Docstanya

docs/environment.yml

@@ -3,107 +3,98 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - alabaster=0.7.11=py_3
-  - asn1crypto=0.24.0=py27_2
-  - babel=2.6.0=py_1
-  - bzip2=1.0.6=h470a237_2
-  - ca-certificates=2018.8.13=ha4d7672_0
-  - cdat_info=8.0=py27_0
-  - cdms2=3.0.1=py27h6091dcd_1
-  - cdtime=3.0=py27h6091dcd_1
-  - certifi=2018.8.13=py27_0
-  - cffi=1.11.5=py27h5e8e0c9_1
-  - chardet=3.0.4=py27_3
-  - clapack=3.2.1=0
-  - colorama=0.3.9=py_1
-  - colorlog=3.1.2=py27_0
-  - cryptography=2.3.1=py27hdffb7b8_0
-  - cryptography-vectors=2.3.1=py27_0
-  - curl=7.61.0=h93b3f91_1
-  - distarray=2.12.2=py27_0
-  - docutils=0.14=py27_0
+  - alabaster=0.7.12=py37_0
+  - asn1crypto=0.24.0=py37_1003
+  - attrs=19.1.0=py_0
+  - babel=2.6.0=py37_0
+  - blas=1.1=openblas
+  - bzip2=1.0.6=h14c3975_1002
+  - ca-certificates=2019.1.23=0
+  - cdat_info=8.1.1=py_2
+  - cdtime=3.1.2=py37h6091dcd_1
+  - certifi=2019.3.9=py37_0
+  - cffi=1.12.2=py37hf0e25f4_1
+  - chardet=3.0.4=py37_1003
+  - colorama=0.4.1=py_0
+  - colorlog=4.0.2=py37_1000
+  - cryptography=2.6.1=py37h72c5cf5_0
+  - curl=7.64.1=hf8cf82a_0
+  - decorator=4.4.0=py_0
+  - distarray=2.12.2=py_1
+  - docutils=0.14=py37_0
   - easydev=0.9.36=py_1
-  - enum34=1.1.6=py27_1
-  - esmf=7.1.0r=1
-  - esmpy=7.1.0r=py27_1
-  - future=0.16.0=py27_2
-  - g2clib=1.6.0=3
-  - hdf4=4.2.13=0
-  - hdf5=1.10.1=2
-  - idna=2.7=py27_2
-  - imagesize=1.0.0=py_1
-  - ipaddress=1.0.22=py_1
-  - jasper=1.900.1=4
-  - jinja2=2.10=py_1
-  - jpeg=9c=h470a237_0
-  - krb5=1.14.6=0
-  - lapack=3.6.1=1
-  - libcdms=3.0.1=h9ac9557_2
-  - libcf=1.0.1=py27_2
-  - libdrs=3.0.1=h6e3784b_3
-  - libdrs_f=3.0.1=h2cd7f18_3
-  - libffi=3.2.1=hfc679d8_4
-  - libgcc=7.2.0=h69d50b8_2
-  - libgfortran=3.0.0=1
-  - libgfortran-ng=7.2.0=hdf63c60_3
-  - libnetcdf=4.6.1=2
-  - libpng=1.6.35=ha92aebf_0
-  - libssh2=1.8.0=h5b517e9_2
-  - libtiff=4.0.9=he6b73bb_1
-  - markupsafe=1.0=py27_0
-  - mpi=1.0=mpich
-  - mpich=3.2.1=h26a2512_4
-  - ncurses=6.1=hfc679d8_1
-  - netcdf-fortran=4.4.4=7
-  - numpydoc=0.8.0=py_1
-  - openssl=1.0.2o=h470a237_1
-  - ossuuid=1.6.2=hfc679d8_0
-  - packaging=17.1=py_0
-  - pexpect=4.6.0=py27_0
-  - ptyprocess=0.6.0=py27_0
-  - pycparser=2.18=py_1
-  - pygments=2.2.0=py_1
-  - pyopenssl=18.0.0=py27_0
-  - pyparsing=2.2.0=py_1
-  - pysocks=1.6.8=py27_1
-  - python=2.7.15=h9fef7bc_0
-  - pytz=2018.5=py_0
-  - readline=7.0=haf1bffa_1
-  - requests=2.19.1=py27_1
-  - setuptools=40.0.0=py27_1
-  - six=1.11.0=py27_1
-  - snowballstemmer=1.2.1=py_1
-  - sphinxcontrib-websupport=1.0.1=py27_0
-  - sqlite=3.24.0=h2f33b56_0
-  - tk=8.6.8=0
-  - typing=3.6.4=py27_2
-  - urllib3=1.23=py27_1
-  - xz=5.2.4=h470a237_1
-  - zlib=1.2.11=h470a237_3
-  - binutils_impl_linux-64=2.31.1=h6176602_0
-  - binutils_linux-64=2.31.1=h6176602_2
-  - freetype=2.9.1=h8a8886c_0
-  - funcsigs=1.0.2=py27_0
-  - gcc_impl_linux-64=7.3.0=habb00fd_0
