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--- other:uvcdat:cdat_conda:miniconda3_install [2021/03/08 14:59]
jypeter [Post-Miniconda3 installation]
+++ other:uvcdat:cdat_conda:miniconda3_install [2024/04/18 11:52] (current)
jypeter Started reorganizing the sections to better take Windows into account and avoid duplication
@@ Line 1: / Line 1: @@
 ====== JYP steps for installing Miniconda3 ======
-===== What? Why? =====
+===== Why should you use Miniconda3 ? =====
-  * //Miniconda3// is a minimal python environment/distribution that can be used for creating more complete working environments. It will basically make ''conda'' available on your computer, and then you can use ''conda'' to install and update more //stuff//.
+  * **//Miniconda3// is a minimal/bootstrap Python distribution** that can be used for creating more complex Python distributions.\\ It will basically make a recent ''conda'' command available on your computer, and you can then use this ''conda'' executable to select an existing distribution, or create new and independent Python distributions.
-  * A python //environment// is basically where and how you install python. A python //distribution// is more which packages you have chosen to install together in the environment. Hmmm, well, these are very similar things!
+  * A **conda //environment//** is basically (the short name of the directory) where you install the Python that you will use (independently of //Miniconda3// itself). You have to ''activate'' this environment in order to use it\\ A **python //distribution//** is the collection of packages (and their dependencies) you have chosen to install together in a given environment.
+    * Example: initializing an environment named ''cdatm_py3'' (assuming it exists)<code>$ source /path_to_miniconda/etc/profile.d/conda.sh
-  * You don't need to be (and **you should not be**) //root// when you install Miniconda3. You just need enough disk space where you have write access
+$ which conda
+/path_to_miniconda/condabin/conda
-  * If you are installing Miniconda3 in a Linux environment on a [[other:win10wsl|Windows 10 computer using Windows Subsystem for Linux (WSL)]], pay special attention to the instructions on the **WSL** lines
+$ conda env list
+[...]
+cdatm_py3                /path_to_miniconda/envs/cdatm_py3
+some_other_env           /path_to_miniconda/envs/some_other_env
-  * The way you do things will depend on how you are going to use python? Are you installing the environment just for you, or for multiple users?
+$ conda activate cdatm_py3
+(cdatm_py3) $ which python
+/path_to_miniconda/envs/cdatm_py3/bin/python
+</code>
+    * 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
+/path_to_miniconda/bin/python
+</code>
+  * You **don't need to be (and you should not be) //root//** when you install //Miniconda3//. You just **need //enough// disk space** on a disk where you have write access
+    * **WARNING**: by default, //Miniconda3// will install itself and subsequent Python environments in a sub-directory of your home directory (''~/miniconda3'' on Linux). **Do not use the default installation location**, if you want to avoid disk space related problems (//disk full//, //quota exceeded//, ...)
+      * **WARNING**: older versions of //Miniconda3// used a **hidden sub-directory** of your home directory (''~/.conda'' on Linux) for the installation
+    * Choose carefully where you will install //Miniconda3//, because the size of the installation directory will start at a few Gb and will keep on growing
+  * 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,
+    * 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**
+===== Downloading Miniconda3, and BASIC installation =====
+==== Miniconda3 on a Windows computer ====
+<WRAP center round info 60%>
+**//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> .\miniconda.exe
+PS C:\Scratch\your_login> del .\miniconda.exe
+</code>
+</WRAP>
+=== Downloading on Windows ===
+=== BASIC installation on Windows ===
-  * We could also start with the //Anaconda// installer that will install a much more complete python environment, ready for use, but we choose not to do that because Anaconda requires more disk space at the beginning, with all its components coming from the ''default'' //channel// (or //repository//) provided by the [[https://docs.conda.io/projects/conda/en/latest/glossary.html#conda-repository|conda repository]]. It's not useful because we will be mostly using (the same) packages provided by the [[https://conda-forge.org/feedstock-outputs/|conda-forge]] channel.
-The steps on this page are adapted from the much older (but with lots of extra and possibly useful details) [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions
+==== Miniconda3 on a Linux-like computer ====
-===== Installing miniconda3 in a Linux-like computer =====
 <WRAP center round tip 60%>
-By //Linux-like//, we mean:
+By **//Linux-like//**, we mean:
-  * A native Linux computer
+  * 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>
-  * Get the [[https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh|Python 3.8 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]])
-    * Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]])
-      * e.g. Linux at LSCE:\\ ''cd /home/scratch01/<your_login>''
-      * e.g. WSL, assuming that there is a ''C:\Scratch\<your_login>'' directory:\\ ''cd /mnt/c/Scratch/<your_login>''
-    * Use ''wget'' to download the installer:\\ ''wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (90 Mb, 26 Feb 2021)
-  * Execute the installer
+=== Downloading the Miniconda3 installer ===
-    * ''bash Miniconda3-latest-Linux-x86_64.sh''
-      * Accept the license
-      * Note: at the end of the installation (next step), **answer //no// to the following question**, so that the installer does **not** change your existing shell initialization files!\\ ''Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]'' => **NO**
-      * Specify an explicit installation path **outside of your //home// directory**, with enough disk space (more than 3 Gb if you are going to install CDAT and some extra packages), preferably on a disk that is not backed up:
-        * Installations by //JYP//:
-          * Linux at LSCE: ''/home/share/unix_files/cdat/miniconda3'', or a ''miniconda3<some_version>'' subdirectory of ''/home/share/unix_files/cdat/''
-          * Linux on ciclad: ''/data/jypmce/cdat/miniconda3'', or a ''miniconda3<some_version>'' sub-directory of ''/data/jypmce/cdat/''
-        * WSL: installing to a directory that is not in ''/home/'' <wrap hi>does not work</wrap> (e.g. ''/mnt/h/CDAT/miniconda3'',assuming there is a ''H:\CDAT\'' directory, does not work)\\ You need to accept the installation in the default location: ''/home/<your_login>/miniconda3''
-      * The resulting ''miniconda3'' directory size is 342M\\ <code> > du -sh miniconda3
-M    miniconda3
- > cd miniconda3
+  * 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
+      * 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**
- > du -sh *
+  * Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]])
-M     bin
+    * e.g. Linux at **LSCE**:\\ ''$ cd /home/scratch01/$USER''
-       compiler_compat
+    * e.g. Linux at **spiritx**:<code>$ mkdir /homedata/$USER/Scratch
-.0K    condabin
+$ cd /homedata/$USER/Scratch</code>
-K    conda-meta
+    * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a scratch/temporary directory with //enough// space
-       envs
-K     etc
-.5M    include
-.0K    info
-M    lib
-K     LICENSE.txt
-M    pkgs
-K    share
-.0K    shell
-       ssl
-       x86_64-conda_cos6-linux-gnu</code>
-  * Initialize the newly installed conda environment (this will initialize the environment only in the current terminal):
+  * Use ''wget'' to download the latest installer (138 Mb as of 22 Mar 2024):\\ <code>$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    * bash shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.sh''
+$ ls -lh Miniconda3-latest-Linux-x86_64.sh
-    * tcsh shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.csh''
+[...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code>
+=== Using the Miniconda3 installer ===
+We assume below that we are in the [[#downloading_the_installer|directory where we have downloaded the installer]]
+  * **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**
+    * **If you want to share this installation with other users**, the directory has to be readable by these users
+    * At LSCE, **do not** install in a sub-directory of your home directory!
+      * On other servers and computers, you should also **avoid installing in your //home// directory**, 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. Linux at **LSCE**: ''/home/share/unix_files/cdat/miniconda3_2024-03''
+    * e.g. Linux at **spiritx**: ''/homedata/$USER/miniconda3_2024-03''
+    * Linux (including WSL) on a **personal PC/Mac desktop/laptop**: find a directory with enough space (including space for adding more packages and their future updates)
+      * You may want to use a directory that you are not backing up, if you want to avoid having to save thousands of files...
+  * Execute the installer with ''$ 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 $SHELL''
+        * or at least disable the automatic activation of the environment (that might have side effect) by typing: ''conda config --set auto_activate_base false''
+      * The resulting ''miniconda3'' directory size is 647 Mb (as of March 2024)\\ <code>$ du -sh miniconda3_2024-03
+M    miniconda3_2024-03
+$ du -sh miniconda3_2024-03/*
+M     miniconda3_2024-03/bin
+K     miniconda3_2024-03/cmake
+.0K    miniconda3_2024-03/compiler_compat
+M     miniconda3_2024-03/_conda
+.0K    miniconda3_2024-03/condabin
+K    miniconda3_2024-03/conda-meta
+.0K    miniconda3_2024-03/envs
+K     miniconda3_2024-03/etc
+M     miniconda3_2024-03/include
+M    miniconda3_2024-03/lib
+K     miniconda3_2024-03/LICENSE.txt
+.1M    miniconda3_2024-03/man
+M    miniconda3_2024-03/pkgs
+K    miniconda3_2024-03/sbin
+.5M    miniconda3_2024-03/share
+K     miniconda3_2024-03/shell
+.0K    miniconda3_2024-03/ssl
+.0K    miniconda3_2024-03/x86_64-conda_cos7-linux-gnu
+.0K    miniconda3_2024-03/x86_64-conda-linux-gnu
+</code>
+  * Initialize the newly installed conda environment (this will initialize the environment **only in the current terminal**):
+    * **bash shell**: ''source /path_to_miniconda3/etc/profile.d/conda.sh''
+      * e.g. (spiritx): ''source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh''
+    * **tcsh shell**: ''source /path_to_miniconda3/etc/profile.d/conda.csh''
+      * e.g. (LSCE): ''source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh''
   * Check if you can use the ''conda'' command, and use it to initialize the //base// environment
-    * <code>$ which conda
+    * e.g. on **spiritx1**: <code>$ which conda
-<installation_path>/miniconda3/condabin/conda
 $ which python
 /usr/bin/python
-$ conda activate
+$ source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh
+$ which conda
+/homedata/jypmce/miniconda3_2024-03/condabin/conda
+$ which python
+/usr/bin/python
+$ conda activate base
+(base) $ which conda
+/homedata/jypmce/miniconda3_2024-03/bin/conda
 (base) $ which python
-<installation_path>/miniconda3/bin/python</code>
+/homedata/jypmce/miniconda3_2024-03/bin/python
-  * Update the new installation
-    * <code>$ conda update --all
-[...]</code>
-    * During the update, the ''miniconda3'' directory size goes from 432 Mb to 581 Mb. This directory will keep on growing, which is the reason why you should put it on a (preferably non backed up) disk where you have //enough// space
-  * Make sure we have the latest ''conda'' package (just in case we did not get it with the //update//)\\ ''conda update -n base conda''
+(base) $ conda deactivate
-  * Remove the installer later, when you have tester your installation:\\ ''rm Miniconda3-latest-Linux-x86_64.sh''
+$ which conda
+/homedata/jypmce/miniconda3_2024-03/condabin/conda
+$ which python
+/usr/bin/python
+</code>
-===== Initializing conda in new terminals =====
+  * Remove the //Miniconda3// installer: ''$ rm Miniconda3-latest-Linux-x86_64.sh''
-When you open a terminal, your shell needs to know where to find the ''conda'' command used to initialize an environment, or switch between environments
+===== Fine-tuning conda to use (only) conda-forge =====
-==== General case ====
+  * ''conda'' will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies.
-You were asked the following question when installing miniconda3: //Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]//
+  * ''conda'' works much better and faster since the end of 2023 (''conda'' versions starting at ''23.10''), now that it is [[https://conda.org/blog/2023-07-05-conda-libmamba-solver-rollout/|using the mamba solver]] instead of the default solver.
+    * If you have followed all the steps of this section in order to **use only //conda-forge// packages**, and there are still some problems with a recent version of ''conda'', try to install and use [[https://mamba.readthedocs.io/|mamba]], as a drop-in replacement of conda
+    * Historical note: before ''conda'' used ''libmamba'', we had to use ''mamba'' (instead of ''conda'') for dealing with our complex Python environments:
+      * [[https://wolfv.medium.com/making-conda-fast-again-4da4debfb3b7|Making conda fast again]]
+      * [[https://github.com/conda/conda/issues/9367#issuecomment-793968239|Solving environment: failed with initial frozen solve. Retrying with flexible solve.]]
