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====== UV-CDAT 2.10 installation notes ======

[ [[.:index|Back to all versions]] ]

<WRAP center round tip 60%>
Follow the instructions about the [[other:python:starting#conda-based_versions_of_uv-cdat|conda-based versions of UV-CDAT initialization]] for actually using an installed version of ''2.10''
</WRAP>

===== What's New? =====

  * [[https://github.com/UV-CDAT/uvcdat/releases/tag/v2.10|2.10 announcement]] and features summary ([[https://github.com/UV-CDAT/uvcdat/releases|all versions]])
  * Full [[https://uvcdat.llnl.gov/changelog.html#2.10|Change log]]

===== Installation with Miniconda2 =====

<note important>\\ We used the [[other:uvcdat:cdat_conda:cdat_2_8_0#downgrading_conda|recommended downgraded version of conda]] that was available after installing UV-CDAT 2.8</note>

DIsk space used before 2.10 installation (after running ''conda clean --all'')

<code> > du -sh /home/share/unix_files/cdat/miniconda2
6.5G	/home/share/unix_files/cdat/miniconda2

 > du -sh /home/share/unix_files/cdat/miniconda2/* 
4.4M	/home/share/unix_files/cdat/miniconda2/bin
4.0K	/home/share/unix_files/cdat/miniconda2/conda-bld
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
6.4G	/home/share/unix_files/cdat/miniconda2/envs
20K	/home/share/unix_files/cdat/miniconda2/etc
3.8M	/home/share/unix_files/cdat/miniconda2/include
99M	/home/share/unix_files/cdat/miniconda2/lib
4.0K	/home/share/unix_files/cdat/miniconda2/LICENSE.txt
76K	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl

 >du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
1.7G	/home/share/unix_files/cdat/miniconda2/envs/keras
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0</code>

Actual installation

<code>bash-4.1$ conda create -n uvcdat-2.10 -c conda-forge -c uvcdat uvcdat=2.10

# Generate the list of installed packages
conda list -n uvcdat-2.10 > /home/scratch01/jypeter/uvcdat-2.10_list_170721.txt</code>

List of installed packages: {{:other:uvcdat:cdat_conda:uvcdat-2.10_list_170721.txt}}

Disk space after 2.10 installation

<code>bash-4.1$ conda env list
cdatm14                  /home/share/unix_files/cdat/miniconda2/envs/cdatm14
keras                    /home/share/unix_files/cdat/miniconda2/envs/keras
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
uvcdat-2.8.0             /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
root                  *  /home/share/unix_files/cdat/miniconda2

 > du -sh /home/share/unix_files/cdat/miniconda2
11G	/home/share/unix_files/cdat/miniconda2

 > du -sh /home/share/unix_files/cdat/miniconda2/* 
4.4M	/home/share/unix_files/cdat/miniconda2/bin
4.0K	/home/share/unix_files/cdat/miniconda2/conda-bld
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
9.2G	/home/share/unix_files/cdat/miniconda2/envs
20K	/home/share/unix_files/cdat/miniconda2/etc
3.8M	/home/share/unix_files/cdat/miniconda2/include
99M	/home/share/unix_files/cdat/miniconda2/lib
4.0K	/home/share/unix_files/cdat/miniconda2/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl

 > du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
1.7G	/home/share/unix_files/cdat/miniconda2/envs/keras
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
</code>

Disk space after removing the keras environment that we don't need any more

<code>jypeter@asterix2 - ...cdat - 67 >du -sh /home/share/unix_files/cdat/miniconda2
9.0G	/home/share/unix_files/cdat/miniconda2
jypeter@asterix2 - ...cdat - 68 >du -sh /home/share/unix_files/cdat/miniconda2/*
4.4M	/home/share/unix_files/cdat/miniconda2/bin
4.0K	/home/share/unix_files/cdat/miniconda2/conda-bld
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
7.5G	/home/share/unix_files/cdat/miniconda2/envs
20K	/home/share/unix_files/cdat/miniconda2/etc
3.8M	/home/share/unix_files/cdat/miniconda2/include
99M	/home/share/unix_files/cdat/miniconda2/lib
4.0K	/home/share/unix_files/cdat/miniconda2/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl
jypeter@asterix2 - ...cdat - 69 >du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0</code>

Disk space used in <wrap em>a brand new directory hierarchy</wrap> (''cdat/miniconda2b'', on the obelix servers)

