Issue 1707 curvsetaxis (#199)

* 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

* fix squeeze CDAT/cdat/issues/1707

* fix squeeze CDAT/cdat/issues/1707

* fix ci netcdf-fortran

* fix ci netcdf-fortran to number 4.4.4=5

* flake8

.travis.yml

@@ -20,7 +20,7 @@ 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 netcdf-fortran=4.4.4=3
+- conda install -n py3 -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient netcdf-fortran=4.4.4=5
 - 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 netcdf-fortran=4.4.4=3; fi
 - export UVCDAT_ANONYMOUS_LOG=False

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
@@ -343,6 +343,15 @@ 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

@@ -588,14 +588,16 @@ def getGridSlices(self, domainlist, newaxislist, slicelist):
         k = 0
         i = j = -1
         for d in domainlist:
-            if d is iaxis:
-                inewaxis = newaxislist[k]
-                islice = slicelist[k]
-                i = k
-            if d is jaxis:
-                jnewaxis = newaxislist[k]
-                jslice = slicelist[k]
-                j = k
+            if d.shape == iaxis.shape:
+                if numpy.allclose(d[:], iaxis[:]) is True:
+                    inewaxis = newaxislist[k]
+                    islice = slicelist[k]
+                    i = k
+            if d.shape == jaxis.shape:
+                if numpy.allclose(d[:], jaxis[:]) is True:
+                    jnewaxis = newaxislist[k]
+                    jslice = slicelist[k]
+                    j = k
             k += 1
 
         if i == -1 or j == -1:
@@ -677,7 +679,8 @@ 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 all [False, False, ....] result=0
+            if not any([allclose(item[:], axis[:]) 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 netcdf-fortran=4.4.4=3"
+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 netcdf-fortran=4.4.4=5"
 echo $cmd
 $cmd
 
-cmd="conda install -n py3 -c nadeau1 -c conda-forge esmf esmpy netcdf-fortran=4.4.4=3"
+cmd="conda install -n py3 -c nadeau1 -c conda-forge esmf esmpy netcdf-fortran=4.4.4=5"
 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 netcdf-fortran=4.4.4=3"
+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=5"
 echo $cmd
 $cmd
 

tests/test_curvilinear_grid.py

@@ -5,9 +5,19 @@
 import os
 import sys
 import basetest
+import copy
 
 
 class TestCurvilinearGrids(basetest.CDMSBaseTest):
+
+    def testReadCurvGrid(self):
+        f = self.getDataFile('sampleCurveGrid4.nc')
+        data = f("sample")
+        attrs = copy.copy(data.attributes)
+        axes = list([x[0].clone() for x in data.getDomain()])
+        data2 = cdms2.createVariable(data, copy=0, attributes=attrs, axes=axes)
+        data3=data2(*(),squeeze=1)
+
     def testCurvilinear(self):
         datb = numpy.array(
             [[697., 698., 699., 700., 701., 702., ],