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--- other:uvcdat:extra [2015/05/27 10:01]
jypeter Started adding cartopy and GEOS
+++ other:uvcdat:extra [2016/06/01 11:52] (current)
jypeter Added scikit-learn
@@ Line 3: / Line 3: @@
 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 =====
@@ Line 15: / Line 174: @@
 ^  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 ====
-  * 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 ====
-Check the installed version with:
+Check the installed version with: ''python -c 'import cartopy; print cartopy.%%__version__%%' ''
 ===== GEOS =====
@@ Line 29: / Line 203: @@
   * 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 ====
@@ Line 40: / Line 215: @@
 ==== 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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