3.3.1 (#301)

* update to 3.2.9 in cmor.h

* update tables to 01.00.17

* use CdUnif

* fix Table memory

* fix Table version 6.0 to 6.2

* Fix licences and conventions; Fix memory issue

* insure that cdms2 is not loaded

* update tables

* fix cronjob message for CMIP6_CV push

* update to version 3.3.0

* use 1024 character, fix regex

* Make sure buffer does not overflow due to license

* Add multiprocessing to PrePARE

* pep8 code

* create parallelization for PrePARE

* fix typo

* Fix basin integer missing value; add test; move code around in PrePARE.py

* update test tables

* fix conda recipe

* pinning anaconda-client to 1.6.5 due to network issue

* check in source section is defined in CV souce_id

* fix external variable issue

* add test for branch_time...

* fix climatology issue

* change geo_region to sector

* update upload scripts

* add then to script

* fix travis; branch_time.. message; license(OSX)

* use gcc_linux-64

* try miniconda 4.3.21

* change docker to centos 6.8

* change branch_time message

* fix time_bnds issue and missing_value for Ofx test

* Release 3.3.1

* use GCC instead of gcc_linux-64

* add gfortran to .travis

* use gfortran_linux-64

* revert to miniconda 4.3.21

.travis.yml

@@ -9,8 +9,7 @@ services:
 sudo: false
 
 before_install:
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-    -O miniconda.sh; fi
+  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then wget --no-check https://repo.continuum.io/miniconda/Miniconda2-4.3.21-Linux-x86_64.sh  -O miniconda.sh ; fi
   - if [ "$TRAVIS_OS_NAME" = "osx" ]; then wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh
     -O miniconda.sh; fi
   - export PATH="$HOME/miniconda/bin:$PATH"
@@ -23,8 +22,10 @@ before_install:
   - conda install openssl=1.0.2d
   - conda install cdms2 -c uvcdat/label/nightly -c conda-forge -c uvcdat
   - conda install udunits2 -c uvcdat/label/nightly  -c conda-forge -c uvcdat
-  - conda install gcc
-
+  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then conda install gcc; fi
+  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then conda install gcc; fi
+  - source deactivate root
+  - source activate root
 install:
   - git clone https://github.com/PCMDI/cmip6-cmor-tables
   - ln -s cmip6-cmor-tables/Tables Tables
@@ -50,4 +51,4 @@ env:
 
 after_success:
   - if [ "$TRAVIS_OS_NAME" = "osx" ]; then bash scripts/conda_upload.sh ${TRAVIS_BRANCH} ; fi
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then docker run -v `pwd`:/travis_home -e CONDA_UPLOAD_TOKEN=${CONDA_UPLOAD_TOKEN} -a STDOUT -a STDERR cdat/conda:conda-forge-cdms2 /travis_home/scripts/conda_upload.sh ${TRAVIS_BRANCH} ; fi
+  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then docker run -v `pwd`:/travis_home -e CONDA_UPLOAD_TOKEN=${CONDA_UPLOAD_TOKEN} -a STDOUT -a STDERR centos:6.8 /travis_home/scripts/conda_upload.sh ${TRAVIS_BRANCH} ; fi

INSTALL

@@ -1,6 +1,6 @@
 INSTALLATION INSTRUCTIONS  
 ------------------------- 
-Climate Model Output Rewriter (CMOR) version 3.3.0 installation instructions.
+Climate Model Output Rewriter (CMOR) version 3.3.1 installation instructions.
 
 
 DOWNLOAD 
@@ -13,7 +13,7 @@ cd CMOR
 
 INSTALLATION
 ------------ 
-CMOR 3.3.0 requires external packages that need to be installed first. 
+CMOR 3.3.1 requires external packages that need to be installed first. 
 It can be compiled/linked against either NetCDF3 or NetCDF4. If you
 decide to go with NetCDF4 be sure to build NetCDF4 with the
  --enable-netcdf-4 option! 

Lib/__init__.py

@@ -11,7 +11,8 @@
     close, grid, set_grid_mapping, time_varying_grid_coordinate, dataset_json,
     set_cur_dataset_attribute, get_cur_dataset_attribute,
     has_cur_dataset_attribute, set_variable_attribute, get_variable_attribute,
-    has_variable_attribute, get_final_filename, set_deflate, set_furtherinfourl)
+    has_variable_attribute, get_final_filename, set_deflate, set_furtherinfourl, 
+    set_climatology, get_climatology)
 
 try:
     from check_CMOR_compliant import checkCMOR

Lib/pywrapper.py

@@ -6,6 +6,9 @@
 import _cmor
 from _cmor import CMORError
 
+global climatology 
+climatology = False
+
 try:
     import cdtime
     has_cdtime = True
@@ -297,6 +300,16 @@ def set_grid_mapping(grid_id, mapping_name, parameter_names,
     pvals = numpy.ascontiguousarray(pvals).astype('d')
     return _cmor.set_grid_mapping(grid_id, mapping_name, pnms, pvals, punit)
 
+def set_climatology(entry):
+    global climatology 
+    if( entry == True ):
+      climatology = True 
+    else:
+      climatology = False
+
+def get_climatology():
+    global climatology 
+    return climatology
 
 def axis(table_entry, units=None, length=None,
          coord_vals=None, cell_bounds=None, interval=None):
@@ -321,6 +334,9 @@ def axis(table_entry, units=None, length=None,
         raise Exception(
             "You need to pass a table_entry to match in the cmor table")
 
+    if(table_entry in ['time2', 'time3']):
+        set_climatology(True)
+
     if coord_vals is None:
         if cell_bounds is not None:
             raise Exception("you passed cell_bounds but no coords")
@@ -740,7 +756,7 @@ def write(var_id, data, ntimes_passed=None, file_suffix="",
 
     data = numpy.ascontiguousarray(numpy.ravel(data))
 
-    if time_bnds is not None:
+    if time_bnds is not None: 
         if numpy.ma.isMA(time_bnds):
             time_bnds = numpy.ascontiguousarray(time_bnds.filled())
         elif has_oldma and numpy.oldnumeric.ma.isMA(time_bnds):
@@ -762,7 +778,7 @@ def write(var_id, data, ntimes_passed=None, file_suffix="",
                 raise Exception(
                     "error time_bnds' 2nd dimension must be of length 2")
             bnds = []
-            if time_bnds.shape[0] > 1:
+            if time_bnds.shape[0] > 1 and get_climatology() is False:
                 _check_time_bounds_contiguous(time_bnds)
                 bnds = _flatten_time_bounds(time_bnds)
             else: