Renamed the root package from jasmin_cis to cis. Updated version numb…

…er to reflect this major change.

.gitignore

@@ -1,12 +1,10 @@
-/jasmin_cis/test/test_details.txt
-/jasmin_cis/test/manual/.~lock.test_plot_script_expected_results.ods#
 .project
 .pydevproject
 /.idea
 *.log
 *.pyc
 build/
 dist/
-jasmin_cis.egg-info/
+cis.egg-info/
 *~
 doc/_build

MANIFEST.in

@@ -1 +1 @@
-include jasmin_cis/logging.conf
+include cis/logging.conf

README

@@ -1,4 +1,4 @@
-This package contains code for the JASMIN Community Inter-comparison Suite.  Development is documented at http://proj.badc.rl.ac.uk/cedaservices/wiki/JASMIN/CommunityIntercomparisonSuite
+This package contains code for the Community Inter-comparison Suite.  Development is documented at http://proj.badc.rl.ac.uk/cedaservices/wiki/JASMIN/CommunityIntercomparisonSuite
 
 Contact
 -------
@@ -12,7 +12,7 @@ Copyright and licence
 
 (C) University of Oxford 2013
 
-This file is part of the JASMIN Community Inter-comparison Suite (CIS).
+This file is part of the Community Inter-comparison Suite (CIS).
 
 CIS is free software: you can redistribute it and/or modify it under
 the terms of the GNU Lesser General Public License as published by the

bin/cis

@@ -2,5 +2,5 @@
 # This file is part of the CIS package.  
 # http://proj.badc.rl.ac.uk/cedaservices/wiki/JASMIN/CommunityIntercomparisonSuite
 
-from jasmin_cis.cis import main
+from cis.cis import main
 main()

jasmin_cis/__init__.py → cis/__init__.py

@@ -1,5 +1,5 @@
 
 __author__ = "David Michel, Daniel Wallis, Duncan Watson-Parris, Richard Wilkinson, Ian Bush, Matt Kendall, John Holt"
-__version__ = "1.0.2"
-__status__ = "Dev"
+__version__ = "1.1.0"
+__status__ = "Stable"
 __website__ = "http://proj.badc.rl.ac.uk/cedaservices/wiki/JASMIN/CommunityIntercomparisonSuite"

jasmin_cis/aggregation/aggregate.py → cis/aggregation/aggregate.py

@@ -3,13 +3,13 @@
 import iris.coords
 import iris.coord_categorisation
 
-from jasmin_cis.data_io.data_reader import DataReader
-from jasmin_cis.data_io.data_writer import DataWriter
-from jasmin_cis.aggregation.aggregator import Aggregator
-from jasmin_cis.col_framework import get_kernel
-from jasmin_cis.exceptions import CISError, InvalidVariableError
-from jasmin_cis.cis import __version__
-from jasmin_cis.aggregation.aggregation_kernels import aggregation_kernels
+from cis.data_io.data_reader import DataReader
+from cis.data_io.data_writer import DataWriter
+from cis.aggregation.aggregator import Aggregator
+from cis.col_framework import get_kernel
+from cis.exceptions import CISError, InvalidVariableError
+from cis.cis import __version__
+from cis.aggregation.aggregation_kernels import aggregation_kernels
 from iris.exceptions import IrisError
 
 

jasmin_cis/aggregation/aggregator.py → cis/aggregation/aggregator.py

@@ -4,14 +4,14 @@
 import iris.analysis.cartography
 from iris.coords import DimCoord
 import numpy
-from jasmin_cis.col_implementations import GeneralGriddedColocator, BinnedCubeCellOnlyConstraint
-from jasmin_cis.data_io.gridded_data import make_from_cube
-import jasmin_cis.parse_datetime as parse_datetime
-from jasmin_cis.subsetting.subset import Subset
-from jasmin_cis.utils import isnan, guess_coord_axis
-from jasmin_cis.exceptions import ClassNotFoundError, CoordinateNotFoundError
-from jasmin_cis.aggregation.aggregation_kernels import MultiKernel
-from jasmin_cis.data_io.gridded_data import GriddedDataList
+from cis.col_implementations import GeneralGriddedColocator, BinnedCubeCellOnlyConstraint
+from cis.data_io.gridded_data import make_from_cube
+import cis.parse_datetime as parse_datetime
+from cis.subsetting.subset import Subset
+from cis.utils import isnan, guess_coord_axis
+from cis.exceptions import ClassNotFoundError, CoordinateNotFoundError
+from cis.aggregation.aggregation_kernels import MultiKernel
+from cis.data_io.gridded_data import GriddedDataList
 
 
 class Aggregator(object):

jasmin_cis/cis.py → cis/cis.py

@@ -6,10 +6,10 @@
 import traceback
 import logging
 
-from jasmin_cis.data_io.data_reader import DataReader
-from jasmin_cis.data_io.data_writer import DataWriter
-from jasmin_cis.exceptions import CISError, NoDataInSubsetError
-from jasmin_cis import __version__, __status__
+from cis.data_io.data_reader import DataReader
+from cis.data_io.data_writer import DataWriter
+from cis.exceptions import CISError, NoDataInSubsetError
+from cis import __version__, __status__
 
 
 logger = logging.getLogger(__name__)
@@ -36,7 +36,7 @@ def __check_variable_is_valid(main_arguments, data, axis):
     :param var_axis_dict: A dictionary where the key will be the name of a variable and the value will be the axis it will be plotted on.
     :param axis: The axis on which to plot the variable on
     '''
-    from jasmin_cis.exceptions import InvalidVariableError
+    from cis.exceptions import InvalidVariableError
 
     user_specified_variable = main_arguments.pop(axis + "axis")
 
