Merge branch 'MPAS-Dev/MPAS-Analysis/develop'

xylar · xylar · commit a28d8d2ae443 · 2022-09-12T21:26:48.000-06:00
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.7.0" %}
+{% set version = "1.7.1" %}
 
 package:
   name: {{ name|lower }}
diff --git a/docs/versions.rst b/docs/versions.rst
@@ -16,6 +16,7 @@ Documentation    On GitHub
 `v1.6.0`_        `1.6.0`_
 `v1.6.1`_        `1.6.1`_
 `v1.7.0`_        `1.7.0`_
+`v1.7.1`_        `1.7.1`_
 ================ ===============
 
 .. _`stable`: ../stable/index.html
@@ -30,6 +31,7 @@ Documentation    On GitHub
 .. _`v1.6.0`: ../1.6.0/index.html
 .. _`v1.6.1`: ../1.6.1/index.html
 .. _`v1.7.0`: ../1.7.0/index.html
+.. _`v1.7.1`: ../1.7.1/index.html
 .. _`master`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/master
 .. _`develop`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/develop
 .. _`1.2.6`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.2.6
@@ -42,3 +44,4 @@ Documentation    On GitHub
 .. _`1.6.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.6.0
 .. _`1.6.1`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.6.1
 .. _`1.7.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.7.0
+.. _`1.7.1`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.7.1
diff --git a/mpas_analysis/__init__.py b/mpas_analysis/__init__.py
@@ -3,5 +3,5 @@
 import matplotlib as mpl
 mpl.use('Agg')
 
-__version_info__ = (1, 7, 0)
+__version_info__ = (1, 7, 1)
 __version__ = '.'.join(str(vi) for vi in __version_info__)
diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py
@@ -328,7 +328,7 @@ def _compute_nino34_index(self, regionSST, calendar):
         regionSST : xarray.DataArray object
            values of SST in the nino region
 
-        calendar: {'gregorian', 'gregorian_noleap'}
+        calendar: {'gregorian', 'noleap'}
             The name of the calendars used in the MPAS run
 
         Returns
diff --git a/mpas_analysis/ocean/regional_ts_diagrams.py b/mpas_analysis/ocean/regional_ts_diagrams.py
@@ -77,7 +77,7 @@ def __init__(self, config, mpasClimatologyTask, regionMasksTask,
         regionMasksTask : ``ComputeRegionMasks``
             A task for computing region masks
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlConfig : mpas_tools.config.MpasConfigParser, optional
             Configuration options for a control run (if any)
         """
         # Authors
@@ -658,12 +658,9 @@ def _write_mpas_t_s(self, config):
 
             ds = ds.where(cellMask, drop=True)
 
-            self.logger.info("Don't worry about the following dask "
-                             "warnings.")
             depthMask = numpy.logical_and(ds.zMid >= zmin,
                                           ds.zMid <= zmax)
             depthMask.compute()
-            self.logger.info("Dask warnings should be done.")
             ds['depthMask'] = depthMask
 
             for var in variableList:
@@ -715,7 +712,7 @@ def _write_obs_t_s(self, obsDict, zmin, zmax):
                 xarray.open_dataset(regionMaskFileName).chunk(chunk).stack(
                         nCells=(obsDict['latVar'], obsDict['lonVar']))
             dsRegionMask = dsRegionMask.reset_index('nCells').drop_vars(
-                [obsDict['latVar'], obsDict['lonVar']])
+                [obsDict['latVar'], obsDict['lonVar'], 'nCells'])
 
             maskRegionNames = decode_strings(dsRegionMask.regionNames)
             regionIndex = maskRegionNames.index(self.regionName)
@@ -745,7 +742,7 @@ def _write_obs_t_s(self, obsDict, zmin, zmax):
             ds = xarray.open_dataset(obsFileName, chunks=chunk)
             ds = ds.stack(nCells=(obsDict['latVar'], obsDict['lonVar']))
             ds = ds.reset_index('nCells').drop_vars(
-                [obsDict['latVar'], obsDict['lonVar']])
+                [obsDict['latVar'], obsDict['lonVar'], 'nCells'])
 
