Environment Management with Conda

Courses

Essential Computing Tools for Scientists

Authors

Dr. Atle Rimehaug | Dr. Ole Bialas | Dr. Nicholas Del Grosso | Dr. Sangeetha Nandakumar

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Most software we use comes with a list of dependencies which, in turn, have their own dependencies. This means that any given piece of software requires a specific environment of other packages to function properly. The larger the tree of dependencies, the more likely it is that two pieces of software have a version conflict because they require different versions of the same dependency. This can be prevented by using virtual environments. Virtual environments are self-contained boxes that are used only within a specific narrow scope. By creating a dedicated virtual environment for every project we can isolate the software and avoid conflicts. We can also improve the reproducibility of our research because the virtual environment can be shared together with the code and data.

In this notebook, you are going to learn how to use Conda - an established and widely used tool for creating and managing virtual environments. Conda allows us to create new virtual environments, either directly in the project folder or system wide, install packages and run code in them. Conda can also export the current environment to a environment.yml file which can be used to reproduce the computational environment.

Setup

The exercises in this notebook assume that you have installed Conda from Miniforge and Visual Studio Code. If you haven’t, just click on the link and follow the instructions for your operating system on the website. To test if Conda was installed correctly, open a terminal (in VSCode select View>Terminal from the menu bar or press Ctrl+`) and type conda --version. If you are getting an error saying that the command was not found, try restarting VSCode.

conda --version

conda 24.11.3

Section 1: Creating and Managing Environments

Background

One of the key advantages of Conda is its ability to create isolated environments, which are essentially self-contained workspaces with their own packages and dependencies. This allows you to experiment, develop, and analyze data without worrying about conflicts between different package versions, which can often disrupt workflows. This is especially helpful for reproducible research: by keeping dependencies organized, you ensure that your projects are replicable across systems.

When creating a new Conda environment, you give it a name using the -n flag and Conda will store it in a new subfolder in the directory where Conda is installed which defaults to C:\Users\<username>\miniforge3 on Windows and ~/miniforge3 on Linux/MacOS. For example, a new environment called new_env will be stored in miniforge3/new_env. To activate an environment, type conda activate <environment name> and Conda will look in the installation directory for an environment that matches the name.

Exercises

In the following exercises, you will learn how to create new environments, activate and deactivate them and get a list of your existing environments. Here are the different commands required to solve the exercises:

Code	Description
`conda create -n env_name`	Create a new environment named `env_name`
`conda env list`	List all existing Conda environments
`conda activate env_name`	Activate the environment `env_name`
`conda deactivate`	Deactivate the current Conda environment
`ls folder/subfolder`	List the content of `folder/subfolder`

Exercise: Create a new Conda environment with the name (-n) test_env and confirm the action by typing y.

Solution

conda create -n test_env


Retrieving notices: done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/test_env


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate test_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Exercise: List all environments to verify that test_env was created.

Solution

conda env list



# conda environments:
#
test_env               /home/olebi/miniforge3/envs/test_env

Exercise: Activate test_env. You should see (test_env) appear on the left of your terminal’s input line.

Solution

conda activate test_env

Exercise: Deactivate test_env again.

Solution

conda deactivate

Exercise: Create a new Conda environment with the name (-n) test_env2 and confirm the action by typing y.

Solution

conda create -n test_env2


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/test_env2


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate test_env2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Exercise: List all environments and note the path where test_env2 is stored.

Solution

conda env list



# conda environments:
#
test_env               /home/olebi/miniforge3/envs/test_env
test_env2              /home/olebi/miniforge3/envs/test_env2

Exercise: View the content of the test_env2/ folder, either by moving to that directory using your file explorer or by using the ls command.

Solution

ls /home/olebi/miniforge3/envs/test_env2  # change the path to reflect the location on your machine

conda-meta

Exercise: Activate test_env2, then deactivate it again.

