Clean up the nino34 index task

mpas_analysis/ocean/meridional_heat_transport.py

@@ -6,15 +6,12 @@
 import numpy as np
 import netCDF4
 import os
-import warnings
 
 from ..shared.plot.plotting import plot_vertical_section,\
     setup_colormap, plot_1D
 
 from ..shared.io.utility import build_config_full_path
 
-from ..shared.timekeeping.utility import get_simulation_start_time
-
 from ..shared import AnalysisTask
 from ..shared.html import write_image_xml
 
@@ -119,8 +116,8 @@ def setup_and_check(self):  # {{{
             if os.path.exists(observationsFile):
                 self.observationsFile = observationsFile
             else:
-                warnings.warn('No MHT observations file found: skip plotting '
-                              'obs')
+                print('Warning: No MHT observations file found: skip plotting '
+                      'obs')
 
         mainRunName = self.config.get('runs', 'mainRunName')
 

mpas_analysis/shared/analysis_task.py

@@ -10,7 +10,6 @@
 from __future__ import absolute_import, division, print_function, \
     unicode_literals
 
-import warnings
 from multiprocessing import Process, Value
 import time
 import traceback
@@ -451,13 +450,12 @@ def check_analysis_enabled(self, analysisOptionName, default=False,
         except ValueError:
             enabled = default
             if default:
-                message = 'WARNING: namelist option {} not found.\n' \
-                          'This likely indicates that the simulation you ' \
-                          'are analyzing was run with an\n' \
-                          'older version of MPAS-O that did not support ' \
-                          'this flag.  Assuming enabled.'.format(
-                              analysisOptionName)
-                warnings.warn(message)
+                print('Warning: namelist option {} not found.\n'
+                      'This likely indicates that the simulation you '
+                      'are analyzing was run with an\n'
+                      'older version of MPAS-O that did not support '
+                      'this flag.  Assuming enabled.'.format(
+                              analysisOptionName))
 
         if not enabled and raiseException:
             raise RuntimeError('*** MPAS-Analysis relies on {} = .true.\n'

mpas_analysis/shared/climatology/mpas_climatology_task.py

@@ -4,7 +4,6 @@
 
 import xarray
 import os
-import warnings
 import subprocess
 from distutils.spawn import find_executable
 
@@ -288,14 +287,13 @@ def _update_climatology_bounds_from_file_names(self):  # {{{
         endYear = years[lastIndex]
 
         if startYear != requestedStartYear or endYear != requestedEndYear:
-            message = "climatology start and/or end year different from " \
-                      "requested\n" \
-                      "requestd: {:04d}-{:04d}\n" \
-                      "actual:   {:04d}-{:04d}\n".format(requestedStartYear,
-                                                         requestedEndYear,
-                                                         startYear,
-                                                         endYear)
-            warnings.warn(message)
+            print("Warning: climatology start and/or end year different from "
+                  "requested\n"
+                  "requestd: {:04d}-{:04d}\n"
+                  "actual:   {:04d}-{:04d}\n".format(requestedStartYear,
+                                                     requestedEndYear,
+                                                     startYear,
+                                                     endYear))
             config.set('climatology', 'startYear', str(startYear))
             config.set('climatology', 'endYear', str(endYear))
 

mpas_analysis/shared/plot/plotting.py

@@ -1144,42 +1144,6 @@ def setup_colormap(config, configSectionName, suffix=''):
     return (colormap, colorbarLevels)
 
 
-def plot_size_y_axis(plt, xaxisValues, **data):
-    '''
-    Resize the y-axis limit based on the curves being plotted
-
-    Parameters
-    ----------
-    plt : plot handle
-
-    xaxisValues : numpy.array
-       Values plotted along the x-axis
-
-    data : dictionary entries must be numpy.array
-       data for curves on plot
-
-    Authors
-    -------
-    Luke Van Roekel
-    '''
-
-    ax = plt.gca()
-    xmin = ax.get_xlim()[0]
-    xmax = ax.get_xlim()[1]
-
-    # find period/frequency bounds for chosen xmin/xmax
-    minIndex = np.abs(xaxisValues - xmin).argmin()
-    maxIndex = np.abs(xaxisValues - xmax).argmin()
-
-    # find maximum value of three curves plotted
-    maxCurveVal = -1E20
-    for key in data:
-        maxTemp = data[key][minIndex:maxIndex].max()
-        maxCurveVal = max(maxTemp, maxCurveVal)
-
-    return maxCurveVal
-
-
 def plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks):
     '''
     Formats tick labels and positions along the x-axis for time series

mpas_analysis/shared/time_series/mpas_time_series_task.py

@@ -3,7 +3,6 @@
     unicode_literals
 
 import os
-import warnings
 import subprocess
 from distutils.spawn import find_executable
 import xarray as xr
@@ -42,7 +41,7 @@ class MpasTimeSeriesTask(AnalysisTask):  # {{{
     '''
 
     def __init__(self, config, componentName, taskName=None,
-                 subtaskName=None):  # {{{
+                 subtaskName=None, section='timeSeries'):  # {{{
         '''
         Construct the analysis task for extracting time series.
 
