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other:uvcdat:cdat_conda:miniconda3_install [2024/04/16 12:56] jypeter [conda resources] Added subsections and some content |
other:uvcdat:cdat_conda:miniconda3_install [2024/04/19 09:43] jypeter [Miniconda3 on a Windows computer] More instructions, based on Linux-like |
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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 | ||
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* You //could// also start with the full //Anaconda// (instead of //Miniconda//) installer that will install a much more complete python environment, ready for use.\\ **We choose not to use the full //Anaconda// installer** because: | * You //could// also start with the full //Anaconda// (instead of //Miniconda//) installer that will install a much more complete python environment, ready for use.\\ **We choose not to use the full //Anaconda// installer** because: | ||
* it requires more disk space than //Miniconda3// during the initial installation, | * it requires more disk space than //Miniconda3// during the initial installation, | ||
- | * 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 ===== | ||
- | <WRAP center round tip 60%> | + | ===== Downloading Miniconda3, and BASIC installation ===== |
- | By **//Linux-like//**, we mean: | + | |
- | * A native Linux computer (or server) | + | ==== Miniconda3 on a Windows computer ==== |
- | * A windows 10 computer with [[other:win10wsl|WSL+Ubuntu installed]] | + | |
- | * A Mac where you can use Linux in a terminal | + | Some of the steps below are 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 |
- | </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 | ||
PS C:\Scratch\your_login> del .\miniconda.exe | PS C:\Scratch\your_login> del .\miniconda.exe | ||
</code> | </code> | ||
+ | </WRAP> | ||
+ | |||
+ | === Downloading the Miniconda3 installer on Windows === | ||
+ | |||
+ | * We use a download link that always point to the [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|latest version of the Windows installer]] | ||
+ | * https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe | ||
+ | * The installer is based on **Python 3.12.2 and Conda 24.3.0 as of April 2024** | ||
+ | |||
+ | * Find some temporary space on Windows | ||
+ | * e.g. ''C:\Scratch\your_login'' | ||
+ | |||
+ | * Use ''curl'' to download the latest installer (78 Mb as of April 2024): <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> dir miniconda.exe | ||
+ | [...] | ||
+ | -a---- 19/04/2024 11:18 81274240 miniconda.exe</code> | ||
+ | |||
+ | === BASIC Miniconda3 installation on Windows === | ||
+ | |||
+ | * **Determine the directory where you will install miniconda3 and all the Python environments** based on this version of miniconda3, but **do not create the directory** (the installation script will do it)\\ **We will later refer to this location as ''/path_to_miniconda3/''** | ||
+ | * Remember that **you will need a few Gb of available space** | ||
+ | * You should also **avoid installing in your Windows //home// directory** (''C:\Users\your_login''), if you want to be able to easily make backups or your //home//, without backing up thousands of files related to your Python installation... | ||
+ | * We add some date or version information at the end of the directory, in order to differentiate it from other (older of future) installations | ||
+ | * e.g. ''C:\Utils\miniconda3_2024-03'' | ||
+ | |||
+ | * Execute the installer with ''$ bash Miniconda3-latest-Linux-x86_64.sh'' | ||
+ | * Review the license (type ''<SPACE>'' several times...) and accept it | ||
+ | * When asked for the installation directory, specify the directory location chosen in the previous step, and **not the default directory** | ||
+ | * e.g. specify\\ ''/path_to_miniconda3/''\\ instead of the default\\ ''$HOME/miniconda3'' | ||
+ | * **Answer ''no'' to the question ''Do you wish to update your shell profile to automatically initialize conda?''**.\\ Otherwise the installation will make changes to your shell configuration files | ||
+ | * If you forget to answer ''no'', you can apparently: | ||
+ | * remove the changes to your shell configuration files by typing later: ''conda init --reverse $SHELL'' | ||
+ | * or at least disable the automatic activation of the environment (that might have side effect) by typing: ''conda config --set auto_activate_base false'' | ||
+ | ==== Miniconda3 on a Linux-like computer ==== | ||
+ | |||
+ | |||
+ | <WRAP center round tip 60%> | ||
+ | By **//Linux-like//**, we mean: | ||
+ | * A **Linux** desktop/laptop | ||
+ | * The installation will be used by **one** person | ||
+ | * A **Linux** server | ||
+ | * The installation will be used by **one or more** persons | ||
+ | * A **windows computer with [[other:win10wsl|WSL+Ubuntu installed]]** | ||
+ | * You should use the [[#miniconda3_on_a_windows_computer|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> | ||
- | ==== Downloading the Miniconda3 installer ==== | + | === Downloading the Miniconda3 installer === |
* We use a download link that always point to the [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|latest version of the Linux installer]] | * We use a download link that always point to the [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|latest version of the Linux installer]] | ||
* For the Linux computers we commonly use, we need the //Miniconda3 Linux 64-bit// link: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | * For the Linux computers we commonly use, we need the //Miniconda3 Linux 64-bit// link: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | ||
* Note: Mac users should use the latest [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|macOS installer]] appropriate for their computer | * Note: Mac users should use the latest [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|macOS installer]] appropriate for their computer | ||
- | * The installer is based on **Python 3.12 as of March 2024** | + | * The installer is based on **Python 3.12.2 and Conda 24.3.0 as of April 2024** |
* Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]]) | * Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]]) | ||
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[...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code> | [...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code> | ||
- | ==== Using the Miniconda3 installer ==== | + | === Using the Miniconda3 installer === |
We assume below that we are in the [[#downloading_the_installer|directory where we have downloaded the installer]] | We assume below that we are in the [[#downloading_the_installer|directory where we have downloaded the installer]] | ||
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* Remove the //Miniconda3// installer: ''$ rm Miniconda3-latest-Linux-x86_64.sh'' | * Remove the //Miniconda3// installer: ''$ rm Miniconda3-latest-Linux-x86_64.sh'' | ||
- | ==== Fine-tuning conda to use (only) conda-forge ==== | + | |
+ | ===== Fine-tuning conda to use (only) conda-forge ===== | ||
* ''conda'' will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies. | * ''conda'' will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies. | ||
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===== 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. | + | |
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* [[https://docs.conda.io/projects/conda/en/stable/|Official conda website]] | * [[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/user-guide/cheatsheet.html|Cheat sheet]] (2 pages, for people in a hurry) |
* [[https://docs.conda.io/projects/conda/en/stable/commands/|Commands' reference]] | * [[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 commands ==== | + | ==== 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 ==== | ==== 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 ==== | ||