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- | ====== CDAT 8.2.1 installation notes ====== | + | ====== Python distribution based on CDAT 8.2.1 notes ====== |
[ [[.:index|Back to all versions]] ] | [ [[.:index|Back to all versions]] ] | ||
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===== Using JYP version ===== | ===== Using JYP version ===== | ||
- | If you mostly want to use the CDAT 8.2.1 installed by JYP, just use the following steps and then read the //What should I do now?// section below | + | If you mostly want to use the **python distribution based on CDAT 8.2.1** installed by JYP, just use the following steps and then read the [[#what_should_i_do_now|What should I do now?]] section below |
* Initialize //conda// with: | * Initialize //conda// with: | ||
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* python 3.x: ''conda activate cdatm_py3'' | * python 3.x: ''conda activate cdatm_py3'' | ||
- | * Type ''which python'' (or the ''wp'' alias) and make sure you get something like\\ ''[...]/miniconda3/envs/env_name/bin/python'' | + | * Type ''which python'' (or the ''wp'' alias) and make sure you get something looking like |
+ | * ''[...]/miniconda3<possibly_some_version>/envs/<some_env_name>/bin/python'' | ||
+ | * e.g. ''cdatm_py3'' environment at LSCE:\\ ''/home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3/bin/python'' | ||
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==== You want to replicate this installation on your own server or desktop/laptop ==== | ==== You want to replicate this installation on your own server or desktop/laptop ==== | ||
+ | Read the next sections of this web page | ||
+ | |||
+ | There are some slight differences if you want to install this distribution: | ||
+ | * just for you. This is the usual case. Well, if you break something you can always remove everything and start from scratch | ||
+ | * for sharing a stable version with several other people | ||
+ | |||
+ | The notes at the beginning of each section will tell you if you can skip the section if you are just installing for you | ||
===== What's New in CDAT 8.2.1? ===== | ===== What's New in CDAT 8.2.1? ===== | ||
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* Full [[https://uvcdat.llnl.gov/changelog.html#8.2.1|Change log]] | * Full [[https://uvcdat.llnl.gov/changelog.html#8.2.1|Change log]] | ||
- | Note: this particular CDAT installation at LSCE (and on other machines/servers) provides **many extra (non-CDAT) packages**. You can jump directly to the [[#extra_packages_list|Extra package list]] at the bottom of this page to see what is available | + | Note: this particular CDAT installation at LSCE (and on other machines/servers) provides **many extra (non-CDAT) packages**. You can jump directly to the [[#extra_packages_list|Extra package list]] at the bottom of this page, if you want to see what is available |
===== Installation with Miniconda3 ===== | ===== Installation with Miniconda3 ===== | ||
- | We assume that Miniconda3 is already installed. Otherwise, follow the the [[other:uvcdat:cdat_conda:cdat_8_0_py2#installing_miniconda3|Installing Miniconda]] steps (and the //Post-Miniconda3 installation// section) we followed when installing CDAT 8.0 | + | ==== Installing Miniconda3 ==== |
+ | |||
+ | If //Miniconda3// is not already installed, or if you want to start over with a brand new version, read [[other:uvcdat:cdat_conda:miniconda3_install|JYP steps for installing Miniconda3]]. | ||
- | ==== Updating conda ==== | ||
- | The conda package itself can be updated (if need be) with\\ ''conda update -n base -c defaults conda'' | ||
==== Installing CDAT 8.2.1 ==== | ==== Installing CDAT 8.2.1 ==== | ||
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577M /home/share/unix_files/cdat/miniconda3_21-02</code> | 577M /home/share/unix_files/cdat/miniconda3_21-02</code> | ||
- | We can also use ''conda env list'' and remove some obsolete versions with ''conda remove -n obsolete_name --all'' to get some space | + | We can also use ''conda env list'' and remove some obsolete versions with ''conda remove -n obsolete_environment %%--%%all'', in order to free up some space |
=== Python 2.7 version === | === Python 2.7 version === | ||