Solution

conda activate test_env2
conda deactivate

Section 2: Installing Packages in Environments

Background

Managing packages within Conda environments allows you to install libraries and dependencies specific to each project. This helps avoid the challenges of “dependency hell” where incompatible package versions interfere with each other. For researchers, Conda’s ability to install non-Python packages (like r-base or system libraries) provides flexibility and power, especially for complex data workflows involving multiple languages.

When running conda install <package name>, Conda will look through the conda-forge repository for a package with a matching name, download and install it. If no package with that name can be found, you’ll get an error. The conda-forge repository contains a wealth of scientific packages for download. You can view a full list here: https://conda-forge.org/packages/ To install a package into a specific environment, you can either activate the environment or use the -n flag to specify the name of the environment where the package should be installed.

Exercises

In the following exercises, you are going to create new environments to install interpreters for the programming languages Python and R. Here are the commands you need to know:

Code	Description
`conda install package_name`	Install `package_name` in the active environment
`conda install -n env_name package_name`	Install `package_name` into `env_name`
`conda list`	List all installed packages in the active environment

Exercise: Create new environment named py_env and activate it.

Solution

conda create -n py_env
conda activate py_env


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/py_env


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate py_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Exercise: Install python=3.12 in py_env and confirm the installation by entering y.

Solution

conda install python=3.12


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done



## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/py_env

  added / updated specs:
    - python=3.12


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    icu-78.1                   |       h33c6efd_0        12.1 MB  conda-forge
    ld_impl_linux-64-2.45      |default_hbd61a6d_105         714 KB  conda-forge
    libgcc-15.2.0              |      he0feb66_16        1018 KB  conda-forge
    libgcc-ng-15.2.0           |      h69a702a_16          27 KB  conda-forge
    libgomp-15.2.0             |      he0feb66_16         589 KB  conda-forge
    libsqlite-3.51.1           |       hf4e2dac_1         921 KB  conda-forge
    libstdcxx-15.2.0           |      h934c35e_16         5.6 MB  conda-forge
    libuuid-2.41.3             |       h5347b49_0          39 KB  conda-forge
    pip-25.3                   |     pyh8b19718_0         1.1 MB  conda-forge
    python-3.12.12             |hd63d673_1_cpython        30.1 MB  conda-forge
    readline-8.3               |       h853b02a_0         337 KB  conda-forge
    tk-8.6.13                  |noxft_ha0e22de_103         3.1 MB  conda-forge
    tzdata-2025c               |       hc9c84f9_1         116 KB  conda-forge
    zstd-1.5.7                 |       hb78ec9c_6         587 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        56.3 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hda65f42_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2026.1.4-hbd8a1cb_0 
  icu                conda-forge/linux-64::icu-78.1-h33c6efd_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.45-default_hbd61a6d_105 
  libexpat           conda-forge/linux-64::libexpat-2.7.3-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h9ec8514_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-he0feb66_16 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_16 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-he0feb66_16 
  liblzma            conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1 
  libsqlite          conda-forge/linux-64::libsqlite-3.51.1-hf4e2dac_1 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_16 
  libuuid            conda-forge/linux-64::libuuid-2.41.3-h5347b49_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.6.0-h26f9b46_0 
  pip                conda-forge/noarch::pip-25.3-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.12-hd63d673_1_cpython 
  readline           conda-forge/linux-64::readline-8.3-h853b02a_0 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_ha0e22de_103 
  tzdata             conda-forge/noarch::tzdata-2025c-hc9c84f9_1 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done                                                                                                                                                                                                                                                                                                                    
Verifying transaction: done                                                                                                                                                                                                                                                                                                                    
Executing transaction: done

Exercise: Install the numpy package in py_env.

Solution

conda install numpy


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/py_env

  added / updated specs:
    - numpy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-2.4.0                |  py312h33ff503_0         8.3 MB  conda-forge
    python_abi-3.12            |          8_cp312           7 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         8.4 MB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-64::libblas-3.11.0-5_h4a7cf45_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.11.0-5_h0358290_openblas 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_16 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-h68bc16d_16 
  liblapack          conda-forge/linux-64::liblapack-3.11.0-5_h47877c9_openblas 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_4 
  numpy              conda-forge/linux-64::numpy-2.4.0-py312h33ff503_0 
  python_abi         conda-forge/noarch::python_abi-3.12-8_cp312 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done                                                                                                                                                                                                                                                                                                                    
Verifying transaction: done
Executing transaction: done

Exercises: List all installed packages to verify that Python 3.12 and Numpy were installed.

