Extra packages installed in UV-CDAT

This page lists the packages (usually) installed in the LSCE-IPSL CDAT versions that are not available in the standard UV-CDAT (i.e. there are no ccmake configuration switches to get them installed).

pip documentation

• To install the latest version of “SomeProject”:
  pip install 'SomeProject'
• To install a specific version:
  pip install 'SomeProject==1.4'
• To upgrade an installed version:
  pip install SomeProject --upgrade

• Web site: http://docs.python-requests.org/en/latest/
• Required by: find_agg

• HOWTO: http://docs.python-requests.org/en/latest/user/install/
• pip install requests

Check the installed version with: python -c 'import requests; print requests.__version__'

• Web site: http://cmip5-find-agg.readthedocs.org/en/latest/

• HOWTO: http://cmip5-find-agg.readthedocs.org/en/latest/installation.html
• pip install findagg

Check the installed version with: find_agg -V

Clean this section!

PIL does not seem to be maintained any longer and should be replaced by pillow

• Web site: https://pillow.readthedocs.org/
• Required by: basemap
  • implicitely used by basemap to plot etopo, bluemarble, etc

More information

pip uninstall PIL
pip install pillow

Check the installed version with

python -c 'import PIL; print dir(PIL)'
['PILLOW_VERSION', 'VERSION', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', '_plugins']

Use one of the basemap examples to check if everything is working

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
# setup Lambert Conformal basemap.
# set resolution=None to skip processing of boundary datasets.
m = Basemap(width=12000000,height=9000000,projection='lcc',
            resolution=None,lat_1=45.,lat_2=55,lat_0=50,lon_0=-107.)
m.bluemarble()
plt.show()

• Web site: http://labix.org/python-dateutil
• Required by: pandas

• Bundled with another package?
• A newer version of python-dateutil was installed during pandas installation in the old CDAT 1.5.1…

Check the installed version with: python -c 'import dateutil; print dateutil.__version__'

• Web site: http://pytz.sourceforge.net/
• Required by: pandas

Bundled?

Check the installed version with: python -c 'import pytz; print pytz.__version__'

• Web site: http://pandas.pydata.org/

• Dependencies:
  • numpy >= 1.7.0
  • python_dateutil >= 1.5
  • pytz
• Optional dependencies (http://pandas.pydata.org/pandas-docs/version/0.16.2/install.html#dependencies): not checked!
• pip install pandas
  • JYP install: setenv mydate `date +“%Y%m%d_%H%M”` ; setenv mylogf $ALL_LOGS_DIR/pandas_install_${CDAT_ID}_${mydate}.log ; ( /usr/bin/nohup /usr/bin/time pip install pandas > & $mylogf & ) ; sleep 10 ; tail -n +1 -f $mylogf

Check the installed version with: python -c 'import pandas; print pandas.__version__'

• Web site: http://rpy.sourceforge.net/rpy2/doc-2.5/html/index.html

• Web site: http://scitools.org.uk/cartopy/

• HOWTO: http://scitools.org.uk/cartopy/docs/latest/installing.html#installing
• Checked that the non standard requirements were already installed, or installed them:
  • geos >= 3.3.3
  • shapely >= 1.1.4
    • Cartopy actually required a more recent version of shapely and installed it automatically
  • pyshp >= 1.1.4
  • proj4 >= 4.8.0
  • six >= 1.3.0
• Optional dependencies (http://scitools.org.uk/cartopy/docs/latest/installing.html#optional-dependencies): not checked!
• pip install cartopy
  • Check proj4 if there is a *proj* related error
  • The installation may bump shapely to a newer version: e.g. 1.3.2 to 1.5.8
    • Shapely seems to have non-blocking Cython speedup compilation errors

Check the installed version with: python -c 'import cartopy; print cartopy.__version__'

• Web site: http://trac.osgeo.org/geos/
• Required by: cartopy
• Bundled with CDAT if we use -D CDAT_BUILD_BASEMAP=ON ([INFO] Setting build package – GEOS ON – as required by basemap)

Check the installed version with: which geos-config and geos-config --version

• Web site: https://code.google.com/p/pyshp/
• Required by: cartopy

• pip install pyshp

Check the installed version with: python -c 'import shapefile; print shapefile.__version__'

• Web site: http://trac.osgeo.org/proj/
• Required by: cartopy

We use the PROJ.4 library already installed on the system!

Note: if proj-devel is not installed, you will get the following kind of error when trying to install Cartopy. Just install it with yum install proj-devel and try installing Cartopy again

    lib/cartopy/trace.cpp:237:22: fatal error: proj_api.h: No such file or directory
     #include "proj_api.h"
                          ^
    compilation terminated.
    error: command 'gcc' failed with exit status 1

Check the installed version with: rpm -qa | grep '^proj'

• Web site:
  • http://pythonhosted.org/spectrum/
  • https://github.com/cokelaer/spectrum

• pip install spectrum

Check the installed version with: python -c 'import spectrum'

• Web site: http://statsmodels.sourceforge.net/stable/index.html

• pip install statsmodels

Check the installed version with: python -c 'import statsmodels; print statsmodels.version.version'

• Web site: https://stanford.edu/~mwaskom/software/seaborn/index.html

• pip install seaborn

Check the installed version with: python -c 'import seaborn; print seaborn.__version__'

• Web site: http://scikit-image.org/

• for CDAT up to 2.1.0: pip install 'scikit-image==0.8.2'

Check the installed version with: python -c 'import skimage; print skimage.__version__'

• Web site: http://scikit-learn.org/stable/

• pip install scikit-learn

Check the installed version with: python -c 'import sklearn; print sklearn.__version__'

• Web site: http://cython.org/
• Version: python -c 'import Cython; print Cython.__version__'

• Web site: http://numpy.scipy.org/
• Version: python -c 'import numpy; print numpy.__version__'

• CDAT cmake option: -D CDAT_BUILD_SHAPELY=ON
• Web site: https://github.com/Toblerity/Shapely
• If needed, explicit install/updgrade with: pip install shapely –upgrade
• Version: python -c 'import shapely; print shapely.__version__'
• Required by: cartopy

• Web site: http://pythonhosted.org/six/
• Version: python -c 'import six; print six.__version__'
• Required by: cartopy
• Bundled with CDAT if we use -D CDAT_BUILD_MATPLOTLIB=ON ([INFO] Setting build package – SIX ON – as required by Matplotlib)

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