3. Setting Up Software

This chapter will show you how to set up a computer so that it has the software you need and it’s a comfortable place to work. Along the way, you’ll learn two fundamental skills:

• How to install software, whether or not you have administrator access

• How to edit configuration files, particularly for the Unix shell

The examples in this chapter focus on remote computers, but these skills are also useful for configuring laptops and desktops.

Learning Objectives

• Use Farm’s module system

• List popular tools for installing software on POSIX computers

• Explain what virtual environments are and why they’re useful

• Explain the difference between conda and mamba

• Install mamba via miniforge

• Create virtual environments with mamba

• Install software with mamba

• Explain the difference between .bashrc, .profile, and .bash_profile

• Create shell aliases

• Create and modify environment variables

3.1. What’s an Environment?

A computing environment is a collection of hardware, software, and associated settings. Whenever you run software (including code) on your computer, it runs in a computing environment. Being able to set up, inspect, maintain, and document computing environments is important because:

• A computer may not have the software you need pre-installed. Often the best and sometimes the only solution is to install the software yourself. Doing it yourself gives you more control over what’s installed and is typically faster than asking an administrator to do it for you. For your personal computer, you may be the sole administrator. You can use the same tools to set up and maintain environments on your computer as you do on remote computers.

• Differences between software versions can cause subtle bugs. Specifying a required software environment, with versions, can make it easier to collaborate on, distribute, and revisit research projects.

• Different projects may require different computing environments, and you may need to switch between them frequently. Switching software environments and settings can be quick and painless with the right tools. With modern compute clusters and cloud computing services, even switching hardware environments can be relatively easy.

• Inspecting the computing environment is the first step to diagnosing most computing problems. If you ask someone for help, they’ll likely want to know which hardware, software, and settings you’re using.

This chapter focuses on software environments and settings, because configuring these is often the first thing you’ll need to do, and because it’s not always possible to choose your hardware environment.

3.2. Installing Software

3.2.1. Package and Environment Managers

A package manager is a software tool that downloads and installs software packages. If you’ve used R or Python, you may already be familiar with the package managers these languages provide. Many modern operating systems also provide a package manager, because package managers have several benefits. They can:

• Automatically select software compatible with the computing environment

• Automatically install dependencies for software

• Update installed software, often automatically or with a single command

• In some cases, provide guarantees that software packages are not malicious

Note

Most Linux distributions provide a package manager as the recommended way to install software. Nevertheless, it is possible to install software on Linux without a package manager. One way is to download the source code for the software and compile it yourself; another is to download a pre-built binary. FlatPak and AppImage are two popular formats for distributing pre-built binaries.

Install software via a package manager when possible, but be aware that there are alternatives when it’s not.

Sometimes you may need to simultaneously work with several conflicting versions of software. For example, suppose you’re working on a new project that requires Python 3.12 or newer, but you also want to be able to examine results from an older project that requires Python 3.9 or older. What should you do?

A lightweight solution is to use an environment manager, a software tool that can create virtual environments. Each virtual environment behaves like an independent software environment, so you can install conflicting software in separate virtual environments. Many environment managers have a package manager built in.

Micromamba is the environment manager we recommend. Micromamba is based on the Mamba environment manager, which is, in-turn, based on the Conda environment manager. The three tools are drop-in replacements for one another, and it’s common to refer to the virtual environments created by all three as conda environments. We recommend Micromamba over Mamba and Conda because it is substantially faster and because it eliminates some of the pitfalls of the other two. That said, Micromamba is less mature than Mamba and Conda, so you may occasionally encounter missing features or bugs. Section 3.2.3 goes into detail about how to install and use micromamba.

Examples of other popular package and environment managers are:

• Homebrew for macOS and Linux

• Chocolatey for Windows

• Advanced Packaging Tool (APT) for Debian-based Linux distributions

• Nix for Linux and macOS

• Spack for Linux and macOS, focused on high-performance computing

• EasyBuild for Linux, focused on research computing

Note

A more complex solution is to use virtualization tools, such as Podman, Docker, and VirtualBox. These provide complete control over the operating system and software in a computing environment, so they provide stronger guarantees of reproducibility. The cost is that these tools are often slower than environment managers and using them requires more technical knowledge.

For most research projects, using an environment manager provides adequate flexibility and reproducibility.

