other:uvcdat:cdat_conda:miniconda3_install
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other:uvcdat:cdat_conda:miniconda3_install [2024/07/03 14:50] jypeter [Cleaning up Miniconda3...] Improved |
other:uvcdat:cdat_conda:miniconda3_install [2024/08/09 15:42] (current) jypeter Added a new "Creating Windows menu shortcuts to start environments" section |
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| * ''Anaconda Prompt'' | * ''Anaconda Prompt'' | ||
| * ''Anaconda Powershell Prompt'' | * ''Anaconda Powershell Prompt'' | ||
| - | * **We will now use this //Anaconda PowerShell// shortcut each time we need to use Miniconda3 or Python** | + | * **We will now use this //Anaconda Powershell// shortcut each time we need to use Miniconda3 or Python** |
| + | * It is **highly recommended to [[other:win10apps#windows_terminal|install Windows Terminal and make it the default terminal application]]**, so that the ''conda'' prompts will open in a modern (and highly configurable) terminal | ||
| * Remove the installer<code>PS C:\Scratch\your_login> del .\miniconda.exe</code> | * Remove the installer<code>PS C:\Scratch\your_login> del .\miniconda.exe</code> | ||
| Line 438: | Line 439: | ||
| <WRAP center round important 60%> | <WRAP center round important 60%> | ||
| - | It seems **safe** to reclaim some disk space by cleaning up the initial (//base//) installation, **when no other environments have been installed yet**\\ \\ Use cleaning with caution after installing other environments... | + | It seems **safe** to reclaim some disk space by cleaning up the initial (//base//) installation, **when no other (shared) environments have been installed yet**\\ \\ Use cleaning with caution after installing other environments (besides ''base''), especially environments **shared** by several users. But it should not break your installation |
| </WRAP> | </WRAP> | ||
| - | You can [[https://docs.conda.io/projects/conda/en/latest/commands/clean.html|clean]] the initial //Miniconda3// installation to free up some disk space. | + | * ''conda clean %%--%%all'' |
| - | + | * [[https://docs.conda.io/projects/conda/en/latest/commands/clean.html|Documentation]] | |
| - | The documentation specifies //WARNING: This will break environments with packages installed using symlinks back to the package cache.// | + | * There is **no ''-n'' option to specify an environment name**, because ''clean'' will //Remove **unused** packages and caches// shared by **all** the environments |
| - | + | * The ''clean'' command will mostly deal with the content of the ''/path_to_miniconda/pkgs/'' directory | |
| - | **You should probably avoid using ''clean'' once you have used //Miniconda3// to install new Python environments** (unless you are desperate for disk space, and know how to do a complete re-installation if something breaks...) | + | * Example:<code>(base) $ conda clean --all |
| - | + | ||
| - | <code>(base) $ conda clean --all | + | |
| Will remove 154 (180.9 MB) tarball(s). | Will remove 154 (180.9 MB) tarball(s). | ||
| Proceed ([y]/n)? y | Proceed ([y]/n)? y | ||
| Line 463: | Line 462: | ||
| 457M /homedata/jypmce/miniconda3_2024-03 | 457M /homedata/jypmce/miniconda3_2024-03 | ||
| </code> | </code> | ||
| + | |||
| + | * It //should// be safe to use ''conda clean %%--%%all'' even in a multi-user installation with several environments, **if you don't use the ''-f'' option** | ||
| + | * The ''-f''/''%%--%%force-pkgs-dirs'' documentation specifies //WARNING: This will break environments with packages installed using symlinks back to the package cache.// | ||
| + | * ...but Linux installations probably use [[https://www.redhat.com/sysadmin/linking-linux-explained|hard links]] rather than soft/symbolic links | ||
| + | * ...and you will probably never need this option anyway | ||
| + | |||
| + | * Remember that **your Python installation will keep on growing and growing and growing, and you will need to do some cleaning at some point** | ||
| + | |||
| + | |||
| + | |||
| ===== Initializing conda in terminals ===== | ===== Initializing conda in terminals ===== | ||
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| * FIXME: update/rewrite the [[other:uvcdat:cdat_conda:cdat_2024_03]] page | * FIXME: update/rewrite the [[other:uvcdat:cdat_conda:cdat_2024_03]] page | ||
