{"id":32175944,"url":"https://github.com/erdc/proteus","last_synced_at":"2025-12-16T15:56:32.051Z","repository":{"id":37502781,"uuid":"2212385","full_name":"erdc/proteus","owner":"erdc","description":"A computational methods and simulation toolkit","archived":false,"fork":false,"pushed_at":"2024-09-16T20:16:52.000Z","size":33859,"stargazers_count":92,"open_issues_count":106,"forks_count":58,"subscribers_count":19,"default_branch":"main","last_synced_at":"2025-10-21T19:52:50.336Z","etag":null,"topics":["c","c-plus-plus","code-mil","proteus","python","simulation-toolkit"],"latest_commit_sha":null,"homepage":"http://proteustoolkit.org","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/erdc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2011-08-15T21:28:25.000Z","updated_at":"2025-10-02T22:47:39.000Z","dependencies_parsed_at":"2024-01-26T21:47:29.293Z","dependency_job_id":null,"html_url":"https://github.com/erdc/proteus","commit_stats":{"total_commits":3549,"total_committers":71,"mean_commits":"49.985915492957744","dds":0.5849535080304311,"last_synced_commit":"bf2bf666000b9c4ae16d6f1d1191e9766bb200ad"},"previous_names":[],"tags_count":32,"template":false,"template_full_name":null,"purl":"pkg:github/erdc/proteus","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erdc%2Fproteus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erdc%2Fproteus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erdc%2Fproteus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erdc%2Fproteus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/erdc","download_url":"https://codeload.github.com/erdc/proteus/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erdc%2Fproteus/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27767434,"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":"2025-12-16T02:00:10.477Z","response_time":57,"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":["c","c-plus-plus","code-mil","proteus","python","simulation-toolkit"],"created_at":"2025-10-21T19:52:18.444Z","updated_at":"2025-12-16T15:56:32.042Z","avatar_url":"https://github.com/erdc.png","language":"Python","readme":"# Proteus: Computational Methods and Simulation Toolkit [![Build Status](https://travis-ci.com/cekees/proteus.svg?branch=main)](https://app.travis-ci.com/github/cekees/proteus) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/erdc/proteus_tutorial/master?filepath=index.ipynb)  [![DOI](https://zenodo.org/badge/2212385.svg)](https://zenodo.org/badge/latestdoi/2212385)\n\n\nProteus (http://proteustoolkit.org) is a Python package for\nrapidly developing computer models and numerical methods.\n\n# Installation\n\n\n\n```bash\nmamba install proteus -c conda-forge\n```\n\nFor a development installation, you want to install Proteus's dependencies and compile Proteus from source:\n\n```bash\nmamba env create -f environment-dev.yml #environment-dev-up.yml to try unpinned dependencies\nmamba activate proteus-dev\npip install -v -e .\n```\n\n# HPC Installation\n\nFor installation on high performance environments you may want to install Proteus's dependencies from source as well. We recommend using the PETSc build system to install most of the dependencies. The following is general outline:\n\nCreate a basic python environment you can install into:\n\n```\nmamba env create -f petsc-dev.yml\nmamba activate petsc-dev\n```\n\nor\n\n```\npython -m venv petsc-dev\npip install setuptools make cmake cython swig pybind11 numpy\n```\n\nNext, build petsc from source\n\n```\nbash scripts/petsc_config_linux_conda_seq.sh #see https://petsc.org/release/install/\n```\n\nNext, build additional C++ dependencies and install into environment prefix (e.g $CONDA_PREFIX or $VIRTUAL_ENV)\n\nhttps://github.com/projectchrono/chrono #\u003e=9.0.1, with python bindings\nhttps://github.com/scorec/core #\u003e=2.2.8, shared, python bindinds not needed\nhttps://github.com/xtensor-stack/xtl\nhttps://github.com/xtensor-stack/xtensor\nhttps://github.com/xtensor-stack/xtensor-python\n\nFinally, locally build and install remaining python dependencies into environment\n\n```\nCC=mpicc CXX=mpicxx MPI_DIR=$MPI_ROOT pip install -v mpi4py==3.1.6 --no-build-isolation --no-binary=:all:\nPETSC_DIR=$CONDA_PREFIX PETSC_ARCH=\"\" pip install -v ../petsc/src/binding/petsc4py --no-build-isolation --no-binary=:all:\nHDF5_MPI=ON HDF5_DIR=${CONDA_PREFIX} CC=mpicc CXX=mpicxx pip install -v h5py --no-build-isolation --no-binary=:all: #note h5py depends on mpi4py for this config\nCC=mpicc CXX=mpicxx pip install -v . --no-build-isolation --no-binary=:all:\n```\n\nSome optional packages can be installed with pip/mamba: py2gmsh, memory_profiler, scipy, pytest.\n\nSee https://github.com/erdc/proteus/wiki/How-to-Build-Proteus for old information on building the entire stack.\n\n# Developer Information\n\nThe source code, wiki, and issue tracker are on GitHub at\n\nhttps://github.com/erdc/proteus.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferdc%2Fproteus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ferdc%2Fproteus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferdc%2Fproteus/lists"}