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| other:uvcdat:cdat_conda:miniconda3_install [2024/04/12 16:24] – [Why should you use Miniconda3 ?] Cleaned jypeter | other:uvcdat:cdat_conda:miniconda3_install [2024/04/19 15:49] – [Miniconda3 on a Windows computer] Improved jypeter |
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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 |
| * 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) | |
| * A windows 10 computer with [[other:win10wsl|WSL+Ubuntu installed]] | |
| * A Mac where you can use Linux in a terminal | |
| </WRAP> | |
| |
| <WRAP center round info 60%> | ==== Miniconda3 on a Windows computer ==== |
| **//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 | |
| | 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 |
| | |
| | === 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'' or whatever you use as a [[other:win10config#local_scratch_folder|local Scratch folder]] |
| | |
| | * Open a //terminal//, where you can type the required installation commands |
| | * Windows //Powershell terminal//: ''Start'' => ''W'' => ''Windows PowerShell'' => ''Windows PowerShell'' |
| | * [[other:win10apps#windows_terminal|Windows Terminal]] |
| | |
| | * 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> 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> dir miniconda.exe |
| PS C:\Scratch\your_login> del .\miniconda.exe | [...] |
| </code> | -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 your future Python environments** based on this version of Miniconda3\\ **We will later refer to this location as ''/path_to_miniconda3/''** in the Linux sections |
| | * Remember that **you will need a few Gb of available space** |
| | * You should **avoid installing Miniconda3 in your Windows //home// directory** (''C:\Users\your_login'' or [[other:win10config#local_home_folder|<some_disk_different_from_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 environments... |
| | * 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'' |
| | |
| | * Launch the installer with<code>PS C:\Scratch\your_login> .\miniconda.exe</code> |
| | |
| | * In the installer window: |
| | * (Review and) accept the License Agreement |
| | * Choose to install for //Just Me// (the recommended default choice) |
| | * Specify the //Destination Folder// selected above, e.g. ''C:\Utils\miniconda3_2024-03'' |
| | * Use the pre-selected //Advanced Installation Options//, i.e |
| | * //Create start menu shortcutes// |
| | * //Register Miniconda3 as my default Python 3.12// <= Useful? |
| | |
| | * When the installer has finished running, you should have two new shortcuts in the Windows ''Start menu'' |
| | * ''Anaconda Prompt'' |
| | * ''Anaconda Powershell Prompt'' |
| | * **We will now use this //Anaconda PowerShell// shortcut each time we need to use Miniconda3 or Python** |
| | |
| | * Remove the installer<code>PS C:\Scratch\your_login> del .\miniconda.exe</code> |
| | |
| | ==== 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]]) |
| [...] 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]] |
| |
| * 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. |
| * ask //tcsh// users to add to ''~/.cshrc'' something like\\ ''source ~main_installer_login/.conda3_jyp.csh''\\ \\ with a ''.conda3_jyp.csh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp.csh.txt |}} | * ask //tcsh// users to add to ''~/.cshrc'' something like\\ ''source ~main_installer_login/.conda3_jyp.csh''\\ \\ with a ''.conda3_jyp.csh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp.csh.txt |}} |
| |
| ===== 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 |
| | |
| | * The ''base'' (miniconda3) and the other environments are all independent and can be updated independently |
| | |
| | * It is up to you to decide if you want to update environments or not |
| | ===== conda resources ===== |
| | |
| | |
| | |
| | |
| | ==== 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 ===== |
| |
| ===== FIXME Using mamba instead of conda ===== | ==== Windows computer ==== |
| |
| Even when using a proper ''.condarc'' in order to get packages coming only from //conda-forge//, ''conda install'' may fail to solve the dependencies after meditating during an enormous time (e.g. [[https://github.com/conda/conda/issues/9367#issuecomment-793968239|Solving environment: failed with initial frozen solve. Retrying with flexible solve.]]), when we try to deal with **complex environments** (i.e. we already have lots of installed packages and we want to add even more packages). | Miniconda3 can be removed like a regular Windows application |
| |
| Using CDAT as a base environment, and adding a lot of extra packages is a **complex environment**. | * 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'' |
| |
| The only solution seems to replace ''conda'' with [[https://github.com/mamba-org/mamba|mamba]], a reimplementation of the conda package manager in C++ ([[https://wolfv.medium.com/making-conda-fast-again-4da4debfb3b7|Making conda fast again]]): | ==== Linux-like computer ==== |
| * Install ''mamba'' in the //base// (i.e. //miniconda//) environment\\ ''conda install mamba -n base -c conda-forge'' | |
| * Use ''mamba'' instead of ''conda'' when installing packages.\\ Theoretically, you don't need to specify ''install -c conda forge'' any more, because ''conda-forge'' is now the default source of new packages\\ ''mamba install lots_of_packages'' | |
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