- | Python 2 is deprecated in CDAT, starting with CDAT 8.2.1. If you still need to use python 2.7, please use [[other:uvcdat:cdat_conda:cdat_8_1|CDAT 8.1]] | + | <wrap hi>Python 2.x is deprecated in CDAT, starting with CDAT 8.2.1</wrap>. |
+ | |||
+ | If you still need to use python 2.7, please use [[other:uvcdat:cdat_conda:cdat_8_1|CDAT 8.1]] | ||
=== Python 3.8 version === | === Python 3.8 version === | ||
<WRAP center round important 60%> | <WRAP center round important 60%> | ||
- | It's possible that, when using the tcsh shell and trying to use the ''conda create -n cdat-8.2.1_py3 lots_of_parameters_with_stars'' line, you will get the following error message: | + | It's possible that, when using the //tcsh// shell and trying to use the ''conda create -n cdat-8.2.1_py3 lots_of_parameters_with_wildcards'' line, you will get the following error message: |
**conda: No match** | **conda: No match** | ||
- | This may be due to [[https://gitmemory.com/issue/conda/conda/9771/608209654|CSH install/search fail with '*' variable in an argument]]. In that case, just type ''bash'' and run the installation command in a //bash// shell | + | Apparently the //tcsh// version of conda does not like wildcards too much ([[https://gitmemory.com/issue/conda/conda/9771/608209654|CSH install/search fail with '*' variable in an argument]])... |
+ | |||
+ | In that case, just type ''bash'' and run the installation command in a //bash// shell | ||
</WRAP> | </WRAP> | ||
The installation line below is based on information from the [[https://github.com/CDAT/cdat/wiki/install#for-linux-python|CDAT wiki page]]. See also [[https://github.com/CDAT/cdat/issues/2265|Some questions and notes about 8.2.1 installation]] | The installation line below is based on information from the [[https://github.com/CDAT/cdat/wiki/install#for-linux-python|CDAT wiki page]]. See also [[https://github.com/CDAT/cdat/issues/2265|Some questions and notes about 8.2.1 installation]] | ||
+ | <code> | ||
+ | bash-4.2$ conda config --env --add channels conda-forge | ||
+ | bash-4.2$ conda config --set channel_priority strict | ||
+ | bash-4.2$ cat .condarc | ||
+ | channels: | ||
+ | - conda-forge | ||
+ | - defaults | ||
+ | $ conda config --describe channel_priority | ||
+ | |||
+ | $ conda create -n cdat-8.2.1_nompi_py3 -c conda-forge -c cdat/label/v8.2.1 cdat "libnetcdf=*=nompi_*" "mesalib=18.3.1" "python=3"</code> | ||
<code>$ conda create -n cdat-8.2.1_py3 -c conda-forge -c cdat/label/v8.2.1 cdat "libnetcdf=*=mpi_openmpi_*" "mesalib=18.3.1" "python=3"</code> | <code>$ conda create -n cdat-8.2.1_py3 -c conda-forge -c cdat/label/v8.2.1 cdat "libnetcdf=*=mpi_openmpi_*" "mesalib=18.3.1" "python=3"</code> | ||
- | ===== Cloning CDAT before adding specific packages for LSCE ===== | + | Resulting list of installed packages |
+ | * ''conda list -n cdat-8.2.1_nompi_py3 > cdat_8.2.1_nompi_21-03-05.txt'' | ||
+ | * no mpi: {{ :other:uvcdat:cdat_conda:cdat_8.2.1_nompi_21-03-05.txt |}} | ||
+ | * with mpî: {{ :other:uvcdat:cdat_conda:cdat_8.2.1_installed_packages.txt |}} | ||
+ | |||
+ | [[https://github.com/CDAT/cdat/issues/2265|Some extra installation notes]] | ||
+ | ===== Cloning the base CDAT environment before adding specific packages for LSCE ===== | ||
<WRAP center round alert 60%> | <WRAP center round alert 60%> | ||
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Notes: | Notes: | ||
- | * Why //cloning//? The initial CDAT environment is strictly the one created at PCMDI and certified by PCMDI. Rather than making changes directly in there, we keep it as it is, clone it, and work on the clone | + | * Why //cloning//? The initial CDAT environment is strictly the one created at PCMDI and certified by PCMDI. Rather than making changes directly in there, we keep it as it is, clone it, and make changes in the cloned environment |
- | * Carefully working on different python environments (possibly cloned) is safer in a multi-user environment | + | * Carefully working on different python environments (possibly cloned) is safer in a multi-user environment (i.e. you can have people use a specific environment, and make tests in another environment) |
