Setup.md

Setup.md

1. Environment Update

sudo apt update #Update Package Lists
sudo apt install -y latexmk texlive texlive-latex-extra texlive-xetex #Install latexmk and TeX Live for Myst
latexmk --version # Latexmk, John Collins, 31 Jan. 2024. Version 4.83

2. Install UV

pip install uv

3. Create a virtual environment and then activate it.

uv init # Creates a new or initialize the current directory and generates following files :  pyproject.toml, README.md, .python-version, main.py
#Another example : uv venv --python=3.12 .venv
uv venv # creates a new virtual environment for isolating Python packages and dependencies.
#Activate the venv
source .venv/bin/activate

3. [Optional] Install the locked requirements

#uv pip sync requirements.txt
#uv sync # run this to install what is present in your lock file exactly 
#uv lock # generated automaticall the first time you run uv add, uv remove or uv sync
#uv.lock file : The lockfile ensures reproducible builds by recording the exact versions of all dependencies that were resolved. 

4. Install some typical python libraries that are needed.

#pip install pandas ipykernel jupyter matplotlib plotly 
uv add pandas ipykernel jupyter matplotlib seaborn groq

5. Install Ruff

#pip install ruff
uv tool install ruff
ruff version # ruff 0.12.0
ruff check   # Lint all files in the current directory. or specify a file name to check for that file.
ruff format  # Format all files in the current directory.
# ruff check --fix

6. Run your Jupyter Notebook

   • Install the following extensions : Python [Microsoft microsoft.com]
   • Install the following extensions : Jupyter [Microsoft microsoft.com]
   • Choose the Python Virtual Environment created ealier.
   • Run the cells and play around with the prompts.

7. Install MyST

• Install Myst(https://mystmd.org/guide/installing), https://mystmd.org/guide/quickstart-myst-documents

At the terminal type:

#pip install mystmd
uv tool install mystmd
myst --version
myst init
myst start
# ctrl + Z to stop the myst 
# Install a PDF viewer : PDF Viewer [Mathematic Inc]
# to generate the pdf report : myst build 03_publication/01-article.md --pdf --output 03_publication/01-article.pdf

8. Generate uv.lock file or alternatively Requirements.txt

#pip freeze > requirements.txt
# uv pip freeze > requirements.txt
uv lock

9. Checkin the code to Github
10. Make a Release
    • Open the Releases Page
    • Click on "Draft a new release"
    • Choose the appropriate target branch
    • Choose a Tag Version else GitHub will create it.
    • Add a Release Title & Description
    • Click "Publish Release"
11. Try to upload the Release in Zenodo
    • Follow the steps mentioned here : https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content