other:uvcdat:cdat_conda:cdat_8_2_1
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other:uvcdat:cdat_conda:cdat_8_2_1 [2021/03/08 20:34] jypeter [Extra packages list] Started updating the list |
other:uvcdat:cdat_conda:cdat_8_2_1 [2021/09/13 12:22] jypeter [Extra packages list] Added pygrib (and indirectly eccodes) |
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| === Pre-installation check with the dry-run option === | === Pre-installation check with the dry-run option === | ||
| - | <code>/usr/bin/time mamba install -n cdatm19_nompi_py3 --dry-run -c conda-forge basemap basemap-data-hires cartopy cmocean cmor ferret_datasets gdal gdal glances gsw iris joblib netcdf4 palettable pandas pillow pyferret rpy2 scikit-image scikit-learn seaborn seawater shapely spyder statsmodels windspharm wrf-python xarray xlsxwriter | + | <code>/usr/bin/time mamba install -n cdatm19_nompi_py3 --dry-run -c conda-forge basemap basemap-data-hires cartopy cmocean cmor ferret_datasets gdal gdal geopandas glances gsw iris joblib netcdf4 palettable pandas pillow pyferret rpy2 scikit-image scikit-learn seaborn seawater shapely spyder statsmodels windspharm wrf-python xarray xlsxwriter |
| [... lots of information about what would be done followed by some information about how long it took ...] | [... lots of information about what would be done followed by some information about how long it took ...] | ||
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| === Actual installation === | === Actual installation === | ||
| - | <code>/usr/bin/time mamba install -n cdatm19_nompi_py3 -c conda-forge basemap basemap-data-hires cartopy cmocean cmor ferret_datasets gdal gdal glances gsw iris joblib netcdf4 palettable pandas pillow pyferret rpy2 scikit-image scikit-learn seaborn seawater shapely spyder statsmodels windspharm wrf-python xarray xlsxwriter</code> | + | <code>/usr/bin/time mamba install -n cdatm19_nompi_py3 -c conda-forge basemap basemap-data-hires cartopy cmocean cmor ferret_datasets gdal gdal geopandas glances gsw iris joblib netcdf4 palettable pandas pillow pyferret rpy2 scikit-image scikit-learn seaborn seawater shapely spyder statsmodels windspharm wrf-python xarray xlsxwriter</code> |
| Resulting list of installed packages | Resulting list of installed packages | ||
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| * Get version number with: ''python -c 'from cmor import *; print( (CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH) )' '' | * Get version number with: ''python -c 'from cmor import *; print( (CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH) )' '' | ||
| * <wrap hi>Warning!</wrap> [[https://github.com/PCMDI/cmor/issues/449|CMOR currently requires Python 2.7]] | * <wrap hi>Warning!</wrap> [[https://github.com/PCMDI/cmor/issues/449|CMOR currently requires Python 2.7]] | ||
| - | |||
| - | * [[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 | ||
| - | * ''conda install -n cdatm19_py3 -c conda-forge -c vacumm vacumm'' | ||
| - | * <wrap hi>Warning!</wrap> [[https://github.com/VACUMM/vacumm/issues/15|standard install of vacumm does not work for Python3]] | ||
| - | |||
| - | * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library | ||
| - | * ''conda install -n cdatm19_py3 -c stefraynaud -c conda-forge spanlib'' | ||
| - | * 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 | * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses | ||
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| * [[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 cdatm19_py3 -c conda-forge palettable'' | ||
| ==== TODO ==== | ==== TODO ==== | ||
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| ===== Extra packages list ===== | ===== Extra packages list ===== | ||
| - | * [[https://python-pillow.org/|pillow]]: the friendly PIL (//Python Imaging Library//) fork | + | FIXME: need to clean the list below, and move the packages to the ordered list further down |
| - | * [[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://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://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 Python | ||
| * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret | * [[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'' | ||
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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 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 | ||
| - | * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography | ||
| - | * [[http://www.gdal.org/|OSGeo/GDAL]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats | ||
| - | * [[https://pcjericks.github.io/py-gdalogr-cookbook/|Python GDAL/OGR Cookbook]] | ||
| - | * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library | ||
| * [[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 | ||
| + | |||
| + | <WRAP center round tip 60%> | ||
