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Instructions for local install of these notes

To install these notes, first set up the reaquired software [requirements]. Do not proceed unless you have set up all of these pieces of software. These are:

Then set up and test the notes in a [local install] following the intsructions below.

These instructions assume that you will run these commands in a bash shell. You might need to modify in places for other shells such as zsh for OS X. Make sure you asre aware of which shell you are using.

We assume you will setup the repository in your home directory (~). If not, then replace ~ below by where you want to setup.

Local install of GEOG0111

1. Clone this repository and cd to the local directory

    cd ~ && git clone https://github.com/UCL-EO/geog0111.git
    cd ~/geog0111
    cd notebooks && tar xvzf data/cacheData.tar.Z

2. Download/update required Python packages

This will be faster if you first install the package mamba. To do this:

    conda create -n mamba
    conda activate mamba
    conda install -c conda-forge mamba

Answer 'Y' to any prompts to install.

If you choose to use mamba then you can install the geog0111 environment with:

    mamba env create -y --force -n geog0111 -f environment.yml

This may take minutes/tens of minutes. If you do not have mamba, just use conda (Warning: this is much slower):

    conda env create -y --force -n geog0111 -f environment.yml

3. Set up anaconda.

In the Terminal (shell), type either, if using windows WSL or linux:

    conda init
    echo "conda activate geog0111" >> ~/.bashrc

Or if using OS X:

    conda init
    echo "conda activate geog0111" >> ~/.zshrc

Then, open a new shell (or type bash) and type:

    conda env list

This should now show:

    # conda environments:
    #
    base                     /Users/plewis/anaconda3
    geog0111              *  /Users/plewis/anaconda3/envs/geog0111

4. Set up notebook kernel and extensions

Do this by running the following in shell (Terminal):

    python -m ipykernel install --name=conda-env-geog0111-geog0111-py --display-name 'conda env:geog0111-geog0111' --user
    ~/geog0111/notebooks/bin/postBuild

5. Set up your NASA Earthdata login

Go to the site https://urs.earthdata.nasa.gov/. Make sure you know your Earthdata login and password for when you come across it in the notes.

6. Launch jupyter or jupyterlab server

      jupyter notebook

This will respond with something like:

    [I 06:58:25.120 NotebookApp] Serving notebooks from local directory: /Users/plewis/Documents/GitHub/geog0111
    [I 06:58:25.120 NotebookApp] Jupyter Notebook 6.4.4 is running at:
    [I 06:58:25.120 NotebookApp] http://The-Brain.local:8888/?token=146dbb8eb09948a20f219c69256926ca6ab62c4fae03d0c1
    [I 06:58:25.120 NotebookApp]  or http://127.0.0.1:8888/?token=146dbb8eb09948a20f219c69256926ca6ab62c4fae03d0c1
    [I 06:58:25.120 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
    [C 06:58:25.164 NotebookApp] 

        To access the notebook, open this file in a browser:
            file:///Users/plewis/Library/Jupyter/runtime/nbserver-88431-open.html
        Or copy and paste one of these URLs:
            http://The-Brain.local:8888/?token=146dbb8eb09948a20f219c69256926ca6ab62c4fae03d0c1
         or http://127.0.0.1:8888/?token=146dbb8eb09948a20f219c69256926ca6ab62c4fae03d0c1

The main things for you that o see from this are:

A. How to stop the jupyter server:

Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Use Control-C in the shell you started the server. You might try that now to familiarise yourself with it, and then restart jupyter notebook

B. The URL of the server (with the security token). In this case:

    http://127.0.0.1:8888/?token=146dbb8eb09948a20f219c69256926ca6ab62c4fae03d0c1

Launch a browser that points to that (your one, not te example here!!). That should take you to the Jupyter server homepage.

After this initial setup, just do:

      cd ~/geog0111/notebooks
      jupyter notebook

to get to this point.

8. Test

Now, test things:

  • navigate to the coursenotes geog0111 then notebooks

  • select the fist notebook 001_Notebook_use.ipynb

  • go through the notes and run the code in the cells

  • if that doesn't launch for any reason, try re-stopping and starting the server

  • failing that, ask for help in the Monday class, or come along to office hours or the Thursday help sessions

One issue to look out for is if the notebook kernel doesn't start. That normally means that either you haven't set up the geog0111 environment properly, and/or you didn't setup the notebook kernel properly. Look back over sections 3. and 4. above.

You should test that your setup is robust.

  • Try logging out and in again on your computer and launch jupyter again

9. Use of the notes and updates

There are some things to be aware of when using and updating the notes, so make sure to look over these instructions