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).

2. 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 a run.py file.
• Inside the shell/ directory, create a submit.sbatch and a submit.sh file.
• Inside the experiments/ directory, create a config.yaml file.
• Inside the test/ directory, create a 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 the 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