| + | The extra packages below are (more or less) listed in package name alphabetical order. These are the extra packages that we explicitly installed, but there are many more packages installed (e.g. {{ :other:uvcdat:cdat_conda:cdatm19_nompi_py3_21-03-06.txt |}})! | ||
| + | |||
| + | Initialize the environment and type ''conda list'' if you need an up-to-date list, including the packages' version and where they came from (conda-forge for most packages | ||
| + | </WRAP> | ||
| + | |||
| + | |||
| + | * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses | ||
| + | * see also ''iris'' | ||
| + | * [[https://github.com/Try2Code/cdo-bindings|python-cdo]]: Python scripting interface of [[https://code.mpimet.mpg.de/projects/cdo/wiki/Cdo#Documentation|cdo]] | ||
| + | * ''python-cdo'' will install the ''cdo'' package (providing the ''cdo ''executable) as a dependency | ||
| + | * see also [[https://code.mpimet.mpg.de/projects/cdo/wiki/Cdo%7Brbpy%7D|Using CDO from python or ruby]] | ||
| + | * [[https://www.fabiocrameri.ch/colourmaps/|cmcrameri]]: Crameri's Scientific colour maps ''[color]'' | ||
| + | * the colormaps are also available in [[https://jiffyclub.github.io/palettable/scientific/|palettable.scientific]] | ||
| + | * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography ''[color]'' | ||
| + | * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]] and ''ferret_datasets'': Ferret encapsulated in Python | ||
| + | * [[https://github.com/jswhit/pygrib|pygrib]]: high-level interface to the ECWMF ECCODES C library for reading GRIB files | ||
| + | * OSGeo/[[http://www.gdal.org/|gdal]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats | ||
| + | * [[https://pcjericks.github.io/py-gdalogr-cookbook/|Python GDAL/OGR Cookbook]] | ||
| + | * [[https://github.com/TEOS-10/GSW-python|gsw]]: Python implementation of the Thermodynamic Equation Of Seawater | ||
| + | * see also //seawater// | ||
| + | * [[https://scitools-iris.readthedocs.io/en/stable/|iris]]: a powerful, format-agnostic, community-driven Python package for analysing and visualising Earth science data | ||
| + | * see also ''cartopy'' | ||
| + | * install sample data with ''conda install -c conda-forge iris-sample-data'' | ||
| * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | ||
| - | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | + | * [[https://opencv.org/|OpenCV]]: OpenCV (Open Source Computer Vision Library) is an open-source library that includes several hundreds of computer vision algorithms. See also [[https://www.geeksforgeeks.org/opencv-python-tutorial/|OpenCV Python Tutorial]] and **scikit-image** |
| + | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python ''[color]'' | ||
| + | * [[http://pandas.pydata.org/|pandas]]: Python Data Analysis Library | ||
| + | * [[https://geopandas.org/|geopandas]]: an open source project to make working with geospatial data in python easier | ||
| + | * [[https://peakutils.readthedocs.io/|PeakUtils]]: utilities related to the detection of peaks on 1D data | ||
| + | * [[https://python-pillow.org/|pillow]]: the friendly PIL (//Python Imaging Library//) fork | ||
| + | * [[https://proplot.readthedocs.io/en/latest/|proplot]]: a lightweight **matplotlib wrapper** for making beautiful, publication-quality graphics | ||
| + | * [[https://rpy2.github.io/|rpy2]]: an interface to R running embedded in a Python process | ||
| * [[http://scikit-image.org/|scikit-image]]: image processing in Python | * [[http://scikit-image.org/|scikit-image]]: image processing in Python | ||
| * [[https://scikit-learn.org/stable/index.html|scikit-learn]]: Machine Learning in Python | * [[https://scikit-learn.org/stable/index.html|scikit-learn]]: Machine Learning in Python | ||
| + | * [[https://seaborn.pydata.org/|seaborn]]: statistical data visualization | ||
| + | * [[http://pythonhosted.org/seawater/|seawater]]: Python re-write of the CSIRO seawater toolbox | ||
| + | * see also //gsw// | ||
| + | * [[http://statsmodels.sourceforge.net/|statsmodels]]: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests | ||
| + | * [[https://xoa.readthedocs.io/en/latest/|xoa]]: xarray-based ocean analysis library | ||
| + | * ''xoa'' is the successor of [[http://www.ifremer.fr/vacumm/|vacumm]] (vacumm does **not** support Python3) | ||
| ==== Removed packages ==== | ==== Removed packages ==== | ||
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| * NO removed packages! | * NO removed packages! | ||
| + | ==== Packages NOT supported in Python3 ==== | ||
| + | |||
| + | * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library | ||
| + | * [[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 | ||
| + | * Check the ''xoa'' replacement package | ||
| ===== Environments summary ===== | ===== Environments summary ===== | ||
other/uvcdat/cdat_conda/cdat_8_2_1.txt · Last modified: 2024/06/21 10:31 by jypeter
