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Anaconda

Python is a high level programming language that is widely used in many branches of science. As a result, many scientific packages have been developed in Python, leading to the development of a package manager called Anaconda. Anaconda is the standard in Python package management for scientific research.

Benefits of Anaconda:

  • Shareability: environments can be shared via human-readable text-based YAML files.
  • Maintainability: the same YAML files can be version controlled using git.
  • Repeatability: environments can be rebuilt using those same YAML files.
  • Simplicity: dependency matrices are computed and solved by Anaconda, and libraries are pre-built and stored on remote servers for download instead of being built on your local machine.
  • Ubiquity: nearly all Python developers are aware of the usage of Anaconda, especially in scientific research, so there are many resources available for learning how to use it, and what to do if something goes wrong.

Anaconda can also install Pip and record which Pip packages are installed, so Anaconda can do everything Pip can, and more.

Important

If using Anaconda on Cheaha, please see our Anaconda on Cheaha page for important details and restrictions.

Using Anaconda

Anaconda is a package manager, meaning it handles all of the difficult mathematics and logistics of figuring out exactly what versions of which packages should be downloaded to meet your needs, or inform you if there is a conflict.

Anaconda is structured around environments. Environments are self-contained collections of researcher-selected packages. Environments can be changed out using a simple package without requiring tedious installing and uninstalling of packages or software, and avoiding dependency conflicts with each other. Environments allow researchers to work and collaborate on multiple projects, each with different requirements, all on the same computer. Environments can be installed from the command line, from pre-designed or shared YAML files, and can be modified or updated as needed.

The following subsections detail some of the more common commands and use cases for Anaconda usage. More complete information on this process can be found at the Anaconda documentation. Need some hands-on experience, you can find instructions on how to install PyTorch and TensorFlow using Anaconda in this tutorial.

Important

If using Anaconda on Cheaha, please see our Anaconda on Cheaha page for important details and restrictions.

Create an Environment

In order to create a basic environment with the default packages, use the conda create command:

# create a base environment. Replace <env> with an environment name
conda create -n <env>

If you are trying to replicate a pipeline or analysis from another person, you can also recreate an environment using a YAML file, if they have provided one. To replicate an environment using a YAML file, use:

# replicate an environment from a YAML file named env.yml
conda create -n <env> -f <path/to/env.yml>

By default, all of your conda environments are stored in /home/<user>/.conda/envs.

Activate an Environment

From here, you can activate the environment using either source or conda:

# activate the virtual environment using source
source activate <env>

# or using conda
conda activate <env>

To know your environment has loaded, the command line should look like:

(<env>) [blazerid@c0XXX ~]$

Once the environment is activated, you are allowed to install whichever python libraries you need for your analysis.

Install Packages

To install packages using Anaconda, use the conda install command. The -c or --channel command can be used to select a specific package channel to install from. The anaconda channel is a curated collection of high-quality packages, but the very latest versions may not be available on this channel. The conda-forge channel is more open, less carefully curated, and has more recent versions.

# install most recent version of a package
conda install <package>

# install a specific version
conda install <package>=version

# install from a specific conda channel
conda install -c <channel> <package><=version>

Generally, if a package needs to be downloaded from a specific conda channel, it will mention that in its installation instructions.

Installing Packages with Pip

Some packages are not available through Anaconda. Often these packages are available via PyPi and thus using the Python built-in Pip package manager. Pip may also be used to install locally-available packages as well.

Important

Make sure pip is installed within the conda environment and use it for installing packages within the conda environment to prevent Pip related issues.

# install most recent version of a package
pip install \<package\>

# install a specific version, note the double equals sign
pip install \<package\>==version

# install a list of packages from a text file
pip install -r packages.txt

Finding Packages

You may use the Anaconda page to search for packages on Anaconda, or use Google with something like <package name> conda. To find packages in PyPi, either use the PyPi page to search, or use Google with something like <package name> pip.

Packages for Jupyter

For more information about using Anaconda with Jupyter, see the section Working with Anaconda Environments.

Update packages in an environment

To ensure packages and their dependencies are all up to date, it is a best practice to regularly update installed packages, and libraries in your activated environment.

conda update -β€”all

Deactivating an Environment

An environment can be deactivated using the following command.

# Using conda
conda deactivate

Anaconda may say that using source deactivate is deprecated, but environment will still be deactivated.

Closing the terminal will also close out the environment.

Deleting an Environment

To delete an environment, use the following command. Remember to replace <env> with the existing environment name.

conda env remove β€”-name <env>

Working with Environment YAML Files

Exporting an Environment

To easily share environments with other researchers or replicate it on a new machine, it is useful to create an environment YAML file. You can do this using:

# activate the environment if it is not active already
conda activate <env>

# export the environment to a YAML file
conda env export > env.yml

Creating an Environment from a YAML File

To create an environment from a YAML file env.yml, use the following command.

conda env create --file env.yml

Sharing your environment file

To share your environment for collaboration, there are primarily 3 ways to export environments, the below commands show how to create environment files that can be shared for replication. Remember to replace <env> with the existing environment name.

