{"id":18658696,"url":"https://github.com/mcellteam/mcell_tools","last_synced_at":"2026-02-28T17:02:15.015Z","repository":{"id":152893644,"uuid":"201977882","full_name":"mcellteam/mcell_tools","owner":"mcellteam","description":"Package build repository","archived":false,"fork":false,"pushed_at":"2025-05-07T18:12:03.000Z","size":186,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-05-18T01:36:33.182Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mcellteam.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":"2019-08-12T17:28:54.000Z","updated_at":"2025-05-07T17:00:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"3833eacd-0c5d-46e6-8171-cd5ba968670c","html_url":"https://github.com/mcellteam/mcell_tools","commit_stats":null,"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/mcellteam/mcell_tools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mcellteam","download_url":"https://codeload.github.com/mcellteam/mcell_tools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_tools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29943662,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-28T13:49:17.081Z","status":"ssl_error","status_checked_at":"2026-02-28T13:48:50.396Z","response_time":90,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2024-11-07T07:34:04.164Z","updated_at":"2026-02-28T17:02:14.965Z","avatar_url":"https://github.com/mcellteam.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mcell_tools\n\nThis repository contains all tools to clone MCell repositories and build them.\n\nRequired system packages (on Debian 9) are:\n\n```\n  sudo apt install git cmake build-essential bison flex swig python3 python3-dev libboost-dev zip\n```\n\nTo checkout all the repositories and build mcell along with other tools, run the following commands:\n\n```\n  mkdir mcell\n  git clone https://github.com/mcellteam/mcell_tools.git\n  cd mcell_tools\n  python3 run.py # optional argument -b BRANCH_NAME selects branch, mcell4_dev is the default branch\n```\n  \nThe resulting build directory of mcell is then located in work/build_mcell.\n\n\nTo run tests afterwards, these packages need to be installed (on Debian 9):\n\n```\n  sudo apt install python3-pip python3-tk\n  pip3 install toml pyparsing lxml pyyaml psutil matplotlib pathlib pandas\n```\n\nAnd this is how the test are run:\n\n```\n  cd ../mcell_tests\n  python3 run-tests.py # optional argument -c TEST_CONFIG selects test configuration, test_configs/default.tomp is the default config\n```\n\n\n## Windows System Setup\n\nThese sections desribe how to setup a Windows build\u0026test system. \n\n### 1) Downloads\n\nhttps://visualstudio.microsoft.com/vs/features/cplusplus/\n- install C++ compiler, might need recent windows upgrades\n\nhttps://repo.msys2.org/distrib/x86_64/msys2-x86_64-20210105.exe\n\nhttps://github.com/cmderdev/cmder/releases/download/v1.3.17/cmder.zip\n\nhttps://www.eclipse.org/downloads/packages/\n\nhttps://www.python.org/ftp/python/3.5.0/python-3.5.0-amd64.exe\n\nhttps://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5-win64-x64.msi\n\nhttps://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win32/Personal%20Builds/mingw-builds/installer/mingw-w64-install.exe/download\n\n### 2) Add Python, visual studio, mingw, msys, and cmake to PATH\n\nExample PATH value for tools under c:\\mcell\\tools and user name tester:\n\nC:\\mcell\\tools\\mingw-w64\\x86_64-8.1.0-posix-seh-rt_v6-rev0\\mingw64\\bin;C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Community\\VC\\Tools\\MSVC\\14.28.29333\\bin\\Hostx64\\x64;C:\\mcell\\tools\\Python35;C:\\mcell\\tools\\msys64\\usr\\bin;C:\\Users\\tester\\AppData\\Local\\Microsoft\\WindowsApps;C:\\mcell\\tools\\cmder\\vendor\\git-for-windows\\mingw64\\bin;C:\\mcell\\tools\\cmder\\vendor\\git-for-windows\\usr\\bin;C:\\mcell\\tools\\cmder\n\n\n### 3) Make a python3.exe copy\n\ncp /c/mcell/tools/Python35/python.exe /c/mcell/tools/Python35/python3.exe\n\n### 4) Install python libs\nOld versions of pip cannot install the dependencies and newer version e.g. 20.x is not compatible with 3.5\nso we must use 10.0.\n\npython.exe -m pip install pip==10.0.1\npython -m pip install toml pyparsing lxml pyyaml psutil\n\n### 5) Install zip and gcc\n\npacman -S zip unzip flex bison make swig\n\n### 6) Fix python installation according to notes in cellblender/windows_build_readme.txt\n\n### 7) Remove unzip from git installation\nwhich unzip\n-\u003e make sure that unzip comes from msys\n\n### 8) Update python.py according to notes in cellblender\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell_tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmcellteam%2Fmcell_tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell_tools/lists"}