====== 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 related notes ===== [[http://python-packaging-user-guide.readthedocs.io/en/develop/|pip documentation]] You may need to do some cleaning, in order to be sure that pip is not going to get something from its installation cache! Go check the content of ''/tmp/pip-build/''... * 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'' ===== Requests ===== * Web site: http://docs.python-requests.org/en/latest/ * Required by: [[#find_agg]] ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 2.1.0 | LSCE_13 | 2.8.1 | Oct 20 2015 | | 2.1.0 | ciclad_13 | 2.8.1 | Oct 20 2015 | ==== Installing ==== * HOWTO: http://docs.python-requests.org/en/latest/user/install/ * ''pip install requests'' ==== Testing ==== Check the installed version with: ''python -c 'import requests; print requests.%%__version__%%' '' ===== find_agg ===== * Web site: http://cmip5-find-agg.readthedocs.org/en/latest/ ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 2.1.0 | LSCE_13 | 0.5.1 - v0.5 2015-07-06 | Oct 20 2015 | | 2.1.0 | ciclad_13 | 0.5.1 - v0.5 2015-07-06 | Oct 20 2015 | ==== Installing ==== * HOWTO: http://cmip5-find-agg.readthedocs.org/en/latest/installation.html * ''pip install findagg'' ==== Testing ==== Check the installed version with: ''find_agg -V'' ===== PIL and pillow ===== FIXME **Clean this section!** FIXME 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 [[http://matplotlib.org/basemap/users/geography.html|plot etopo, bluemarble, etc]] === Replacing PIL with pillow === [[http://stackoverflow.com/questions/8915296/python-image-library-fails-with-message-decoder-jpeg-not-available-pil|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 [[http://matplotlib.org/basemap/users/geography.html|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 [[https://github.com/SciTools/cartopy/issues/622|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' '' ===== spectrum ===== * Web site: * http://pythonhosted.org/spectrum/ * https://github.com/cokelaer/spectrum ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 2.1.0 | LSCE_13 | 0.6.1 | Apr 14 2016 | ==== Installing ==== * ''pip install spectrum'' ==== Testing ==== Check the installed version with: ''python -c 'import spectrum' '' ===== statsmodels ===== * Web site: http://statsmodels.sourceforge.net/stable/index.html ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 2.1.0 | LSCE_13 | 0.6.1 | Apr 14 2016 | ==== Installing ==== * ''pip install statsmodels'' ==== Testing ==== Check the installed version with: ''python -c 'import statsmodels; print statsmodels.version.version' '' ===== seaborn ===== * Web site: https://stanford.edu/~mwaskom/software/seaborn/index.html ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 2.1.0 | LSCE_13 | 0.7.0 | Apr 14 2016 | ==== Installing ==== * ''pip install seaborn'' ==== Testing ==== Check the installed version with: ''python -c 'import seaborn; print seaborn.%%__version__%%' '' ===== scikit-image ===== * Web site: http://scikit-image.org/ ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 1.5.1 | LSCE_10 | 0.8.2\\ Newer versions fail because we have Cython 0.16, but require >= 0.21 | Jun 01 2016 | | 2.1.0 | LSCE_13 | 0.8.2\\ Newer versions fail because we have Cython 0.16, but require >= 0.21 | Jun 01 2016 | ==== Installing ==== * for CDAT up to 2.1.0: ''pip install 'scikit-image==0.8.2' '' ==== Testing ==== Check the installed version with: ''python -c 'import skimage; print skimage.%%__version__%%' '' ===== scikit-learn ===== * Web site: http://scikit-learn.org/stable/ ==== Versions installed ==== ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | 1.5.1 | LSCE_10 | 0.17.1 | Jun 01 2016 | | 2.1.0 | LSCE_13 | 0.17.1 | Jun 01 2016 | ==== Installing ==== * ''pip install scikit-learn'' ==== Testing ==== Check the installed version with: ''python -c 'import sklearn; print sklearn.%%__version__%%' '' ===== 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// | /* standard page footer */ \\ \\ \\ ---- [ [[pmip3:|PMIP3 Wiki Home]] ] - [ [[pmip3:wiki_help|Help!]] ] - [ [[wiki:syntax|Wiki syntax]] ]