3.2.2. UC Davis HPC Modules

Important

This section is specific to UC Davis HPC clusters. While some other servers and clusters may have a similar module system, many do not.

On most of UC Davis’ HPC clusters, the HPC Core Facility staff maintain a collection of ready-to-use virtual environments called modules. These are an alternative to setting up environments yourself.

Note

After learning to use Micromamba or another environment manager, you may find it more convenient and less of a cognitive burden to just manage environments yourself rather than use modules.

You can list all of the modules available on a cluster with the module avail command. For example, as of writing, the output from module avail on Farm begins:

----------------------------------------------------------------- /share/apps/22.04/modulefiles/spack/core -----------------------------------------------------------------
cuda/11.7.1  gcc/5.5.0  hwloc/2.9.3                      jdk/17.0.1   julia/1.9.0  julia/1.9.3      nvhpc/23.1         openjdk/16.0.2  pigz/2.7    slurm/23.02.6
gcc/4.9.4    gcc/7.5.0  intel-oneapi-compilers/2022.2.1  julia/1.8.5  julia/1.9.2  libevent/2.1.12  openjdk/11.0.17_8  openmpi/4.1.5   pmix/4.2.6  ucx/1.14.1

----------------------------------------------------------------- /share/apps/22.04/modulefiles/spack/libs -----------------------------------------------------------------
amdfftw/3.2   bzip2/1.0.8  eigen/3.4.0  gmp/6.2.1  h5z-zfp/1.1.0  hypre/2.26.0               librsvg/2.51.0  mpfr/4.1.0      netcdf-cxx4/4.3.1     nvhpc/23.1  zlib/1.2.13
boost/1.80.0  cgal/5.4.1   fftw/3.3.10  gsl/2.7.1  hdf5/1.12.2    intel-oneapi-mkl/2022.2.1  libszip/2.1.1   netcdf-c/4.9.0  netcdf-fortran/4.6.0  pigz/2.7

Modules are displayed in groups defined by the server administrators. Each module has a name and a version number, separated by a slash. For instance, julia/1.9.3 is the julia module, version 1.9.3.

To get help with a module, use the module help command with the module’s name and optionally its version. For example, to get help with the julia module:

module help julia

-------------------------------------------------------------------
Module Specific Help for /share/apps/22.04/modulefiles/spack/core/julia/1.9.3:

The Julia Language: A fresh approach to technical computing
-------------------------------------------------------------------

To load a module, use the module load command. Again, you need to specify the module’s name and optionally its version. As an example, suppose you decide you want to try out the Julia programming language on Farm. If you try to run julia, you’ll see an error message saying it’s not installed:

julia

julia: command not found

You can load the julia module to switch to an environment where Julia is installed:

module load julia

Now running julia will open the Julia interpreter (you can exit Julia by typing exit() and pressing enter).

You can check which modules are loaded at any given time with the module list command:

module list

Currently Loaded Modulefiles:
 1) slurm/23.02.6   2) openmpi/4.1.5

You might see different output if you’ve loaded or unloaded modules.

Finally, to unload a module, you can use the module unload command with the module’s name:

module unload julia

Note that when you log out, Farm will automatically unload any modules you loaded.

3.2.3. Micromamba

3.2.3.1. Installing Micromamba

The Micromamba documentation includes official installation instructions. We recommend the “install script” method for installing Micromamba, which we describe below with slight changes. You can use these instructions to install Micromamba on a server or on your personal computer.

Important

Before following the instructions below, make sure to review the official installation instructions, as they may have changed since this was written. At the time of writing, the official installation command was:

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

This command downloads the install script and immediately runs it. In the instructions below, we separate the download and install steps, to make it easier to troubleshoot problems and because it’s generally a good idea to read a script you downloaded before running it, to make sure it doesn’t do anything malicious.

Note

On Windows, we recommend installing Micromamba in Git Bash or the Windows Subsystem for Linux.

While it is possible to install Micromamba in Windows’ native CMD.exe or PowerShell terminals, these terminals do not support Unix shell commands, so we recommend against using them for research computing.

The first step is to download the install script. The official installation instructions suggest using the curl command line tool to do this. Since curl is not pre-installed on some servers, we’ve also provided instructions for how to do it with the wget command line tool. In a terminal, run:

curl

curl -O -L micro.mamba.pm/install.sh

The -O flag saves the file with the same name it had on the server (install.sh), while the -L flag ensures curl follows redirects.