Solution

conda list


# packages in environment at /home/olebi/miniforge3/envs/py_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                hda65f42_8    conda-forge
ca-certificates           2026.1.4             hbd8a1cb_0    conda-forge
icu                       78.1                 h33c6efd_0    conda-forge
ld_impl_linux-64          2.45            default_hbd61a6d_105    conda-forge
libblas                   3.11.0          5_h4a7cf45_openblas    conda-forge
libcblas                  3.11.0          5_h0358290_openblas    conda-forge
libexpat                  2.7.3                hecca717_0    conda-forge
libffi                    3.5.2                h9ec8514_0    conda-forge
libgcc                    15.2.0              he0feb66_16    conda-forge
libgcc-ng                 15.2.0              h69a702a_16    conda-forge
libgfortran               15.2.0              h69a702a_16    conda-forge
libgfortran5              15.2.0              h68bc16d_16    conda-forge
libgomp                   15.2.0              he0feb66_16    conda-forge
liblapack                 3.11.0          5_h47877c9_openblas    conda-forge
liblzma                   5.8.1                hb9d3cd8_2    conda-forge
libnsl                    2.0.1                hb9d3cd8_1    conda-forge
libopenblas               0.3.30          pthreads_h94d23a6_4    conda-forge
libsqlite                 3.51.1               hf4e2dac_1    conda-forge
libstdcxx                 15.2.0              h934c35e_16    conda-forge
libuuid                   2.41.3               h5347b49_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
ncurses                   6.5                  h2d0b736_3    conda-forge
numpy                     2.4.0           py312h33ff503_0    conda-forge
openssl                   3.6.0                h26f9b46_0    conda-forge
pip                       25.3               pyh8b19718_0    conda-forge
python                    3.12.12         hd63d673_1_cpython    conda-forge
python_abi                3.12                    8_cp312    conda-forge
readline                  8.3                  h853b02a_0    conda-forge
setuptools                80.9.0             pyhff2d567_0    conda-forge
tk                        8.6.13          noxft_ha0e22de_103    conda-forge
tzdata                    2025c                hc9c84f9_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
zstd                      1.5.7                hb78ec9c_6    conda-forge

Exercise: Create new environment named r_env and activate it.

Solution

conda create -n r_env
conda activate r_env


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done



## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/r_env



Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate r_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Exercise: Install r-base into r_env, then list all packages to confirm that the installation was successful.

