Merge branch 'master' of github.com:/PCMDI/cmor

.travis.yml

@@ -49,5 +49,5 @@ env:
     secure: V5q+wzxrJ5Rmk1vVYXimIdHgWUwZSHINd5W+oi3mTmfbtVyrngau9XQVZyiPyg8S309vHAbys9uMaplp83to7OY1Cw3+w002oMWkCaLwlVMn4UWs+xU7lJGn/wwLwN1OikZnTtiXF8RqrtBZpYsbAxjdebqZ8uZx/zDJXHVvvZY=
 
 after_success:
-  #- if [ "$TRAVIS_OS_NAME" = "osx" ]; then bash scripts/conda_upload.sh ${TRAVIS_BRANCH} ; fi
+  - if [ "$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

INSTALL

@@ -1,6 +1,6 @@
 INSTALLATION INSTRUCTIONS  
 ------------------------- 
-Climate Model Output Rewriter (CMOR) version 3.2.5 installation instructions.
+Climate Model Output Rewriter (CMOR) version 3.2.6 installation instructions.
 
 
 DOWNLOAD 
@@ -13,7 +13,7 @@ cd CMOR
 
 INSTALLATION
 ------------ 
-CMOR 3.2.5 requires external packages that need to be installed first. 
+CMOR 3.2.6 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 +11,7 @@
     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)
+    has_variable_attribute, get_final_filename, set_deflate, set_furtherinfourl)
 
 try:
     from check_CMOR_compliant import checkCMOR

Lib/pywrapper.py

@@ -730,7 +730,7 @@ def write(var_id, data, ntimes_passed=None, file_suffix="",
                         "Error: your data shape (%s) does not match the expected variable shape (%s)\nCheck your variable dimensions before caling cmor_write" %
                         (str(osh), str(ogoodshape)))
             j += 1
-        elif ntimes_passed != 1:
+        else:
             j += 1
 
     data = numpy.ascontiguousarray(numpy.ravel(data))
@@ -952,6 +952,15 @@ def get_cur_dataset_attribute(name):
         return None
 
 
+def set_furtherinfourl(varid):
+    """Sets further_url_info attribute for ES-DOC
+    Usage:
+      cmor.set_futherurlinfo(var_id)
+    Where:
+      var_id: is cmor variable id
+    """
+    return _cmor.set_furtherinfourl(varid)
+
 def set_variable_attribute(var_id, name, value):
     """Sets an attribute onto a cmor variable
     Usage:

LibCV/PrePARE/PrePARE.py

@@ -277,6 +277,15 @@ def ControlVocab(self):
         varmissing = self.infile[self.var[0]]._FillValue[0]
         varid = cmip6_cv.setup_variable(self.var[0], varunits, varmissing, startime, endtime,
                                         startimebnds, endtimebnds)
+        if(varid == -1):
+            print bcolors.FAIL
+            print "====================================================================================="
+            print " Could not find variable '%s' in table '%s' " % (self.var[0], self.cmip6_table)
+            print "====================================================================================="
+            print bcolors.ENDC
+            cmip6_cv.set_CV_Error()
+            return
+
         fn = os.path.basename(self.infile.id)
         cmip6_cv.check_filename(
             self.table_id,
@@ -337,6 +346,7 @@ def ControlVocab(self):
                     file_value = file_value[:idx]
                     table_value = table_value[:idx]
 
+
                 file_value = str(file_value)
                 table_value = str(table_value)
                 if table_value != file_value:
@@ -350,6 +360,9 @@ def ControlVocab(self):
             else:
                 # That attribute is not in the file
                 table_value = prepLIST[key]
+                if key == "cell_measures":
+                    if((table_value.find("OPT") != -1) or (table_value.find("MODEL") != -1)):
+                        continue
                 if isinstance(table_value, numpy.ndarray):
                     table_value = table_value[0]
                 if isinstance(table_value, float):