If you see a message like curl: command not found, try the wget version instead.

wget

wget micro.mamba.pm/install.sh

If you see a message like wget: command not found, try the curl version instead.

If the command was successful, you’ll have a file install.sh in your working directory. Take a moment to inspect the script with your preferred text editor. If everything looks okay, make the script executable:

chmod +x install.sh

Then run the script:

./install.sh

The script will prompt you about several installation details:

• Micromamba binary folder: where the micromamba tool will be installed. For most computers, it’s fine to accept the default by pressing Enter without typing anything.

• Init shell: whether to configure the shell to find the micromamba tool. Enter Y here unless you know how to configure this yourself.

• Configure conda-forge: whether to default to installing packages from the conda-forge package repository, which provides additional community-maintained packages. Enter Y here.

• Prefix location: where environments and packages will be installed. Once again, it’s fine to accept the default by pressing Enter without typing anything.

Once the script finishes, you must reload your shell’s settings before running Micromamba. To do so, run this command in the terminal:

source ~/.bashrc

Section 3.3.1 provides more details about what this command is doing.

Then check that your shell can find Micromamba. In the terminal, run:

micromamba --version

If the installation was successful, you should see a version number like 1.5.3. It’s okay if you have a different version. If you see an error message like micromamba: command not found, try running source ~/.bashrc and then try the command above again. If you still see an error message, some possible fixes are to run the install script again or to edit the shell configuration files (and check the PATH environment variable).

3.2.3.2. Creating Environments

The Micromamba documentation is intended for users already familiar with Conda. If you’re new to environment management or the Conda family of tools, you may find the Conda documentation more helpful for understanding what commands do and how to use them. There’s also a Conda cheat sheet.

Tip

In almost all cases, Conda commands are the same as Micromamba commands—just replace conda with micromamba.

Caution

If you find a different Conda cheat sheet online, make sure it’s up-to-date! There are a few very old cheat sheets that rank highly in search engines but list commands that will not work in Micromamba and recent versions of Conda.

To practice using Micromamba, let’s create a new virtual environment and install a few useful command line tools. You can create a new virtual environment with the create subcommand. Run this command in the terminal to create a new virtual evironment called utils:

micromamba create --name utils

Empty environment created at prefix: /home/USERNAME/micromamba/envs/utils

When the create subcommand runs successfully, it prints out Empty environment created at prefix: and a path. The path is the location where packages installed in the environment will be stored.

Tip

Creating a new virtual environment for each project you work on is a good way to avoid software version conflicts and keep track of the software each project requires. For some projects, you may need to create multiple virtual environments to accommodate distinct research directions and collections of software.

Virtual environments are easy to create and remove (aside from the time it takes to download and install software), so experiment until you find a workflow that works well for you.

You can list all of the virtual environments Micromamba detects with the env list subcommand. Try running this command in the terminal:

micromamba env list

  Name      Active  Path
────────────────────────────────────────────────────────────────
  utils             /home/USERNAME/micromamba/envs/utils

In order to use an environment and its installed packages, you must first activate the environment. You can activate an environment with the activate subcommand. Go ahead and activate the utils environment:

micromamba activate utils

By default, the name of the active virtual environment (if any) is displayed as a prefix on the shell prompt. So after running the activate subcommand above, you should see (utils) at the beginning of the shell prompt. The environment will remain active as long as your terminal is open. If you close the terminal (or log out, for SSH connections) the environment will be deactivated.

Note

You can also deactivate the currently active environment by running micromamba deactivate. It is not necessary to do this before activating a different environment.

Let’s install a file search tool, [ripgrep][rg], in the utils environment. The ripgrep (rg) tool searches for files which contain a given text string (or regular expression). You can use the install subcommand to install packages. The default is to install packages into the active environment. You can list any number of packages after install. For instance, to install ripgrep:

micromamba install ripgrep

The subcommand will list the packages that will be installed and prompt you to confirm. If you see more than just the requested packages in the listing, it’s because the requested packages have dependencies.

Caution

Whenever you run the install subcommand, it will also try to update packages that are already installed. This is good for keeping your software up-to-date, but a problem if your project requires specific versions. You can use the --freeze-installed flag to prevent updates to packages that are already installed.

Tip

You can install a specific version of a package by quoting the name of the package and using =, <, <=, >, or >= to indicate the version. For instance, to install Python 3.9:

micromamba install 'python=3.9'

After the installation is complete, try out one of the commands. For example, create a file called foo.txt with the text hello world, and then try finding it with rg:

echo "hello world" > foo.txt
rg hello

You can list all of the packages installed in a virtual environment with the list subcommand. The default is to list packages in the active environment:

micromamba list

List of packages in environment: "/home/nick/micromamba/envs/utils"

  Name           Version  Build        Channel
────────────────────────────────────────────────────
  _libgcc_mutex  0.1      conda_forge  conda-forge
  _openmp_mutex  4.5      2_gnu        conda-forge
  libgcc-ng      13.2.0   h807b86a_5   conda-forge
  libgomp        13.2.0   h807b86a_5   conda-forge
  ripgrep        14.1.0   he8a937b_0   conda-forge

The list might differ slightly on your computer because of different operating systems and new versions of packages released since this was written. However, you should see ripgrep in the list. All of the other packages—which we did not request directly—are dependencies.

The create, activate, and install subcommands are fundamental to using Micromamba. There are many other subcommands, which you can learn about by reading the Conda documentation.

Tip

The ripgrep search tool is worth knowing about if you work in the command line frequently. It can help you find files quickly. It’s a faster, modernized versions of the classic grep tool.

3.2.3.3. Exporting Environments

One of the benefits of using conda environments is that they can be exported and then recreated later, possibly by other people or on other computers. You can export a conda environment with the env export subcommand. In most cases, you should also use the --from-history flag, which exports only the packages you installed directly. For example, run this command in the utils environment:

micromamba env export --from-history

name: utils
channels:
- conda-forge
- pkgs/main
dependencies:
- ripgrep

The subcommand prints out the environment specification in YAML, a human-readable markup language. The dependencies section lists the packages as you installed them, so each package’s version is omitted unless you installed a specific version. The channels section lists the channels (package repositories) from which you downloaded the packages.

You’ll probably want to save the environment specification rather than just print it out. You can use the shell > command to pipe the output to a file, to save or share with others. It’s a good idea to include the environment name in the name of the file, and to use a .yml or .yaml extension. So for the utils environment:

micromamba env export --from-history > utils.yml

After running the command, there will be a utils.yml file in your working directory. You can use a text editor to check its contents.

You can recreate an environment from a specification file with the env create subcommand and the --file flag. Let’s remove the utils environment from Micromamba, so that we can recreate it from the utils.yml file. To remove the environment, run this command:

micromamba env remove --name utils

Then recreate the environment from utils.yml:

micromamba env create --file utils.yml

After the packages finish installing, activate the environment and test that ripgrep (rg) is there.

Keep environment specification files with the code for the project to which they belong. For instance, if you version your code with git, version your environment file(s) too. Share the environment specification files with anyone who needs to work on your project, so that you can make sure their environment is set up with the same software as yours.

The environment specification files produced by env export with the --from-history flag do not include version info for most packages. This is by design: the format is meant to be cross-platform, and sometimes specific versions are not available on all platforms. The tradeoff is that when the environment is recreated, Micromamba might install newer versions of packages, which might cause compatibility issues. If you know your project depends on specific versions of packages, make sure to specify the versions when you install the packages. Alternatively, you can export to a specification format that has complete version information but is not cross-platform by omitting the --from-history flag. The command to recreate an environment from a specification file in this format is the same.

Note

Environment export is still under development in both the Conda and Mamba (which includes Micromamba) projects, and there’s no consensus yet. As of writing:

• The conda-lock subproject is a relatively mature tool for exporting environments.

• The Conda developers might add an option to include version information in the cross-platform format.

• The Mamba developers might create a new format.

3.2.3.4. Managing Storage

Depending on which packages you install, conda environments can potentially use 10s of gigabytes of storage. Micromamba automatically caches installed packages and shares them between environments when possible, but there are also a few things you can do to keep storage usage under control.

First, make sure you use env remove to remove old environments that you no longer use. If you export these environments before removing them, you can recreate them if you need them again later.

