# Installing and configuring packages In Nextjournal’s runtimes you can install any package or library, and configure them in whatever way works best for you. For most programming languages, the preferred way of installing packages will be to use a Bash script, but some, like R, might use their own runtime for it. Here, we first recap quickly on how to use Bash cells for installing packages (that you can skip if you've already read [this guide](https://nextjournal.com/help/how-to-install-packages?version=published)), and then provide a collection of examples of package installations in different languages. # Using Bash for package installation Currently, the language used for code cells and their corresponding runtimes are coupled, meaning a Python runtime will only use Python cells, a R runtime only R cells, and so on. Bash is an *exception* here. Since Bash is often used to install packages, Nextjournal allows assigning Bash cells to other language runtimes. Nextjournal tries to facilitate the process by guessing your intent when you add a Bash cell: If **no other runtimes exist**, Nextjournal will add a standalone Bash runtime. If **other, non-Bash runtimes exist**, Nextjournal will take the most recent cell’s runtime and assign the Bash cell to that runtime, assuming that you want to install packages for it. This will be indicated by *Bash in \[Language\]* in the bottom right corner of a code cell: ```bash id=4fe6f15a-d155-4b80-a034-d25e75322bf6 pip install climt ``` ## Manually assigning cells to runtimes You can always manually assign your Bash cells to different runtimes: simply open the Bash cell’s options menu and select *Change runtime…*, then select the runtime you want it to assign to: ![Changing Runtimes.png][nextjournal#file#bdd103c0-dd02-46b8-8d44-0fcbcc04031d] # Installing Packages Each Nextjournal runtime comes with an environment based on Ubuntu 18.04 LTS. This means that you can install packages from files via `dpkg`, or fetch them from repositories with `apt-get`. Nextjournal’s default environments don’t have package lists stored so an `apt-get update` might be required first: ```bash id=d4d1df75-8804-4dd0-b03f-ebd5b6ddb682 apt-get update apt-get install fortune cowsay /usr/games/fortune | /usr/games/cowsay ``` ## Prevent having to re-install packages A Nextjournal runtime’s file system state is transient by default. This means that whenever the runtime shuts down or is reset (either by your action or because it automatically shut down after 20 minutes of idle time), all installed packages are lost and have to be re-installed again. To prevent this, save your environment after installing packages to persist their file system state and all installed packages. You might want to read [How to reuse your environments](https://nextjournal.com/help/how-to-reuse-your-environments) for a short tutorial. Once you saved the runtime’s environment, you can assign it to your runtime so your code cells have the packages available to them. What follows here is a collection of examples on how to install packages for individual programming languages. ## Installing Python Packages Nextjournal's [default Python 2 and 3 environments](/nextjournal/python-environment) have a number of basic data and plotting packages installed, including `numpy`, `matplotlib`, and `plotly`: ```bash id=c69baac6-9153-4c3f-9b14-4bff41a3c40e pip freeze ``` When additional Python packages are required, you can install them in multiple ways. The easiest is to use `conda`, which will attempt to install all packages and dependencies in a consistent manner, including system packages and libraries. The [Anaconda Cloud](https://anaconda.org/) has a searchable database of packages and channels — by default `conda` will select only from the [anaconda channel](https://anaconda.org/anaconda/repo). ```bash id=e453efaf-3ea7-4de7-8416-835597daa2ca conda install descartes pysal ``` Additional channels can be added with the `-c` flag. ```bash id=5ea4b8ff-a6ee-414f-a0b8-4257553d6aa6 conda install -c conda-forge cartopy ``` For packages and versions unavailable via `conda`, or for installing packages distributed as *wheel files*, `pip` is available. For any packages that require compilation, `gcc` is available along with the most common build tools. ```bash id=73266fe0-945f-42ca-8075-950cca48efad pip install quilt mapclassify ``` You can also use `pip` to install development versions from git repos. ```bash id=1702c2f4-cf2b-42ce-90fd-ca4feb4bba27 pip install git+https://github.com/geopandas/geopandas@master ``` Finally, if a package has a `setup.py`, you can download and install with that. ```bash