@@ -55,8 +55,8 @@ def plot_cmd(main_arguments):
     :param main_arguments:    The command line arguments
     '''
     from plotting.plot import Plotter
-    from jasmin_cis.data_io.read import read_data
-    import jasmin_cis.exceptions as ex
+    from cis.data_io.read import read_data
+    import cis.exceptions as ex
     from iris.exceptions import IrisError
 
     # create a list of data object (ungridded or gridded(in that case, a Iris cube)), concatenating data from various files
@@ -103,7 +103,7 @@ def info_cmd(main_arguments):
     filename = main_arguments.filename
     data_type = main_arguments.type
 
-    from jasmin_cis.info import info
+    from cis.info import info
 
     try:
         info(filename, variables, data_type)
@@ -117,8 +117,8 @@ def col_cmd(main_arguments):
 
     :param main_arguments:    The command line arguments (minus the col command)
     '''
-    from jasmin_cis.exceptions import ClassNotFoundError, CISError
-    from jasmin_cis.col import Colocate
+    from cis.exceptions import ClassNotFoundError, CISError
+    from cis.col import Colocate
 
     output_file = main_arguments.output
     data_reader = DataReader()
@@ -162,7 +162,7 @@ def subset_cmd(main_arguments):
 
     :param main_arguments:    The command line arguments (minus the subset command)
     '''
-    from jasmin_cis.subsetting.subset import Subset
+    from cis.subsetting.subset import Subset
 
     if len(main_arguments.datagroups) > 1:
         __error_occurred("Subsetting can only be performed on one data group")
@@ -185,7 +185,7 @@ def aggregate_cmd(main_arguments):
 
     :param main_arguments: The command line arguments (minus the aggregate command)
     """
-    from jasmin_cis.aggregation.aggregate import Aggregate
+    from cis.aggregation.aggregate import Aggregate
 
     if len(main_arguments.datagroups) > 1:
         __error_occurred("Aggregation can only be performed on one data group")
@@ -222,7 +222,7 @@ def stats_cmd(main_arguments):
     :param main_arguments: The command line arguments (minus the stats command)
     """
     from stats import StatsAnalyzer
-    from jasmin_cis.data_io.gridded_data import GriddedDataList
+    from cis.data_io.gridded_data import GriddedDataList
     data_reader = DataReader()
     data_list = data_reader.read_datagroups(main_arguments.datagroups)
     analyzer = StatsAnalyzer(*data_list)

jasmin_cis/col.py → cis/col.py

@@ -3,9 +3,9 @@
 """
 import logging
 
-import jasmin_cis.col_implementations as ci
-from jasmin_cis.col_framework import get_kernel
-from jasmin_cis.exceptions import InvalidCommandLineOptionError
+import cis.col_implementations as ci
+from cis.col_framework import get_kernel
+from cis.exceptions import InvalidCommandLineOptionError
 
 
 class _GenericKernel(object):
@@ -165,9 +165,9 @@ def colocate(self, data, col_name=None, col_params=None, kern=None, kern_params=
         :param kern_params: the kernel parameters to use
         :return: colocated data
         """
-        from jasmin_cis.exceptions import CoordinateNotFoundError
+        from cis.exceptions import CoordinateNotFoundError
         from time import time
-        from jasmin_cis.cis import __version__
+        from cis.cis import __version__
 
         # Find colocator, constraint and kernel to use
         col_params['missing_data_for_missing_sample'] = self.missing_data_for_missing_sample

jasmin_cis/col_framework.py → cis/col_framework.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from jasmin_cis.utils import index_iterator_for_non_masked_data, index_iterator_nditer
+from cis.utils import index_iterator_for_non_masked_data, index_iterator_nditer
 
 
 class Colocator(object):
@@ -120,7 +120,7 @@ def get_iterator(self, missing_data_for_missing_sample, coord_map, coords, data_
         :return: iterator which iterates through sample indices, hyper point and constrained points to be placed in
             these points
         """
-        from jasmin_cis.col_implementations import HyperPoint
+        from cis.col_implementations import HyperPoint
         if missing_data_for_missing_sample:
             iterator = index_iterator_for_non_masked_data(shape, points)
         else:
@@ -154,7 +154,7 @@ class CellConstraint(Constraint):
     __metaclass__ = ABCMeta
 
     def get_iterator(self, missing_data_for_missing_sample, coord_map, coords, data_points, shape, points, output_data):
-        from jasmin_cis.col_implementations import HyperPoint
+        from cis.col_implementations import HyperPoint
         if missing_data_for_missing_sample:
             iterator = index_iterator_for_non_masked_data(shape, points)
         else:
@@ -179,7 +179,7 @@ class IndexedConstraint(Constraint):
     __metaclass__ = ABCMeta
 
     def get_iterator(self, missing_data_for_missing_sample, coord_map, coords, data_points, shape, points, output_data):
-        from jasmin_cis.col_implementations import HyperPoint
+        from cis.col_implementations import HyperPoint
         if missing_data_for_missing_sample:
             iterator = index_iterator_for_non_masked_data(shape, points)
         else:
@@ -206,11 +206,11 @@ def __get_class(parent_class, name=None):
     :param name: name of the class to find
     :return: a subclass of the parent_class
     '''
-    from jasmin_cis.plugin import find_plugin_classes
-    from jasmin_cis.exceptions import ClassNotFoundError
+    from cis.plugin import find_plugin_classes
+    from cis.exceptions import ClassNotFoundError
     import logging
 
-    all_classes = find_plugin_classes(parent_class, 'jasmin_cis.col_implementations')
+    all_classes = find_plugin_classes(parent_class, 'cis.col_implementations')
     for cls in all_classes:
 
         if name is None: