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--- other:uvcdat:cdat_conda:miniconda3_install [2024/04/10 15:13]
jypeter [Fine-tuning conda to use (only) conda-forge] Improved
+++ other:uvcdat:cdat_conda:miniconda3_install [2024/04/19 09:00]
jypeter [Miniconda3 on a Linux-like computer] Some updates
@@ Line 21: / Line 21: @@
 /path_to_miniconda/envs/cdatm_py3/bin/python
 </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
@@ Line 32: / Line 32: @@
     * 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:
+  * 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// at the beginning,
+    * it requires more disk space than //Miniconda3// during the initial installation,
-    * and all its packages come from the ''default'' //channel// (or //repository//) provided by the [[https://docs.conda.io/projects/conda/en/latest/glossary.html#conda-repository|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**
-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.
-===== Installing miniconda3 on a Linux-like computer =====
+===== Downloading Miniconda3, and BASIC installation =====
-<WRAP center round tip 60%>
+==== Miniconda3 on a Windows computer ====
-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%>
-**//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> .\miniconda.exe
 PS C:\Scratch\your_login> del .\miniconda.exe
 </code>
+</WRAP>
+=== Downloading on Windows ===
+=== BASIC installation on Windows ===
+==== 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>
-==== 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]]
     * 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**
+    * 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]])
@@ Line 74: / Line 99: @@
 [...] 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]]
@@ Line 87: / Line 112: @@
     * 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''
@@ Line 155: / Line 181: @@
   * 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.
@@ Line 316: / Line 343: @@
       * 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''
+    * 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 add a ''conda activate env_name'' line to the shell configuration files, in order to avoid future side effects.
+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
@@ Line 331: / Line 358: @@
   * 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 |}}
-==== Using mamba instead of conda ====
+===== 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 =====
+==== 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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