-  * If you answered //yes//, the installer probably added some very complicated lines to your shell configuration files, but you probably have ''conda'' directly available when you open a new terminal
+  * We are power users, and **we intend to create complex Python environments** combining lots (and lots) of packages available from ''conda-forge'', with complex dependencies, and we may run into dependency problems when combining packages coming from both conda and conda-forge.
-  * if you answered //no// (as suggested), use a text editor to add an extra line to the appropriate configuration file
+    * => **The solution is to configure conda to always use conda-forge**, and completely update //Miniconda3// itself with packages coming only from conda-forge
-    * //bash// user: add this line to ''~/.bashrc''\\ ''source <installation_path>/miniconda3/etc/profile.d/conda.sh''
-    * //tcsh// user: add this line to ''~/.cshrc''\\ ''source <installation_path>/miniconda3/etc/profile.d/conda.csh''
-We choose **not** to add a ''conda activate env_name'' line to the shell configuration files, in order to avoid side effects. When we open a new terminal, we get the default python available on the system. When we need a specific python environment, we just open a new window and then explicitly type: ''conda activate env_name''
+=== Changing the .condarc file ===
-==== Multi-user installation ====
+The following steps will **make sure that we only get packages from //conda-forge//**  (same thing as using the ''-c conda-forge'' option) by default unless the requested packages really don't exist on //conda-forge//. More details in [[https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html|Managing channels]]
-In the case of python environments installed by a single user, but used by several users, we could do the same as above, but it can be useful to have the users //source// an intermediate initialization file, that will the //source// the lines above. This makes it easier to maintain the
+<code>$ cat ~/.condarc
+cat: /home/jypmce/.condarc: No such file or directory
+$ conda config --get channels
+$ conda config --prepend channels conda-forge
-The idea is not to use the miniconda3 initialization lines that the miniconda3 installer could have automatically added at the end of shell configuration file and put them (and other useful commands) in a special initialization file, that can be sourced only when we actually want to use conda and CDAT (in order to avoid potential side effects)
+$ conda config --set channel_priority strict
-==== bash shell users ====
+$ conda config --get channels
+--add channels 'defaults'   # lowest priority
+--add channels 'conda-forge'   # highest priority
-See the ''~your_login/.conda3_jyp.sh'' file below, and how to use it, **in a bash shell**. In a **tcsh shell**, see the ''~jypeter/.conda3_jyp.csh'' further down. In both shell cases, if you are installing your own version of python, you need to use your own location of the initialization files in the ''source'' lines, and you can use another file name than ''conda3_jyp''
+$ cat ~/.condarc
+channels:
+  - conda-forge
+  - defaults
+channel_priority: strict
+</code>
-<code>$ which python
+=== Getting conda configuration information ===
-/usr/bin/python
-$ cat ~jypeter/.conda3_jyp.sh
+  * [[https://docs.conda.io/projects/conda/en/latest/commands/config.html|conda config]] documentation
+  * Basic information: ''conda info''
+  * Full configuration: ''conda config %%--%%show''
-# Conda initialization by JYP, NEW style
+==== Updating (Mini)conda ====
-#
-# Use this for working with conda and CDAT centrally managed by JYP
-#
-# Execute this file in a BASH shell with
-#     source path/this_file
-# Then get the list of available python distributions with
-#     conda env list
-# Then activate a specific distribution with
-#     conda activate version_name
-#
-# More details in:
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
-#
-# Jean-Yves Peterschmitt - LSCE - 11/2018
-source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.sh
+We have to **completely update //Miniconda3// at least once after installing //Miniconda3//** and [[#fine-tuning_conda_to_use_only_conda-forge|making conda-forge the highest priority channel]]
-# Use the alias below to easily determine where your python
+  * Check the current version of ''conda''
-# interpreter is located
+    * <code>$ conda list -n base | grep conda
-alias wp="which python"
+# packages in environment at /path_to_miniconda:
+conda                     24.1.2          py312h06a4308_0
+conda-libmamba-solver     23.12.0            pyhd3eb1b0_1
+[... and other packages with 'conda' in their name]
+</code>
-# Where are ALL the python interpreters in the search path
+  * Completely update the //Miniconda3// installation
-alias wpa="which -a python"
+    * <code>$ conda update -n base --all
+Channels:
+ - conda-forge
+ - defaults
+Platform: linux-64
+Collecting package metadata (repodata.json): done
+Solving environment: done
-# The end
+## Package Plan ##
-$ source ~jypeter/.conda3_jyp.sh
+  environment location: /homedata/jypmce/miniconda3_2024-03
-$ conda activate
-(base) $ which python
-/home/share/unix_files/cdat/miniconda3/bin/python
+The following packages will be downloaded:
+    package                    |            build
+    ---------------------------|-----------------
+    conda-24.3.0               |  py312h7900ff3_0         1.1 MB  conda-forge
+    conda-libmamba-solver-24.1.0|     pyhd8ed1ab_0          40 KB  conda-forge
+    python-3.12.2              |hab00c5b_0_cpython        30.8 MB  conda-forge
+[...]