-  - gcc_linux-64=7.3.0=h553295d_2
+  - esmf=7.1.0=hdfb41a0_1004
+  - esmpy=7.1.0=py37h24bf2e0_3
+  - freetype=2.9.1=h8a8886c_1
+  - future=0.17.1=py37_1000
+  - g2clib=1.6.0=hf3f1b0b_9
+  - hdf4=4.2.13=h9a582f1_1002
+  - hdf5=1.10.4=nompi_h3c11f04_1106
+  - idna=2.8=py37_1000
+  - imagesize=1.1.0=py37_0
+  - ipython_genutils=0.2.0=py_1
+  - jasper=1.900.1=h07fcdf6_1006
+  - jinja2=2.10=py37_0
+  - jpeg=9c=h14c3975_1001
+  - jsonschema=3.0.1=py37_0
+  - jupyter_core=4.4.0=py_0
+  - krb5=1.16.3=h05b26f9_1001
+  - lazy-object-proxy=1.3.1=py37h14c3975_1000
+  - libcdms=3.1.2=hcbdc9ef_1000
+  - libcf=1.0.2=py37h6e3784b_1006
+  - libcurl=7.64.1=hda55be3_0
+  - libdrs=3.1.2=h6e3784b_1
+  - libdrs_f=3.1.2=h750f5ca_1
+  - libedit=3.1.20170329=hf8c457e_1001
+  - libffi=3.2.1=he1b5a44_1006
   - libgcc-ng=8.2.0=hdf63c60_1
-  - libopenblas=0.2.20=h9ac9557_7
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libnetcdf=4.6.2=hbdf4f91_1001
+  - libpng=1.6.36=h84994c4_1000
+  - libssh2=1.8.2=h22169c7_2
   - libstdcxx-ng=8.2.0=hdf63c60_1
-  - mock=2.0.0=py27_0
-  - numpy=1.14.3=py27h28100ab_1
-  - numpy-base=1.14.3=py27h0ea5e3f_1
-  - olefile=0.45.1=py27_0
-  - pbr=4.2.0=py27_0
-  - pillow=5.2.0=py27heded4f4_0
-  - pip=10.0.1=py27_0
-  - sphinx=1.7.6=py27_0
-  - sphinx_rtd_theme=0.4.1=py27_0
-  - wheel=0.31.1=py27_0
-  - pip:
-    - commonmark==0.5.4
-    - mv2==3.0.0
-    - readthedocs-sphinx-ext==0.5.14
-    - recommonmark==0.4.0
-    - regrid2==3.0.0
-prefix: /export/reshel3/anaconda52/envs/cdms2
-
+  - libtiff=4.0.10=h648cc4a_1001
+  - markupsafe=1.1.1=py37h7b6447c_0
+  - mock=2.0.0=py37_0
+  - mpi=1.0=mpich
+  - mpich=3.2.1=h1c2f66e_1008
+  - nbformat=4.4.0=py_1
+  - ncurses=6.1=hf484d3e_1002
+  - netcdf-fortran=4.4.5=hea25ff8_1000
+  - numpy=1.16.2=py37_blas_openblash1522bff_0
+  - numpydoc=0.8.0=py37_0
+  - olefile=0.46=py37_0
+  - openblas=0.3.3=h9ac9557_1001
+  - openssl=1.1.1b=h7b6447c_1
+  - ossuuid=1.6.2=hf484d3e_1000
+  - packaging=19.0=py37_0
+  - pbr=5.1.3=py_0
+  - pexpect=4.7.0=py37_0
+  - pillow=5.4.1=py37h34e0f95_0
+  - pip=19.0.3=py37_0
+  - ptyprocess=0.6.0=py37_1000
+  - pycparser=2.19=py37_1
+  - pygments=2.3.1=py37_0
+  - pyopenssl=19.0.0=py37_0
+  - pyparsing=2.3.1=py37_0
+  - pyrsistent=0.14.11=py37h14c3975_0
+  - pysocks=1.6.8=py37_1002
+  - python=3.7.3=h5b0a415_0
+  - pytz=2018.9=py37_0
+  - readline=7.0=hf8c457e_1001
+  - requests=2.21.0=py37_1000
+  - setuptools=41.0.0=py37_0
+  - six=1.12.0=py37_1000
+  - snowballstemmer=1.2.1=py37_0
+  - sphinx=1.8.5=py37_0
+  - sphinx_rtd_theme=0.4.3=py_0
+  - sphinxcontrib=1.0=py37_1
+  - sphinxcontrib-websupport=1.1.0=py37_1
+  - sqlite=3.26.0=h67949de_1001
+  - tk=8.6.9=h84994c4_1001
+  - traitlets=4.3.2=py37_1000
+  - urllib3=1.24.1=py37_1000
+  - wheel=0.33.1=py37_0
+  - xz=5.2.4=h14c3975_1001
+  - zlib=1.2.11=h14c3975_1004
+prefix: /software/anaconda53/envs/cdms2

