Add python 2 and 3 support

.travis.yml

@@ -8,13 +8,14 @@ matrix:
   fast_finish: true
   include:
   - python: 2.7
-    env: CONDA_ENV=py27
+  - python: 3.5
+  - python: 3.6
 
 before_install:
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget http://repo.continuum.io/miniconda/Miniconda-3.16.0-Linux-x86_64.sh -O miniconda.sh;
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
     else
-      wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh;
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
     fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
@@ -24,8 +25,10 @@ before_install:
   - conda info -a
 
 install:
-  - conda env create --file ci/requirements-$CONDA_ENV.yml
+  - conda create -n test_env -c conda-forge python=$TRAVIS_PYTHON_VERSION
+  - conda env update -n test_env -f ci/requirements.yml
   - source activate test_env
+  - conda list
 
 script:
-  - py.test
+  - pytest

ci/requirements-py27.yml → ci/requirements.yml

@@ -1,9 +1,8 @@
-name: test_env
 channels:
   - conda-forge
 dependencies:
-  - python=2.7
   - pytest
+  - six
   - numpy
   - scipy
   - lxml

mpas_analysis/analysis_task_template.py

@@ -33,6 +33,9 @@
 Xylar Asay-Davis
 '''
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 # import python modules here
 import numpy
 import matplotlib.pyplot as plt
@@ -351,10 +354,10 @@ def _make_plot(self, plotParameter, optionalArgument=None):  # {{{
         # self.myArg is a copy of the argument we passed in to __init__ when we
         # built the task.  It is available in any method after that for us to
         # use as needed.
-        print 'myArg:', self.myArg
-        print 'plotParameter:', plotParameter
+        print('myArg: {}'.format(self.myArg))
+        print('plotParameter: {}'.format(plotParameter))
         if optionalArgument is not None:
-            print 'optionalArgument:', optionalArgument
+            print('optionalArgument: {}'.format(optionalArgument))
 
         # get the file name based on the plot parameter
         filePrefix = self.filePrefixes[plotParameter]

mpas_analysis/configuration/MpasAnalysisConfigParser.py

@@ -9,11 +9,18 @@
 Xylar Asay-Davis, Phillip J. Wolfram
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import numbers
 import ast
+import six
 import numpy as np
-from ConfigParser import ConfigParser
 
+from six.moves.configparser import ConfigParser
+
+if six.PY3:
+    xrange = range
 
 npallow = dict(linspace=np.linspace, xrange=xrange, range=range,
                arange=np.arange, pi=np.pi, Pi=np.pi, __builtins__=None)

mpas_analysis/ocean/__init__.py

@@ -1,7 +1,7 @@
-from climatology_map import ClimatologyMapSST, ClimatologyMapMLD, \
+from .climatology_map import ClimatologyMapSST, ClimatologyMapMLD, \
     ClimatologyMapSSS
-from time_series_ohc import TimeSeriesOHC
-from time_series_sst import TimeSeriesSST
-from index_nino34 import IndexNino34
-from streamfunction_moc import StreamfunctionMOC
-from meridional_heat_transport import MeridionalHeatTransport
+from .time_series_ohc import TimeSeriesOHC
+from .time_series_sst import TimeSeriesSST
+from .index_nino34 import IndexNino34
+from .streamfunction_moc import StreamfunctionMOC
+from .meridional_heat_transport import MeridionalHeatTransport

mpas_analysis/ocean/climatology_map.py

@@ -8,6 +8,9 @@
 Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 import datetime
 import numpy as np

mpas_analysis/ocean/index_nino34.py

@@ -1,4 +1,8 @@
 # -*- coding: utf-8 -*-
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import datetime
 import xarray as xr
 import pandas as pd
@@ -394,7 +398,7 @@ def _running_mean(self, inputData, wgts):  # {{{
         """
 
         nt = len(inputData)
-        sp = (len(wgts) - 1)/2
+        sp = (len(wgts) - 1) // 2
         runningMean = inputData.copy()
         for k in range(sp, nt-(sp+1)):
             runningMean[k] = sum(wgts*inputData[k-sp:k+sp+1].values)

mpas_analysis/ocean/meridional_heat_transport.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 import numpy as np
 import netCDF4

mpas_analysis/ocean/streamfunction_moc.py

@@ -1,4 +1,8 @@
 # -*- coding: utf-8 -*-
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 import numpy as np
 import netCDF4

mpas_analysis/ocean/time_series_ohc.py

@@ -1,4 +1,8 @@
 # -*- coding: utf-8 -*-
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import numpy as np
 import netCDF4
 
