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other:uvcdat:extra [2015/05/27 14:24] jypeter Added pyshp |
other:uvcdat:extra [2016/04/14 10:01] jypeter Added spectrum |
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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). | ||
+ | |||
+ | ===== 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 164: | ||
^ 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, [[#shapely]]>=1.1.4, [[#pyshp]]>=1.1.4 | + | * 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 193: | ||
* 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 205: | ||
==== Testing ==== | ==== Testing ==== | ||
- | Check the installed version with: ''geos-config --version'' | + | Check the installed version with: ''which geos-config'' and ''geos-config %%--version%%'' |
===== pyshp ===== | ===== pyshp ===== | ||
Line 61: | Line 226: | ||
==== Testing ==== | ==== Testing ==== | ||
- | Check the installed version with: ''python -c 'import shapefile; print shapefile.__version__''' | + | 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' '' | ||
Line 69: | Line 281: | ||
* Web site: http://cython.org/ | * Web site: http://cython.org/ | ||
- | * Version: ''python -c 'import Cython; print Cython.__version__' '' | + | * Version: ''python -c 'import Cython; print Cython.%%__version__%%' '' |
^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | ||
Line 80: | Line 292: | ||
* Web site: http://numpy.scipy.org/ | * Web site: http://numpy.scipy.org/ | ||
- | * Version: ''python -c 'import numpy; print numpy.__version__' '' | + | * Version: ''python -c 'import numpy; print numpy.%%__version__%%' '' |
^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | ||
Line 90: | Line 302: | ||
==== shapely ==== | ==== shapely ==== | ||
- | * Web site: http://toblerity.org/shapely/ | + | * CDAT cmake option: ''-D CDAT_BUILD_SHAPELY=ON'' |
- | * Version: ''python -c 'import shapely; print shapely.__version__' '' | + | * 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 ^ | ^ UV-CDAT\\ version ^ JYP\\ installation ^ Package\\ version ^ Date ^ | ||
- | | 1.5.1 | LSCE_10 | 1.2.14 | //bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')// | | + | | 1.5.1 | LSCE_10 | 1.2.14 | //bundled with UV-CDAT?// | |
- | | 1.5.1 | VB_10 | 1.2.14 | //bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')// | | + | | 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 | 1.3.2 | //bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')// | | + | | 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 | 1.3.2 | //bundled with UV-CDAT (''-D CDAT_BUILD_SHAPELY=ON'')// | | + | | 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// | | ||