             ds = ds.where(cellMask, drop=True)
 
diff --git a/mpas_analysis/ocean/time_series_ocean_regions.py b/mpas_analysis/ocean/time_series_ocean_regions.py
@@ -871,7 +871,7 @@ def run_task(self):
             xarray.open_dataset(regionMaskFileName).stack(
                     nCells=(obsDict['latVar'], obsDict['lonVar']))
         dsRegionMask = dsRegionMask.reset_index('nCells').drop_vars(
-            [obsDict['latVar'], obsDict['lonVar']])
+            [obsDict['latVar'], obsDict['lonVar'], 'nCells'])
 
         maskRegionNames = decode_strings(dsRegionMask.regionNames)
         regionIndex = maskRegionNames.index(self.regionName)
@@ -956,7 +956,7 @@ def run_task(self):
             dsMonth = dsMonth.stack(nCells=(obsDict['latVar'],
                                             obsDict['lonVar']))
             dsMonth = dsMonth.reset_index('nCells').drop_vars(
-                [obsDict['latVar'], obsDict['lonVar']])
+                [obsDict['latVar'], obsDict['lonVar'], 'nCells'])
 
             dsMonth = dsMonth.where(cellMask, drop=True)
 
diff --git a/mpas_analysis/sea_ice/time_series.py b/mpas_analysis/sea_ice/time_series.py
@@ -525,7 +525,7 @@ def _replicate_cycle(self, ds, dsToReplicate, calendar):
             length of dsToReplicate plus the time between the first two time
             values (typically one year total).
 
-        calendar : {'gregorian', 'gregorian_noleap'}
+        calendar : {'gregorian', 'noleap'}
             The name of one of the calendars supported by MPAS cores
 
         Returns:
diff --git a/mpas_analysis/shared/climatology/climatology.py b/mpas_analysis/shared/climatology/climatology.py
@@ -147,7 +147,7 @@ def compute_monthly_climatology(ds, calendar=None, maskVaries=True):
         A data set with a ``Time`` coordinate expressed as days since
         0001-01-01 or ``month`` coordinate
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores, used to
         determine ``month`` from ``Time`` coordinate, so must be supplied if
         ``ds`` does not already have a ``month`` coordinate or data array
@@ -201,7 +201,7 @@ def compute_climatology(ds, monthValues, calendar=None,
     monthValues : int or array-like of ints
         A single month or an array of months to be averaged together
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores, used to
         determine ``month`` from ``Time`` coordinate, so must be supplied if
         ``ds`` does not already have a ``month`` coordinate or data array
@@ -242,7 +242,7 @@ def add_years_months_days_in_month(ds, calendar=None):
     """
     Add ``year``, ``month`` and ``daysInMonth`` as data arrays in ``ds``.
     The number of days in each month of ``ds`` is computed either using the
-    ``startTime`` and ``endTime`` if available or assuming ``gregorian_noleap``
+    ``startTime`` and ``endTime`` if available or assuming ``noleap``
     calendar and ignoring leap years.  ``year`` and ``month`` are computed
     accounting correctly for the the calendar.
 
@@ -252,7 +252,7 @@ def add_years_months_days_in_month(ds, calendar=None):
         A data set with a ``Time`` coordinate expressed as days since
         0001-01-01
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores, used to
         determine ``year`` and ``month`` from ``Time`` coordinate
 
diff --git a/mpas_analysis/shared/climatology/ref_year_mpas_climatology_task.py b/mpas_analysis/shared/climatology/ref_year_mpas_climatology_task.py
@@ -100,10 +100,12 @@ def get_start_and_end(self):
         startDate = '{:04d}-01-01_00:00:00'.format(startYear)
         endDate = '{:04d}-12-31_23:59:59'.format(endYear)
 
