Python Well SFM - pyWellSFM

pyWellSFM, which stands for Python Well SFM (Stratigraphic Forward Modeling), is a Python package dedicated to the analysis of accommodation along wells and the simulation of sedimentary layers over time.

pyWellSFM consists in:

  • a data structure that stores well information (e.g. depth, age, lithology, etc.) and the results of the accommodation analysis and simulations

  • tools to compute accommodation along wells

  • tools to simulate sedimentary layers over time using a stratigraphic forward modeling approach

  • tools to visualize the results of the accommodation analysis and simulations

Note

If you use pyWellSFM, please refer to the GitHub repository and cite the software as follows:

Installation

To install pyWellSFM, you can clone the GitHub repository. It is recommended to use a virtual Python environment.

Run the following commands: - using pip and a virtual environment:

cd path/to/install/dir/
git clone https://github.com/martin-lemay/pyWellSFM.git
cd pyWellSFM
source .venv/bin/activate
pip install -e ./

  • using conda:

cd path/to/install/dir/
git clone https://github.com/martin-lemay/pyWellSFM.git
cd pyWellSFM
conda activate venv
conda install ./

Testing

You can test pyWellSFM package using pytest (see the homepage).

  • To test the source distribution, run the following commands from pyWellSFM root directory:

pytest ./

  • To test the installed package, run the following commands:

pytest --pyargs pywellsfm

Contributing

Contributions are welcome — bug reports, feature requests, docs improvements, and code changes.

Workflow (issues + PR/MR)

  • Create an issue first to describe the bug / enhancement (with a minimal

    reproducible example when relevant).

  • Create a Pull Request / Merge Request that addresses one issue.

    • Reference the issue in the PR description (e.g. Fixes #123).

    • Keep changes focused and include tests/docs updates when applicable.

Local setup

pip install -e .[dev,test]

If you plan to build the docs locally, install the doc build dependencies as well:

pip install -r requirements.txt

Formatting, linting, typing, tests

Run these from the repository root:

# Format
ruff format .

# Lint (optionally auto-fix)
ruff check .
ruff check --fix .

# Type-check
mypy .

# Tests
pytest

# Coverage gate (configured in pyproject.toml)
# Test run fails if total coverage is below 80%
pytest --cov=pywellsfm --cov-fail-under=80

# To mirror CI more closely (includes doctests)
pytest ./ --doctest-modules

Build the docs locally

python -m sphinx -b html docs docs/_build/html

Then open docs/_build/html/index.html in your browser.

What is checked in CI

On each Pull Request, GitHub Actions runs:

  • ruff check (lint; currently non-blocking in CI)

  • mypy (static type checks)

  • pytest (tests + doctests)

  • Coverage threshold: test run fails if total coverage is below 80%

  • sphinx (documentation build)

Contents