Merge pull request #1002 from MPAS-Dev/develop

Merge develop into main

ci/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.10.0" %}
+{% set version = "1.11.0rc1" %}
 
 package:
   name: {{ name|lower }}
@@ -27,7 +27,7 @@ requirements:
     - cartopy_offlinedata
     - cmocean
     - dask
-    - esmf >=8.4.2,<8.5.0
+    - esmf >=8.4.2,<8.7.0
     - esmf=*=mpi_mpich_*
     - f90nml
     - geometric_features >=1.2.0
@@ -46,7 +46,7 @@ requirements:
     - pyremap >=1.2.0,<2.0.0
     - python-dateutil
     - requests
-    - scipy
+    - scipy >=1.7.0
     - setuptools
     - shapely >=2.0,<3.0
     - xarray >=0.14.1

dev-spec.txt

@@ -8,7 +8,7 @@ cartopy >=0.18.0
 cartopy_offlinedata
 cmocean
 dask
-esmf >=8.4.0,<8.5.0
+esmf >=8.4.2,<8.7.0
 esmf=*=mpi_mpich_*
 f90nml
 geometric_features>=1.2.0
@@ -29,7 +29,7 @@ pyproj
 pyremap>=1.2.0,<2.0.0
 python-dateutil
 requests
-scipy
+scipy >=1.7.0
 setuptools
 shapely>=2.0,<3.0
 xarray>=0.14.1

docs/versions.rst

@@ -21,6 +21,7 @@ Documentation    On GitHub
 `v1.8.0`_        `1.8.0`_
 `v1.9.0`_        `1.9.0`_
 `v1.10.0`_       `1.10.0`_
+`v1.11.0`_       `1.11.0`_
 ================ ===============
 
 .. _`stable`: ../stable/index.html
@@ -40,6 +41,7 @@ Documentation    On GitHub
 .. _`v1.8.0`: ../1.8.0/index.html
 .. _`v1.9.0`: ../1.9.0/index.html
 .. _`v1.10.0`: ../1.10.0/index.html
+.. _`v1.11.0`: ../1.11.0/index.html
 .. _`main`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/main
 .. _`develop`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/develop
 .. _`1.2.6`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.2.6
@@ -57,3 +59,4 @@ Documentation    On GitHub
 .. _`1.8.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.8.0
 .. _`1.9.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.9.0
 .. _`1.10.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.10.0
+.. _`1.11.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.11.0

mpas_analysis/__init__.py

@@ -3,5 +3,5 @@
 import matplotlib as mpl
 mpl.use('Agg')
 
-__version_info__ = (1, 10, 0)
+__version_info__ = (1, 11, 0)
 __version__ = '.'.join(str(vi) for vi in __version_info__)

mpas_analysis/default.cfg

@@ -3970,6 +3970,9 @@ areaSH = IceArea_timeseries/iceAreaSH_climo_20180710.nc
 volNH = PIOMAS/PIOMASvolume_monthly_climo_20180710.nc
 volSH = none
 
+# mask sea ice that is thicker than this a threshold (m)
+maxAllowedSeaIceThickness = None
+
 
 [climatologyMapSeaIceProductionNH]
 # options related to plotting horizontally remapped climatologies of

mpas_analysis/ocean/index_nino34.py

@@ -16,6 +16,7 @@
 import pandas as pd
 import numpy as np
 from scipy import signal, stats
+from scipy.signal.windows import tukey
 import matplotlib.pyplot as plt
 
 from mpas_analysis.shared.climatology import climatology
@@ -400,7 +401,7 @@ def _compute_nino34_spectra(self, nino34Index):
 
         # Move nino34Index to numpy to allow functionality with scipy routines
         ninoIndex = nino34Index.values
-        window = signal.tukey(len(ninoIndex), alpha=0.1)
+        window = tukey(len(ninoIndex), alpha=0.1)
         f, Pxx = signal.periodogram(window * ninoIndex,
                                     1.0 / constants.sec_per_month)
 

mpas_analysis/sea_ice/time_series.py

@@ -9,6 +9,7 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/MPAS-Analysis/main/LICENSE
 