* Cloning a full environment uses Linux hard links and requires less disk space than making a real copy | * Cloning a full environment uses Linux hard links and requires less disk space than making a real copy | ||
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- | ===== Getting ready for a moving default CDAT ===== | + | ===== Getting ready for a moving default CDAT environment ===== |
- | <note warning>This step should probably be listed at the **end**, especially in a multi-user environment! If there is already a ''cdatm'' link, make sure that the new version is stable and working correctly before updating the ''cdatm'' link</note> | + | <WRAP center round alert 60%> |
+ | You can skip this section if you are **installing CDAT just for one user (yourself)** on a Linux machine (or a Windows 10 machine with WSL) | ||
- | 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 | + | You will directly make changes and install packages in **your** main python environment |
+ | </WRAP> | ||
- | <code>$ cd /home/share/unix_files/cdat/miniconda3/envs | + | <WRAP center round tip 60%> |
- | $ ln -s cdatm19_py2 cdatm_py2</code> | + | This step could probably be listed at the **end**, especially in a multi-user environment! |
- | ===== Customizing UV-CDAT for LSCE ===== | + | If there is already a ''cdatm_py3'' link (pointing to an older environment), make sure that the new CDAT environment is stable and working correctly before updating the ''cdatm_py3'' link |
+ | </WRAP> | ||
- | ==== Testing vcs ==== | + | We create a **//cdatm_py3// symbolic link** in the ''envs'' directory, that has a //stable name// but can be moved to point to the latest default (and hopefully stable) CDAT environment. In that case, most users can just activate this //cdatm_py3// environment and always get the latest stable version. |
- | Start python and paste the following lines | + | <code>$ cd /home/share/unix_files/cdat/miniconda3_21-02/envs |
+ | $ ln -s cdatm19_py3 cdatm_py3 | ||
- | <code>import numpy as np, vcs | + | conda env list |
- | id100 = np.identity(100) | + | # conda environments: |
- | x = vcs.init() | + | # |
- | x.plot(id100) | + | base * /home/share/unix_files/cdat/miniconda3_21-02 |
+ | cdat-8.2.1_py3 /home/share/unix_files/cdat/miniconda3_21-02/envs/cdat-8.2.1_py3 | ||
+ | cdatm19_py3 /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3 | ||
+ | cdatm_py3 /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3 | ||
+ | |||
+ | $ ls -l /home/share/unix_files/cdat/miniconda3_21-02/envs/ | ||
+ | drwxr-xr-x [...] cdat-8.2.1_py3/ | ||
+ | drwxr-xr-x [...] cdatm19_py3/ | ||
+ | lrwxrwxrwx [...] cdatm_py3 -> cdatm19_py3/ | ||
</code> | </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)... | + | ===== Customizing CDAT for LSCE ===== |
- | 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 | + | ==== A quick test of cdms2 and vcs ==== |
- | <code>x.png('test_mesalib') | + | You can use the quick test shown in [[https://github.com/CDAT/cdat/wiki/install#to-test-your-cdat-installation|To Test Your CDAT Installation]], and check if you get the expected png file |
- | 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 | + | You can also check the [[other:uvcdat:cdat_conda:cdat_8_1#testing_vcs|Testing vcs]] section of the LSCE installation of CDAT 8.1 |
==== Downloading cdms2/vcs test data ==== | ==== Downloading cdms2/vcs test data ==== | ||
- | You should download the test data (174M of 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...) | + | You should download the test data (174M of 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...). The downloaded data files will be available in: ''vcs.sample_data'' |
- | <code>$ conda activate cdatm19_py2 | + | <code>$ conda activate cdatm19_py3 |
- | (cdatm19_py2) $ python -c 'import vcs; vcs.download_sample_data_files(); print("\nFinished downloading sample data to " + vcs.sample_data)' | + | (cdatm19_py3) $ 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/miniconda3/envs/cdatm19_py2/share/cdat/sample_data | + | Finished downloading sample data to /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data |
- | (cdatm19_py2) $ du -sh /home/share/unix_files/cdat/miniconda3/envs/cdatm19_py2/share/cdat/sample_data | + | (cdatm19_py3) $ du -sh /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data |
