Check if the Python package you are desperately seeking is not already installed, before installing your own Python on shared interactive Linux servers, or on batch computing clusters !!

• Ask other users who know the local environment

• Read the servers/clusters documentation: Python at LSCE by JYP, LSCE, ESPRI Computing and Data Center, …

• Use module avail [mod_name] to find out the Python versions available, and then module load and conda list to get more information on the available Python packages
  • e.g. on spiritx (modules on spirit)):

    $ module avail python
    python/meso-3.8  python/meso-3.9  python/meso-3.10  python/meso-3.11
    
    $ module avail anaconda
    anaconda-meso/2022.10    anaconda3-py/2020.11
    anaconda-meso/2023.09-0  anaconda3-py/2021.11
    
    $ module avail pangeo
    pangeo-meso/2023.04.15  pangeo-meso/2024.01.22
    
    $ module load pangeo-meso/2024.01.22
    (pangeo-meso-2024.01.22) $ which python
    /net/nfs/tools/u20/Python/miniconda3_py311_23.11.0-2/envs/pangeo-meso-2024.01.22/bin/python
    
    $ conda list | grep cartopy
    cartopy                   0.22.0          py311h320fe9a_1    conda-forge

• Lots of Python packages do very similar things. Maybe you can use another similar package that is already installed…

• If the packages you need are not available, it may be faster and easier to ask the local system administrators if they can install the packages, rather than doing everything yourself

If there is a jupyter notebook server connected to your system, and a Python environment providing all the packages you need, but that is not directly available on the notebook server, follow the using a non-standard kernel instructions, rather than starting your own local server

• 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/executable 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 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) in a bash shell

    $ source /path_to_miniconda/etc/profile.d/conda.sh
    
    $ which conda
    /path_to_miniconda/condabin/conda
    
    $ conda env list
    [...]
    cdatm_py3                /path_to_miniconda/envs/cdatm_py3
    some_other_env           /path_to_miniconda/envs/some_other_env
    
    $ conda activate cdatm_py3
    
    (cdatm_py3) $ which python
    /path_to_miniconda/envs/cdatm_py3/bin/python

  • 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

    $ conda activate base
    
    (base) $ which python
    /path_to_miniconda/bin/python

• 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, …) during the inittial installation or later
    • WARNING: older versions of Miniconda3 used a hidden sub-directory of the home directory of the person installing Miniconda3 (~/.conda on Linux)
  • 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 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 conda-forge channel, in order to avoid complex package dependency problems

Some of the steps below are adapted from the Windows section of "Quick command line install" to install a pure Windows version of Miniconda3

• We use a download link that always point to the 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 disk space on Windows
  • e.g. C:\Scratch\your_login or whatever you use as a local Scratch folder

• Open a terminal, where you can type the required installation commands
  • Windows Powershell terminal: Start ⇒ W ⇒ Windows PowerShell ⇒ Windows PowerShell
  • PowerShell in a Windows Terminal

• Use curl to download the latest installer (78 Mb as of April 2024):

  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

• Determine the folder where you will install Miniconda3 and ALL your future Python environments based on this version of Miniconda3
  We will later refer to this installation location as /path_to_miniconda3/ in the Linux sections below
  • Remember that you will need a few Gb of available space
  • You should avoid installing Miniconda3 in your Windows home folder (C:\Users\your_login or <some_disk_different_from_c>:\Users\<your_login>), if you want to be able to easily make backups or your home folder, without backing up thousands of files related to your Python environments…
  • We add some date or version information at the end of the folder name, in order to differentiate it from other (older of future) installations
  • Example installation folder: C:\Utils\miniconda3_2024-03 (if we start installing in March 2024)

• Launch the Miniconda3 installer with

  PS C:\Scratch\your_login> .\miniconda.exe

• 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?
  • There is no need to bookmark the web pages suggested by the installer at the end, since this web page gives all the required information

• When the installer has finished running, you should have:
  • A new C:\Utils\miniconda3_2024-03 folder
    • This folder size will be ~650 Mb and will keep on growing (up to several Gb) as you add more Python environments and packages
      • ⇒ Be sure to have enough space on this disk!
  • Two new shortcuts in the Windows Start⇒M⇒Miniconda3 menu:
    • Anaconda Prompt
    • Anaconda Powershell Prompt
      • We will now use this Anaconda Powershell shortcut each time we need to use Miniconda3 or Python
    • It is highly recommended to 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

  PS C:\Scratch\your_login> del .\miniconda.exe

• Open an Anaconda PowerShell Prompt, and type a few commands to make sure that conda is working
  • Start⇒M⇒Miniconda3 ⇒ Anaconda Powershell Prompt

  • (base) PS C:\Users\your_login> conda env list
    base                  *  C:\Utils\miniconda3_2024-03
    
    (base) PS C:\Users\your_login> conda list
    # packages in environment at C:\Utils\miniconda3_2024-03:
    # Name                    Version                   Build  Channel
    [...]
    conda                     24.3.0          py312haa95532_0
    [...]
    python                    3.12.2               h1d929f7_0
    [...]
    
    (base) PS C:\Users\your_login> conda deactivate
    
    PS C:\Users\your_login> conda env list
    base                     C:\Utils\miniconda3_2024-03

• Next: be sure to follow the steps in the Fine-tuning conda to use (only) conda-forge, and all the other Miniconda3 related instructions
  • conda commands will work the same way on all Operating Systems (Windows and Linux-like)
  • The .condarc is located in your Windows home folder
    ⇒ C:\Users\your_login\.condarc (or $HOME\.condarc)

• Important: do not install your own Python environment(s) on shared computers before you have made sure that the packages you need are not already installed, or cannot be easily installed in an existing environment (by the person who maintains this environment)!
  • Read again the Before installing Python on a shared computer section

• We use a download link that always point to the 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 macOS installer appropriate for their computer
  • 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 WSL)
  • e.g. Linux on the LSCE servers:
    $ cd /home/scratch01/$USER
  • e.g. Linux on the IPSL spiritx cluster:

    $ mkdir /homedata/$USER/Scratch
    $ cd /homedata/$USER/Scratch

  • e.g. Linux on a personal PC/Mac desktop/laptop: use a local scratch/temporary directory with enough space

• Use wget to download the latest installer (138 Mb as of 22 Mar 2024):
  

  $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  $ ls -lh Miniconda3-latest-Linux-x86_64.sh
  [...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh

We assume below that we are in the 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
  • Always 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. JYP shared Linux installation at LSCE: /home/share/unix_files/cdat/miniconda3_2024-03
    • e.g. Linux at spiritx: /homedata/$USER/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:
      • later remove the changes to your shell configuration files by typing: 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 initial miniconda3 directory size is 647 Mb (as of March 2024).
    Remember that this directory size will keep on growing!
    

    $ du -sh miniconda3_2024-03
    647M    miniconda3_2024-03
    
    $ du -sh miniconda3_2024-03/*
    47M     miniconda3_2024-03/bin
    16K     miniconda3_2024-03/cmake
    8.0K    miniconda3_2024-03/compiler_compat
    32M     miniconda3_2024-03/_conda
    8.0K    miniconda3_2024-03/condabin
    976K    miniconda3_2024-03/conda-meta
    4.0K    miniconda3_2024-03/envs
    28K     miniconda3_2024-03/etc
    18M     miniconda3_2024-03/include
    317M    miniconda3_2024-03/lib
    92K     miniconda3_2024-03/LICENSE.txt
    1.1M    miniconda3_2024-03/man
    232M    miniconda3_2024-03/pkgs
    396K    miniconda3_2024-03/sbin
    1.5M    miniconda3_2024-03/share
    12K     miniconda3_2024-03/shell
    8.0K    miniconda3_2024-03/ssl
    8.0K    miniconda3_2024-03/x86_64-conda_cos7-linux-gnu
    8.0K    miniconda3_2024-03/x86_64-conda-linux-gnu

• Initialize the newly installed conda environment. This will initialize the environment only in the current terminal. When you have checked that things work properly, you can later make the initialization easier by following the steps in Initializing conda on a Linux-like computer
  • You have to execute a configuration script, and then activate the environment
    1. Run the init script: source /some_path/conda_init_script
    2. Activate the base environment (these two commands have the same result):
       • conda activate
       • or conda activate base
  • 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

• After initializing the environment, check if you can access the conda command, and use it to initialize the base environment
  • e.g. on spiritx1:

    $ 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
    /homedata/jypmce/miniconda3_2024-03/bin/python
    
    (base) $ conda deactivate
    
    $ which conda
    /homedata/jypmce/miniconda3_2024-03/condabin/conda
    $ which python
    /usr/bin/python

• Remove the Miniconda3 installer: $ rm Miniconda3-latest-Linux-x86_64.sh

• conda will probably work fine with the default settings if you create simple new environments with just one package and its dependencies.

