fix setGrid (#193)

* fix setGrid

* add squeeze array to MV2

* pinned libnetcdf=4.4.1.1=9

* pinned libnetcdf=4.4.1.1=9 for MAC

* fix documentation for squeeze

* fix ci machines

* flake8

.travis.yml

@@ -20,9 +20,9 @@ before_install:
 script:
 #- conda install -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8
 - conda create -n py3 python=3.6
-- conda install -n py3 -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient
+- conda install -n py3 -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient libnetcdf netcdf-fortran=4.4.4=3
 - source activate py3
-- if [ "$TRAVIS_OS_NAME" = "linux" ]; then conda install -n py3 -c nesii/channel/dev-esmf -c conda-forge esmpy=7.1.0.dev34; fi
+- if [ "$TRAVIS_OS_NAME" = "linux" ]; then conda install -n py3 -c nesii/channel/dev-esmf -c conda-forge esmpy=7.1.0.dev34 netcdf-fortran=4.4.4=3; fi
 - if [ "$TRAVIS_OS_NAME" = "osx" ]; then conda install -n py3 -c nadeau1 -c conda-forge esmf esmpy; fi
 - export UVCDAT_ANONYMOUS_LOG=False
 - echo $TRAVIS_BRANCH
@@ -38,7 +38,7 @@ script:
 - conda create -n py2 python=2.7
 - source activate py2
 - which python
-- conda install -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8 
+- conda install -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8 netcdf-fortran=4.4.4=3
 - export UVCDAT_ANONYMOUS_LOG=False
 - python setup.py install
 - python run_tests.py -v2 -s

Lib/MV2.py

@@ -5,7 +5,7 @@
 import numpy
 from numpy import character, float, float32, float64  # noqa
 from numpy import int, int8, int16, int32, int64, byte  # noqa
-from numpy import  ubyte, uint8, uint16, uint32, uint64, long   # noqa
+from numpy import ubyte, uint8, uint16, uint32, uint64, long   # noqa
 from numpy.ma import allclose, allequal, common_fill_value  # noqa
 from numpy.ma import make_mask_none, dot, filled  # noqa
 from numpy.ma import getmask, getmaskarray, identity  # noqa
@@ -341,6 +341,15 @@ def _conv_axis_arg(axis):
     return axis
 
 
+def squeeze(x):
+    "call numpy.squeeze on ndarray and rebuild tvariable."
+    # ta = _makeMaskedArg(x)
+    maresult = numpy.squeeze(x._data)
+    axes, attributes, id, grid = _extractMetadata(x)
+    return TransientVariable(
+        maresult, axes=axes, attributes=attributes, grid=grid, id=id)
+
+
 def is_masked(x):
     "Is x a 0-D masked value?"
     return isMaskedArray(x) and x.size == 1 and x.ndim == 0 and x.mask.item()

Lib/avariable.py

@@ -1497,6 +1497,9 @@ def getGridIndices(self):
 
     # numpy.ma overrides
 
+    def squeeze(self):
+        return(MV.squeeze(self))
+
     def __getitem__(self, key):
         if isinstance(key, tuple):
             speclist = self._process_specs(key, {})

Lib/hgrid.py

@@ -676,7 +676,7 @@ def isClose(self, g):
     def checkAxes(self, axes):
         """Return 1 iff every element of self.getAxisList() is in the list 'axes'."""
         for item in self.getAxisList():
-            if item not in axes:
+            if item.shape not in [axis.shape for axis in axes]:
                 result = 0
                 break
         else:

Lib/tvariable.py

@@ -121,6 +121,8 @@ def __array_finalize__(self, obj):
     def __copy__(self):
         return numpy.ma.MaskedArray.copy(self)
 
+    squeeze = AbstractVariable.squeeze
+
     __mul__ = AbstractVariable.__mul__
     __rmul__ = AbstractVariable.__rmul__
     __imul__ = AbstractVariable.__imul__

ci-support/circleci_mac_dep.sh

@@ -12,11 +12,11 @@ echo $cmd
 $cmd
 
 # Create Python 3 environment
-cmd="conda create -n py3 -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient"
+cmd="conda create -n py3 -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient libnetcdf netcdf-fortran=4.4.4=3"
 echo $cmd
 $cmd
 
-cmd="conda install -n py3 -c nadeau1 -c conda-forge esmf esmpy"
+cmd="conda install -n py3 -c nadeau1 -c conda-forge esmf esmpy netcdf-fortran=4.4.4=3"
 echo $cmd
 $cmd
 
@@ -30,7 +30,7 @@ cmd="source activate py2"
 echo $cmd
 $cmd 
 
-cmd="conda install -n py2  -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8 myproxyclient"
+cmd="conda install -n py2  -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8 myproxyclient netcdf-fortran=4.4.4=3"
 echo $cmd
 $cmd