- | 174M /home/share/unix_files/cdat/miniconda3/envs/cdatm19_py2/share/cdat/sample_data | + | 174M /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data |
- | </code> | + | |
+ | $ python | ||
+ | >>> import os, vcs | ||
+ | >>> vcs.sample_data | ||
+ | '/home/jypeter/miniconda3_21-02/envs/cdat-8.2.1_py3/share/cdat/sample_data' | ||
+ | |||
+ | >>> os.listdir(vcs.sample_data) | ||
+ | ['BlueMarble.ppm', 'clt.nc', 'geo.1deg.ctl', 'geo.1deg.gmp', 'geo.1deg.grb', ...]</code> | ||
==== Packages that have no dependency problems ==== | ==== Packages that have no dependency problems ==== | ||
- | After cloning, we are ready to install some extra packages that may be requested by LSCE users | + | After [[#cloning_the_base_cdat_environment_before_adding_specific_packages_for_lsce|cloning]], we are ready to install some extra (e.g. not directly related to CDAT) packages that may be useful to LSCE users |
- | * We first try to install together as many packages as possible that don't require other channels than //conda-forge//, and that don't request a downgrade of what is already installed | + | * We first install together as many packages as possible that don't require other channels than //conda-forge//, and that don't request a significant downgrade of what is already installed |
- | * We then install individual extra packages with ''conda install'' or ''pip install'' | + | * We use the //dry-run// option of conda in order to check the version (theoretically the latest) and origin (theoretically //conda-forge//) of the packages that would be installed. Or maybe the result will be that there are too many conflicts and the installation cannot proceed with the requested packages combination |
+ | * conda may take a very long time to report that there are too many conflicts and we have started using [[https://github.com/mamba-org/mamba|mamba]] that uses different solving libraries and is much (**much!**) faster than conda | ||
+ | * if the dry-run reports too many conflicts or requests too many downgrades, we try to remove some (not really important) packages and check if it works better | ||
+ | * the last resort is too create a new environment with a smaller set of packages if a user really needs a conflicting package | ||
+ | * We later install individual extra packages with ''conda install'', ''mamba install'' or ''pip install'' | ||
- | <code># You can use the following to keep a trace of what will be installed | + | === Pre-installation check with the dry-run option === |
- | #$ conda install --dry-run -n cdatm19_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm > somewhere/extra_packages.txt | + | |
- | # Install... | + | <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 |
- | $ conda install -n cdatm19_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret ferret_datasets basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm | + | |
- | [...] | + | |
- | # Use a similar install line if you want to install the same packages in the python3 version</code> | + | [... lots of information about what would be done followed by some information about how long it took ...] |
+ | |||
+ | Summary: | ||
+ | |||
+ | Install: 167 packages | ||
+ | Downgrade: 3 packages | ||
+ | |||
+ | Total download: 474 MB | ||
+ | |||
+ | DryRunExit: Dry run. Exiting. | ||
+ | |||
+ | 8.31user 0.51system 0:11.45elapsed 77%CPU</code> | ||
+ | |||
+ | === 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 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 | ||
+ | * ''conda list -n cdatm19_nompi_py3 > cdatm19_nompi_py3_21-03-06.txt'' | ||
+ | * no mpi: {{ :other:uvcdat:cdat_conda:cdatm19_nompi_py3_21-03-06.txt |}} | ||
+ | |||
+ | === Extra packages installed with pip === | ||
- | List of installed packages: {{ :other:uvcdat:cdat_conda:lsce-extra_01_install_190304.txt |}} | ||
- | Packages installed with //pip// | ||
* [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API | * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API | ||
- | * ''conda activate cdatm19_py2''\\ ''pip install dreqPy'' | + | * ''conda activate cdatm19_py3''\\ ''pip install dreqPy'' |
* Update with: ''pip install %%--%%upgrade dreqPy'' | * Update with: ''pip install %%--%%upgrade dreqPy'' | ||