README.md

@@ -5,7 +5,7 @@ CMOR 3.2 documentation can be found here: http://cmor.llnl.gov
 
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.827366.svg)](https://doi.org/10.5281/zenodo.827366)
-[![stable version](https://img.shields.io/badge/stable%20version-3.2.5-brightgreen.svg)](https://github.com/PCMDI/cmor/releases/tag/3.2.5)
+[![stable version](https://img.shields.io/badge/stable%20version-3.2.6-brightgreen.svg)](https://github.com/PCMDI/cmor/releases/tag/3.2.6)
 ![platforms](https://img.shields.io/badge/platforms-linux%20|%20osx-lightgrey.svg)
 [![Anaconda-Server Badge](https://anaconda.org/pcmdi/cmor/badges/installer/conda.svg)](https://conda.anaconda.org/pcmdi)
 [![Anaconda-Server Badge](https://anaconda.org/pcmdi/cmor/badges/downloads.svg)](https://anaconda.org/pcmdi)

RELEASE-NOTES

@@ -1,3 +1,4 @@
+2018-08-31 : Release 3.2.6
 2017-00-00 : Release 3.2.5
 2017-06-16 : Release 3.2.4
 2017-04-19 : Release 3.2.3

Src/_cmormodule.c

@@ -889,6 +889,30 @@ static PyObject *PyCMOR_time_varying_grid_coordinate(PyObject * self,
     return (Py_BuildValue("i", coord_var_id));
 }
 
+/************************************************************************/
+/*                            PyCMOR_grid()                             */
+/************************************************************************/
+static PyObject *PyCMOR_set_furtherinfourl(PyObject * self, PyObject * args) 
+{
+    int varid;
+    int ierr;
+
+    signal(signal_to_catch, signal_handler);
+
+    if (!PyArg_ParseTuple (args, "i", &varid)) {
+        return NULL;
+    }
+
+    ierr = cmor_CV_checkFurtherInfoURL(varid);
+
+    if (ierr != 0 || raise_exception) {
+        raise_exception = 0;
+        PyErr_Format(CMORError, exception_message, "set_futherurlinfo");
+        return NULL;
+    }
+
+    return (Py_BuildValue("i", ierr));
+}
 /************************************************************************/
 /*                            PyCMOR_grid()                             */
 /************************************************************************/
@@ -1006,6 +1030,7 @@ static PyMethodDef MyExtractMethods[] = {
     {"has_variable_attribute", PyCMOR_has_variable_attribute,
      METH_VARARGS},
     {"get_original_shape", PyCMOR_get_original_shape, METH_VARARGS},
+    {"set_furtherinfourl", PyCMOR_set_furtherinfourl, METH_VARARGS},
     {"get_final_filename", PyCMOR_getFinalFilename, METH_VARARGS},
     {"set_deflate", PyCMOR_set_deflate, METH_VARARGS},
     {NULL, NULL}                /*sentinel */

Src/_controlvocabulary.c

@@ -4,8 +4,8 @@
 #include "numpy/arrayobject.h"
 #include "cmor.h"
 
-extern int cmor_CV_variable(int *, char *, char *, float *,
-                            float, float, float, float);
+extern int cmor_CV_variable(int *, char *, char *, double *,
+                            double, double, double, double);
 
 /************************************************************************/
 /*                       PyCV_checkFilename                             */
@@ -555,15 +555,15 @@ static PyObject *PyCV_setup_variable(PyObject * self, PyObject * args)
 {
     char *name;
     char *units;
-    float missing;
-    float startime;
-    float endtime;
-    float startimebnds;
-    float endtimebnds;
+    double missing;
+    double startime;
+    double endtime;
+    double startimebnds;
+    double endtimebnds;
 
     int var_id;
 
-    if (!PyArg_ParseTuple(args, "ssfffff", &name, &units, &missing,
+    if (!PyArg_ParseTuple(args, "ssddddd", &name, &units, &missing,
                           &startime, &endtime, &startimebnds, &endtimebnds)) {
         return (Py_BuildValue("i", -1));
     }