Installing new packages

Predefined Environments should already include most of the scenarios, but they cannot possibly include all existing libraries, so you might want to install something necessary for your research.

There are generally 3 ways to install new packages in Polus Notebooks:

1. Temporary installation using base conda environment. Open Terminal and run installation commands. Base environment is activated by default. Please, keep in mind that base environment only comes with Python by default, so if you would like to install R, Julia, Java or Octave packages, you need to install it first. Any changes done to the base environment will be lost after the server is shut down. Use this method for quickly checking something, for more long-term project, please utilize the next method

2. User-defined Conda environment is a workaround to create user-defined and editable environments that persist the server restarts.

   • Creating environment

     1. Open Terminal

     2. Create folder for storing conda environment in your persistent storage: mkdir -p work/my-conda-envs/my-test-env. my-test-env could be any name you like.

     3. Create Conda environment with packages you’d like mamba create -y --prefix work/my-conda-envs/my-test-env python=3.10 pip ipykernel numpy scipy. Alternatively, create a conda environment.yaml file with the list of packages: https://carpentries-incubator.github.io/introduction-to-conda-for-data-scientists/04-sharing-environments/index.html and install with mamba env create --prefix work/my-conda-envs/my-test-env --file environment.yaml. In either case, make sure to include ipykernel in the list of dependencies.

     4. Rename environment folder so it does not clash with ipykernel: mv /home/jovyan/work/my-conda-envs/my-test-env/share/jupyter/kernels/python3 /home/jovyan/work/my-conda-envs/my-test-env/share/jupyter/kernels/my-test-env

     5. Add your kernel to the list of kernels: /home/jovyan/work/my-conda-envs/my-test-env/bin/python -m ipykernel install --user --name my-test-env --display-name "My Test Environment" . Kernel will appear in Launcher. Unfortunately, you would have to re-run this command every time you login to Notebooks to get access to your kernel.

   • Activating environment Open Terminal and run conda activate /home/jovyan/work/my-conda-envs/my-test-env and then run any required conda commands: conda install ...

   This method is good for medium-term development, but if you find yourself needing to share the Conda environment, please consider the next method.

3. Create new or update existing Environment. There are multiple actions involved into creating or updating the Environment, but it often boils down to creating Conda environmnet YAML

Tips for different languages/package managers

Python 3

Python packages are managed with conda package manager. You can use both conda or pip to install and update new packages

With conda

1. Use Anaconda Cloud to search for package you are interested in

anaconda_cloud_1

2. Choose the package you are looking for. Most of the community packages are published through conda-forge account

anaconda_cloud_2

3. Copy the install command and paste it to the notebook cell

anaconda_cloud_3

You have to append --yes to the end of the command

anaconda_cloud_4

With pip

1. Use Python Package Index (PyPi) to search for package you are interested in

pypi_1

2. Choose the package you are looking for.

pypi_2

3. Copy the install command and paste it to the notebook cell

pypi_3

You have to use exclamation mark before the command to let Jupyter know that this is shell command

pypi_4

You can specify the version to install using =<version> afer name of the package

!pip install opencv-python=4.1.1.26

R

You can use both conda or R to install and update new packages

With Anaconda

1. Use Anaconda Cloud to search for R packages you are interested in

anaconda_cloud_1

2. Choose the package you are looking for. Many R packages are published through r/ or conda-forge/ repos and their names start with r-

r_anaconda_cloud_

3. Copy the install command and paste it to the notebook cell

r_anaconda_cloud_3

You have to append --yes to the end of the command

system("conda install -c r r-tidyverse --yes", intern=TRUE)

From CRAN

Install packages from CRAN-like repositories or from local files using install.packages("<PACKAGE_NAME>") command

install.packages("tidyverse")

More documentation on install.packages available here: https://www.rdocumentation.org/packages/utils/versions/3.6.1/topics/install.packages

Julia

Install packages using Pkg as shown below

using Pkg
Pkg.add("CSV")

then load them with using statement:

using CSV

Java

You can add maven dependencies at runtime using magic command %maven. Full list of supported magic commands is here.

%mavenRepo scijava.public https://maven.scijava.org/content/groups/public
%maven net.imagej:imagej:2.0.0-rc-71
%maven net.imagej:imagej-notebook:0.7.1

You can search Maven Central for available packages

Octave

Octave Forge is a central location for development of packages for GNU Octave, similar to Matlab’s toolboxes. To install a package, use the pkg command from the Octave prompt by typing:

pkg install -forge package_name
pkg load package_name

C++

C++ does not have a built-in package manager. There are multiple existing package manager and if you are interested we may support one of them in the future.