Solution

conda install r-base
conda list


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


## Package Plan ##

  environment location: /home/olebi/miniforge3/envs/r_env

  added / updated specs:
    - r-base


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    binutils_impl_linux-64-2.45|default_hfdba357_105         3.5 MB  conda-forge
    c-ares-1.34.6              |       hb03c661_0         203 KB  conda-forge
    curl-8.17.0                |       h4e3cde8_1         183 KB  conda-forge
    gcc_impl_linux-64-15.2.0   |      hc5723f1_16        76.6 MB  conda-forge
    gfortran_impl_linux-64-15.2.0|      h281d09f_16        19.1 MB  conda-forge
    gxx_impl_linux-64-15.2.0   |      hda75c37_16        15.6 MB  conda-forge
    kernel-headers_linux-64-6.12.0|       he073ed8_5         1.5 MB  conda-forge
    libblas-3.11.0             |5_h4a7cf45_openblas          18 KB  conda-forge
    libcblas-3.11.0            |5_h0358290_openblas          18 KB  conda-forge
    libcurl-8.17.0             |       h4e3cde8_1         449 KB  conda-forge
    libdeflate-1.25            |       h17f619e_0          72 KB  conda-forge
    libgcc-devel_linux-64-15.2.0|     hcc6f6b0_116         3.0 MB  conda-forge
    libgfortran-15.2.0         |      h69a702a_16          27 KB  conda-forge
    libgfortran-ng-15.2.0      |      h69a702a_16          27 KB  conda-forge
    libgfortran5-15.2.0        |      h68bc16d_16         2.4 MB  conda-forge
    libglib-2.86.3             |       h6548e54_0         3.8 MB  conda-forge
    liblapack-3.11.0           |5_h47877c9_openblas          18 KB  conda-forge
    libpng-1.6.53              |       h421ea60_0         310 KB  conda-forge
    libsanitizer-15.2.0        |      h90f66d4_16         7.3 MB  conda-forge
    libstdcxx-devel_linux-64-15.2.0|     hd446a21_116        19.8 MB  conda-forge
    libstdcxx-ng-15.2.0        |      hdf11a46_16          27 KB  conda-forge
    libtiff-4.7.1              |       h9d88235_1         425 KB  conda-forge
    pcre2-10.47                |       haa7fec5_0         1.2 MB  conda-forge
    r-base-4.5.2               |       h835929b_3        26.1 MB  conda-forge
    sysroot_linux-64-2.39      |       hc4b9eeb_5        39.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:       221.1 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  _r-mutex           conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 
  binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.45-default_hfdba357_105 
  bwidget            conda-forge/linux-64::bwidget-1.10.1-ha770c72_1 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hda65f42_8 
  c-ares             conda-forge/linux-64::c-ares-1.34.6-hb03c661_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2026.1.4-hbd8a1cb_0 
  cairo              conda-forge/linux-64::cairo-1.18.4-h3394656_0 
  curl               conda-forge/linux-64::curl-8.17.0-h4e3cde8_1 
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_3 
  fontconfig         conda-forge/linux-64::fontconfig-2.15.0-h7e30c49_1 
  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-hc364b38_1 
  freetype           conda-forge/linux-64::freetype-2.14.1-ha770c72_0 
  fribidi            conda-forge/linux-64::fribidi-1.0.16-hb03c661_0 
  gcc_impl_linux-64  conda-forge/linux-64::gcc_impl_linux-64-15.2.0-hc5723f1_16 
  gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-15.2.0-h281d09f_16 
  graphite2          conda-forge/linux-64::graphite2-1.3.14-hecca717_2 
  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0 
  gxx_impl_linux-64  conda-forge/linux-64::gxx_impl_linux-64-15.2.0-hda75c37_16 
  harfbuzz           conda-forge/linux-64::harfbuzz-12.2.0-h15599e2_0 
  icu                conda-forge/linux-64::icu-75.1-he02047a_0 
  kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-6.12.0-he073ed8_5 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.45-default_hbd61a6d_105 
  lerc               conda-forge/linux-64::lerc-4.0.0-h0aef613_1 
  libblas            conda-forge/linux-64::libblas-3.11.0-5_h4a7cf45_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.11.0-5_h0358290_openblas 
  libcurl            conda-forge/linux-64::libcurl-8.17.0-h4e3cde8_1 
