other:uvcdat:conda_notes
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other:uvcdat:conda_notes [2017/02/27 16:37] jypeter Improved page |
other:uvcdat:conda_notes [2019/11/05 13:45] jypeter [What should I install?] Added a link to "Why You Need Python Environments and How to Manage Them with Conda " |
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| * If you know that you are going to use UV-CDAT, you might as well use the ''conda'' from //Miniconda// to avoid uselessly duplicating packages downloaded from the official Anaconda repository (used by Anaconda) with the same packages downloaded from the conda-forge repository (used by UV-CDAT). | * If you know that you are going to use UV-CDAT, you might as well use the ''conda'' from //Miniconda// to avoid uselessly duplicating packages downloaded from the official Anaconda repository (used by Anaconda) with the same packages downloaded from the conda-forge repository (used by UV-CDAT). | ||
| + | * When you are done with this page (not just this section), you should have a look at the [[https://www.freecodecamp.org/news/why-you-need-python-environments-and-how-to-manage-them-with-conda-85f155f4353c/|Why You Need Python Environments and How to Manage Them with Conda]] page that covers interesting topics | ||
| ===== Miniconda ===== | ===== Miniconda ===== | ||
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| * Get the [[https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh|Python 2.7 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]]) | * Get the [[https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh|Python 2.7 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]]) | ||
| * ''cd /home/scratch01/jypeter'' (some temporary storage space for the installer) | * ''cd /home/scratch01/jypeter'' (some temporary storage space for the installer) | ||
| - | * ''wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'' (28 Mo, 16 Feb 2017) | + | * ''wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'' (28 Mo, 02 Aug 2017) |
| * Execute the installer | * Execute the installer | ||
| * ''bash Miniconda2-latest-Linux-x86_64.sh'' | * ''bash Miniconda2-latest-Linux-x86_64.sh'' | ||
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| 8.0K ssl</code> | 8.0K ssl</code> | ||
| * Accept the automatic update of the //PATH// variable in ''.bashrc'' (note: the installer automatically creates a backup of ''.bashrc'') | * Accept the automatic update of the //PATH// variable in ''.bashrc'' (note: the installer automatically creates a backup of ''.bashrc'') | ||
| - | * ''# added by Miniconda2 4.3.11 installer''\\ ''export PATH="/home/share/unix_files/cdat/miniconda2/bin:$PATH"'' | + | * ''# added by Miniconda2 4.3.21 installer''\\ ''export PATH="/home/share/unix_files/cdat/miniconda2/bin:$PATH"'' |
| * Open a new terminal (if you use bash) or type ''bash'' and check if the python from the conda distribution has been correctly installed | * Open a new terminal (if you use bash) or type ''bash'' and check if the python from the conda distribution has been correctly installed | ||
| * Update and clean the new installation | * Update and clean the new installation | ||
| - | * ''conda updpate --all'' | + | * ''conda update %%--%%all'' |
| - | * ''conda clean --all'' | + | * ''conda clean %%--%%all'' |
| * <code>bash-4.1$ which python | * <code>bash-4.1$ which python | ||
| /home/share/unix_files/cdat/miniconda2/bin/python | /home/share/unix_files/cdat/miniconda2/bin/python | ||
| Line 146: | Line 147: | ||
| * Deleting an environment | * Deleting an environment | ||
| * ''conda remove %%--%%name crap_environment %%--%%all''\\ ''conda clean --all'' | * ''conda remove %%--%%name crap_environment %%--%%all''\\ ''conda clean --all'' | ||
| - | * Activating or going back to //root// | + | * The following seems to do the same: ''conda env remove -n crap_environment'' |
| - | * ''source activate existing_environment'' | + | * Activating or going back to //root/base// |
| - | * ''source activate'' will activate the //root// environment | + | * ''conda activate existing_environment'' (used to be ''source activate existing_environment'' in older versions of conda) |
| - | * You can use ''which python'' to determine where is the current Python you are using, or ''which -a python'' to display all the Python executables in the currrent search path | + | * ''conda activate'' will activate the //root/base// environment |
| - | * ''source deactivate'' | + | * You can use ''which python'' to determine where is the current Python you are using, or ''which -a python'' (''-a'' will only work in //bash//) to display all the Python executables in the current search path |