@@ -62,19 +61,22 @@ def __init__(self, config, componentName, taskName=None,
         subtaskName : str, optional
             The name of the subtask (if any)
 
+        section : str, optional
+            The section of the config file from which to read the start and
+            end times for the time series, also added as a tag
 
         Authors
         -------
         Xylar Asay-Davis
         '''
         self.variableList = []
-        self.seasons = []
+        self.section = section
+        tags = [section]
 
-        tags = ['timeSeries']
-
-        suffix = componentName[0].upper() + componentName[1:]
         if taskName is None:
-            taskName = 'mpasTimeSeries{}'.format(suffix)
+            suffix = section[0].upper() + section[1:] + \
+                componentName[0].upper() + componentName[1:]
+            taskName = 'mpas{}'.format(suffix)
 
         # call the constructor from the base class (AnalysisTask)
         super(MpasTimeSeriesTask, self).__init__(
@@ -138,8 +140,8 @@ def setup_and_check(self):  # {{{
 
         # get a list of timeSeriesStats output files from the streams file,
         # reading only those that are between the start and end dates
-        startDate = config.get('timeSeries', 'startDate')
-        endDate = config.get('timeSeries', 'endDate')
+        startDate = config.get(self.section, 'startDate')
+        endDate = config.get(self.section, 'endDate')
         streamName = 'timeSeriesStatsMonthlyOutput'
         self.inputFiles = self.historyStreams.readpath(
                 streamName, startDate=startDate, endDate=endDate,
@@ -200,7 +202,7 @@ def _update_time_series_bounds_from_file_names(self):  # {{{
         """
 
         config = self.config
-        section = 'timeSeries'
+        section = self.section
 
         requestedStartYear = config.getint(section, 'startYear')
         requestedEndYear = config.getint(section, 'endYear')
@@ -222,14 +224,14 @@ def _update_time_series_bounds_from_file_names(self):  # {{{
         endYear = years[lastIndex]
 
         if startYear != requestedStartYear or endYear != requestedEndYear:
-            message = "time series start and/or end year different from " \
-                      "requested\n" \
-                      "requestd: {:04d}-{:04d}\n" \
-                      "actual:   {:04d}-{:04d}\n".format(requestedStartYear,
-                                                         requestedEndYear,
-                                                         startYear,
-                                                         endYear)
-            warnings.warn(message)
+            print("Warning: {} start and/or end year different from "
+                  "requested\n" \
+                  "requestd: {:04d}-{:04d}\n" \
+                  "actual:   {:04d}-{:04d}\n".format(section,
+                                                     requestedStartYear,
+                                                     requestedEndYear,
+                                                     startYear,
+                                                     endYear))
             config.set(section, 'startYear', str(startYear))
             config.set(section, 'endYear', str(endYear))
 
@@ -280,7 +282,7 @@ def _compute_time_series_with_ncrcat(self):
 
             with xr.open_dataset(self.outputFile) as ds:
                 dates = [bytes.decode(name) for name in
-                           ds.xtime_startMonthly.values]
+                         ds.xtime_startMonthly.values]
                 lastDate = dates[-1]
 
             lastYear = int(lastDate[0:4])

mpas_analysis/shared/time_series/time_series.py

@@ -12,7 +12,6 @@
 import xarray as xr
 import numpy
 import os
-import warnings
 
 from ..timekeeping.utility import days_to_datetime
 
@@ -87,7 +86,7 @@ def cache_time_series(timesInDataSet, timeSeriesCalcFunction, cacheFileName,
             message = 'Deleting cache file {}, which appears to have ' \
                       'been corrupted.'.format(cacheFileName)
             if logger is None:
-                warnings.warn(message)
+                print('Warning: {}'.format(message))
             else:
                 logger.warning(message)
             os.remove(cacheFileName)

mpas_analysis/test/test_mpas_climatology_task.py

@@ -142,8 +142,7 @@ def test_update_climatology_bounds_from_file_names(self):
         config.set('climatology', 'startDate', startDate)
         config.set('climatology', 'endDate', endDate)
 
-        with pytest.warns(UserWarning):
-            mpasClimatologyTask._update_climatology_bounds_from_file_names()
+        mpasClimatologyTask._update_climatology_bounds_from_file_names()
 
         startYear = 2
         endYear = 2

run_mpas_analysis

@@ -70,6 +70,9 @@ def build_analysis_list(config):  # {{{
                                               componentName='ocean')
     oceanTimeSeriesTask = MpasTimeSeriesTask(config=config,
                                              componentName='ocean')
+    oceanIndexTask = MpasTimeSeriesTask(config=config,
+                                        componentName='ocean',
+                                        section='index')
     analyses.append(oceanClimatolgyTask)
     analyses.append(ocean.ClimatologyMapMLD(config, oceanClimatolgyTask))
     analyses.append(ocean.ClimatologyMapSST(config, oceanClimatolgyTask))
@@ -81,7 +84,7 @@ def build_analysis_list(config):  # {{{
     analyses.append(ocean.TimeSeriesSST(config, oceanTimeSeriesTask))
     analyses.append(ocean.MeridionalHeatTransport(config, oceanClimatolgyTask))
     analyses.append(ocean.StreamfunctionMOC(config, oceanClimatolgyTask))
-    analyses.append(ocean.IndexNino34(config, oceanTimeSeriesTask))
+    analyses.append(ocean.IndexNino34(config, oceanIndexTask))
 
     # Sea Ice Analyses
     seaIceClimatolgyTask = MpasClimatologyTask(config=config,