  libdeflate         conda-forge/linux-64::libdeflate-1.25-h17f619e_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libexpat           conda-forge/linux-64::libexpat-2.7.3-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h9ec8514_0 
  libfreetype        conda-forge/linux-64::libfreetype-2.14.1-ha770c72_0 
  libfreetype6       conda-forge/linux-64::libfreetype6-2.14.1-h73754d4_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-he0feb66_16 
  libgcc-devel_linu~ conda-forge/noarch::libgcc-devel_linux-64-15.2.0-hcc6f6b0_116 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_16 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_16 
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-15.2.0-h69a702a_16 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-h68bc16d_16 
  libglib            conda-forge/linux-64::libglib-2.86.3-h6548e54_0 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-he0feb66_16 
  libiconv           conda-forge/linux-64::libiconv-1.18-h3b78370_2 
  libjpeg-turbo      conda-forge/linux-64::libjpeg-turbo-3.1.2-hb03c661_0 
  liblapack          conda-forge/linux-64::liblapack-3.11.0-5_h47877c9_openblas 
  liblzma            conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_4 
  libpng             conda-forge/linux-64::libpng-1.6.53-h421ea60_0 
  libsanitizer       conda-forge/linux-64::libsanitizer-15.2.0-h90f66d4_16 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_16 
  libstdcxx-devel_l~ conda-forge/noarch::libstdcxx-devel_linux-64-15.2.0-hd446a21_116 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-hdf11a46_16 
  libtiff            conda-forge/linux-64::libtiff-4.7.1-h9d88235_1 
  libuuid            conda-forge/linux-64::libuuid-2.41.3-h5347b49_0 
  libwebp-base       conda-forge/linux-64::libwebp-base-1.6.0-hd42ef1d_0 
  libxcb             conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  make               conda-forge/linux-64::make-4.4.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.6.0-h26f9b46_0 
  pango              conda-forge/linux-64::pango-1.56.4-hadf4263_0 
  pcre2              conda-forge/linux-64::pcre2-10.47-haa7fec5_0 
  pixman             conda-forge/linux-64::pixman-0.46.4-h54a6638_1 
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 
  r-base             conda-forge/linux-64::r-base-4.5.2-h835929b_3 
  readline           conda-forge/linux-64::readline-8.3-h853b02a_0 
  sed                conda-forge/linux-64::sed-4.9-h6688a6e_0 
  sysroot_linux-64   conda-forge/noarch::sysroot_linux-64-2.39-hc4b9eeb_5 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_ha0e22de_103 
  tktable            conda-forge/linux-64::tktable-2.10-h8d826fa_7 
  tzdata             conda-forge/noarch::tzdata-2025c-hc9c84f9_1 
  xorg-libice        conda-forge/linux-64::xorg-libice-1.1.2-hb9d3cd8_0 
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.6-he73a12e_0 
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0 
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.12-hb03c661_1 
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb03c661_1 
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.12-hb9d3cd8_0 
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.3.1-hb9d3cd8_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done                                                                                                                                                                                                                                                                                                                    
Verifying transaction: done                                                                                                                                                                                                                                                                                                                    
Executing transaction: done                                                                                                                                                                                                                                                                                                                    