• conda works much better and faster since the end of 2023 (conda versions starting at 23.10), now that it is using the mamba solver instead of the default solver.
  • Use conda --version version to determine which version you are using

    $ conda --version
    conda 24.5.0

• 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.
  • ⇒ The sections below configure conda to always use conda-forge, and completely update Miniconda3 itself with packages coming only from conda-forge

• Very unlikely situation: if you use a recent version of conda (>= 23.10), and you have followed all the steps below, in order to use only conda-forge packages, and there are still some package installation problems, try to install and use 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:
    • Making conda fast again
    • Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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 do not exist on conda-forge. More details in Managing channels

$ cat ~/.condarc  # On Windows use: cat $HOME\.condarc
cat: /home/jypmce/.condarc: No such file or directory

$ conda config --get channels

$ conda config --prepend channels conda-forge

$ conda config --set channel_priority strict

$ conda config --get channels
--add channels 'defaults'   # lowest priority
--add channels 'conda-forge'   # highest priority

$ cat ~/.condarc  # On Windows use: cat $HOME\.condarc
channels:
  - conda-forge
  - defaults
channel_priority: strict

Before you go further, do not forget to update conda at least once in order to take all the changes above into account!

mamba is a fast, robust, and cross-platform package manager […] fully compatible with conda packages, and supports most of conda’s commands

• mamba is used to manage environments, and has to be installed in the base environment (i.e. in the same environment as conda)!
• If :
  1. You are sure that you need ''mamba'', even if the developers advise not to mix conda and mamba
  2. You have configured conda to use conda-forge by default
  3. Then (and only then!) you can install mamba:
     ⇒ conda install -n base mamba

• The useful mamba commands (we need) are listed in the Useful conda commands section
  • We mostly need mamba repoquery
• Mamba User Guide

• Just type conda update -n base --all, (review) and accept the changes
  • Things should be OK if no package downgrades are requested

• The base (Miniconda3 itself) and the other Python environments installed with the conda executable provided by the base environment are all independent, and can be updated independently

• It is up to you to decide if and when you want to update environments…
  • …but you have to update the base environment at least once in order to replace all of its packages by their equivalent conda-forge packages

• You can later update again the full Miniconda3, or just the conda command.
  This should not make any changes to the other Python environment(s) installed with Miniconda3

  • $ conda update -n base --all
    [...]
    # All requested packages already installed.
    
    (base) $ conda update -n base conda
    [...]
    # All requested packages already installed.

• Note: during our initial 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 free space

  • $ du -sh /homedata/jypmce/miniconda3_2024-03
    736M    /homedata/jypmce/miniconda3_2024-03
    [... update]
    $ du -sh /homedata/jypmce/miniconda3_2024-03
    1.6G    /homedata/jypmce/miniconda3_2024-03

We have to completely update Miniconda3 at least once after installing Miniconda3 and making conda-forge the highest priority channel

• Check the current version of conda

  • $ conda --version
    conda 24.1.2

• Completely update the Miniconda3 installation

  • $ conda update -n base --all
    Channels:
     - conda-forge
     - defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): done
    Solving environment: done
    
    ## Package Plan ##
    
      environment location: /homedata/jypmce/miniconda3_2024-03
    
    
    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

• Check the updated version of conda and python. Note that (almost) all the packages should now specify that they are provided by conda-forge

  • $ 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
    [...]

