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Practical session 1


Everybody has to start somewhere - Haruki Murakami


Development Tools for Scientific Computing 2024/2025

Pasquale Claudio Africa, Dario Coscia
11 Feb 2025

Part 1: Setting up your development environment

  1. Install required tools:
    • Ensure that Python is installed on your system.
    • Install Git, and create a GitHub account if you haven't already.
    • Install Miniconda on your system (refer to the installation guide here).
  1. Set up a git repository and virtual environment:
    • Open your terminal and create a conda environment named devtools_scicomp with Python 3.9 by running: 
      conda create --name devtools_scicomp python=3.9
    • Install essential packages by running: 
      python -m pip install pytest
      Note: Always install packages inside the conda environment using python -m pip, which ensures that you're using the Python interpreter and pip package manager within the environment.
    • Open GitHub in your web browser and follow these steps:
      1. Create a new empty repository titled devtools_scicomp_project_2025, and select a specific license and the Python .gitignore file.
      2. Open your terminal or command prompt, clone the repository, create a README.md file, and push your changes to the origin with the commit message first commit.

A small note on pushing:

  • Add your changes using: 
    git add [FILES]
  • Commit your changes with: 
    git commit -m "[COMMIT MESSAGE]"
  • Push your commits with: 
    git push origin HEAD:main

Part 2: Structuring the package

  • Inside your cloned GitHub repository, create the following directories: src/pyclassify/, scripts, test, shell, and experiments.
  • Inside the src/pyclassify/ directory, create an __init__.py and utils.py file.
  • Inside the scripts/ directory, create an run.py file.
  • Inside the shell/ directory, create an submit.sbatch and submit.sh file.
  • Inside the experiments/ directory, create an config.yaml file.
  • Inside the test/ directory, create an test_.py file.
  • Generate a requirements.txt file from the devtools_scicomp conda environment by running: 
    python -m pip freeze > requirements.txt

Add the requirements.txt file to the root of your project folder (devtools_scicomp_project_2025/).

  • Create a pyproject.toml file for your project from this template, and complete the [INSERT] placeholders.
  • Add in the .gitignore file a removal of .dat and .data files.
  • Add, commit, and push these changes to the origin repository with the commit message structuring the package.

Solutions

The repository with the right structure and commits is available here: GitHub repo