+import numpy as np
 import xarray as xr
 
 from mpas_analysis.shared import AnalysisTask
@@ -590,6 +591,14 @@ def _compute_area_vol(self):
         config = self.config
         chunkYears = config.getint('timeSeriesSeaIceAreaVol', 'chunkYears')
 
+        maxAllowedSeaIceThickness = config.get(
+            'timeSeriesSeaIceAreaVol', 'maxAllowedSeaIceThickness')
+
+        if maxAllowedSeaIceThickness == 'None':
+            maxAllowedSeaIceThickness = None
+        else:
+            maxAllowedSeaIceThickness = float(maxAllowedSeaIceThickness)
+
         outFileNames = {}
         for hemisphere in ['NH', 'SH']:
             baseDirectory = build_config_full_path(
@@ -612,6 +621,10 @@ def _compute_area_vol(self):
             startDate=self.startDate,
             endDate=self.endDate)
 
+        ds = ds.rename(
+            {'timeMonthly_avg_iceAreaCell': 'iceConc',
+                'timeMonthly_avg_iceVolumeCell': 'iceThick'})
+
         nTime = ds.sizes['Time']
         # chunk into 10-year seguments so we don't run out of memory
         if nTime > 12 * chunkYears:
@@ -624,22 +637,26 @@ def _compute_area_vol(self):
             else:
                 mask = dsMesh.latCell < 0
 
+            if maxAllowedSeaIceThickness is not None:
+                mask = np.logical_and(mask,
+                                      ds.iceThick <= maxAllowedSeaIceThickness)
+
             dsAreaSum = (ds.where(mask) * dsMesh.areaCell).sum('nCells')
             dsAreaSum = dsAreaSum.rename(
-                {'timeMonthly_avg_iceAreaCell': 'iceArea',
-                 'timeMonthly_avg_iceVolumeCell': 'iceVolume'})
+                {'iceConc': 'iceArea',
+                 'iceThick': 'iceVolume'})
             dsAreaSum['iceThickness'] = (dsAreaSum.iceVolume /
                                          dsMesh.areaCell.sum('nCells'))
 
             dsAreaSum['iceArea'].attrs['units'] = 'm$^2$'
             dsAreaSum['iceArea'].attrs['description'] = \
-                'Total {} sea ice area'.format(hemisphere)
+                f'Total {hemisphere} sea ice area'
             dsAreaSum['iceVolume'].attrs['units'] = 'm$^3$'
             dsAreaSum['iceVolume'].attrs['description'] = \
-                'Total {} sea ice volume'.format(hemisphere)
+                f'Total {hemisphere} sea ice volume'
             dsAreaSum['iceThickness'].attrs['units'] = 'm'
             dsAreaSum['iceThickness'].attrs['description'] = \
-                'Mean {} sea ice volume'.format(hemisphere)
+                f'Mean {hemisphere} sea ice volume'
 
             dsTimeSeries[hemisphere] = dsAreaSum
 

setup.py

@@ -31,7 +31,7 @@
      'pyproj',
      'python-dateutil',
      'requests',
-     'scipy',
+     'scipy>=1.7.0',
      'setuptools',
      'shapely>=2.0,<3.0',
      'six',
@@ -41,9 +41,8 @@
 with open(os.path.join(here, 'mpas_analysis', '__init__.py')) as f:
     init_file = f.read()
 
-# version = re.search(r'{}\s*=\s*[(]([^)]*)[)]'.format('__version_info__'),
-#                     init_file).group(1).replace(', ', '.')
-version = '1.10.0rc2'
+version = re.search(r'{}\s*=\s*[(]([^)]*)[)]'.format('__version_info__'),
+                    init_file).group(1).replace(', ', '.')
 
 setup(name='mpas_analysis',
       version=version,