<code>bash-4.2$ conda env list
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
4.3G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/*
4.4M	/home/share/unix_files/cdat/miniconda2b/bin
4.0K	/home/share/unix_files/cdat/miniconda2b/conda-bld
280K	/home/share/unix_files/cdat/miniconda2b/conda-meta
2.8G	/home/share/unix_files/cdat/miniconda2b/envs
20K	/home/share/unix_files/cdat/miniconda2b/etc
3.8M	/home/share/unix_files/cdat/miniconda2b/include
100M	/home/share/unix_files/cdat/miniconda2b/lib
8.0K	/home/share/unix_files/cdat/miniconda2b/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2b/pkgs
16K	/home/share/unix_files/cdat/miniconda2b/share
376K	/home/share/unix_files/cdat/miniconda2b/ssl
</code>


===== Cloning uvcdat to add specific packages for LSCE =====

<WRAP center round tip 60%>
This section is about the creation of the **cdatm15** environment

Notes about [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat|actually using the cdatm15 conda-based python]]
</WRAP>


Note: using hard links, cloning a full environment //only// adds an extra 500M of disk space

<code>bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
9.0G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

bash-4.1$ conda create -n cdatm15 --clone uvcdat-2.10 
Source:      /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
Destination: /home/share/unix_files/cdat/miniconda2/envs/cdatm15
[...]

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
9.5G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm15
573M	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
</code>

Disk space used after cloning, in <wrap em>in the  new directory hierarchy</wrap> (''cdat/miniconda2b'', on the obelix servers)

<code>bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
4.8G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/*
4.4M	/home/share/unix_files/cdat/miniconda2b/bin
4.0K	/home/share/unix_files/cdat/miniconda2b/conda-bld
280K	/home/share/unix_files/cdat/miniconda2b/conda-meta
3.4G	/home/share/unix_files/cdat/miniconda2b/envs
20K	/home/share/unix_files/cdat/miniconda2b/etc
3.8M	/home/share/unix_files/cdat/miniconda2b/include
100M	/home/share/unix_files/cdat/miniconda2b/lib
8.0K	/home/share/unix_files/cdat/miniconda2b/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2b/pkgs
16K	/home/share/unix_files/cdat/miniconda2b/share
376K	/home/share/unix_files/cdat/miniconda2b/ssl

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2b/envs/cdatm15
574M	/home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
</code>

===== Getting ready for a moving default CDAT =====

We create a **//cdatm// symbolic link** in the ''envs'' directory, that has a //stable name// but can be moved to point to the latest default CDAT. In that case, most users can just activate this //cdatm// version and always get the latest stable version

<code>bash-4.2$ cd /home/share/unix_files/cdat/miniconda2b/envs

bash-4.2$ conda env list
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ ln -s cdatm15 cdatm

bash-4.2$ conda env list
cdatm                    /home/share/unix_files/cdat/miniconda2b/envs/cdatm
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ source activate cdatm

(cdatm) bash-4.2$ conda env list
cdatm                 *  /home/share/unix_files/cdat/miniconda2b/envs/cdatm
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                     /home/share/unix_files/cdat/miniconda2b
</code>

===== Customizing UV-CDAT for LSCE =====


==== Downloading cdms2/vcs test data ====

You should download the test data and use it in the example scripts that you want to distribute, and scripts you write for reporting the errors you find (if any...)

<code>bash-4.1$ source activate cdatm15

(cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data'
[...]
Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data

(cdatm15) bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data
174M	/home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data</code>


==== Packages that have no dependency problems ====

After cloning, we are ready to install some extra packages that may be requested by LSCE users

<code># Keep a trace of what will be installed
bash-4.1$ conda install --dry-run -n cdatm15 -c conda-forge -c uvcdat -c pcmdi pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires pcmdi_metrics xlsxwriter cmor shapely cartopy rpy2 > /home/scratch01/jypeter/lsce-extra_01_install_170808.txt

# Install...
bash-4.1$ conda install -n cdatm15 -c conda-forge -c uvcdat -c pcmdi pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires pcmdi_metrics xlsxwriter cmor shapely cartopy rpy2
[...]

# Check the disk space after installation
bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
11G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
0	/home/share/unix_files/cdat/miniconda2/envs/cdatm
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
3.7G	/home/share/unix_files/cdat/miniconda2/envs/cdatm15
574M	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

# Check the disk space again after cleaning
bash-4.1$ conda clean --all

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
9.9G	/home/share/unix_files/cdat/miniconda2</code>

List of installed packages: {{ :other:uvcdat:cdat_conda:lsce-extra_01_install_170808.txt |}}

Disk space used after adding the extra packages, in <wrap em>in the  new directory hierarchy</wrap> (''cdat/miniconda2b'', on the obelix servers)

<code>bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b 
6.4G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/envs/*
0	/home/share/unix_files/cdat/miniconda2b/envs/cdatm
3.8G	/home/share/unix_files/cdat/miniconda2b/envs/cdatm15
630M	/home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10