  • You can use the following (on Linux) to determine if some packages were not available in conda-forge

    • $ 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

    • 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: version 3.1.20191231 @ conda-forge and version 3.1.20230828 @ anaconda

• conda clean --all
  • Documentation
  • 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
  • Example:

    (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
    457M    /homedata/jypmce/miniconda3_2024-03

• 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 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

• Open a PowerShell terminal with: Start⇒ M ⇒ Miniconda3 ⇒ Anaconda Powershell Prompt
• The base environment will be activated by default
  • If you need another environment, just type: conda activate name_of_the_environment_you_want

TODO

• Find out how to use menuinst in order to directly initialize an existing environment (different from base) from the Start menu and from a Windows Terminal
  • Adding Windows Start menu items
  • menuinst documentation
  • Add Windows Terminal profile option

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 your shell configuration files (.bashrc, .cshrc, …)

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 installed python are probably directly available when you open a new terminal.
  
  Warning! The automatic activation might have subtle side effects. You can:
  • Remove the changes to your shell configuration files by typing: conda init --reverse $SHELL
  • Or at least disable the automatic activation of the environment by typing: conda config --set auto_activate_base false

• If you answered no (as suggested), use a text editor to add extra lines to the appropriate shell configuration file
  The changes will apply to all the new terminals you open
  
  
  • bash shell user : add these lines to ~/.bashrc
    

    source /path_to_miniconda3/etc/profile.d/conda.sh
    alias pynit='conda activate base'

    • e.g. (spiritx):

      source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh
      alias pynit='conda activate base'

  • tcsh shell user: add these lines to ~/.cshrc
    

    source /path_to_miniconda3/etc/profile.d/conda.csh''
    alias pynit 'conda activate base'

    • e.g. (LSCE):

      source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh
      alias pynit 'conda activate base'

  • After changing your configuration file, just type pynit in any (new) terminal you open, when you need to use Python
  • 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 could use the same configuration file as in the single-user case, but it is more efficient to have the users source an intermediate initialization file. This intermediate init file will:

• source the conda initialization file used in the single-user case
• Define some aliases that will be useful to all the people using these environments:
  • pynit ⇒ initialize the base environment (or another default environment chosen by the central maintainer)
  • wp ⇒ which python
  • wconda ⇒ which python
  • more aliases, if required
• If changes have to be made later, it is very easy to update this central initialization file accordingly, without asking the other users to make changes
  • Do not forget to keep a copy of the previous version of the init file!
  • Use a symbolic link (ln -s) to point from the unchanging central initialization file name to the latest initialization file.
    conda@LSCE example in /home/share/unix_files/cdat/conda_init_files/:

    $ ls -l
    -rw-r--r-- Jun 14 16:37 conda3_jyp_2024-03.csh
    -rw-r--r-- Jun 14 17:48 conda3_jyp_2024-03.sh
    lrwxrwxrwx Jun 17 15:56 conda3_jyp_latest.csh -> conda3_jyp_2024-03.csh
    lrwxrwxrwx Jun 17 15:57 conda3_jyp_latest.sh -> conda3_jyp_2024-03.sh

• bash users should add to their ~/.bashrc file something like
  source /some_path_accessible_by_all_users/shared_conda_init_file.sh
  
  with a shared_conda_init_file.sh file looking like conda3_jyp_2024-03.sh.txt
  
  Examples:
  
  
  • LSCE:
    • Add to ~/.bashrc: source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_latest.sh
    • Note: conda3_jyp_latest.sh is a link to the latest version of the init file,
      currently /home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.sh
  • spiritx and spirit:
    • We use the fact that file systems on spiritx are accessible in read-only mode on spirit
      • The python environments are installed on local disks of spiritx, but they can also be used on spirit, even if the remote disks access will add some latency
    • Add to ~/.bashrc: source /homedata/jypmce/conda_init_files/conda3_jyp_spiritx_latest.sh
    • Note: conda3_jyp_spiritx_latest.sh is a link to the latest version of the init file,
      currently /homedata/jypmce/conda_init_files/conda3_jyp_spiritx_2024-03.sh

• tcsh users should add to their ~/.cshrc file something like
  source /some_path_accessible_by_all_users/shared_conda_init_file.csh
  
  with a shared_conda_init_file.csh file looking like conda3_jyp_2024-03.csh.txt
  
  Examples:
  • LSCE:
    • Add to ~/.cshrc: source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_latest.csh
    • Note: conda3_jyp_latest.csh is a link to the latest version of the init file,
      currently /home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.csh

• Once conda is installed (in the base environment provided by Miniconda3), configured and updated, you can use it to create a new environment with the packages that you (or other users, in a shared environment) need
  • Use the commands described in Useful conda commands

• Detailed example: the xcdat environment
  • : update/rewrite the cdat_2024_03 page

⇒ Move this section somewhere else?

