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other:uvcdat:extra [2015/05/27 12:01] – Started adding cartopy and GEOS jypeterother:uvcdat:extra [2016/06/01 13:52] (current) – Added scikit-learn jypeter
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 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). 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]]
 +
 +<note important>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/''...</note>
 +
 +  * 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]]
 +
 +<code>pip uninstall PIL
 +pip install pillow
 +</code>
 +
 +=== Testing ===
 +
 +Check the installed version with
 +
 +<code>python -c 'import PIL; print dir(PIL)'
 +['PILLOW_VERSION', 'VERSION', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', '_plugins']
 +</code>
 +
 +Use one of the [[http://matplotlib.org/basemap/users/geography.html|basemap examples]] to check if everything is working
 +
 +<code>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()
 +</code>
 +
 +===== 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  |  <del>1.5-mpl</del>\\ 2.4.2  |  ? (//bundled?//)\\ Sep 11 2015 (with pandas)  |
 +|  1.5.1  |  VB_10  |  <del>1.5-mpl</del>\\ 2.4.2  |  <del>? (//bundled?//)</del>\\ 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 ===== ===== rpy2 =====
Line 15: Line 174:
  
 ^  UV-CDAT\\ version  ^  JYP\\ installation  ^  Package\\ version  ^  Date  ^ ^  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 ==== ==== Installing ====
  
-  * http://scitools.org.uk/cartopy/docs/latest/installing.html#installing +  * HOWTO: http://scitools.org.uk/cartopy/docs/latest/installing.html#installing 
-  * Non //standard// requirements: [[#geos]]>=3.3.3+  * 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 ==== ==== Testing ====
  
-Check the installed version with: +Check the installed version with: ''python -c 'import cartopy; print cartopy.%%__version__%%' ''
  
 ===== GEOS ===== ===== GEOS =====
Line 29: Line 203:
   * Web site: http://trac.osgeo.org/geos/   * Web site: http://trac.osgeo.org/geos/
   * Required by: [[#cartopy]]   * 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 ==== ==== Versions installed ====
Line 40: Line 215:
 ==== Testing ==== ==== Testing ====
  
-Check the installed version with: ''geos-config --version''+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 
 + 
 +<code> 
 +    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 
 +</code> 
 + 
 +==== 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  |  <del>1.2.14</del>\\ 1.5.8  |  <del>//bundled with UV-CDAT?//</del>\\ May 27 2015 (with Cartopy)  | 
 +|  2.1.0  |  LSCE_13  |  <del>1.3.2</del>\\ 1.5.9  |  <del>//bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')//</del>\\ May 29 2015  | 
 +|  2.1.0  |  VB_13  |  <del>1.3.2</del>\\ 1.5.8  |  <del>//bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')//</del>\\ 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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other/uvcdat/extra.1432720912.txt.gz · Last modified: by jypeter
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