# packages in environment at /home/olebi/miniforge3/envs/r_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.45            default_hfdba357_105    conda-forge
bwidget                   1.10.1               ha770c72_1    conda-forge
bzip2                     1.0.8                hda65f42_8    conda-forge
c-ares                    1.34.6               hb03c661_0    conda-forge
ca-certificates           2026.1.4             hbd8a1cb_0    conda-forge
cairo                     1.18.4               h3394656_0    conda-forge
curl                      8.17.0               h4e3cde8_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.15.0               h7e30c49_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                    hc364b38_1    conda-forge
freetype                  2.14.1               ha770c72_0    conda-forge
fribidi                   1.0.16               hb03c661_0    conda-forge
gcc_impl_linux-64         15.2.0              hc5723f1_16    conda-forge
gfortran_impl_linux-64    15.2.0              h281d09f_16    conda-forge
graphite2                 1.3.14               hecca717_2    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gxx_impl_linux-64         15.2.0              hda75c37_16    conda-forge
harfbuzz                  12.2.0               h15599e2_0    conda-forge
icu                       75.1                 he02047a_0    conda-forge
kernel-headers_linux-64   6.12.0               he073ed8_5    conda-forge
keyutils                  1.6.3                hb9d3cd8_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.45            default_hbd61a6d_105    conda-forge
lerc                      4.0.0                h0aef613_1    conda-forge
libblas                   3.11.0          5_h4a7cf45_openblas    conda-forge
libcblas                  3.11.0          5_h0358290_openblas    conda-forge
libcurl                   8.17.0               h4e3cde8_1    conda-forge
libdeflate                1.25                 h17f619e_0    conda-forge
libedit                   3.1.20250104    pl5321h7949ede_0    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.7.3                hecca717_0    conda-forge
libffi                    3.5.2                h9ec8514_0    conda-forge
libfreetype               2.14.1               ha770c72_0    conda-forge
libfreetype6              2.14.1               h73754d4_0    conda-forge
libgcc                    15.2.0              he0feb66_16    conda-forge
libgcc-devel_linux-64     15.2.0             hcc6f6b0_116    conda-forge
libgcc-ng                 15.2.0              h69a702a_16    conda-forge
libgfortran               15.2.0              h69a702a_16    conda-forge
libgfortran-ng            15.2.0              h69a702a_16    conda-forge
libgfortran5              15.2.0              h68bc16d_16    conda-forge
libglib                   2.86.3               h6548e54_0    conda-forge
libgomp                   15.2.0              he0feb66_16    conda-forge
libiconv                  1.18                 h3b78370_2    conda-forge
libjpeg-turbo             3.1.2                hb03c661_0    conda-forge
liblapack                 3.11.0          5_h47877c9_openblas    conda-forge
liblzma                   5.8.1                hb9d3cd8_2    conda-forge
libnghttp2                1.67.0               had1ee68_0    conda-forge
libopenblas               0.3.30          pthreads_h94d23a6_4    conda-forge
libpng                    1.6.53               h421ea60_0    conda-forge
libsanitizer              15.2.0              h90f66d4_16    conda-forge
libssh2                   1.11.1               hcf80075_0    conda-forge
libstdcxx                 15.2.0              h934c35e_16    conda-forge
libstdcxx-devel_linux-64  15.2.0             hd446a21_116    conda-forge
libstdcxx-ng              15.2.0              hdf11a46_16    conda-forge
libtiff                   4.7.1                h9d88235_1    conda-forge
libuuid                   2.41.3               h5347b49_0    conda-forge
libwebp-base              1.6.0                hd42ef1d_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
make                      4.4.1                hb9d3cd8_2    conda-forge
ncurses                   6.5                  h2d0b736_3    conda-forge
openssl                   3.6.0                h26f9b46_0    conda-forge
pango                     1.56.4               hadf4263_0    conda-forge
pcre2                     10.47                haa7fec5_0    conda-forge
pixman                    0.46.4               h54a6638_1    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
r-base                    4.5.2                h835929b_3    conda-forge
readline                  8.3                  h853b02a_0    conda-forge
sed                       4.9                  h6688a6e_0    conda-forge
sysroot_linux-64          2.39                 hc4b9eeb_5    conda-forge
tk                        8.6.13          noxft_ha0e22de_103    conda-forge
tktable                   2.10                 h8d826fa_7    conda-forge
tzdata                    2025c                hc9c84f9_1    conda-forge
xorg-libice               1.1.2                hb9d3cd8_0    conda-forge
xorg-libsm                1.2.6                he73a12e_0    conda-forge
xorg-libx11               1.8.12               h4f16b4b_0    conda-forge
xorg-libxau               1.0.12               hb03c661_1    conda-forge
xorg-libxdmcp             1.1.5                hb03c661_1    conda-forge
xorg-libxext              1.3.6                hb9d3cd8_0    conda-forge
xorg-libxrender           0.9.12               hb9d3cd8_0    conda-forge
xorg-libxt                1.3.1                hb9d3cd8_0    conda-forge
zstd                      1.5.7                hb78ec9c_6    conda-forge