docs/source/conf.py

@@ -28,9 +28,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0,os.path.join(sys.prefix,"lib","python3.7","site-packages"))
 sys.path.insert(0,os.path.join(sys.prefix,"lib","python2.7","site-packages"))
-print os.path.join(sys.prefix,"lib","python2.7","site-packages")
+print(os.path.join(sys.prefix,"lib","python3.7","site-packages"))
 os.environ['UVCDAT_ANONYMOUS_LOG']="False"
+import MV2
 
 
 

docs/source/manual/cdms_2.rst

@@ -344,15 +344,16 @@ Cdms Module Functions(cont'd)
                      NOT be generated; the ``getBounds`` method will return ``None`` for the boundaries. 
                    **Note:** In versions of CDMS prior to V4.0, the default ``mode`` was ``'on'``."
    "None", "``setClassifyGrids(mode)``:
-             Set the grid classification mode. 
-             This affects how grid type is determined, for the purpose of generating grid boundaries.
-                  * If ``mode`` is ``'on'`` (the default), grid type is determined by a grid classification method, 
+            Set the grid classification mode. 
+             This affects how grid type is determined, for the purpose of generating grid
+             boundaries.
+                   * If ``mode`` is ``'on'`` (the default), grid type is determined by a grid classification method, 
                     regardless of the value of ``grid.get-Type()``.
-                  * If ``mode`` is ``'off'``, the value of ``grid.getType()`` determines the grid type." 
+                   * If ``mode`` is ``'off'``, the value of ``grid.getType()`` determines the grid type." 
    "None", "``writeScripGrid(path, grid, gridTitle=None)``:
              Write a grid to a SCRIP grid file. 
-                * ``path`` is a string, the path of the SCRIP file to be created. 
-                * ``grid`` is a CDMS grid object. It may be rectangular. ``gridTitle`` is a string ID for the grid."
+                   * ``path`` is a string, the path of the SCRIP file to be created. 
+                   * ``grid`` is a CDMS grid object. It may be rectangular. ``gridTitle`` is a string ID for the grid."
 
 
 
@@ -794,16 +795,16 @@ CdmsFile Methods(cont'd)
            * ``datatype`` is an ``MV2`` typecode, e.g., ``MV2.Float``, ``MV2.Int``. 
            * ``axes`` is a list of Axis and/or Grid objects. 
            * ``fill_value`` is the missing value (optional)."
-   "Variable", "``createVariableCopy (var, newname=None)``", "Create a new ``Variable``, with the   same name, 
-               axes, and attributes as the input variable.
-        An error is raised if a variable of the same name exists
-        in the file. 
+   "Variable", "``createVariableCopy (var, newname=None)``", "Create a new ``Variable``, with the same name, axes, and
+    attributes as the input variable. An error is raised if a 
+    variable of the same name exists in the file.
            * ``var`` is the ``Variable`` to be copied. 
            * ``newname``, if specified is the name of the new variable. 
            * If unspecified, the returned variable has the same name as ``var``.
         **Note:** Unlike copyAxis, the actual data is not copied to the new variable."
-   "CurveGrid or Generic-Grid", "``readScripGrid (self,whichGrid= 'destination',check-Grid=1)``", "Read a curvilinear or generic grid from a SCRIP netCDF file. 
-         The file can be a SCRIP grid file or remapping file. 
+   "CurveGrid or Generic-Grid", "``readScripGrid (self,whichGrid= 'destination',check-Grid=1)``", "Read a curvilinear or generic grid from a SCRIP netCDF file.
+           The file can be a SCRIP grid file or remapping file.  
+
            * If a mapping file, ``whichGrid`` chooses the grid to read, either ``'source'`` or ``'destination'``. 
            * If ``checkGrid`` is ``1`` (default), the grid cells are checked for convexity, and 'repaired' if necessary.  
            * Grid cells may appear to be nonconvex if they cross a ``0 / 2pi`` boundary. 

readthedocs.yml

@@ -10,6 +10,6 @@ conda:
 build:
   image: latest
 python:
-  version: 2.70
+  version: 3.70
   setup_py_install: true
 

run_tests.py

@@ -23,6 +23,7 @@ def __setup_cdms(self):
         cacert_pem = ""
         if hostname.endswith('.llnl.gov'):
             cmd = "curl https://access.llnl.gov/cspca.cer -o {h}/cspca.cer".format(h=home)
+            cmd = "curl -k https://www-csp.llnl.gov/content/assets/csoc/cspca.crt -o {h}/cspca.cer".format(h=home)
             ret_code, out = run_command(cmd)
             if ret_code != SUCCESS:
                 return ret_code