https://github.com/briochemc/aibecs_demo
Demo of package use for JKM students
https://github.com/briochemc/aibecs_demo
Last synced: 3 months ago
JSON representation
Demo of package use for JKM students
- Host: GitHub
- URL: https://github.com/briochemc/aibecs_demo
- Owner: briochemc
- Created: 2019-04-23T23:50:49.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2019-05-10T10:56:55.000Z (about 6 years ago)
- Last Synced: 2024-10-12T10:30:19.048Z (7 months ago)
- Language: Jupyter Notebook
- Size: 294 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# AIBECS Demo
This repository contains a Jupyter notebook to beta test the AIBECS package.
First, to download this notebook, you can either click on the download button on this page, or using git, type
```bash
git clone https://github.com/briochemc/AIBECS_demo.git
```
This [README](https://github.com/briochemc/AIBECS_demo/blob/master/README.md) provides a set of instructions and prerequisites to run the notebook.
To run the notebook, you must ensure that you have installed the required software (including the package to run the notebook).
Here are the steps:
## 1. Install Julia
First things first, you must install [Julia](https://julialang.org). Click on the [Julia](https://julialang.org) link, look for the "download" buttons, and install the correct version for your OS.
Once this is done, you should be able to start Julia by typing
```bash
julia
```
in the terminal.
If not, find the Julia executable, and simply double click on it!
This should open a terminal session, and display something like this:
```julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.1.0 (2019-01-21)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia>
```
This is called the Julia REPL (for Read Eval Loop Print) and is used for interactive use of Julia.
Great job, Julia is now running on your computer! Congratulations!
If you want to learn more about Julia, you can read [the documentation](https://docs.julialang.org/en/v1/), there is a [Discourse forum](https://discourse.julialang.org/), and there is a [Slack channel](https://julialang.slack.com/messages) if you need help.
But for now you should not need any of those: The notebook will just require you to press Shift + Enter a couple of times.
## 2. Add some Julia packages
In Julia, you can access the package manager by simply typing `]` in the REPL.
Once you type `]`, the REPL changes to
```julia
(v1.1) pkg>
```
This means you're in the package-manager (or `pkg`) mode.
Note that you can exit the `pkg` mode by pressing the `delete` key, and this will revert the Julia prompt to its original form:
```julia
julia>
```
The packages you must install are:
- **a)** The **AIBECS** package
To create a global steady-state biogeochemistry model, we will be using the [AIBECS](https://github.com/briochemc/AIBECS.jl) package.
Because it is not registered yet (soon though), you have to specify the GitHub URL to install it, via
```julia
add https://github.com/briochemc/AIBECS.jl.git
```
in `pkg` mode, which should look like
```julia
(v1.1) pkg> add https://github.com/briochemc/AIBECS.jl.git
Updating git-repo `https://github.com/briochemc/AIBECS.jl.git`
Resolving package versions...
Updating `~/.julia/environments/v1.1/Project.toml`
[3487739c] + AIBECS v1.0.0 #master (https://github.com/briochemc/AIBECS.jl.git)
(...)
```
This should only take a few seconds.
- **b)** the **Cartopy** packages
In order to plot things, i.e., to look at the output of the beautiful work you will be doing in this demo, you will need a plotting package.
Here, we are going to try Python's [Cartopy](https://scitools.org.uk/cartopy/docs/latest/).
First, we need to install it via the `Conda` package, which we need to install via `add Conda` (and press return), and you should see something like:
```julia
(v1.1) pkg> add Conda
Resolving package versions...
Updating `~/.julia/environments/v1.1/Project.toml`
[8f4d0f93] + Conda v1.2.0
```
Then we install PyPlot:
```julia
(v1.1) pkg> add PyPlot
```
And we also need PyCall:
```julia
(v1.1) pkg> add PyCall
```
And again, this should only take a few seconds.
- **c)** the **IJulia** package
Finally, the [IJulia](https://github.com/JuliaLang/IJulia.jl) package will be your tool to launch JupyterLab from Julia.
Same as above, in `pkg` mode, type `add IJulia` (and press return), and you should see something like:
```julia
(v1.1) pkg> add IJulia
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Installed SoftGlobalScope ─ v1.0.10
Installed ZMQ ───────────── v1.0.0
Installed IJulia ────────── v1.18.1
Updating `~/.julia/environments/v1.1/Project.toml`
[7073ff75] + IJulia v1.18.1
Updating `~/.julia/environments/v1.1/Manifest.toml`
[7073ff75] + IJulia v1.18.1
[b85f4697] + SoftGlobalScope v1.0.10
[c2297ded] + ZMQ v1.0.0
Building ZMQ ───→ `~/.julia/packages/ZMQ/ABGOx/deps/build.log`
Building IJulia → `~/.julia/packages/IJulia/gI2uA/deps/build.log`
```
This should only take a few seconds as well.
- **d)** Building extra packages:
Some of Julia's packages must be built for the notebook to work.
Don't worry, this is pretty easy too.
Get in `pkg` mode (type `]` in the REPL), and then
- type `build CodecZlib`.
It should look like this:
```julia
(v1.1) pkg> build CodecZlib
Building CodecZlib → `~/.julia/packages/CodecZlib/9jDi1/deps/build.log`
```
Great! You can now proceed to starting the notebook!
## 3. Start JupyterLab
The final step is to start JupyterLab.
First, make sure you are in the normal Julia REPL mode (i.e., press `delete` if you are in `pkg` mode.)
Then, tell Julia that you want to "use" IJulia:
```julia
julia> using IJulia
```
Note you can just copy paste the code above (including the `julia>` bits), and the REPL will know to not paste those automatically.
Everytime a package is used for the first time, Julia will precompile it (which can take a few seconds to minutes, depending on the package — don't worry, just let it finish).
Finally, you can start JupyterLab from Julia by simply typing `jupyerlab()` in Julia.
It should look like:
```julia
julia> jupyterlab()
```
If Julia asks you if you want Conda to install JupyterLab, just say "yes" (i.e., type `y`).
After a couple seconds/minutes of downloads and installations, you should be all set up and a browser window should open with JupyterLab!
Just navigate to the notebook within JupyterLab in your browser and double-click on the notebook!