-        config.set('climatology', 'startYear', str(startYear))
-        config.set('climatology', 'startDate', startDate)
-        config.set('climatology', 'endYear', str(endYear))
-        config.set('climatology', 'endDate', endDate)
+        # using "user=True" so these changes take priority over user config
+        # options
+        config.set('climatology', 'startYear', str(startYear), user=True)
+        config.set('climatology', 'startDate', startDate, user=True)
+        config.set('climatology', 'endYear', str(endYear), user=True)
+        config.set('climatology', 'endDate', endDate, user=True)
 
         return startYear, endYear
 
diff --git a/mpas_analysis/shared/generalized_reader/generalized_reader.py b/mpas_analysis/shared/generalized_reader/generalized_reader.py
@@ -47,7 +47,7 @@ def open_multifile_dataset(fileNames, calendar, config,
     fileNames : list of strings
         A lsit of file paths to read
 
-    calendar : {``'gregorian'``, ``'gregorian_noleap'``}, optional
+    calendar : {``'gregorian'``, ``'noleap'``}, optional
         The name of one of the calendars supported by MPAS cores
 
     config : mpas_tools.config.MpasConfigParser
@@ -186,7 +186,7 @@ def _preprocess(ds, calendar, simulationStartTime, timeVariableName,
         an xarray time coordinate and with variable names to be
         substituted.
 
-    calendar : {'gregorian', 'gregorian_noleap'}
+    calendar : {'gregorian', 'noleap'}
         The name of one of the calendars supported by MPAS cores
 
         The name of the time variable (typically 'Time' if using a variableMap
diff --git a/mpas_analysis/shared/io/mpas_reader.py b/mpas_analysis/shared/io/mpas_reader.py
@@ -35,7 +35,7 @@ def open_mpas_dataset(fileName, calendar,
     fileName : str
         File path to read
 
-    calendar : {``'gregorian'``, ``'gregorian_noleap'``}, optional
+    calendar : {``'gregorian'``, ``'noleap'``}, optional
         The name of one of the calendars supported by MPAS cores
 
     timeVariableNames : str or list of 2 str, optional
@@ -120,7 +120,7 @@ def _parse_dataset_time(ds, inTimeVariableName, calendar,
         inTimeVariableName is typically
         ``['xtime_startMonthly', 'xtime_endMonthly']``.
 
-    calendar : {'gregorian', 'gregorian_noleap'}
+    calendar : {'gregorian', 'noleap'}
         The name of one of the calendars supported by MPAS cores
 
     outTimeVariableName : str
diff --git a/mpas_analysis/shared/io/namelist_streams_interface.py b/mpas_analysis/shared/io/namelist_streams_interface.py
@@ -390,7 +390,7 @@ def readpath(self, streamName, startDate=None, endDate=None,
             and added to endDate because the file date might be the first
             or last date contained in the file (or anything in between).
 
-        calendar : {'gregorian', 'gregorian_noleap'}, optional
+        calendar : {'gregorian', 'noleap'}, optional
             The name of one of the calendars supported by MPAS cores, and is
             required if startDate and/or endDate are supplied
 
diff --git a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py
@@ -44,7 +44,7 @@ def open_multifile_dataset(fileNames, calendar,
     fileNames : list of strings
         A lsit of file paths to read
 
-    calendar : {``'gregorian'``, ``'gregorian_noleap'``}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores
 
     simulationStartTime : string, optional
@@ -181,7 +181,7 @@ def preprocess(ds, calendar, simulationStartTime, timeVariableName,
         The data set containing an MPAS time variable to be used to build
         an xarray time coordinate.
 
-    calendar : {``'gregorian'``, ``'gregorian_noleap'``}
+    calendar : {'gregorian', 'noleap'}
         The name of one of the calendars supported by MPAS cores
 
     simulationStartTime : string, optinal
@@ -376,7 +376,7 @@ def _parse_dataset_time(ds, inTimeVariableName, calendar,
         determine the value of the time coordinate.  In such cases,
         inTimeVariableName is typically {['xtime_start', 'xtime_end']}.
 
