{"id":18658709,"url":"https://github.com/mcellteam/mcell_qrg","last_synced_at":"2025-11-05T23:30:38.848Z","repository":{"id":29715117,"uuid":"33258170","full_name":"mcellteam/mcell_qrg","owner":"mcellteam","description":"The MCell Quick Reference Guide","archived":false,"fork":false,"pushed_at":"2015-10-13T17:24:00.000Z","size":240,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":13,"default_branch":"master","last_synced_at":"2024-12-27T15:28:26.411Z","etag":null,"topics":["mcell"],"latest_commit_sha":null,"homepage":"http://mcell.org/documentation/qrg/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","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}},"created_at":"2015-04-01T16:13:27.000Z","updated_at":"2016-09-08T03:38:47.000Z","dependencies_parsed_at":"2022-09-06T08:00:37.429Z","dependency_job_id":null,"html_url":"https://github.com/mcellteam/mcell_qrg","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_qrg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_qrg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_qrg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell_qrg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mcellteam","download_url":"https://codeload.github.com/mcellteam/mcell_qrg/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239475962,"owners_count":19645041,"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":["mcell"],"created_at":"2024-11-07T07:34:06.514Z","updated_at":"2025-11-05T23:30:38.790Z","avatar_url":"https://github.com/mcellteam.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# The README for the MCell Quick Reference Guide\n\n## Overview\n\nThe MCell Quick Reference Guide located at http://mcell.org/documentation/qrg\nis generated with Sphinx (http://sphinx-doc.org/index.html) from\nreStructuredText files.\n\n## Dependencies\n\nWe will be assuming that you are using Debian or Ubuntu, but most of the\ninstructions should be fairly similar for CentOS or other distros.\n\nAlthough it's entirely possible to install all the dependencies manually at the\nsystem level, we will be installing most of the Python libraries with\nvirtualenv. This will minimize possible version conflicts and simplify life\nconsiderably.\n\nFirst, you will want to install pip for Python3:\n\n    sudo apt-get install python3-pip\n\nThen install virtualenv:\n\n    sudo pip3 install virtualenv\n\nCreate a new virtual environment in the cloned mcell_qrg directory:\n\n    cd mcell_qrg\n    virutalenv .\n\nActivate it:\n\n    source bin/activate\n\nInstall sphinx and other necessary python libraries:\n\n    pip3 install -r requirements.txt\n\nIf you want to build the pdf, you'll want to install the following latex\nutilities by typing this command:\n\n    sudo apt-get install -y texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended\n\n## Build the Guide\n\nTo build the html version, use this command:\n\n    make html\n\nTo build the PDF version, use this command:\n\n    make latexpdf\n    \n## Other Notes on Virtualenv\n\nThe virtual environment can be disabled like this:\n\n    deactivate\n\nIt can later be reactivated by using the activate command as was done earlier:\n\n    source bin/activate\n\n## Learn More about Sphinx\n\nHere are some instructions for new developers who want to contribute\nto the QRG but are unfamiliar with ReST and Sphinx:\n\n* Read this page to develop a basic understanding of ReST syntax:\n  http://sphinx-doc.org/rest.html\n    * The official \"quick start\" guide:\n      http://docutils.sourceforge.net/docs/user/rst/quickstart.html\n    * The official ReST reference guide:\n      http://docutils.sourceforge.net/docs/user/rst/quickref.html\n    * Sphinx specific syntax: http://sphinx-doc.org/markup/index.html\n* Follow this tutorial, which will briefly explain how Sphinx projects work:\n  http://sphinx-doc.org/tutorial.html\n* The current implementation of the QRG uses a lot of grid tables which can be\n  difficult to edit out of the box with some text editors. Here are some\n  suggestions.\n    * Vim\n        * The vim-rst-tables plugin can be very useful, although it sometimes\n          behaves oddly.\n        * Consider setting one of the following options\n            * set ve=block\n            * set ve=all\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell_qrg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmcellteam%2Fmcell_qrg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell_qrg/lists"}