other:uvcdat:cdat_conda:miniconda3_install
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other:uvcdat:cdat_conda:miniconda3_install [2024/04/12 15:37] jypeter [FIXME Using mamba instead of conda] REMOVED the old mamba section |
other:uvcdat:cdat_conda:miniconda3_install [2024/04/18 09:43] jypeter [Installing miniconda3 on a Linux-like or Windows computer] |
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| /path_to_miniconda/envs/cdatm_py3/bin/python | /path_to_miniconda/envs/cdatm_py3/bin/python | ||
| </code> | </code> | ||
| - | * The //special// environment where //Miniconda3// itself is installed is called ''base''. Note that the ''python'' binary of the //special// ''base'' environment is not located in the same directory hierarchy as the ''python'' of the other environments (i.e. there is no ''envs/'' subdirectory<code>$ conda activate base | + | * The //special// environment where //Miniconda3// itself is installed is called ''base'' (it also used to be called ''root''). Note that the ''python'' binary of the //special// ''base'' environment is not located in the same directory hierarchy as the ''python'' of the other environments (i.e. there is no ''envs/'' subdirectory<code>$ conda activate base |
| (base) $ which python | (base) $ which python | ||
| Line 36: | Line 36: | ||
| * all the //Anaconda// installer packages come from the ''default'' //channel// (or //repository//) provided by the [[https://anaconda.org/|conda repository]].\\ This is not very useful for us (and could even cause complex dependency problems later) because we will be mostly using (the same) packages provided by the [[https://conda-forge.org/feedstock-outputs/|conda-forge]] //channel//, **in order to avoid complex package dependency problems**. | * all the //Anaconda// installer packages come from the ''default'' //channel// (or //repository//) provided by the [[https://anaconda.org/|conda repository]].\\ This is not very useful for us (and could even cause complex dependency problems later) because we will be mostly using (the same) packages provided by the [[https://conda-forge.org/feedstock-outputs/|conda-forge]] //channel//, **in order to avoid complex package dependency problems**. | ||
| - | ===== Installing miniconda3 on a Linux-like computer ===== | + | ===== Installing miniconda3 on a Linux-like or Windows computer ===== |
| <WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
| By **//Linux-like//**, we mean: | By **//Linux-like//**, we mean: | ||
| - | * A native Linux computer (or server) | + | * A **Linux** desktop/laptop |
| - | * A windows 10 computer with [[other:win10wsl|WSL+Ubuntu installed]] | + | * The installation will be used by **one** person |
| - | * A Mac where you can use Linux in a terminal | + | * A **Linux** server |
| + | * The installation will be used by **one or more** persons | ||
| + | * A **windows computer with [[other:win10wsl|WSL+Ubuntu installed]]** | ||
| + | * You may want to use the //Pure Windows// installer, if all the packages you need are available for Windows | ||
| + | * The installation will be used by **one** person | ||
| + | * A **Mac** where you can use Linux in a terminal | ||
| + | * The installation will be used by **one** person | ||
| </WRAP> | </WRAP> | ||
| <WRAP center round info 60%> | <WRAP center round info 60%> | ||
| - | **//Pure Windows//** Note: you can also follow the steps listed in the [[https://docs.anaconda.com/free/miniconda/#quick-command-line-install|Windows section of "Quick command line install"]] to install a //pure Windows// version of miniconda3, and then follow the steps listed in the next sections of this page.\\ We assume below that the installer is downloaded in the ''C:\Scratch\your_login'' directory, and we install Miniconda3 in a ''C:\Utils\miniconda3_2024-03'' directory. <code>PS C: cd C:\Scratch\your_login | + | **//Pure Windows//** Note: |
| + | |||
| + | * Follow the steps just below adapted from the [[https://docs.anaconda.com/free/miniconda/#quick-command-line-install|Windows section of "Quick command line install"]] to install a //pure Windows// version of miniconda3 | ||
| + | * And then follow the steps in the next sections of this page. | ||
| + | |||
| + | We assume below that: | ||
| + | * The Windows installer is downloaded in the ''C:\Scratch\your_login'' directory | ||
| + | * We want to install Miniconda3 in the ''C:\Utils\miniconda3_2024-03'' directory (and we have a few Gb of available space on that disk) | ||
| + | |||
| + | <code>PS C: cd C:\Scratch\your_login | ||
| PS C:\Scratch\your_login> curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe | PS C:\Scratch\your_login> curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe | ||
| PS C:\Scratch\your_login> .\miniconda.exe | PS C:\Scratch\your_login> .\miniconda.exe | ||
| Line 332: | Line 347: | ||
| ===== Keeping Miniconda3 up-to-date ===== | ===== Keeping Miniconda3 up-to-date ===== | ||
| - | * Just type ''conda update -n base --all'' as shown in the [[#updating_mini_conda|Updating (Mini)conda]] section | + | * Just type ''conda update -n base %%--%%all'' as shown in the [[#updating_mini_conda|Updating (Mini)conda]] section |
| * The ''base'' (miniconda3) and the other environments are all independent and can be updated independently | * The ''base'' (miniconda3) and the other environments are all independent and can be updated independently | ||
| Line 339: | Line 354: | ||
| ===== conda resources ===== | ===== conda resources ===== | ||
| - | Note: some extra details are available on the much older page //Installing and maintaining UV-CDAT with conda//. You can check later the [[other:uvcdat:conda_notes#useful_conda_commands|Useful conda commands]], but the [[https://docs.conda.io/projects/conda/en/latest/index.html|official conda documentation]] and the [[https://docs.conda.io/projects/conda/en/latest/user-guide/cheatsheet.html|Cheat sheet]] are probably more up-to-date. | + | |
| + | |||
| + | |||
| + | ==== Web sites ==== | ||
| + | |||
| + | * [[https://docs.conda.io/projects/conda/en/stable/|Official conda website]] | ||
| + | * [[https://docs.conda.io/projects/conda/en/stable/user-guide/cheatsheet.html|Cheat sheet]] (2 pages, for people in a hurry) | ||
| + | * [[https://docs.conda.io/projects/conda/en/stable/commands/|Commands' reference]] | ||
| + | * Package repositories | ||
| + | * [[https://conda-forge.org/packages/|conda-forge]] <= recommended source of packages | ||
| + | * [[https://anaconda.org/|default]] | ||
| + | |||
| + | |||
| + | ==== Useful conda commands ==== | ||
| + | |||
| + | This is just a subset of some of the commands, and a subset of their options! For a complete reference, use the [[https://docs.conda.io/projects/conda/en/stable/|official conda website]] | ||
| + | |||
| + | * **Get help** | ||
| + | * ''conda -h'' | ||
| + | * ''conda //command// %%--%%help'': help for a specific //command// | ||
| + | |||
| + | * **Available environments** | ||
| + | * ''conda env list'' | ||
| + | * The currently active environment has a "*****" character on its line<code>(base) $ conda env list | ||
| + | # conda environments: | ||
| + | # | ||
| + | base * /homedata/jypmce/miniconda3_2024-03</code> | ||
| + | |||
| + | * **Activate** an existing environment (available in ''conda env list'') or **deactivate**, in order to go back to the default Python | ||
| + | * ''conda activate existing_environment'' | ||
| + | * ''conda activate'' (without specifying an environment name) will **activate the ''base'' Miniconda3 environment** | ||
| + | * Go back to the default Python available on the system | ||
| + | * ''conda deactivate'' | ||
| + | * You can type ''which python'' to determine where is the current ''python'' executable you are using is\\ You should **always know which Python you are using!** | ||
| + | * <code>(base) $ which python | ||
| + | /homedata/jypmce/miniconda3_2024-03/bin/python | ||
| + | |||
| + | (base) $ conda deactivate | ||
| + | |||
| + | $ which python | ||
| + | /usr/bin/python</code> | ||
| + | * Note: //before conda ''4.6''//, you had to type ''**source** activate existing_environment'' and ''**source** deactivate'' | ||
| + | |||
| + | * Get the **list of installed packages**, their version, and where they come from (e.g. ''conda-forge'', ''pip'') | ||
| + | * ''conda list [-n existing_environment]'' | ||
| + | |||
| + | * **Create an environment** and install a few packages and their dependencies | ||
| + | * ''conda create -n new_environment_name package1 package2 packageN'' | ||
| + | |||
| + | * **Delete an environment** | ||
| + | * ''conda remove -n crap_environment %%--%%all'' | ||
| + | |||
| + | * **Find out if a package is available** on the //conda-forge// channel (or other channels) | ||
| + | * Note: you should always install a package with ''conda'' instead of ''pip'', if it is available on a //conda channel// | ||
| + | * ''conda search package_exact_name''\\ ''conda search '*package_partial_name*''' | ||
| + | * Note: ''search'' with wildcards fails in a //tcsh// shell, as of April 2024 ([[https://github.com/conda/conda/issues/9771|CSH install/search fail with '*' variable in an argument]]) | ||
| + | |||
| + | * **Install and remove packages**\\ Add ''-n target_environment'' to make changes in another environment than the active one | ||
| + | * ''conda install package1 package2 packageN'' | ||
| + | * ''conda'' should already be [[#fine-tuning_conda_to_use_only_conda-forge|configured to use conda-forge by default]] if you have read this page carefully | ||
| + | * Add ''-c channel_url_or_alias'' to install from a specific //channel// | ||
| + | * ''conda remove package1 package2 packageN'' | ||
| + | |||
| + | * **Update** just ''conda'' (update the //conda// package, not the full Miniconda3 //base// environment) | ||
| + | * ''conda update -n base conda'' | ||
| + | |||
| + | * **Completely update an environment** (all the packages) | ||
| + | * ''conda update -n existing_environment %%--%%all'' | ||
| + | |||
| + | * **Cleaning... <wrap em>Dangerous</wrap>**!\\ If you have several environments, ''conda clean'' may remove packages that are not needed in an environment, but are still used in other environments, and **you may end up with a broken installation...**\\ ''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, pip and virtualenv ==== | ||
| + | |||
| + | * Read the [[https://docs.conda.io/projects/conda/en/stable/commands/#conda-vs-pip-vs-virtualenv-commands|Conda vs. pip vs. virtualenv commands]] section | ||
| + | |||
| + | * Read the [[https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-environments.html#using-pip-in-an-environment|Using pip in an environment]] | ||
| + | ==== Installation history ==== | ||
| + | |||
| + | |||
| + | ===== Uninstalling Miniconda3 ===== | ||
| + | |||
| + | ==== Windows computer ==== | ||
| + | |||
| + | Miniconda3 can be removed like a regular Windows application | ||
| + | |||
| + | * Go to the //Apps & features// panel | ||
| + | * ''Start'' => ''Settings'' => ''Apps'' => ''Apps & features'' | ||
| + | * Select ''Miniconda3 py3xxxxx'' | ||
| + | * Click on ''Uninstall'' and follow the instructions displayed by the uninstaller window\\ This will remove: | ||
| + | * The (very big) directory that you specified when you installed //Miniconda3// | ||
| + | * The ''conda'' shortcuts from the ''Start Menu'' | ||
| + | |||
| + | ==== Linux-like computer ==== | ||
| /* standard page footer */ | /* standard page footer */ | ||
other/uvcdat/cdat_conda/miniconda3_install.txt · Last modified: 2024/07/08 13:28 by jypeter
