Development

If you are developing or contributing to Solosis, follow the steps below to set up your local development environment.

git

Clone the Solosis Git repository

git clone git@github.com:haniffalab/solosis.git
cd solosis

Export required environment variables

Replace placeholders with values specific to your environment:

export LSB_DEFAULT_USERGROUP=<USERGROUP>
export TEAM_DATA_DIR=<DATA_DIR>
export TEAM_LOGS_DIR=<LOG_DIR>

Environment

Create and activate a virtual environment

python -m venv .venv
source .venv/bin/activate

Install dependencies and pre-commit hooks

pip install --upgrade pip
python -m pip install -r envs/requirements.txt
python -m pip install -r envs/dev-requirements.txt
python -m pip install -r envs/doc-requirements.txt
pre-commit install

The pre-commit configuration includes checks for code formatting using black and import ordering using isort. You can run these manually as follows:

black path/to/file.py
isort path/to/file.py

Branches

Check your current branch

git status

Expected output

On branch main
Your branch is up-to-date with 'origin/main'.

Switch to the `dev` branch

git checkout dev

Create a new branch from `dev`

git checkout -b <new-branch>

For more information on branching, see: - Git checkout guide - Branch naming conventions

Executing Solosis

When developing, run Solosis as follows:

python -m solosis.cli

Committing Changes

Commit and push your changes

git add .
git commit -m "ADD MESSAGE HERE"
git push

Once changes are ready, create a Pull Request to merge them into dev.

pip-compile

Solosis uses pip-tools to manage and lock dependencies. Dependencies are declared in pyproject.toml and compiled into pinned requirements files to ensure reproducible environments.

To update locked dependencies:

pip-compile --output-file=envs/requirements.txt
pip-compile --extra=dev --output-file=envs/dev-requirements.txt
pip-compile --extra=dev --output-file=envs/doc-requirements.txt

Synchronise your environment:

pip-sync envs/requirements.txt
pip-sync envs/dev-requirements.txt
pip-sync envs/doc-requirements.txt

This will install exactly the packages and versions listed in the specified files, removing any packages not included.

To upgrade dependencies, add --upgrade:

pip-compile --upgrade --output-file=envs/requirements.txt

pytest

To run tests using pytest:

python -m pytest -q tests/test_cli.py