Second, periodically clean up Micromamba’s cache to remove old, unused packages. To do this, run:

micromamba clean --all

This will remove all packages from the cache that are not installed in any environments. Unless you install packages via symlinks, which is beyond the scope of this reader, then this is a safe command and will not break your environments.

3.3. Editing Configurations

After installing software in your computing environment, you’ll likely want to configure it. Many software, especially command-line software, read settings from a configuration file when they run. By editing configuration files, you can customize your computing environment to make it do what you want and make it more comfortable to use.

3.3.1. Bash

Bash is a shell: a programming language and prompt that serves as a command line interface for computers. Bash is widely used, and is the default shell for most Linux distributions. Knowing how to configure Bash can make it much easier to work in a terminal.

Important

This section is about configuring Bash, but some POSIX computers default to other shells (such as the Z Shell (Zsh) or Fish). These shells can also be configured, but the files and commands needed to do so may be different; see their documentation for details.

You can check the default shell on a POSIX computer with this command:

echo $SHELL

On macOS, the default shell for versions 10.3 through 10.14 is Bash. Beginning with version 10.15, the default shell is Zsh.

Three files in your home directory are especially important for configuring Bash. Each one is a script, which means they contain commands for Bash (bash) or its predecessor, the Bourne shell (sh). The files are:

• ~/.bash_profile runs every time you log in (to a server, for example).

• ~/.profile also runs every time you log in, but only if .bash_profile doesn’t exist. It can only contain sh commands, not bash commands.

• ~/.bashrc runs every time you open a shell when you’re already logged in.

When these files don’t exist or are empty, Bash uses default settings. If they alredy exist on your computer and contain commands, they may have been set up by your operating system or by your computer’s administrator. Leave them intact until you have enough experience to know what the commands do—they might be important. You can still add your own settings to the files.

Note

You can learn more about how Bash reads configuration files at startup in the Bash Startup Files section of the Bash manual.

Note

Configuration files are also called dotfiles, because they usually have names that begin with a dot.

We recommend setting up the Bash configuration files so that .bash_profile always runs .profile and .bashrc. Then use .profile to set environment variables (Section 3.3.1.2) and use .bashrc for everything else. This approach ensures that your environment variables are loaded whenever you use any sh-compatible shell and that your Bash configuration is loaded whenever you use Bash. To set this up, use a text editor (such as vi) to add these lines to your .bash_profile:

#
# .bash_profile
#
# This file is runs on login to a Bash shell.

[[ -r ~/.profile ]] && source ~/.profile
[[ -r ~/.bashrc  ]] && source ~/.bashrc

These commands check that .profile and .bashrc exist, and run them if they do. Leave the rest of your .bash_profile blank.

3.3.1.1. Aliases

While learning about Micromamba, did you ever feel like typing out micromamba for every command was a little bit tedious? One way you can customize the shell is by creating aliases for commands that are long or hard to remember. Let’s create an alias mm for the micromamba command, so that you can just type mm instead of typing micromamba.

The command to create an alias is alias, followed by a space, the name of the alias, an equals sign, and then the aliased command in quotes.

For example, try adding this code to your .bashrc:

alias mm='micromamba'

Important

Be careful to match the spacing and quotes exactly. In Bash, spacing often matters and single quotes have a distinct meaning from double quotes.

After adding the alias command to .bashrc, save and close the file. You can make Bash “reload” the settings in .bashrc with this command:

source ~/.bashrc

Alternatively, you can restart or open a new terminal, since .bashrc runs every time you open a new interactive shell. Then try using the alias to list your conda environments:

mm env list

This should print a list of environments. Notice that you can add arguments as you would normally after the aliased command.

Note

If the alias doesn’t work, or the shell prints mm: command not found, double-check that your saved the alias command in ~/.bashrc and that you ran the source command.

If you ever decide you don’t like an alias, you can use the unalias command to unset aliases in your current shell (for example, unalias mm). Make sure to remove the alias from .bashrc as well, or else it will return next time you open a new shell.

Tip

For many shell commands, you can set an argument several times and only the last setting applies. As a result, you can use aliases to set your preferred defaults for a command, and then override them as needed.

For example, to make the ls command color-code file names and display file sizes in human-readable units by default, add this alias to your .bashrc:

alias ls='ls --color=auto --human-readable'

You can find many examples of helpful aliases online; try searching for bash aliases or bash dotfiles.