| + | * ''conda deactivate'' (used to be ''source deactivate'') | ||
| * Installed packages | * Installed packages | ||
| * ''conda list'' | * ''conda list'' | ||
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| * ''conda remove package1 package2 packageN'' | * ''conda remove package1 package2 packageN'' | ||
| * Updating conda (update the //conda// package, not the full Miniconda) | * Updating conda (update the //conda// package, not the full Miniconda) | ||
| - | * ''conda update conda'' | + | * ''conda update -n base -c defaults conda'' |
| + | * Downgrading conda (required for installing UV-CDAT 2.10) | ||
| + | * <code>bash-4.1$ conda install -n root "conda<4.3.13" | ||
| + | Fetching package metadata ......... | ||
| + | Solving package specifications: . | ||
| + | |||
| + | Package plan for installation in environment /home/share/unix_files/cdat/miniconda2: | ||
| + | |||
| + | The following packages will be DOWNGRADED due to dependency conflicts: | ||
| + | |||
| + | conda: 4.3.13-py27_0 --> 4.3.11-py27_0 | ||
| + | |||
| + | Proceed ([y]/n)? y | ||
| + | |||
| + | conda-4.3.11-p 100% |###############################################################| Time: 0:00:00 4.28 MB/s | ||
| + | |||
| + | bash-4.1$ conda info | ||
| + | Current conda install: | ||
| + | |||
| + | platform : linux-64 | ||
| + | conda version : 4.3.11 | ||
| + | conda is private : False | ||
| + | conda-env version : 4.3.11</code> | ||
| * conda does not automatically clean the content of the ''pkgs'' directory! Use the following to //Remove index cache, lock files, tarballs, unused cache packages, and source cache// | * conda does not automatically clean the content of the ''pkgs'' directory! Use the following to //Remove index cache, lock files, tarballs, unused cache packages, and source cache// | ||
| * ''conda clean %%--%%all'' | * ''conda clean %%--%%all'' | ||
| + | ==== Installation history ==== | ||
| + | |||
| + | You can get the current list of installed packages with ''conda list'', but it may also be useful to know the installation order: | ||
| + | |||
| + | * ''conda list %%--%%revisions'' revisions will display **exactly** what was installed and when (including the updates, and automatic dependencies installation) | ||
| + | * You can theoretically roll back to a previous //revision// with: ''conda install %%--%%revision RR'' | ||
| + | * There is more information in the ''conda-meta/history'' installation log files. e.g., if you need to know the list of installation commands used:\\ <code> $ egrep -e 'cmd:' -e '==>' /home/share/unix_files/cdat/miniconda3/envs/cdatm18_py2/conda-meta/history | ||
| + | ==> 2019-03-07 16:19:55 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda create -n cdatm18_py2 --clone cdat-8.1_py2 | ||
| + | ==> 2019-03-07 16:35:11 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda install -n cdatm18_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm | ||
| + | ==> 2019-03-07 16:57:50 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda install -n cdatm18_py2 -c conda-forge -c vacumm vacumm | ||
| + | ==> 2019-03-12 14:35:31 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda install -n cdatm18_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm | ||
| + | ==> 2019-03-12 15:49:54 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda install -n cdatm18_py2 -c stefraynaud -c conda-forge spanlib | ||
| + | ==> 2019-03-12 17:30:26 <== | ||
| + | # cmd: /home/share/unix_files/cdat/miniconda3/bin/conda install -n cdatm18_py2 -c conda-forge cmor</code> | ||
| + | * You can also, use a script and the ''conda'' module available **in the ''base'' environment**: [[https://github.com/conda/conda/issues/4545#issuecomment-469984684|example]] | ||
| ==== Misc ==== | ==== Misc ==== | ||
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| * [[https://conda.io/docs/|conda Full documentation]] | * [[https://conda.io/docs/|conda Full documentation]] | ||
| * [[https://conda.io/docs/faq.html|conda FAQ]] | * [[https://conda.io/docs/faq.html|conda FAQ]] | ||
| - | * [[https://conda.io/docs/using/envs.html#share-an-environment|Sharing (replicating) an environment]] | + | * [[https://conda.io/docs/user-guide/tasks/manage-environments.html#sharing-an-environment|Sharing (replicating) an environment]] |
| * [[https://conda.io/docs/install/central.html|Centralized installation]] | * [[https://conda.io/docs/install/central.html|Centralized installation]] | ||
other/uvcdat/conda_notes.txt · Last modified: 2021/12/21 10:33 by jypeter