-    calendar : {'gregorian', 'gregorian_noleap'}
+    calendar : {'gregorian', 'noleap'}
         The name of one of the calendars supported by MPAS cores
 
 
diff --git a/mpas_analysis/shared/time_series/time_series.py b/mpas_analysis/shared/time_series/time_series.py
@@ -135,7 +135,7 @@ def cache_time_series(timesInDataSet, timeSeriesCalcFunction, cacheFileName,
         The absolute path to the cache file where the times series will be
         stored
 
-    calendar : {'gregorian', 'gregorian_noleap'}
+    calendar : {'gregorian', 'noleap'}
         The name of one of the calendars supported by MPAS cores, used to
         determine ``year`` and ``month`` from ``Time`` coordinate
 
diff --git a/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py b/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py
@@ -31,7 +31,7 @@ class MpasRelativeDelta(relativedelta):
 
     def __init__(self, dt1=None, dt2=None, years=0, months=0, days=0,
                  hours=0, minutes=0, seconds=0, calendar='gregorian'):
-        if calendar not in ['gregorian', 'gregorian_noleap']:
+        if calendar not in ['gregorian', 'noleap', 'gregorian_noleap']:
             raise ValueError('Unsupported MPAs calendar {}'.format(calendar))
         self.calendar = calendar
         super(MpasRelativeDelta, self).__init__(dt1=dt1, dt2=dt2, years=years,
@@ -79,15 +79,15 @@ def __add__(self, other):
 
         if self.calendar == 'gregorian':
             daysInMonth = monthrange(year, month)[1]
-        elif self.calendar == 'gregorian_noleap':
+        elif self.calendar in ['noleap', 'gregorian_noleap']:
             # use year 0001, which is not a leapyear
             daysInMonth = monthrange(1, month)[1]
 
         day = min(daysInMonth, other.day)
         repl = {"year": year, "month": month, "day": day}
 
         days = self.days
-        if self.calendar == 'gregorian_noleap' and isleap(year):
+        if self.calendar in ['noleap', 'gregorian_noleap'] and isleap(year):
             if month == 2 and day + days >= 29:
                 # skip forward over the leap day
                 days += 1
diff --git a/mpas_analysis/shared/timekeeping/utility.py b/mpas_analysis/shared/timekeeping/utility.py
@@ -137,7 +137,7 @@ def string_to_relative_delta(dateString, calendar='gregorian'):
         Note: either underscores or spaces can be used to separate the date
         from the time portion of the string.
 
-    calendar: {'gregorian', 'gregorian_noleap'}, optional
+    calendar: {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores
 
     Returns
@@ -189,7 +189,7 @@ def string_to_days_since_date(dateString, calendar='gregorian',
         Note: either underscores or spaces can be used to separate the date
         from the time portion of the string.
 
-    calendar: {'gregorian', 'gregorian_noleap'}, optional
+    calendar: {'gregorian', 'noleap'}, optional
         The name of one of the calendars supported by MPAS cores
 
     referenceDate : str, optional
@@ -232,14 +232,14 @@ def string_to_days_since_date(dateString, calendar='gregorian',
 def days_to_datetime(days, calendar='gregorian', referenceDate='0001-01-01'):
     """
     Covert days to ``datetime.datetime`` objects given a reference date and an
-    MPAS calendar (either 'gregorian' or 'gregorian_noleap').
+    MPAS calendar (either 'gregorian' or 'noleap').
 
     Parameters
     ----------
     days : float or array-like of floats
         The number of days since the reference date.
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         A calendar to be used to convert days to a ``datetime.datetime``
         object.
 
@@ -293,7 +293,7 @@ def datetime_to_days(dates, calendar='gregorian', referenceDate='0001-01-01'):
         The date(s) to be converted to days since ``referenceDate`` on the
         given ``calendar``.
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         A calendar to be used to convert days to a ``datetime.datetime`` object.
 
     referenceDate : str, optional
@@ -342,7 +342,7 @@ def date_to_days(year=1, month=1, day=1, hour=0, minute=0, second=0,
         The date to be converted to days since ``referenceDate`` on the
         given ``calendar``.
 