@@ -216,7 +220,7 @@ def run_task(self):  # {{{
                                startDate=self.startDate,
                                endDate=self.endDate)
         # rename the variables to shorter names for convenience
-        renameDict = dict((v, k) for k, v in variables.iteritems())
+        renameDict = dict((v, k) for k, v in variables.items())
         ds.rename(renameDict, inplace=True)
 
         timeStart = string_to_datetime(self.startDate)

mpas_analysis/ocean/time_series_sst.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 from ..shared import AnalysisTask
 
 from ..shared.plot.plotting import timeseries_analysis_plot

mpas_analysis/sea_ice/__init__.py

@@ -1,2 +1,2 @@
-from climatology_map import ClimatologyMapSeaIceConc, ClimatologyMapSeaIceThick
-from time_series import TimeSeriesSeaIce
+from .climatology_map import ClimatologyMapSeaIceConc, ClimatologyMapSeaIceThick
+from .time_series import TimeSeriesSeaIce

mpas_analysis/sea_ice/climatology_map.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import os
 import os.path
 

mpas_analysis/sea_ice/sea_ice_analysis_task.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 from ..shared.analysis_task import AnalysisTask
 
 from ..shared.io import StreamsFile

mpas_analysis/sea_ice/time_series.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 
 from .sea_ice_analysis_task import SeaIceAnalysisTask
@@ -551,9 +555,9 @@ def _replicate_cycle(self, ds, dsToReplicate, calendar):  # {{{
 
         # clip dsShift to the range of ds
         dsStartTime = dsShift.Time.sel(Time=ds.Time.min(),
-                                       method='nearest').values
+                                       method=str('nearest')).values
         dsEndTime = dsShift.Time.sel(Time=ds.Time.max(),
-                                     method='nearest').values
+                                     method=str('nearest')).values
         dsShift = dsShift.sel(Time=slice(dsStartTime, dsEndTime))
 
         return dsShift  # }}}

mpas_analysis/shared/__init__.py

@@ -1 +1 @@
-from analysis_task import AnalysisTask
+from .analysis_task import AnalysisTask

mpas_analysis/shared/analysis_task.py

@@ -7,6 +7,9 @@
 
 '''
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import warnings
 from multiprocessing import Process, Value
 import time
@@ -506,11 +509,11 @@ class AnalysisFormatter(logging.Formatter):  # {{{
 
     # printing error messages without a prefix because they are sometimes
     # errors and sometimes only warnings sent to stderr
-    err_fmt = "%(msg)s"
     dbg_fmt = "DEBUG: %(module)s: %(lineno)d: %(msg)s"
     info_fmt = "%(msg)s"
+    err_fmt = info_fmt
 
-    def __init__(self, fmt="%(levelno)s: %(msg)s"):
+    def __init__(self, fmt=info_fmt):
         logging.Formatter.__init__(self, fmt)
 
     def format(self, record):
@@ -558,7 +561,7 @@ def __init__(self, logger, log_level=logging.INFO):
 
     def write(self, buf):
         for line in buf.rstrip().splitlines():
-            self.logger.log(self.log_level, line.rstrip())
+            self.logger.log(self.log_level, str(line.rstrip()))
 
     def flush(self):
         pass

mpas_analysis/shared/climatology/climatology.py

@@ -6,6 +6,9 @@
 Xylar Asay-Davis
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 import os
 import numpy
@@ -327,11 +330,11 @@ def add_years_months_days_in_month(ds, calendar=None):  # {{{
             ds.coords['daysInMonth'] = ds.endTime - ds.startTime
         else:
             if calendar == 'gregorian':
-                print 'Warning: The MPAS run used the Gregorian calendar ' \
-                      'but does not appear to have\n' \
-                      'supplied start and end times.  Climatologies ' \
-                      'will be computed with\n' \
-                      'month durations ignoring leap years.'
+                print('Warning: The MPAS run used the Gregorian calendar '
+                      'but does not appear to have\n'
+                      'supplied start and end times.  Climatologies '
+                      'will be computed with\n'
+                      'month durations ignoring leap years.')
 