| + | |||
| + | ===== Creating Windows menu shortcuts to start environments ===== | ||
| + | |||
| + | FIXME => Move this section somewhere else? | ||
| + | |||
| + | * Use ''conda install'' and what is described in [[https://github.com/conda/menuinst/issues/246|Easily creating shortcuts with the powershell_shortcut_miniconda and console_shortcut_miniconda packages, and can this be replicated with menuinst ?]] | ||
| + | |||
| + | * Can theoretically be done with [[https://conda.github.io/menuinst/|menuinst]] | ||
| + | * [[https://github.com/conda/menuinst|menuinst @ GH]] | ||
| + | |||
| + | * FIXME Find a way to add Windows Terminal profiles | ||
| + | * See ''menuinst''+[[https://github.com/conda/menuinst/issues/196|Add Windows Terminal profile option]] | ||
| ===== conda resources ===== | ===== conda resources ===== | ||
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| ==== Web sites ==== | ==== Web sites ==== | ||
| - | * [[https://docs.conda.io/projects/conda/en/stable/|Official conda website]] | + | * [[https://docs.conda.io/projects/conda/en/stable/|Official Documentation site]] |
| * [[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]] | ||
| + | * [[https://docs.conda.io/projects/conda-build/en/stable/resources/package-spec.html#conda-package-specification|Conda package specification]] | ||
| + | * This helps understand (and [[https://github.com/conda/conda/issues/14026|use]]) the content of the ''/path_to_miniconda/pkgs'' directory | ||
| + | |||
| + | * [[https://conda.org/blog/|conda community site]]: | ||
| + | * [[https://conda.org/blog/|conda Blog]]: ''conda'' new features, etc... | ||
| + | |||
| + | * [[https://github.com/conda/conda|conda @ GitHub]] | ||
| + | |||
| * Package repositories | * Package repositories | ||
| * [[https://conda-forge.org/packages/|conda-forge]] <= recommended source of packages | * [[https://conda-forge.org/packages/|conda-forge]] <= recommended source of packages | ||
| Line 653: | Line 682: | ||
| * **Specific versions can be specified** by using the [[#the_conda_matchspec_format|conda MatchSpec format]] | * **Specific versions can be specified** by using the [[#the_conda_matchspec_format|conda MatchSpec format]] | ||
| * ''conda remove package1 package2 packageN'' | * ''conda remove package1 package2 packageN'' | ||
| - | + | * Matching ''pip'' commands (**only** if the package is not available in conda!) | |
| - | * Display the **dependencies of a package**, and the **packages that need a specific packages** | + | * ''pip install package'' |
| - | * e.g. the ''requests'' package | + | * ''pip uninstall package'' |
| * **Update a package** in the current, or a specific environment | * **Update a package** in the current, or a specific environment | ||
| * ''conda update -n existing_environment installed_package'' | * ''conda update -n existing_environment installed_package'' | ||
| - | * Update only the ''conda'' package (not the full Miniconda3 //base// environment) in the ''base'' environment\\ ''conda update -n base conda'' | + | * Update only the ''conda'' package (not the full Miniconda3 //base// environment) in the ''base'' environment |
| + | * ''conda update -n base conda'' | ||
| + | * Changes and new ''conda'' features are detailed in the [[https://conda.org/blog/|conda Blog]] | ||
| + | * Matching ''pip'' command (**only** if the package is not available in conda!) | ||
| + | * ''pip install %%--%%upgrade package'' | ||
| * **Completely update an environment** (i.e. update **all** the packages) | * **Completely update an environment** (i.e. update **all** the packages) | ||
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| * Note: ''mamba repoquery'' currently [[https://github.com/mamba-org/mamba/issues/3334|only works in the currently active environment]] | * Note: ''mamba repoquery'' currently [[https://github.com/mamba-org/mamba/issues/3334|only works in the currently active environment]] | ||
| * It can be useful to determine: | * It can be useful to determine: | ||
| - | * the packages that are required in order to use a given package => ''depends'' | + | * the packages that are required in order to use a given package => ''mamba repoquery **depends** package'' |