id=547ac8f3-568b-42e2-8d28-59924538acf6 git clone https://github.com/ResidentMario/geoplot cd geoplot git checkout 328cc9d5f8c02470c6257f2bf2fb2f3c5304530f python setup.py install ``` ## Installing Clojure Packages The [default Clojure environment](/nextjournal/clojure-environment) provides *Clojure v1.10.0*. Other versions, and any required libraries or packages, can be installed using a `deps.edn` file. In order to ensure loading when the runtime boots, this file must be created by inserting a *Code Listing*. Simply click the + button between nodes and select Code Listing, then set its language (in the bottom right corner) to *Extensible Data Notation*, and assign it *deps.edn* as its name using its options menu (•••) in the upper left corner. The following example will install the `clj-xchart` library: ```edn no-exec id=d40e705f-2f3b-429e-9a9b-2e25637ea6ac { :deps { com.hypirion/clj-xchart {:mvn/version "0.2.0"} org.clojure/clojure { :mvn/version "1.10.0-beta8" }}} ``` Your `deps.edn` can then be mounted into the Clojure runtime’s file system to be read at boot time using the runtime’s settings panel: ![Mount deps EDN.png][nextjournal#file#c4d1e24f-8b37-42bc-9bd8-445f0ae5bd66] Booting will take an extended length of time because of the installation happening through `deps.edn`. It is advisable to save the environment once all of the packages are installed so you not have to run through this process whenever you reset the runtime. System packages that are required for `clj-xchart` can be installed via a Bash cell: ```bash id=89944356-db4c-498e-a7b5-e04c0cacf42f apt-get update apt-get install --no-install-recommends \ fontconfig libxext6 libxrender1 libxtst6 libxi6 ``` Once everything has been installed, we can require `clj-xchart`: ```clojure id=12e22dba-fe57-43f6-8dbb-c7dde5d26181 (require '[com.hypirion.clj-xchart :as c]) ``` ## Installing Julia Packages The [Julia default environment](/nextjournal/julia-environment) includes a wide variety of file-handling and data processing packages, as well as the [`Plots`](https://github.com/JuliaPlots/Plots.jl) and [`Makie`](https://github.com/JuliaPlots/Makie.jl) graphical frameworks. ```julia id=f5b78a6e-ba83-47cc-8fd8-4a7d83cd1441 inst = Pkg.installed() foreach(key-> println("$key v$(inst[key])"), keys(inst)) ``` Installation of additional packages is done via the the standard Julia [Pkg interface](https://docs.julialang.org/en/v1/stdlib/Pkg/index.html): `update` will upgrade all packages with newer versions available, and `add` will install new packages. Running `precompile` before saving an environment will speed up package loading in the future. ```julia id=ef1acd2f-42b0-453c-9862-2eaba457ed3e pkg"add LightGraphs GraphPlot" pkg"precompile" ``` One can also use the \`\]\` pkg mode to install packages: ```julia id=1f915cd9-299e-4797-b5b0-f140aab5b900 ]up; add UnicodeFun ``` ## Installing R Packages [The R environment](/nextjournal/r-environment) includes the [tidyverse](https://www.tidyverse.org/), and the [plotly](https://plot.ly/r/) and [ggplot2](https://github.com/tidyverse/ggplot2) graphical packages. ```r id=e5e52104-80e5-4547-b8c0-3ae842600f6b inst = installed.packages()[,c("Package","Version")] inst[order(tolower(inst[,"Package"])),] ``` [__out-0.csv][nextjournal#output#e5e52104-80e5-4547-b8c0-3ae842600f6b#__out-0.csv] As always, a Bash cell can install additional dependencies: ```bash id=8d203dd4-b68f-45ea-baff-acffe572dad6 apt-get update apt-get install libudunits2-dev apt-get clean ``` Installation of additional R packages is done via the the standard R function `install.packages()`, or the devtools function `install_github()`. Build tools, including `gcc`, are included for package compilation. ```r id=c2fde22f-5d36-4a65-b7bc-602ee9d54c7f install.packages(c("ggraph","igraph")) devtools::install_github("sjmgarnier/viridis") ``` Once the packages have been installed, we can require them: ```r id=81746dcc-10da-4b45-8eb6-f752910d9296 library(ggraph) library(igraph) library(tidyverse) library(viridis) ``` # Configuring Packages ## Environment Variables Besides using a Bash script for configuration, or a `deps.edn` code listing mounted into Clojure runtimes (see [section above](#installing-clojure-packages)), any runtime also has full control over its environment variables. To create or override env variables, open a runtime’s settings panel, and expand the *Environment Variables & Secrets* section: ![Environment Variables & Secrets.png][nextjournal#file#db1981b9-e8c3-4467-89fb-2f4625577693] ⚠️: the runtime must be booted up in order for its inherited environment variables to be shown. 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