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).

PIL and pillow

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

Replacing PIL with pillow

More information

pip uninstall PIL
pip install pillow

Testing

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()

python-dateutil

Web site: http://labix.org/python-dateutil

Required by: pandas

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	1.5-mpl 2.4.2	? (bundled?) Sep 11 2015 (with pandas)
1.5.1	VB_10	1.5-mpl 2.4.2	? (bundled?) Sep 11 2015 (with pandas)
2.1.0	LSCE_13	2.2	? (bundled?)
2.1.0	VB_13	2.2	? (bundled?)

Installing

Bundled with another package?

A newer version of python-dateutil was installed during pandas installation in the old CDAT 1.5.1…

Testing

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

pytz

Web site: http://pytz.sourceforge.net/

Required by: pandas

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	2014.10	? (bundled?)
1.5.1	VB_10	2015.4	? (bundled?)
2.1.0	LSCE_13	2014.10	? (bundled?)
2.1.0	VB_13	2014.10	? (bundled?)

Installing

Bundled?

Testing

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

pandas

Web site: http://pandas.pydata.org/

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	0.16.2	Sep 11 2015
1.5.1	VB_10	0.16.2	Sep 11 2015
2.1.0	LSCE_13	0.16.2	Sep 11 2015
2.1.0	VB_13	0.16.2	Sep 11 2015

Installing

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

Testing

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

rpy2

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

cartopy

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

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	0.12.0[.5]	May 27 2015
1.5.1	VB_10
2.1.0	LSCE_13
2.1.0	VB_13

Installing

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

Testing

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

GEOS

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)

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	3.3.5	?
1.5.1	VB_10	3.3.5	?
2.1.0	LSCE_13	3.3.5	?
2.1.0	VB_13	3.3.5	?

Testing

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

pyshp

Web site: https://code.google.com/p/pyshp/

Required by: cartopy

Versions installed

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	1.2.1	May 27 2015
1.5.1	VB_10	1.2.1	May 27 2015
2.1.0	LSCE_13	1.2.1	May 27 2015
2.1.0	VB_13	1.2.1	May 27 2015

Installing

pip install pyshp

Testing

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

PROJ.4

Web site: http://trac.osgeo.org/proj/

Required by: cartopy

Versions installed

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

Server	version	JYP installation
asterix obelix	proj-4.7.0-2_0.el6.x86_64 proj-devel-4.7.0-2_0.el6.x86_64	LSCE_nn
ciclad	proj-4.7.0-1.el6.x86_64 proj-devel-4.7.0-1.el6.x86_64	ciclas_nn
Virtual Machine	proj-4.8.0-5.fc20.x86_64 proj-devel.x86_64 0:4.8.0-5.fc20	VB_nn

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

Testing

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

Quick links about packages bundled with UV-CDAT

Cython

Web site: http://cython.org/

Version: python -c 'import Cython; print Cython.__version__'

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	0.16	bundled with UV-CDAT
1.5.1	VB_10	0.16	bundled with UV-CDAT
2.1.0	LSCE_13	0.16	bundled with UV-CDAT
2.1.0	VB_13	0.16	bundled with UV-CDAT

numpy

Web site: http://numpy.scipy.org/

Version: python -c 'import numpy; print numpy.__version__'

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	1.7.1	bundled with UV-CDAT
1.5.1	VB_10	1.7.1	bundled with UV-CDAT
2.1.0	LSCE_13	1.9.0	bundled with UV-CDAT
2.1.0	VB_13	1.9.0	bundled with UV-CDAT

shapely

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

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	1.2.14	bundled with UV-CDAT?
1.5.1	VB_10	1.2.14 1.5.8	bundled with UV-CDAT? May 27 2015 (with Cartopy)
2.1.0	LSCE_13	1.3.2 1.5.9	bundled with UV-CDAT (-D CDAT_BUILD_SHAPELY=ON) May 29 2015
2.1.0	VB_13	1.3.2 1.5.8	bundled with UV-CDAT (-D CDAT_BUILD_SHAPELY=ON) May 27 2015 (with Cartopy)

six

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)

UV-CDAT version	JYP installation	Package version	Date
1.5.1	LSCE_10	1.7.3	?
1.5.1	VB_10	1.9.0	?
2.1.0	LSCE_13	1.7.2	bundled with UV-CDAT
2.1.0	VB_13	1.7.2	bundled with UV-CDAT

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