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other:uvcdat:extra [2015/06/08 16:38] jypeter Started updating the page when preparing for 2.2.0 |
other:uvcdat:extra [2016/04/14 12:15] jypeter Added statsmodels |
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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 ===== | ||
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* Optional dependencies (http://scitools.org.uk/cartopy/docs/latest/installing.html#optional-dependencies): not checked! | * Optional dependencies (http://scitools.org.uk/cartopy/docs/latest/installing.html#optional-dependencies): not checked! | ||
* ''pip install cartopy'' | * ''pip install cartopy'' | ||
- | * Check [[#proj4]] is there is a *proj* related error | + | * 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 | * 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 | * Shapely seems to have non-blocking Cython speedup compilation errors | ||
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==== Testing ==== | ==== Testing ==== | ||
- | Check the installed version with: ''which geos-config'' and ''geos-config --version'' | + | Check the installed version with: ''which geos-config'' and ''geos-config %%--version%%'' |
===== pyshp ===== | ===== pyshp ===== | ||
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Check the installed version with: ''rpm -qa | grep '^proj' '' | 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' '' | ||