| - | * the packages that need a given package => ''whoneeds'' | + | * Without ''mamba repoquery depends'', you would have to follow the steps in [[https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-pkgs.html#listing-package-dependencies|Listing package dependencies]] :-( |
| + | * the packages that need a given package => ''mamba repoquery **whoneeds** package'' | ||
| * Example: the ''[[https://github.com/tqdm/tqdm|tqdm]]'' package | * Example: the ''[[https://github.com/tqdm/tqdm|tqdm]]'' package | ||
| * ''conda'' needs ''tqdm'' to display package download and installation progress, and the base dependencies of ''tqdm'' are ''[[https://github.com/tartley/colorama|colorama]]'', and of course ''python'' | * ''conda'' needs ''tqdm'' to display package download and installation progress, and the base dependencies of ''tqdm'' are ''[[https://github.com/tartley/colorama|colorama]]'', and of course ''python'' | ||
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| </code> | </code> | ||
| - | * **Cleaning... <wrap em>Dangerous</wrap>**! | + | * **Checking the //health// of an environment** with ''[[https://docs.conda.io/projects/conda/en/stable/commands/doctor.html|conda doctor]]'' |
| - | * ''conda'' does not automatically clean the content of the ''pkgs'' directory | + | * Some details in [[https://conda.org/blog/2023-06-01-conda-doctor/|Detecting conda environment inconsistencies easily]] |
| - | * 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 doctor'' does not do much yet, and not necessarily in a useful way, but this will hopefully improve over time! |
| - | * More details in [[#cleaning_up_miniconda3|Cleaning up Miniconda3...]] | + | * [[https://github.com/conda/conda/issues/14017|'conda doctor' output should be improved]] |
| + | * [[https://github.com/conda/conda/issues/13574#issuecomment-2214291304|What exactly are altered files?]] | ||
| + | * ''conda doctor -n base'' | ||
| + | * Example:<code> >conda doctor -n base | ||
| + | Environment Health Report for: /home/share/unix_files/cdat/miniconda3_2024-03 | ||
| + | |||
| + | Altered Files: | ||
| + | |||
| + | python-3.12.3-hab00c5b_0_cpython: 1 | ||
| + | |||
| + | Environment listed in environments.txt file: ✅ | ||
| + | |||
| + | Missing Files: | ||
| + | |||
| + | ✅ There are no packages with missing files. | ||
| + | </code> | ||
| + | |||
| + | * **Cleaning...** | ||
| + | * ''conda'' does not automatically clean the content of the ''/path_to_miniconda/pkgs'' directory and the size of ''/path_to_miniconda/'' will keep on growing, as you add new environments, or update existing ones | ||
| + | * All the details are in the [[#cleaning_up_miniconda3|Cleaning up Miniconda3...]] section | ||
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| * 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/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]] | + | * Read the [[https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-environments.html#using-pip-in-an-environment|Using pip in a conda environment]] |
| + | * //Issues may arise when using pip and conda together//... | ||
| ==== Installation history ==== | ==== Installation history ==== | ||
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| FIXME | FIXME | ||
| + | |||
| + | ===== Improving conda and related tools ===== | ||
| + | |||
| + | There is always room for improvement, and this is is some kind of //TODO// section | ||
| + | |||
| + | ==== conda and mamba ideas ==== | ||
| + | |||
| + | * [[https://github.com/conda/conda/issues/14026|Add a conda command to find the package owning a file]] | ||
| + | * The link also shows how to do it with standard Linux tools (find, grep), based on the [[https://docs.conda.io/projects/conda-build/en/stable/resources/package-spec.html#conda-package-specification|Conda package specification]] page | ||
| + | * [[https://github.com/kelvinou01/conda-which|conda-which]] seems to work (see [[https://github.com/conda/conda/issues/14026#issuecomment-2268821608|test / example]]) ! | ||
| /* standard page footer */ | /* standard page footer */ | ||
other/uvcdat/cdat_conda/miniconda3_install.1720018234.txt.gz · Last modified: 2024/07/03 14:50 by jypeter