Section 3: Exporting and Importing Environments

Background

A powerful feature of Conda is the ability to share environment configurations with collaborators. By exporting an environment to a file, you can create a “snapshot” of all installed packages and dependencies. This is essential for reproducibility in research, as others can recreate the exact environment to ensure consistency in analyses and results. Using Conda environment files can save time and reduce errors, especially when working on collaborative projects.

Removing unused environments and packages helps keep your Conda installation clean and organized, conserving storage space and reducing potential conflicts. Conda makes it easy to remove entire environments or individual packages, allowing you to focus only on the active dependencies you need for your current work.

Section 4: Exercises

In the following exercises, you are going to export your environment to a YAML file and use that file to recreate the environment after deleting it (the same approach could be used to reproduce the environment on a different device). Here are the commands you need to know:

Code	Description
`conda env export > environment.yml`	Save active environment configuration to `environment.yml`
`conda remove -n env_name --all`	Remove the environment `env_name` completely
`conda remove package_name`	Remove `package_name` from the active environment
`conda env create -f environment.yml`	Create an environment from the file `environment.yml`
`conda env list`	List all existing Conda environments

Exercise: Activate the py_env environment from the previous section, then export its content to a file called environment.yml.

Solution

conda activate py_env
conda env export > environment.yml

Exercise: Deactivate and delete py_env. List all environments to confirm it was deleted.

Solution

conda deactivate
conda remove -n py_env --all
conda info --envs


Remove all packages in environment /home/olebi/miniforge3/envs/py_env:

No packages found in /home/olebi/miniforge3/envs/py_env. Continuing environment removal
Everything found within the environment (/home/olebi/miniforge3/envs/py_env), including any conda environment configurations and any non-conda files, will be deleted. Do you wish to continue?
 (y/[n])? y

# conda environments:
#
base                   /home/olebi/miniforge3
r_env                  /home/olebi/miniforge3/envs/r_env
test_env               /home/olebi/miniforge3/envs/test_env
test_env2              /home/olebi/miniforge3/envs/test_env2

Exercise: Recreate py_env from the environment.yml file, then list all environments again.

Solution

conda env create -f environment.yml
conda env list


Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate py_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate


# conda environments:
#
base                   /home/olebi/miniforge3
py_env                 /home/olebi/miniforge3/envs/py_env
r_env                  /home/olebi/miniforge3/envs/r_env
test_env               /home/olebi/miniforge3/envs/test_env
test_env2              /home/olebi/miniforge3/envs/test_env2

Exercise: Verify the recreation by activating py_env and listing the installed packages.

Solution

conda activate py_env
conda list


# packages in environment at /home/olebi/miniforge3/envs/py_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                hda65f42_8    conda-forge
ca-certificates           2026.1.4             hbd8a1cb_0    conda-forge
icu                       78.1                 h33c6efd_0    conda-forge
ld_impl_linux-64          2.45            default_hbd61a6d_105    conda-forge
libblas                   3.11.0          5_h4a7cf45_openblas    conda-forge
libcblas                  3.11.0          5_h0358290_openblas    conda-forge
libexpat                  2.7.3                hecca717_0    conda-forge
libffi                    3.5.2                h9ec8514_0    conda-forge
libgcc                    15.2.0              he0feb66_16    conda-forge
libgcc-ng                 15.2.0              h69a702a_16    conda-forge
libgfortran               15.2.0              h69a702a_16    conda-forge
libgfortran5              15.2.0              h68bc16d_16    conda-forge
libgomp                   15.2.0              he0feb66_16    conda-forge
liblapack                 3.11.0          5_h47877c9_openblas    conda-forge
liblzma                   5.8.1                hb9d3cd8_2    conda-forge
libnsl                    2.0.1                hb9d3cd8_1    conda-forge
libopenblas               0.3.30          pthreads_h94d23a6_4    conda-forge
libsqlite                 3.51.1               hf4e2dac_1    conda-forge
libstdcxx                 15.2.0              h934c35e_16    conda-forge
libuuid                   2.41.3               h5347b49_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
ncurses                   6.5                  h2d0b736_3    conda-forge
numpy                     2.4.0           py312h33ff503_0    conda-forge
openssl                   3.6.0                h26f9b46_0    conda-forge
pip                       25.3               pyh8b19718_0    conda-forge
python                    3.12.12         hd63d673_1_cpython    conda-forge
python_abi                3.12                    8_cp312    conda-forge
readline                  8.3                  h853b02a_0    conda-forge
setuptools                80.9.0             pyhff2d567_0    conda-forge
tk                        8.6.13          noxft_ha0e22de_103    conda-forge
tzdata                    2025c                hc9c84f9_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
zstd                      1.5.7                hb78ec9c_6    conda-forge

Bonus: Remove all the environments you don’t want to keep after this session.