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other:uvcdat:cdat_conda:cdat_8_1 [2019/03/13 14:44] jypeter Updated the top welcome note |
other:uvcdat:cdat_conda:cdat_8_1 [2020/01/23 10:44] jypeter [Using JYP version] |
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<WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
- | You have questions about Python? | + | If you have questions about Python, read: |
- | + | * [[other:python:starting|Working with Python]] | |
- | Read [[other:python:jyp_steps|JYP's recommended steps for learning python]]! | + | * [[other:python:jyp_steps|JYP's recommended steps for learning python]]! |
</WRAP> | </WRAP> | ||
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If you mostly want to use the CDAT 8.1 installed by JYP, just use the following steps and skip the next sections: | If you mostly want to use the CDAT 8.1 installed by JYP, just use the following steps and skip the next sections: | ||
- | * Initialize conda: | + | * Initialize //conda// with: |
^ Server ^ tcsh ^ bash ^ | ^ Server ^ tcsh ^ bash ^ | ||
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| ciclad | ''source ~jypmce/.conda3_jyp.csh'' | ''source ~jypmce/.conda3_jyp.sh'' | | | ciclad | ''source ~jypmce/.conda3_jyp.csh'' | ''source ~jypmce/.conda3_jyp.sh'' | | ||
- | * Activate the default environment: ''conda activate cdatm_py2'' | + | * Choose one of the [[#environments_summary|installed environments]] and activate it with: ''conda activate env_name'' |
- | * Check the [[#environments_summary|Available environments]] for more options | + | * python 2.7.x: ''conda activate cdatm_py2'' |
+ | * python 3.x: ''conda activate cdatm_py3'' (not available on ciclad, but could be installed) | ||
===== What's New? ===== | ===== What's New? ===== | ||
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===== Customizing UV-CDAT for LSCE ===== | ===== Customizing UV-CDAT for LSCE ===== | ||
+ | ==== Testing vcs ==== | ||
+ | Start python and paste the following lines | ||
+ | |||
+ | <code>import numpy as np, vcs | ||
+ | id100 = np.identity(100) | ||
+ | x = vcs.init() | ||
+ | x.plot(id100) | ||
+ | </code> | ||
+ | |||
+ | If you get the kind of errors described in [[https://github.com/CDAT/vcs/issues/393|x.plot crashes with OpenGL2 error]], the drivers on your server are probably not compatible with an interactive use of vcs... The workaround is to **install mesalib and work in //headless mode//** (e.g. without a display)... | ||
+ | |||
+ | Install //mesalib// with ''conda install -c cdat/label/v81 -c conda-forge mesalib vtk-cdat'' and try pasting again the few code lines above in python. If things work as expected, no canvas will be opened, but you'll be able to save the canvas to a file with | ||
+ | |||
+ | <code>x.png('test_mesalib') | ||
+ | x.pdf('test_mesalib')</code> | ||
+ | |||
+ | Note: using //mesalib// for headless mode work makes it possible to work without an X server, and with no DISPLAY variable defined | ||
==== Downloading cdms2/vcs test data ==== | ==== Downloading cdms2/vcs test data ==== | ||
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* Get version number with:\\ <code>$ drq -v | * Get version number with:\\ <code>$ drq -v | ||
dreqPy version 01.00.29 [Version 01.00.29]</code> | dreqPy version 01.00.29 [Version 01.00.29]</code> | ||
+ | |||
+ | * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret | ||
+ | * ''conda activate cdatm18_py2''\\ ''pip install ferretmagic'' | ||
The following packages have no dependency problems and were installed (or updated) //later// | The following packages have no dependency problems and were installed (or updated) //later// | ||
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* ''conda install -n cdatm18_py2 -c stefraynaud -c conda-forge spanlib'' | * ''conda install -n cdatm18_py2 -c stefraynaud -c conda-forge spanlib'' | ||
* Test: ''python -c 'from spanlib.analyzer import Analyzer' '' | * Test: ''python -c 'from spanlib.analyzer import Analyzer' '' | ||
+ | |||
+ | * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses | ||
+ | * ''conda install -n cdatm18_py2 -c conda-forge cartopy'' | ||
+ | |||
+ | * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | ||
+ | * ''conda install -n cdatm18_py2 -c conda-forge joblib'' | ||
* [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | ||
* [[other:uvcdat:cdat_conda:climaf_install|Installation notes]] | * [[other:uvcdat:cdat_conda:climaf_install|Installation notes]] | ||
+ | |||
+ | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
+ | * ''conda install -n cdatm18_py2 -c conda-forge palettable'' | ||
==== TODO ==== | ==== TODO ==== | ||
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* [[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://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://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 | + | * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in Python |
+ | * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret | ||
* [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap'' | * [[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://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests | ||
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* [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module | * [[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://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 | + | * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses |
* [[https://rpy2.readthedocs.io/en/version_2.8.x/|rpy2]]: providing simple and robust access to R from within 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://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography | ||
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* [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python | * [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python | ||
* [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | ||
+ | * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | ||
+ | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
==== Removed packages ==== | ==== Removed packages ==== | ||
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| cdat-8.1_py2 | LSCE\\ ciclad | CDAT 8.1 & Python 2.7 | | | cdat-8.1_py2 | LSCE\\ ciclad | CDAT 8.1 & Python 2.7 | | ||
| cdat-8.1_py3 | LSCE | CDAT 8.1 & Python 3.6 | | | cdat-8.1_py3 | LSCE | CDAT 8.1 & Python 3.6 | | ||
- | | cdatm18_py2 | LSCE\\ ciclad | CDAT 8.1 & P 2.7 //JYP version// | | + | | cdatm18_py2\\ or //cdatm_py2// | LSCE\\ ciclad | CDAT 8.1 & P 2.7 //JYP version// | |
- | | cdatm18_py3 | LSCE | CDAT 8.1 & P 3.7 //JYP version// | | + | | cdatm18_py3\\ or //cdatm_py3// | LSCE | CDAT 8.1 & P 3.7 //JYP version// | |
| cdat-nightly_py2 | LSCE\\ ciclad | CDAT nightly & Python 2.7 | | | cdat-nightly_py2 | LSCE\\ ciclad | CDAT nightly & Python 2.7 | | ||
| cdatm-nightly_py2 | LSCE\\ ciclad | CDAT nightly & P 2.7 //JYP version// | | | cdatm-nightly_py2 | LSCE\\ ciclad | CDAT nightly & P 2.7 //JYP version// | |