+The following NEW packages will be INSTALLED:
+[...]
+The following packages will be UPDATED:
+[...]
+  conda              pkgs/main::conda-24.1.2-py312h06a4308~ --> conda-forge::conda-24.3.0-py312h7900ff3_0
+[...]
+The following packages will be SUPERSEDED by a higher-priority channel:
+[...]
+Proceed ([y]/n)? y
+[...]
+Preparing transaction: done
+Verifying transaction: done
+Executing transaction: done
+</code>
+  * Check the updated version of ''conda''. Note that **(almost) all** the packages should now specify that they are provided by ''conda-forge''
+    * <code>$ conda list -n base
+conda                     24.3.0          py312h7900ff3_0    conda-forge
+conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
+python                    3.12.2          hab00c5b_0_cpython    conda-forge
+</code>
+    * You can use the following to determine if some packages are not provided by ''conda-forge''
+      * <code>$ conda list -n base | grep -v conda-forge
+# Name                    Version                   Build  Channel
+libedit                   3.1.20230828         h5eee18b_0
+libffi                    3.4.4                h6a678d5_0
+xz                        5.4.5                h5eee18b_0
 </code>
+      * It should not be a major problem if a few packages are not provided by ''conda-forge''.\\ It only means that some packages provided by the ''anaconda'' //channel// were more recent than the same packages provided by the ''conda-forge'' //channel// when the packages were updated
+        * ''libedit'' example: [[https://anaconda.org/conda-forge/libedit|version 3.1.20191231 @ conda-forge]] and [[https://anaconda.org/anaconda/libedit|version 3.1.20230828 @ anaconda]]
-==== tcsh shell users ====
+  * You can later update again the full //Miniconda3//, or just the ''conda'' command.\\ This should not make any changes to the Python environment(s) have have installed with ''conda''
+    * <code>$ conda update -n base --all
+[...]
+# All requested packages already installed.
-<code> >which python
+(base) $ conda update -n base conda
-/usr/bin/python
+[...]
+# All requested packages already installed.
+</code>
- >cat ~jypeter/.conda3_jyp.csh
+  * Note: during this installation, the ''miniconda3'' directory size grew from 763 Mb to 1.6 Gb, and we have not installed any custom Python environment yet! This is the reason why you should install //Miniconda3// on a (preferably non backed up) disk where you have //enough// space
-# Conda initialization by JYP, NEW style
+    * <code>$ du -sh /homedata/jypmce/miniconda3_2024-03
+M    /homedata/jypmce/miniconda3_2024-03
+[... update]
+$ du -sh /homedata/jypmce/miniconda3_2024-03
+.6G    /homedata/jypmce/miniconda3_2024-03
+</code>
+  * You can [[https://docs.conda.io/projects/conda/en/latest/commands/clean.html|clean]] the initial //Miniconda3// installation to free up some disk space. The documentation specifies //WARNING: This will break environments with packages installed using symlinks back to the package cache.// and **you should probably avoid using ''clean'' once you have installed new Python environments** (unless you are desperate for disk space and know how to do a complete re-installation if something breaks...)
+    * <code>(base) $ conda clean --all
+Will remove 154 (180.9 MB) tarball(s).
+Proceed ([y]/n)? y
+Will remove 1 index cache(s).
+Proceed ([y]/n)? y
+Will remove 74 (378.0 MB) package(s).
+Proceed ([y]/n)? y
+There are no tempfile(s) to remove.
+There are no logfile(s) to remove.