# Check the disk space again after cleaning
bash-4.2$ conda clean --all

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
5.4G	/home/share/unix_files/cdat/miniconda2b</code>

Packages installed with //pip//
  * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API
    * ''pip install dreqPy''
    * Update with: ''pip install %%--%%upgrade dreqPy''
      * Get version number with:\\ <code>$ drq -v
dreqPy version 01.00.06 [Version 01.00.06]</code>
  * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module
    * ''pip install dtw''
    * Requested by Sentia Goursaud

The following packages have no dependency problems and were installed (or updated) //later//
  * [[http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_7_0_0/esmpy_doc/html/index.html|ESMPy]]: ESMF Python Regridding Interface
    * We used the following to get a more up-to-date version of esmpy than the one bundled with 2.10
    * <code>bash-4.1$ conda list | grep -i esm
esmf                      7.0.0                         6    conda-forge
esmpy                     7.0.0                    py27_1    conda-forge

bash-4.1$ conda install -n cdatm15 -c nesii/channel/dev-esmf -c conda-forge esmpy=7.1.0.dev32
[...]

bash-4.1$ conda list | grep -i esm
esmf                      7.1.0.dev32                   1    nesii/channel/dev-esmf
esmpy                     7.1.0.dev32              py27_1    nesii/channel/dev-esmf</code>
  * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography
    * ''conda install -n cdatm15 -c conda-forge cmocean''
  * [[http://scitools.org.uk/iris/index.html|iris]]: A Python library for Meteorology and Climatology
    * ''conda install -n cdatm15 -c conda-forge -c scitools iris''
  * [[http://www.gdal.org/|OSGeo/GDAL]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats
    * ''conda install -c conda-forge gdal''
    * [[https://pcjericks.github.io/py-gdalogr-cookbook/|Python GDAL/OGR Cookbook]]
  * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library
    * ''conda install -n cdatm15 -c stefraynaud -c conda-forge spanlib''
    * Test: ''python -c 'from spanlib.analyzer import Analyzer' ''
  * [[http://wrf-python.readthedocs.io/en/latest/|wrf-python]]: A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model
    * ''conda install -n cdatm15 -c conda-forge wrf-python''
  * [[https://glances.readthedocs.io/en/stable/index.html|glances]]: a cross-platform monitoring tool (similar to ''top'')
    * ''conda install -n cdatm15 -c conda-forge glances''
    * [[https://github.com/nicolargo/glances|glances@github]]
  * [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python
    * ''conda install -n cdatm15 -c conda-forge windspharm''
    * [[https://github.com/ajdawson/windspharm|windspharm@github]]


==== TODO ====

//Add here packages that would be useful but have some problems that prevent their installation//

  * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
    * As of August 08 2017, installing vacumm in 2.10 requires downgrading to 2.10 (see [[https://github.com/VACUMM/vacumm/issues/9|github issue]])!
    * <wrap hi>Problem solved</wrap> with **vacumm 3.4.1-1** on August 31st! Installation was OK with\\ ''conda install -n cdatm15 -c conda-forge -c vacumm vacumm''

  * Install PySPLIT for Sentia\\ [[https://github.com/mscross/pysplit|PySPLIT]] A package for generating HYSPLIT air parcel trajectories trajectories, performing moisture uptake analyses, expediting HYSPLIT cluster analysis, and for visualizing trajectories, clusters, and along-trajectory meteorological data\\ Works with [[https://ready.arl.noaa.gov/HYSPLIT.php|HYSPLiT]]
    - ''conda install -n cdatm15 -c conda-forge fiona geopandas''
    - ''pip install pysplit''

==== Other packages ====

<note warning>There is no warranty that the packages listed below will work correctly, because it was required to bypass the compatibility checks in order to install them...</note>

  * NO such packages now!

==== Updating some packages ====

Some packages change more often than others, and can be easily updated the following way:

  * [[https://cmor.llnl.gov/|CMOR]]
    * Update with: ''conda update -n cdatm15 -c conda-forge -c pcmdi -c uvcdat cmor''
      * Get version number with: ''python -c 'from cmor import *; print CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH' ''

  * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]
    * Update with: ''pip install %%--%%upgrade dreqPy''
      * Get version number with: ''drq -v''

==== Cleaning up things ====

Some packages may have files that can only be read by the person who installed CDAT and the LSCE extensions (eg [[https://github.com/PCMDI/pcmdi_metrics/issues/496|pcmdi-metrics]] in 2.8.0 and [[https://github.com/UV-CDAT/cdp/issues/21|cdp]] in 2.10)