             daysInMonth = numpy.array([constants.daysInMonth[month-1] for
                                        month in ds.month.values], float)
@@ -527,8 +530,8 @@ def _setup_climatology_caching(ds, startYearClimo, endYearClimo,
                 dsCached = xr.open_dataset(outputFileClimo)
             except IOError:
                 # assuming the cache file is corrupt, so deleting it.
-                print 'Warning: Deleting cache file {}, which appears to ' \
-                      'have been corrupted.'.format(outputFileClimo)
+                print('Warning: Deleting cache file {}, which appears to '
+                      'have been corrupted.'.format(outputFileClimo))
 
                 os.remove(outputFileClimo)
 
@@ -576,7 +579,7 @@ def _cache_individual_climatologies(ds, cacheInfo, printProgress,
         dsYear = ds.where(ds.cacheIndices == cacheIndex, drop=True)
 
         if printProgress:
-            print '     {}'.format(yearString)
+            print('     {}'.format(yearString))
 
         totalDays = dsYear.daysInMonth.sum(dim='Time').values
 
@@ -622,8 +625,8 @@ def _cache_aggregated_climatology(startYearClimo, endYearClimo, cachePrefix,
 
         except IOError:
             # assuming the cache file is corrupt, so deleting it.
-            print 'Warning: Deleting cache file {}, which appears to have ' \
-                  'been corrupted.'.format(outputFileClimo)
+            print('Warning: Deleting cache file {}, which appears to have '
+                  'been corrupted.'.format(outputFileClimo))
             os.remove(outputFileClimo)
 
         if len(cacheInfo) == 1 and outputFileClimo == cacheInfo[0][0]:
@@ -641,8 +644,8 @@ def _cache_aggregated_climatology(startYearClimo, endYearClimo, cachePrefix,
 
     if not done:
         if printProgress:
-            print '   Computing aggregated climatology ' \
-                  '{}...'.format(yearString)
+            print('   Computing aggregated climatology '
+                  '{}...'.format(yearString))
 
         first = True
         for cacheIndex, info in enumerate(cacheInfo):

mpas_analysis/shared/climatology/comparison_descriptors.py

@@ -6,6 +6,9 @@
 Xylar Asay-Davis
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import numpy
 import pyproj
 

mpas_analysis/shared/climatology/mpas_climatology_task.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray
 import os
 import warnings
@@ -425,8 +429,11 @@ def _compute_climatologies_with_ncclimo(self, inDirectory, outDirectory,
         stdout, stderr = process.communicate()
 
         if stdout:
-            self.logger.info(stdout)
+            stdout = stdout.decode('utf-8')
+            for line in stdout.split('\n'):
+                self.logger.info(line)
         if stderr:
+            stderr = stderr.decode('utf-8')
             for line in stderr.split('\n'):
                 self.logger.error(line)
 

mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py

@@ -1,3 +1,7 @@
+
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import xarray as xr
 import os
 

mpas_analysis/shared/constants/constants.py

@@ -1,5 +1,3 @@
-import numpy as np
-
 """
 Constants that are common to all analysis tasks
 
@@ -12,6 +10,11 @@
 03/15/2017
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
+import numpy as np
+
 # set parameters for default climatology comparison grid
 dLongitude = 0.5
 dLatitude = 0.5

mpas_analysis/shared/containers.py

@@ -6,6 +6,9 @@
     10/22/2016
 """
 
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
 import collections
 class ReadOnlyDict(collections.Mapping): #{{{
     """ Read only-dictionary

mpas_analysis/shared/generalized_reader/__init__.py

@@ -1 +1 @@
-from generalized_reader import open_multifile_dataset
+from .generalized_reader import open_multifile_dataset