If you already have conda or anaconda installed, skip to ``Git install`` below
Download miniconda from https://docs.conda.io/en/latest/miniconda.html – choose the correct Miniconda3 MacOSX 64-bit pkg file for your Mac (Intel chip or new M1/M2 Silicon) from the menu and run it, agreeing to the licences and accepting all defaults. You should install for “just me”
To test your installation, open a fresh terminal window and at the prompt type which conda (unless you are using zsh. In that case use whence -p conda). You should see something resembling the following output, with your username instead of phil:
% which conda
/Users/phil/opt/miniconda3/bin/conda
Download miniconda from https://docs.conda.io/en/latest/miniconda.html – choose the Miniconda3 Windows 64-bit. download from the menu and run it, agreeing to the licences and accepting all defaults.
The installer should suggest installing in a path that looks like:
C:\Users\phil\Miniconda3
Once the install completes hit the windows key and start typing anaconda. You should see a shortcut that looks like:
Anaconda Powershell Prompt
(Miniconda3)
Note that Windows comes with two different terminals ``cmd`` (old) and ``powershell`` (new). Always select the powershell version of the anaconda terminal
Select the short cut. If the install was successful you should see something like:
(base) (Miniconda3):Users/phil>
with your username substituted for phil.
Some useful troubleshooting websites if you have issues getting conda installed on windows: https://stackoverflow.com/questions/54501167/anaconda-and-git-bash-in-windows-conda-command-not-found https://stackoverflow.com/questions/44597662/conda-command-is-not-recognized-on-windows-10
Inside your powershell or MacOs terminal, install git using conda:
conda install git
and then set it up
git config --global user.name "Phil"
git config --global user.email phil@example.com
To use the course materials and to work collaboratively for the project, you will need a github account. Sign up for a free account at https://github.com if you don’t already have one - you will need to use the same address you configured git for above.
Once you have your github account, you will need to set up a secure way to connect. If you think you might use github a lot, we recommend setting up an ssh connection - this is a longer set-up process, but then quicker each time you want to connect to git. Follow the instructions here:
https://docs.github.com/en/authentication/connecting-to-github-with-ssh
A quicker set-up is to create a Personal Access Token. Follow the instructions here: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-personal-access-token-classic
Once you have a personal access token, you can enter it instead of your password when performing Git operations over HTTPS (see https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#using-a-personal-access-token-on-the-command-line).
Now go to the course website at https://github.com/rhwhite/numeric_2024 and fork the repository. The ‘fork’ button is on the upper right. This creates a ‘fork’ or copy of the current status of the repository in your account.
You now have your own fork of the course repository and should be taken to that page. Its name will be YourGitHubId/numeric_2024
In the terminal, change directories to your home directory (called ~ for short) and make a new directory called repos to hold the course notebook repository. Change into repos and clone the course (do change YourGitHubId to your actual git hub id):
cd ~
mkdir repos
cd repos
git clone https://github.com/YourGitHubId/numeric_2024.git
In the terminal, execute the following commands:
cd numeric_2024
conda env create -f envs/environment.yaml
conda activate numeric_2024
To make it possible to pull down changes to the repository (for example, as I write this section only lab1 and lab2 are available) you need to work in a copy of the notebook. So always copy the notebook to a new name. See below an example for lab1. I suggest you use your name rather than phil!
cd ~/repos/numeric_2024/notebooks
cp lab1/01-lab1.ipynb lab1/phil-lab1.ipynb
jupyter lab
[ ]: