other:uvcdat:cdat_conda:cdat_8_1
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other:uvcdat:cdat_conda:cdat_8_1 [2019/03/13 14:41] jypeter Added how to initialize CDAT JYP |
other:uvcdat:cdat_conda:cdat_8_1 [2019/10/04 11:50] jypeter Added palettable |
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| <WRAP center round tip 60%> | <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 ''8.1'' | + | If you have questions about Python, read: |
| + | * [[other:python:starting|Working with Python]] | ||
| + | * [[other:python:jyp_steps|JYP's recommended steps for learning python]]! | ||
| </WRAP> | </WRAP> | ||
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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 ==== | ||
| Line 151: | Line 170: | ||
| * 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// | ||
| Line 166: | Line 188: | ||
| * ''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// | | ||
other/uvcdat/cdat_conda/cdat_8_1.txt · Last modified: 2021/03/26 09:10 by jypeter
