filenames when using debug
     Updated 08/2023: add string representation of the harmonics object
@@ -100,28 +102,19 @@
 import logging
 import pathlib
 import zipfile
-import warnings
 import numpy as np
 import gravity_toolkit.version
 from gravity_toolkit.time import adjust_months,calendar_to_grace
 from gravity_toolkit.destripe_harmonics import destripe_harmonics
 from gravity_toolkit.read_gfc_harmonics import read_gfc_harmonics
 from gravity_toolkit.read_GRACE_harmonics import read_GRACE_harmonics
-from gravity_toolkit.utilities import reify
+from gravity_toolkit.utilities import import_dependency, reify
 
 # attempt imports
-try:
-    from geoid_toolkit.read_ICGEM_harmonics import read_ICGEM_harmonics
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("geoid_toolkit not available", ImportWarning)
-try:
-    import h5py
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("h5py not available", ImportWarning)
-try:
-    import netCDF4
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("netCDF4 not available", ImportWarning)
+geoidtk = import_dependency('geoid_toolkit')
+h5py = import_dependency('h5py')
+netCDF4 = import_dependency('netCDF4')
+sparse = import_dependency('sparse')
 
 class harmonics(object):
     """
@@ -520,7 +513,7 @@ def from_gfc(self, filename, **kwargs):
             Ylms = read_gfc_harmonics(self.filename,
                 TIDE=kwargs['tide'])
         else:
-            Ylms = read_ICGEM_harmonics(self.filename,
+            Ylms = geoidtk.read_ICGEM_harmonics(self.filename,
                 TIDE=kwargs['tide'])
         # Output file information
         logging.info(self.filename)
@@ -1188,6 +1181,18 @@ def to_masked_array(self):
             self.squeeze()
         # return the triangular matrix
         return Ylms
+
+    def to_coo_array(self):
+        """
+        Convert data arrays to a COO sparse matrices
+        """
+        # assign degree and order fields
+        self.update_dimensions()
+        # create COO sparse matrices
+        self.clm = sparse.COO(self.clm)
+        self.slm = sparse.COO(self.slm)
+        # return the harmonics object
+        return self
 
     def update_dimensions(self):
         """
@@ -1930,3 +1935,9 @@ def __next__(self):
         # add to index
         self.__index__ += 1
         return temp
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)

gravity_toolkit/read_gfc_harmonics.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 read_gfc_harmonics.py
-Written by Tyler Sutterley (05/2023)
+Written by Tyler Sutterley (06/2023)
 Contributions by Hugo Lecomte
 
 Reads gfc files and extracts spherical harmonics for Swarm and
@@ -55,6 +55,7 @@
     calculate_tidal_offset.py: calculates the C20 offset for a tidal system
 
 UPDATE HISTORY:
+    Updated 06/2024: use wrapper to importlib for optional dependencies
     Updated 05/2023: use pathlib to define and operate on paths
     Updated 03/2023: improve typing for variables in docstrings
     Updated 04/2022: updated docstrings to numpy documentation format
@@ -69,15 +70,12 @@
 """
 import re
 import pathlib
-import warnings
 import numpy as np
 import gravity_toolkit.time
+from gravity_toolkit.utilities import import_dependency
 
 # attempt imports
-try:
-    from geoid_toolkit.read_ICGEM_harmonics import read_ICGEM_harmonics
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("geoid_toolkit not available", ImportWarning)
+geoidtk = import_dependency('geoid_toolkit')
 
 # PURPOSE: read spherical harmonic coefficients of a gravity model
 def read_gfc_harmonics(input_file, TIDE=None, FLAG='gfc'):
@@ -199,7 +197,7 @@ def read_gfc_harmonics(input_file, TIDE=None, FLAG='gfc'):
 
     # python dictionary with model input and headers
     ZIP = bool(re.search('ZIP', SFX, re.IGNORECASE))
-    model_input = read_ICGEM_harmonics(input_file, TIDE=TIDE,
+    model_input = geoidtk.read_ICGEM_harmonics(input_file, TIDE=TIDE,
         FLAG=FLAG, ZIP=ZIP)
 
     # start and end day of the year

gravity_toolkit/read_love_numbers.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 read_love_numbers.py
-Written by Tyler Sutterley (08/2023)
+Written by Tyler Sutterley (05/2024)
 
 Reads sets of load Love numbers from PREM and applies isomorphic parameters
 Linearly interpolates load Love/Shida numbers for missing degrees
@@ -56,6 +56,7 @@
         103(B12), 30205-30229, (1998)
 
 UPDATE HISTORY:
+    Updated 05/2024: make subscriptable and allow item assignment
     Updated 08/2023: add string representation of the love_numbers class
     Updated 05/2023: use pathlib to define and operate on paths
     Updated 03/2023: improve typing for variables in docstrings
@@ -621,3 +622,9 @@ def __iter__(self):
         yield self.hl
         yield self.kl
         yield self.ll
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)

gravity_toolkit/spatial.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 spatial.py
-Written by Tyler Sutterley (10/2023)
+Written by Tyler Sutterley (06/2024)
 
 Data class for reading, writing and processing spatial data
 
@@ -20,6 +20,8 @@
     time.py: utilities for calculating time operations
 
 UPDATE HISTORY:
+    Updated 06/2024: use wrapper to importlib for optional dependencies
+    Updated 05/2024: make subscriptable and allow item assignment
     Updated 10/2023: place time and month variables in try/except block
     Updated 09/2023: prevent double printing of filenames when using debug
     Updated 08/2023: add string representation of the spatial object
@@ -80,20 +82,14 @@
 import logging
 import pathlib
 import zipfile
-import warnings
 import numpy as np
 import gravity_toolkit.version
 from gravity_toolkit.time import adjust_months, calendar_to_grace
+from gravity_toolkit.utilities import import_dependency
 
 # attempt imports
-try:
-    import h5py
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("h5py not available", ImportWarning)
-try:
-    import netCDF4
-except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.warn("netCDF4 not available", ImportWarning)
+h5py = import_dependency('h5py')
+netCDF4 = import_dependency('netCDF4')
 
 class spatial(object):
     """
@@ -2019,3 +2015,9 @@ def update_mask(self):
             if getattr(self, 'magnitude') is not None:
                 self.magnitude[self.mask] = self.fill_value
         return self
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)