• Use conda install and what is described in 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 menuinst
  • menuinst @ GH

• Find a way to add Windows Terminal profiles
  • See menuinst+Add Windows Terminal profile option

• Official Documentation site
  • Cheat sheet (2 pages, for people in a hurry)
  • Commands' reference
  • Conda package specification
    • This helps understand (and use) the content of the /path_to_miniconda/pkgs directory

• conda community site:
  • conda Blog: conda new features, etc…

• conda @ GitHub

• Package repositories
  • conda-forge ⇐ recommended source of packages
  • default

This is just a subset of some of the commands, and a subset of their options! For a complete reference, use the official conda website

• Get help
  • conda -h
    • conda command --help: help for a specific command

• Version and configuration information
  • Version information: conda --version
  • Detailed information: conda info
  • Full configuration: conda config --show
    • conda config documentation

• Available environments
  • conda env list
  • The currently active environment has a “*” character on its line

    (base) $ conda env list
    # conda environments:
    #
    base                  *  /homedata/jypmce/miniconda3_2024-03

• 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!
    • On Linux:

      (base) $ which python
      /homedata/jypmce/miniconda3_2024-03/bin/python
      
      (base) $ conda deactivate
      
      $ which python
      /usr/bin/python

    • On Windows:

      (base) PS C:\> where.exe conda
      C:\Utils\miniconda3_2024-03\Library\bin\conda.bat
      C:\Utils\miniconda3_2024-03\Scripts\conda.exe
      C:\Utils\miniconda3_2024-03\condabin\conda.bat
      
      (base) PS C:\> where.exe python
      C:\Utils\miniconda3_2024-03\python.exe
      C:\Users\jypeter\AppData\Local\Microsoft\WindowsApps\python.exe
      
      (base) PS C:\Users\jypeter> conda deactivate
      
      PS C:\> where.exe conda
      C:\Utils\miniconda3_2024-03\condabin\conda.bat
      
      PS C:\> where.exe python
      C:\Users\jypeter\AppData\Local\Microsoft\WindowsApps\python.exe

  • 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)
  • All the packages: conda list [-n existing_environment]
  • Some packages: conda list [-n existing_environment] full_or_partial_name

    (base) $ conda list libmamba
    # Name                    Version                   Build  Channel
    conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
    libmamba                  1.5.8                had39da4_0    conda-forge
    libmambapy                1.5.8           py312hd9e9ff6_0    conda-forge
    
    (base) $ conda list lib
    _libgcc_mutex             0.1                 conda_forge    conda-forge
    conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
    [...]
    urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
    zlib                      1.3.1                h4ab18f5_1    conda-forge

• 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 or mamba, 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 (CSH install/search fail with '*' variable in an argument)
  • Search results can be filtered by using the conda MatchSpec format
  • Get very detailed information about a package (versions, size, dependencies) with:
    conda search package_exact_name --info
  • : find an option to get only the latest version available for the current platform
    • Did not find a way to do that efficiently (June 20th 2024), even with mamba

• 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 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
  • Specific versions can be specified by using the conda MatchSpec format
  • conda remove package1 package2 packageN
  • Matching pip commands (only if the package is not available in conda!)
    • pip install package
    • pip uninstall package

• Update a package in the current, or a specific environment
  • 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
    • Changes and new conda features are detailed in the 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)
  • conda update -n existing_environment --all
  • 'base' environment update example

• Determine the relationship between installed packages
  • Packages relationships can be listed with mamba repoquery
    • Note: mamba repoquery currently only works in the currently active environment
  • It can be useful to determine:
    • the packages that are required in order to use a given package ⇒ mamba repoquery depends package
      • Without mamba repoquery depends, you would have to follow the steps in Listing package dependencies
    • the packages that need a given package ⇒ mamba repoquery whoneeds package
  • Example: the tqdm package
    • conda needs tqdm to display package download and installation progress, and the base dependencies of tqdm are colorama, and of course python
    • Detailed use:

