{"id":15253579,"url":"https://github.com/4ment/torchtree-scipy","last_synced_at":"2026-01-04T15:05:25.005Z","repository":{"id":92150323,"uuid":"531388975","full_name":"4ment/torchtree-scipy","owner":"4ment","description":"Package providing extra functionalities from SciPy ","archived":false,"fork":false,"pushed_at":"2023-11-22T06:59:44.000Z","size":22,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-03-23T09:42:52.699Z","etag":null,"topics":["phylogenetics","python","pytorch","scipy","torchtree"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/4ment.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}},"created_at":"2022-09-01T06:17:23.000Z","updated_at":"2023-11-22T06:52:59.000Z","dependencies_parsed_at":"2023-11-22T07:40:48.602Z","dependency_job_id":null,"html_url":"https://github.com/4ment/torchtree-scipy","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":"4ment/torchtree-plugin-template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-scipy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-scipy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-scipy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-scipy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/torchtree-scipy/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244638977,"owners_count":20485800,"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","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":["phylogenetics","python","pytorch","scipy","torchtree"],"created_at":"2024-09-29T22:00:25.112Z","updated_at":"2026-01-04T15:05:24.920Z","avatar_url":"https://github.com/4ment.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# torchtree-scipy \n[![Testing](https://github.com/4ment/torchtree-scipy/actions/workflows/python-package.yml/badge.svg)](https://github.com/4ment/torchtree-scipy/actions/workflows/python-package.yml)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n![PyPI](https://img.shields.io/pypi/v/torchtree-scipy)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/torchtree-scipy)\n\n\n## About torchtree-scypi\n`torchtree-scipy` is a package that enhances the functionalities of [torchtree] by incorporating additional features from [SciPy].\n\n## Dependencies\n - [SciPy]\n - [torchtree]\n\n## Installation\n\n### Installing from source\n```bash\ngit clone https://github.com/4ment/torchtree-scipy\npip install torchtree-scipy/\n```\n\n### Installing latest stable version\nYou can install `torchtree-scipy` and its dependencies from PyPI with:\n```\npip install torchtree-scipy\n```\n\n## Check install\nIf the installation was succesfull, this command should print the version of the `torchtree_scipy` library\n```bash\npython -c \"import torchtree_scipy;print(torchtree_scipy.__version__)\"\n```\n\n## Command line arguments\nThe `torchtree-scipy` plugin adds these arguments to the torchtree CLI:\n\n```bash\ntorchtree-cli advi --help\n  ...\n  --scipy_gamma_site    use the GammaSiteModel implemented with SciPy\n```\n\n## Features\n### Discrete gamma site model\nThis model implements the discretized gamma distribution to model rate heterogeity accross sites. The gradient of this model with respect to the shape parameter is calculated numerically using finite differences.\nThe easiest way to use this model is to use the argument `--scipy_gamma_site`. This sets the type of the site model to `torchtree_scipy.GammaSiteModel` in the JSON configuration file. The default step size is `epsilon=1.0e-6` but it can be changed manually in the JSON file.\n\n## License\n\nDistributed under the GPLv3 License. See [LICENSE](LICENSE) for more information.\n\n## Acknowledgements\n\ntorchtree-scipy makes use of the following libraries and tools, which are under their own respective licenses:\n\n - [PyTorch]\n - [SciPy]\n - [torchtree]\n\n[PyTorch]: https://pytorch.org\n[scipy]: https://github.com/scipy/scipy\n[torchtree]: https://github.com/4ment/torchtree\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-scipy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Ftorchtree-scipy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-scipy/lists"}