3.3.1.2. Environment Variables

You can assign variables in your shell just like in most other programming languages. Typically, some variables are assigned automatically when the shell starts.

For example, the PATH variable contains a colon-separated list of paths where the shell should search for commands (software programs). Without PATH, you’d have to type the full path to every command.

Tip

You can use the which command to check where the shell found a command. For instance, to check where the git command is:

which git

In the shell, the echo command prints things, and you can get the value of a variable by putting a dollar sign $ in front of its name. Put these two ideas together to print the value of PATH:

echo $PATH

/home/nick/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin

You should see a colon-separated list of directories, like the one above. Some of the directories listed will probably be different on your computer.

You can assign a variable by typing a name, an equals sign (=), and then a value. The equals sign must not have spaces around it, and if the value contains spaces, it must be quoted. By convention, names of shell variables should be all uppercase. Here’s how to assign a variable FOO with the value Hello world!:

FOO='Hello world!'

Try printing FOO with echo.

Note

You can delete a variable with the unset command. For instance, to delete FOO, run:

unset FOO

If you try this, make sure to reassign FOO again, as we’ll use it in a subsequent example.

An environment variable is a shell variable that’s shared with other programs (including other shells). Environment variables are typically used to configure the computing environment. As it turns out, PATH is an environment variable.

You can get a list of all environment variables with the env command. Here’s an example of a few lines of output from the command:

env

SHELL=/usr/bin/bash
SESSION_MANAGER=local/zen:@/tmp/.ICE-unix/579,unix/zen:/tmp/.ICE-unix/579
R_PROFILE_USER=/home/nick/.config/R/rprofile
LESSHISTFILE=/home/nick/.config/less/history
COLORTERM=truecolor

On your computer, you’ll probably see some environment variables with different names and values.

Shell variables are not automatically environment variables. Notice that the variable FOO, created above, is not in the output from env. To assign an environment variable, you can use the export command. To make FOO an environment variable, run:

export FOO

Now FOO is an environment variable and will appear in the output of env.

Variables you assign interactively will be deleted when you close the shell. If you want to automatically assign or modify a variable every time you open a shell, put the assignment in your ~/.profile file.

As an example, let’s make an executable script that prints Hello, world! and add it to the PATH. To start, create and navigate to a directory called ~/scripts:

mkdir ~/scripts
cd ~/scripts

Open hello.sh in a text editor (for example, nano hello.sh), enter the following, and save the file:

#!/bin/sh
echo Hello world!

Then make the script executable:

chmod +x hello.sh

Try running the script to make sure it works:

./hello.sh

If you want to run the script from any other directory, you’ll have to tell the shell where to find the script by typing the full path ~/scripts/hello.sh.

For instance, navigate back to your home directory and try running hello.sh without the full path:

cd ~
hello.sh

-bash: hello.sh: command not found

The shell is unable to find hello.sh. You can tell the shell where to look by adding ~/scripts to the PATH. The command is:

export PATH="$HOME/scripts:$PATH"

This prepends ~/scripts ($HOME/scripts) and a colon (:) to the PATH.

Caution

Be careful not to overwrite the PATH, as this can break your shell. Instead, prepend or append directories to the PATH.

If you do accidentally overwrite the PATH, you can usually reset it by closing and reopening the shell. On a server, you can do this by logging out and then logging in again.

Now try running hello.sh again:

hello.sh

Hello world!

As it stands, ~/scripts will only stay on the PATH until the shell is closed. You can make the change persistent by adding the export command above to ~/.profile. Open ~/.profile in a text editor and add this line:

export PATH="$HOME/scripts:$PATH"

Now ~/scripts will be on the PATH even if you close and reopen the shell.

Besides the PATH, there are many other environment variables you might want to customize. For instance, you can assign EDITOR to specify your preferred text editor or assign R_LIBS_USER to control where R stores packages. Check the documentation for your favorite software to learn more about how they use environment variables.

3.3.2. Other Configuration Files

Section 3.3.1 focuses on Bash configuration files, but software such as git, tmux, R, Python, and Vim can also be customized through configuration files. For software you use frequently, learning to edit the configuration file(s) is often a worthwhile investment because allows you to tailor the software to your specific needs and workflows.