-    calendar : {'gregorian', 'gregorian_noleap'}, optional
+    calendar : {'gregorian', 'noleap'}, optional
         A calendar to be used to convert days to a ``datetime.datetime``
         object.
 
@@ -469,7 +469,7 @@ def _mpas_to_netcdf_calendar(calendar):
 
     if calendar == 'gregorian_noleap':
         calendar = 'noleap'
-    elif calendar != 'gregorian':
+    if calendar not in ['gregorian', 'noleap']:
         raise ValueError('Unsupported calendar {}'.format(calendar))
     return calendar
 
diff --git a/mpas_analysis/test/test_climatology.py b/mpas_analysis/test/test_climatology.py
@@ -197,7 +197,7 @@ def test_get_observations_remapper(self):
 
     def test_compute_climatology(self):
         config = self.setup_config()
-        calendar = 'gregorian_noleap'
+        calendar = 'noleap'
         ds = self.open_test_ds(config, calendar)
 
         assert('month' not in ds.coords.keys())
@@ -237,7 +237,7 @@ def test_compute_climatology(self):
 
     def test_compute_monthly_climatology(self):
         config = self.setup_config()
-        calendar = 'gregorian_noleap'
+        calendar = 'noleap'
         ds = self.open_test_ds(config, calendar)
 
         monthlyClimatology = compute_monthly_climatology(ds, calendar)
diff --git a/mpas_analysis/test/test_generalized_reader.py b/mpas_analysis/test/test_generalized_reader.py
@@ -56,7 +56,7 @@ def test_variableMap(self):
                         'refBottomDepth', 'daysSinceStartOfSim']
 
         config = self.setup_config()
-        for calendar in ['gregorian', 'gregorian_noleap']:
+        for calendar in ['gregorian', 'noleap']:
             # preprocess_mpas will use variableMap to map the variable names
             # from their values in the file to the desired values in
             # variableList
@@ -80,7 +80,7 @@ def test_open_dataset_fn(self):
             ['time_avg_avgValueWithinOceanRegion_avgSurfaceTemperature']
 
         config = self.setup_config()
-        for calendar in ['gregorian', 'gregorian_noleap']:
+        for calendar in ['gregorian', 'noleap']:
             ds = open_multifile_dataset(
                 fileNames=fileName,
                 calendar=calendar,
@@ -97,7 +97,7 @@ def test_start_end(self):
             ['time_avg_avgValueWithinOceanRegion_avgSurfaceTemperature']
 
         config = self.setup_config()
-        for calendar in ['gregorian', 'gregorian_noleap']:
+        for calendar in ['gregorian', 'noleap']:
             # all dates
             ds = open_multifile_dataset(
                 fileNames=fileName,
diff --git a/mpas_analysis/test/test_mpas_climatology_task/mpas-o_in b/mpas_analysis/test/test_mpas_climatology_task/mpas-o_in
@@ -2,7 +2,7 @@
  config_ocean_run_mode = 'forward'
 /
 &time_management
- config_calendar_type = 'gregorian_noleap'
+ config_calendar_type = 'noleap'
  config_do_restart = .true.
  config_restart_timestamp_name = 'rpointer.ocn'
  config_start_time = 'file'
diff --git a/mpas_analysis/test/test_mpas_xarray.py b/mpas_analysis/test/test_mpas_xarray.py
diff --git a/mpas_analysis/test/test_namelist_streams_interface.py b/mpas_analysis/test/test_namelist_streams_interface.py
diff --git a/mpas_analysis/test/test_namelist_streams_interface/namelist.ocean b/mpas_analysis/test/test_namelist_streams_interface/namelist.ocean
diff --git a/mpas_analysis/test/test_open_mpas_dataset.py b/mpas_analysis/test/test_open_mpas_dataset.py
diff --git a/mpas_analysis/test/test_remap_obs_clim_subtask/mpas-o_in b/mpas_analysis/test/test_remap_obs_clim_subtask/mpas-o_in
diff --git a/mpas_analysis/test/test_timekeeping.py b/mpas_analysis/test/test_timekeeping.py