       >mamba repoquery whoneeds --pretty tqdm
      tqdm
        └─ conda[24.5.0]
      
       >mamba repoquery depends --pretty tqdm
      tqdm[4.66.4]
        ├─ colorama[0.4.6]
        └─ python[3.12.3]

    • The packages that tqdm needs also need packages, and so on…

       >mamba repoquery depends --tree tqdm
      tqdm[4.66.4]
        ├─ colorama[0.4.6]
        │  └─ python[3.12.3]
        │     ├─ bzip2[1.0.8]
        │     │  └─ libgcc-ng[14.1.0]
        │     │     ├─ _libgcc_mutex[0.1]
        │     │     └─ _openmp_mutex[4.5]
        │     │        ├─ _libgcc_mutex already visited
        │     │        └─ libgomp[14.1.0]
        │     │           └─ _libgcc_mutex already visited
        │     ├─ libgcc-ng already visited
        │     ├─ ld_impl_linux-64[2.40]
        │     ├─ libexpat[2.6.2]
        │     │  └─ libgcc-ng already visited
        [...]

• Checking the health of an environment with conda doctor
  • Some details in Detecting conda environment inconsistencies easily
    • conda doctor does not do much yet, and not necessarily in a useful way, but this will hopefully improve over time!
      • 'conda doctor' output should be improved
      • What exactly are altered files?
  • conda doctor -n base
  • Example:

     >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.

• 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... section

• Read the Conda vs. pip vs. virtualenv commands section

• Read the Using pip in a conda environment
  • Issues may arise when using pip and conda together…

You can get the current list of installed packages with conda list -n existing_environment, but it may also be useful to know in which order the packages were installed:

• conda list -n existing_environment --revisions: display exactly what was installed and when (including the updates, and automatic dependencies installation)
  • You can theoretically roll back to a previous RR revision number with: conda install -n existing_environment --revision RR
• There is more information in the /path_to_miniconda/conda-meta/history installation log files.
  • base history file: /path_to_miniconda/conda-meta/history
  • existing_environment history file: /path_to_miniconda/envs/existing_environment/conda-meta/history
  • e.g. installation commands for the base environment:
    

     $ egrep -e 'cmd:' -e '==>' /homedata/jypmce/miniconda3_2024-03/conda-meta/history
    
    ==> 2024-02-23 18:39:23 <==
    # cmd: constructor /tmp/tmp.4um5tGKcqW/miniconda3/ --output-dir /tmp/tmp.4um5tGKcqW
    ==> 2024-03-27 16:10:01 <==
    # cmd: /homedata/jypmce/miniconda3_2024-03/bin/conda update -n base --all
    ==> 2024-03-28 11:38:08 <==
    [...]
    ==> 2024-04-24 17:47:32 <==
    # cmd: /homedata/jypmce/miniconda3_2024-03/bin/conda update -n base --all

  • You can also, use a script and the conda module available in the base environment: example

• The conda search command uses the MatchSpec format

• conda install and conda search probably use the same syntax

• The MatchSpec format is poorly documented…
  • Fortunately, you will usually only specify the package name, and want to install the latest version of a package

• Using == (exact version) is different from = (“fuzzy” value), which can be confusing

  • $ conda search zlib==1.2
    No match found for: zlib==1.2. Search: *zlib*==1.2
    PackagesNotFoundError: The following packages are not available from current channels:
      - zlib==1.2
    
    $ conda search zlib=1.2
    # Name                       Version           Build  Channel
    zlib                           1.2.8               0  conda-forge
    zlib                           1.2.8               1  conda-forge
    [...]
    zlib                          1.2.13      h5eee18b_1  pkgs/main
    zlib                          1.2.13      hd590300_5  conda-forge
    
    $ conda search zlib==1.2.12
    zlib                          1.2.12      h166bdaf_0  conda-forge
    [...]
    zlib                          1.2.12      h7f8727e_2  pkgs/main
    

• Documentation:
  • conda Package match specifications
  • Documentation in the MatchSpec class

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
  • This will not remove your local configuration file C:\Users\your_login\.condarc

There is always room for improvement, and this is is some kind of TODO section

• 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 Conda package specification page
  • conda-which seems to work (see test / example) !

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