+(base) $ du -sh /homedata/jypmce/miniconda3_2024-03
+M    /homedata/jypmce/miniconda3_2024-03
+</code>
+===== Initializing conda in terminals =====
+When you open a terminal, your shell needs to know where to find the ''conda'' command used to initialize an environment, or switch between existing environments. This can be **configured in the //shell// configuration files**
+==== Single-user installation ====
+You were asked the following question when installing //Miniconda3//: //Do you wish to update your shell profile to automatically initialize conda? [yes|no]//
+  * **If you answered //yes//**, the installer probably added some very complicated lines to your shell configuration files, and ''conda'' and the newly installer ''python'' are probably directly available when you open a new terminal.
+  * **If you answered //no//** ([[#using_the_miniconda3_installer|as suggested]]), use a [[other:newppl:starting#text_editors|text editor]] to add extra lines to the appropriate shell configuration file
+    * **bash shell** user : add these lines to ''~/.bashrc''\\ <code>source /path_to_miniconda3/etc/profile.d/conda.sh
+alias pynit='conda activate base'</code>
+      * e.g. (spiritx):<code>source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh
+alias pynit='conda activate base'</code>
+    * **tcsh shell** user: add these lines to ''~/.cshrc''\\ <code>source /path_to_miniconda3/etc/profile.d/conda.csh''
+alias pynit 'conda activate base'</code>
+      * e.g. (LSCE):<code>source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh
+alias pynit 'conda activate base'</code>
+    * When you have a custom Python environment installed (e.g. ''my_power_env'', you can update the ''pynit'' alias to initialize this environment instead of the ''base'' environment (e.g. ''conda activate my_power_env'')
+    * You can also define other aliases, or use another name than ''pynit''!
+We choose **not** to directly add a ''conda activate env_name'' line to the shell configuration files. This would permanently initialize ''env_name'' and may cause future (and obscure) side effects.
+When we open a new terminal, we get the default Python available on the system. If we need a specific Python environment, we just open a new window and then explicitly type ''conda activate env_name'' or the ''pynit'' alias defined above
+==== Multi-user installation ====
+In the case of **python environments maintained by a single user, but used by several users**, we could do the same as in the //General case//, but it can be useful to have the users //source// an intermediate initialization file, that will then //source// the initialization file used in the general case. This makes it easier to maintain and change the environments, without asking users to make changes.
+  * ask //bash// users to add to ''~/.bashrc'' something like\\ ''source  ~main_installer_login/.conda3_jyp.sh''\\ \\ with a ''.conda3_jyp.sh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp.sh.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 =====
+  * 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:
 #
-# Use this for working with conda and CDAT centrally managed by JYP
+base                  *  /homedata/jypmce/miniconda3_2024-03</code>
-#
-# Execute this file in a TCSH shell with
+  * **Activate** an existing environment (available in ''conda env list'') or **deactivate**, in order to go back to the default Python
-#     source path/this_file
+    * ''conda activate existing_environment''
-# Then get the list of available python distributions with
+      * ''conda activate'' (without specifying an environment name) will **activate the ''base'' Miniconda3 environment**
-#     conda env list
+    * Go back to the default Python available on the system
-# Then activate a specific distribution with
+      * ''conda deactivate''
-#     conda activate version_name
+    * 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
-# More details in:
+/homedata/jypmce/miniconda3_2024-03/bin/python
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
+(base) $ conda deactivate
-#
-# Jean-Yves Peterschmitt - LSCE - 11/2018
+$ 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 ====
-source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.csh
-# Use the alias below to easily determine where your python
+===== Uninstalling Miniconda3 =====
-# interpreter is located
-alias wp "which python"
-# The end
+==== Windows computer ====
- >source  ~jypeter/.conda3_jyp.csh
+Miniconda3 can be removed like a regular Windows application
- >conda activate
+  * 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''
-(base) >which python
+==== Linux-like computer ====
-/home/share/unix_files/cdat/miniconda3/bin/python</code>
-You probably don't want to type the //source// line each time you need to use your conda based python, so you can add a ''source  ~jypeter/.conda3_jyp.sh'' line in your ''~/.bashrc'' file, and ''source  ~jypeter/.conda3_jyp.csh'' line in your ''~/.cshrc'' file. Then, when you need a specific python environment, just type ''conda activate name_of_the_specific_environment''
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