  1. Cross-Platform Compatible

    conda env export --from-history > <env>.yml
    
  2. Platform + Package Specific

    Create .yml file to share, replace <envname> (represents the name of your environment) and <env> (represents the name of the file you want to export) with preferred names for file.

    conda env export <envname> > <env>.yml
    
  3. Platform + Package + Channel Specific

    conda list β€”-explicit > <env>.txt
    # OR
    conda list β€”-explicit > <env>.yml
    

Replicability versus Portability

An environment with only python 3.10.4, numpy 1.21.5 and jinja2 2.11.2 installed will output something like the following file when conda env export is used. This file may be used to precisely replicate the environment as it exists on the machine where conda env export was run. Note that the versioning for each package contains two = signs. The code like he774522_0 after the second = sign contains hyper-specific build information for the compiled libraries for that package. Sharing this exact file with collaborators may result in frustration if they do not have the exact same operating system and hardware as you, and they would not be able to build this environment. We would say that this environment file is not very portable.

There are other portability issues:

  • The prefix: C:\... line is not used by conda in any way and is deprecated. It also shares system information about file locations which is potentially sensitive information.
  • The channels: group uses - defaults, which may vary depending on how you or your collaborator has customized their Anaconda installation. It may result in packages not being found, resulting in environment creation failure.
name: test-env
channels:
  - defaults
dependencies:
  - blas=1.0=mkl
  - bzip2=1.0.8=he774522_0
  - ca-certificates=2022.4.26=haa95532_0
  - certifi=2021.5.30=py310haa95532_0
  - intel-openmp=2021.4.0=haa95532_3556
  - jinja2=2.11.2=pyhd3eb1b0_0
  - libffi=3.4.2=h604cdb4_1
  - markupsafe=2.1.1=py310h2bbff1b_0
  - mkl=2021.4.0=haa95532_640
  - mkl-service=2.4.0=py310h2bbff1b_0
  - mkl_fft=1.3.1=py310ha0764ea_0
  - mkl_random=1.2.2=py310h4ed8f06_0
  - numpy=1.21.5=py310h6d2d95c_2
  - numpy-base=1.21.5=py310h206c741_2
  - openssl=1.1.1o=h2bbff1b_0
  - pip=21.2.4=py310haa95532_0
  - python=3.10.4=hbb2ffb3_0
  - setuptools=61.2.0=py310haa95532_0
  - six=1.16.0=pyhd3eb1b0_1
  - sqlite=3.38.3=h2bbff1b_0
  - tk=8.6.11=h2bbff1b_1
  - tzdata=2022a=hda174b7_0
  - vc=14.2=h21ff451_1
  - vs2015_runtime=14.27.29016=h5e58377_2
  - wheel=0.37.1=pyhd3eb1b0_0
  - wincertstore=0.2=py310haa95532_2
  - xz=5.2.5=h8cc25b3_1
  - zlib=1.2.12=h8cc25b3_2
prefix: C:\Users\user\Anaconda3\envs\test-env

To make this a more portable file, suitable for collaboration, some planning is required. Instead of using conda env export we can build our own file. Create a new file called env.yml using your favorite text editor and add the following. Note we've only listed exactly the packages we installed, and their version numbers, only. This allows Anaconda the flexibility to choose dependencies which do not conflict and do not contain unusable hyper-specific library build information.

name: test-env
channels:
  - anaconda
dependencies:
  - jinja2=2.11.2
  - numpy=1.21.5
  - python=3.10.4

This is a much more readable and portable file suitable for sharing with collaborators. We aren't quite finished though! Some scientific packages on the conda-forge channel, and on other channels, can contain dependency errors. Those packages may accidentally pull a version of a dependency that breaks their code.

For example, the package markupsafe made a not-backward-compatible change (a breaking change) to their code between 2.0.1 and 2.1.1. Dependent packages expected 2.1.1 to be backward compatible, so their packages allowed 2.1.1 as a substitute for 2.0.1. Since Anaconda chooses the most recent version allowable, package installs broke. To work around this for our environment, we would need to modify the environment to "pin" that package at a specific version, even though we didn't explicitly install it.

name: test-env
channels:
  - anaconda
dependencies:
  - jinja2=2.11.2
  - markupsafe=2.0.1
  - numpy=1.21.5
  - python=3.10.4

Now we can be sure that the correct versions of the software will be installed on our collaborator's machines.

Note

The example above is provided only for illustration purposes. The error has since been fixed, but the example above really happened and is helpful to explain version pinning.

Good Software Development Practice

Building on the example above, we can bring in good software development practices to ensure we don't lose track of how our environment is changing as we develop our software or our workflows. If you've ever lost a lot of hard work by accidentally deleting an important file, or forgetting what changes you've made that need to be rolled back, this section is for you.

Efficient software developers live the mantra "Don't repeat yourself". Part of not repeating yourself is keeping a detailed and meticulous record of changes made as your software grows over time. Git is a way to have the computer keep track of those changes digitally. Git can be used to save changes to environment files as they change over time. Remember that each time your environment changes to commit the output of Exporting your Environment to a repository for your project.