IRIS 2.0rc1 Install fails on cf_units

[Brian M Hamlin]

Hi - I had a chance to try installing the IRIS 2.0rc1 yesterday, and ran into a problem with cf_units. This is on Ubuntu 1604 Xenial and python 2.7, alongside a Jupyter 4 .   Perhaps there is a step I missed, but this is the error at this time  (tips appreciated):

--

/home/dbb/.local/lib/python2.7/site-packages/scitools_iris-2.0.0rc1-py2.7.egg/iris/_cube_coord_common.py in <module>()

     24 import string

     25 

---> 26 import cf_units

     27 

     28 import iris.std_names

/home/dbb/.local/lib/python2.7/site-packages/cf_units-1.2.0-py2.7.egg/cf_units/__init__.py in <module>()

    399             ctypes.set_errno(0)

    400         raise OSError('[%s] Failed to open UDUNITS-2 XML unit database %s' % (

--> 401             _status_msg, _error_msg))

    402 

    403 

OSError: [UT_OPEN_ARG] Failed to open UDUNITS-2 XML unit database : "No such file or directory"

In [4]: !ls /usr/share/xml/udunits

udunits2-accepted.xml  udunits2-base.xml  udunits2-common.xml  udunits2-derived.xml  udunits2-prefixes.xml  udunits2.xml

-- 

  the last bit of install looks something like this:

 2035  cd iris-2.0.0rc1/

 2036  ls

 2037  python setup.py clean

 2038  python setup.py build

 2039  python setup.py build_ext

 2040  python setup.py install --user

 2041  ipython

 2042  sudo ldconfig

 2043  ipython

 2044  cd ..

 2045  ls

 2046  cd udunits-2.2.26/

 2047  ls

 2048  less udunits2.info 

 2049  apt search udunits

 2050  sudo apt install libudunits2-dev

 2051  sudo apt install udunits-bin

 2052  cd ..

 2053  sudo ldconfig

 2054  ls

 2055  cd iris-2.0.0rc1/

 2056  ls

 2057  python setup.py clean

 2058  python setup.py build

 2059  python setup.py install --user

 2060  cd ..

 2061  sudo ldconfig

 2062  ipython

 2063  sudo updatedb

 2064  locate -i udunit

 2065  export UDUNITS2_XML_PATH=/usr/share/xml/udunits

 2066  ipython

[Phil Elson]

I think cf-units doesn't use the UDUNITS2_XML_PATH environment variable (unfortunately).

The code suggests that you will need to configure cf_units with a file: https://github.com/SciTools/cf_units/blob/master/cf_units/__init__.py#L385

Specifically you will need a site.cfg in cf_units/etc/ that follows the following template: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template

You're welcome to raise an issue on the tracker that relates to this: https://github.com/SciTools/cf_units/issues

Cheers,

Phil

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[Brian M Hamlin]

yes, that does seem to do the trick. 

(following is the output of a somewhat-randomly picked test, which certainly imports cf_units )

iris_tests$ python test_analysis.py 

/home/dbb/.local/lib/python2.7/site-packages/scitools_iris-2.0.0rc1-py2.7.egg/iris/coords.py:1191: UserWarning: Collapsing a non-contiguous coordinate. Metadata may not be fully descriptive for 'lat'.

  warnings.warn(msg.format(self.name()))

/home/dbb/.local/lib/python2.7/site-packages/scitools_iris-2.0.0rc1-py2.7.egg/iris/coords.py:1191: UserWarning: Collapsing a non-contiguous coordinate. Metadata may not be fully descriptive for 'lon'.

  warnings.warn(msg.format(self.name()))

............../home/dbb/.local/lib/python2.7/site-packages/scitools_iris-2.0.0rc1-py2.7.egg/iris/coords.py:1191: UserWarning: Collapsing a non-contiguous coordinate. Metadata may not be fully descriptive for 'wibble'.

  warnings.warn(msg.format(self.name()))

.................sssssssssss.s/home/dbb/.local/lib/python2.7/site-packages/scitools_iris-2.0.0rc1-py2.7.egg/iris/coords.py:1191: UserWarning: Collapsing a non-contiguous coordinate. Metadata may not be fully descriptive for 'dummy'.

  warnings.warn(msg.format(self.name()))

.ssssssssssssssssssssssssssss............sssss

----------------------------------------------------------------------

Ran 90 tests in 0.317s

OK (skipped=45)