We check if some of the installed files are missing read access for the //group// or //other//, and we manually change the permissions
<code>(cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls
50333969    4 -rw-------   2 jypeter  lsce          234 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/PKG-INFO
50333971    4 -rw-------   2 jypeter  lsce          291 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/SOURCES.txt
50333962    4 -rw-------   2 jypeter  lsce            4 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/top_level.txt
50333961    4 -rw-------   2 jypeter  lsce            1 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/dependency_links.txt
50333960    4 -rw-------   2 jypeter  lsce            1 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/not-zip-safe
50333987    8 -rw-------   2 jypeter  lsce         5149 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.pyc
50333986    8 -rw-------   2 jypeter  lsce         4208 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.py
50333966    4 -rw-------   2 jypeter  lsce          150 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.pyc
50333968    4 -rw-------   2 jypeter  lsce          201 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.py
50333988    8 -rw-------   2 jypeter  lsce         5365 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.pyc
50333982    4 -rw-------   2 jypeter  lsce         1821 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.py
50333981    4 -rw-------   2 jypeter  lsce         1773 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.py
50333973    4 -rw-------   2 jypeter  lsce          670 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.py
50333980    4 -rw-------   2 jypeter  lsce         1642 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.pyc
50333979    4 -rw-------   2 jypeter  lsce         1474 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.pyc
50333967    4 -rw-------   2 jypeter  lsce          187 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.py
50333989    0 -rw-------   2 jypeter  lsce            0 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.py
50333985    4 -rw-------   2 jypeter  lsce         3843 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.py
50333984    4 -rw-------   2 jypeter  lsce         2436 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.pyc
50333970    4 -rw-------   2 jypeter  lsce          288 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.py
50333974    4 -rw-------   2 jypeter  lsce          692 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.pyc
50333978    4 -rw-------   2 jypeter  lsce          878 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.pyc
50333976    4 -rw-------   2 jypeter  lsce          734 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.py
50333983    4 -rw-------   2 jypeter  lsce         2269 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.pyc
50333975    4 -rw-------   2 jypeter  lsce          724 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.pyc
(cdatm15) bash-4.2$ chmod -R a+r cdatm15/lib/python2.7/site-packages/cdp*
(cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls</code>


===== Extra packages list =====

  * [[https://python-pillow.org/|pillow]]: the friendly PIL (//Python Imaging Library//) fork
  * [[http://pandas.pydata.org/|pandas]]: Python Data Analysis Library
  * [[http://statsmodels.sourceforge.net/|statsmodels]]: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests
  * [[https://seaborn.pydata.org/|seaborn]]: statistical data visualization
  * [[http://scikit-image.org/|scikit-image]]: image processing in Python
  * [[http://pythonhosted.org/seawater/|seawater]]: Python re-write of the CSIRO seawater toolbox
  * [[https://pypi.python.org/pypi/gsw/|gsw]]: Python implementation of the Thermodynamic Equation Of Seawater
  * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
  * [[http://unidata.github.io/netcdf4-python/|netcdf4]]: a Python interface to the netCDF C library
  * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in 
  * [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap''
  * [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests
  * [[https://xlsxwriter.readthedocs.io/|XlsxWriter]]: a Python module for creating Excel XLSX files
    * Note: <wrap hi>this is a dependency of ''dreqPy''</wrap>
  * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API
  * [[https://cmor.llnl.gov/|CMOR]]:  CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files
  * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module
  * [[http://toblerity.org/shapely/project.html|shapely]]: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane)
  * [[http://scitools.org.uk/cartopy/|cartopy]]: a library providing cartographic tools for python
  * [[https://rpy2.readthedocs.io/en/version_2.8.x/|rpy2]]: providing simple and robust access to R from within Python
  * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography
  * [[http://scitools.org.uk/iris/index.html|iris]]: A Python library for Meteorology and Climatology
  * [[http://www.gdal.org/|OSGeo/GDAL]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats
  * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library
  * [[http://wrf-python.readthedocs.io/en/latest/|wrf-python]]: A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model
  * [[https://glances.readthedocs.io/en/stable/index.html|glances]]: a cross-platform monitoring tool (similar to ''top'')
  * [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python

==== Removed packages ====

  * NO removed packages!

===== Environments summary =====

After following the steps above, we get the following environments. Use the ''conda info %%--%%envs'' or the ''conda env list'' command to get the up-to-date list of available environments

^  Environment\\ name  ^  Server  ^  ''conda list''  ^
|  uvcdat-2.10  |  LSCE  |  {{  |package list}}  |
|  cdatm15  |  LSCE  |  {{ |package list}}  |

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