* Get version number with:\\ <code>$ drq -v | * Get version number with:\\ <code>$ drq -v | ||
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* [[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 | ||
- | * ''conda activate cdatm19_py2''\\ ''pip install ferretmagic'' | + | * ''conda activate cdatm19_py3''\\ ''pip install ferretmagic'' |
+ | |||
+ | === Packages with no dependency problems and were added (or updated) later === | ||
- | The following packages have no dependency problems and were installed (or updated) //later// | ||
* [[https://cmor.llnl.gov/|CMOR]]: CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files | * [[https://cmor.llnl.gov/|CMOR]]: CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files | ||
- | * ''conda install -n cdatm19_py2 -c conda-forge cmor'' | + | * ''conda install -n cdatm19_py3 -c conda-forge cmor'' |
* 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 | * [[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_py2 -c conda-forge -c vacumm vacumm'' | + | * ''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]] | * <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 | * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library | ||
- | * ''conda install -n cdatm19_py2 -c stefraynaud -c conda-forge spanlib'' | + | * ''conda install -n cdatm19_py3 -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 | * [[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 cdatm19_py2 -c conda-forge cartopy'' | + | * ''conda install -n cdatm19_py3 -c conda-forge cartopy'' |
* [[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 | ||
- | * ''conda install -n cdatm19_py2 -c conda-forge joblib'' | + | * ''conda install -n cdatm19_py3 -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 | ||
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* [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
- | * ''conda install -n cdatm19_py2 -c conda-forge palettable'' | + | * ''conda install -n cdatm19_py3 -c conda-forge palettable'' |
==== TODO ==== | ==== TODO ==== | ||
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* [[http://statsmodels.sourceforge.net/|statsmodels]]: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests | * [[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 | * [[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 | * [[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 | * [[https://pypi.python.org/pypi/gsw/|gsw]]: Python implementation of the Thermodynamic Equation Of Seawater | ||
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* [[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 | ||
- | * [[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://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 | ||
Line 291: | Line 356: | ||
* [[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://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
+ | |||
+ | |||
+ | * [[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://geopandas.org/|geopandas]]: an open source project to make working with geospatial data in python easier. | ||
+ | * [[http://scikit-image.org/|scikit-image]]: image processing in Python | ||
+ | * [[https://scikit-learn.org/stable/index.html|scikit-learn]]: Machine Learning in Python | ||
==== Removed packages ==== | ==== Removed packages ==== | ||
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^ Environment\\ name ^ Server ^ Summary ^ | ^ Environment\\ name ^ Server ^ Summary ^ | ||
- | | cdat-8.2.1_py2 | LSCE\\ ciclad | CDAT 8.2.1 & Python 2.7 | | + | | cdat-8.2.1_py3 | LSCE\\ ciclad | CDAT 8.2.1 & Python 2.7 | |
| cdat-8.2.1_py3 | LSCE | CDAT 8.2.1 & Python 3.6 | | | cdat-8.2.1_py3 | LSCE | CDAT 8.2.1 & Python 3.6 | | ||
- | | cdatm19_py2\\ or //cdatm_py2// | LSCE\\ ciclad | CDAT 8.2.1 & P 2.7 //JYP version// | | + | | cdatm19_py3\\ or //cdatm_py3// | LSCE\\ ciclad | CDAT 8.2.1 & P 2.7 //JYP version// | |
| cdatm19_py3\\ or //cdatm_py3// | LSCE | CDAT 8.2.1 & P 3.7 //JYP version// | | | cdatm19_py3\\ or //cdatm_py3// | LSCE | CDAT 8.2.1 & P 3.7 //JYP version// | | ||
- | | cdat-nightly_py2 | LSCE\\ ciclad | CDAT nightly & Python 2.7 | | ||
- | | cdatm-nightly_py2 | LSCE\\ ciclad | CDAT nightly & P 2.7 //JYP version// | | ||
/* standard page footer */ | /* standard page footer */ |