{"id":20751293,"url":"https://github.com/cbg-ethz/pmhn","last_synced_at":"2025-10-07T04:50:02.097Z","repository":{"id":172460726,"uuid":"649324408","full_name":"cbg-ethz/pMHN","owner":"cbg-ethz","description":"Personalised mutual hazard networks: fixed effects in cancer progression modeling","archived":false,"fork":false,"pushed_at":"2025-05-09T18:40:57.000Z","size":4468,"stargazers_count":3,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-09T23:08:31.836Z","etag":null,"topics":["cancer-evolution","probabilistic-models"],"latest_commit_sha":null,"homepage":"https://cbg-ethz.github.io/pMHN/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cbg-ethz.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-06-04T13:56:02.000Z","updated_at":"2025-05-09T18:41:00.000Z","dependencies_parsed_at":null,"dependency_job_id":"c309fbc7-92ec-45f3-af74-323a068d585e","html_url":"https://github.com/cbg-ethz/pMHN","commit_stats":null,"previous_names":["cbg-ethz/pmhn"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/cbg-ethz/pMHN","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FpMHN","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FpMHN/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FpMHN/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FpMHN/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbg-ethz","download_url":"https://codeload.github.com/cbg-ethz/pMHN/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2FpMHN/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278722765,"owners_count":26034461,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-07T02:00:06.786Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cancer-evolution","probabilistic-models"],"created_at":"2024-11-17T08:32:32.440Z","updated_at":"2025-10-07T04:50:02.080Z","avatar_url":"https://github.com/cbg-ethz.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)\n[![build](https://github.com/cbg-ethz/pMHN/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/cbg-ethz/pMHN/actions/workflows/test.yml)\n[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\n# Personalised Mutual Hazard Networks\n\nPrincipled probabilistic modelling with Mutual Hazard Networks.\n\n  - **Documentation:** [https://cbg-ethz.github.io/pMHN](https://cbg-ethz.github.io/pMHN)\n  - **Source code:** [https://github.com/cbg-ethz/pMHN](https://github.com/cbg-ethz/pMHN)\n  - **Bug reports:** [https://github.com/cbg-ethz/pMHN/issues](https://github.com/cbg-ethz/pMHN/issues)\n\n## Running the workflows\n\nTo facilitate reproducibility we use [Snakemake](https://snakemake.readthedocs.io/).\nWe recommend creating a new virtual environment (e.g., using [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)) and installing Snakemake as described in their documentation.\n\nOnce the environment is set, the package can be installed using\n```bash\n$ pip install -e .  # Note -e which will allow modifying the code when needed\n```\n\n## Contributing\n\nWe use [Poetry](https://python-poetry.org/) to control dependencies.\n\nWhen Poetry is installed, clone the repository and type\n\n```bash\n$ poetry install --with dev\n```\n\nto install the package with the dependencies used for development.\n\nAt this stage you should be able to use [Pytest](https://docs.pytest.org/) to run unit tests:\n\n```bash\n$ poetry run pytest\n```\n\nAlternatively, you may want to work inside Poetry environment:\n```bash\n$ poetry shell\n$ pytest\n```\n\nWhen you submit a pull request, automated continuous integration tests will be run.\nThey include unit tests as well as code quality checks.\nTo run the code quality checks automatically at each commit made, we use [pre-commit](https://pre-commit.com/).\nTo activate it run:\n\n```bash\n$ poetry shell  # If it is not already active\n$ pre-commit install\n```\n\n## Acknowledgements\n\nThis package is built around [LearnMHN](https://github.com/spang-lab/LearnMHN) (the backend for Mutual Hazard Networks) and [PyMC](https://www.pymc.io/) (probabilistic programming framework).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fpmhn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fpmhn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fpmhn/lists"}