{"id":32178226,"url":"https://github.com/brsynth/rptools","last_synced_at":"2026-01-05T13:10:13.080Z","repository":{"id":37535618,"uuid":"321697911","full_name":"brsynth/rptools","owner":"brsynth","description":"Suite of tools that work on rpSBML format","archived":false,"fork":false,"pushed_at":"2025-10-16T11:53:01.000Z","size":24119,"stargazers_count":7,"open_issues_count":6,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-21T20:51:40.464Z","etag":null,"topics":["metabolic-engineering","synbio","synthetic-biology","systems-biology"],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/brsynth.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-12-15T14:47:58.000Z","updated_at":"2025-10-16T11:53:05.000Z","dependencies_parsed_at":"2023-10-16T18:44:24.981Z","dependency_job_id":"af34830b-65f6-40a2-a370-8e2f250479ad","html_url":"https://github.com/brsynth/rptools","commit_stats":{"total_commits":646,"total_committers":8,"mean_commits":80.75,"dds":"0.10835913312693501","last_synced_commit":"731f6587e1d42681aa375d43e4eefeaf78564390"},"previous_names":[],"tags_count":38,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/rptools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frptools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frptools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frptools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frptools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/rptools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frptools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280333493,"owners_count":26312845,"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":"2025-10-21T02:00:06.614Z","response_time":58,"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":["metabolic-engineering","synbio","synthetic-biology","systems-biology"],"created_at":"2025-10-21T20:51:53.304Z","updated_at":"2025-10-21T20:51:56.181Z","avatar_url":"https://github.com/brsynth.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rpTools\n\n[![Anaconda-Server Badge](https://anaconda.org/brsynth/rptools/badges/latest_release_date.svg)](https://anaconda.org/brsynth/rptools)\n[![Anaconda-Server Badge](https://anaconda.org/brsynth/rptools/badges/version.svg)](https://anaconda.org/brsynth/rptools)\n![Tests](https://github.com/brsynth/rpTools/workflows/Tests/badge.svg)\n\nrpTools are dedicated to work around rpSBML data structure. Tools are the following:\n\n* rpCompletion: [README.md](rptools/rpcompletion/README.md)\n* rpFBA: [README.md](rptools/rpfba/README.md)\n* rpThermo: [README.md](rptools/rpthermo/README.md)\n* rpExtractSink: [README.md](rptools/rpextractsink/README.md)\n* rpLibs: [README.md](rptools/rplibs/README.md)\n* rpScore: [README.md](rptools/rpscore/README.md)\n* rpRank: [README.md](rptools/rprank/README.md)\n* rpViz: [README.md](rptools/rpviz/README.md)\n* rpReport: [README.md](rptools/rpreport/README.md)\n\n## Install\n```sh\n[sudo] conda install -c conda-forge rptools\n```\n\n## Run\nPlease see tool documentation.\n\n## Tests\nTest can be run with the following commands:\n\n### Natively\n```bash\ncd tests\npytest -v\n```\n\n## CI/CD\nFor further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](./ci/README.md)).\n\n## For developers\n\n### Development installation\n\nAfter a git clone:\n\n```sh\ncd \u003crepository\u003e\nconda env create -f environment.yaml -n \u003cdev_env\u003e\nconda develop -n \u003cdev_env\u003e .\n```\n\nWarning: if you do not specify an environment name with `-n \u003cdev_env\u003e`, \nthen 'rptools-dev' will be used.\n\nTest your installation with:\n\n```sh\nconda activate \u003cdev_env\u003e\npython -m rptools\npython -m rptools.rpcompletion -h\n```\n\nTo uninstall:\n\n```sh\nconda deactivate\nconda env remove -n \u003cdev_env\u003e\n```\n\n### Development installation (alternative using the ci toolkit)\n\nAfter a git clone:\n```sh\ngit clone https://github.com/breakthewall/cicd-toolkit.git\ncd cicd-toolkit\nmake test\ncd ..\nconda develop -n rptools_test .\n```\n\nThis will create a `rptools_test` environnement that can be activated to further develop / debug rptools.\n```sh\nconda activate rptools_test\npython -m rptools\npython -m rptools.rpcompletion -h\n```\n\n## Authors\n\n* **Melchior du Lac**\n* **Joan Hérisson**\n* **Thomas Duigou**\n\n## Licence\nrpTools is released under the MIT licence. See the [LICENCE file](./LICENSE) for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frptools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Frptools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frptools/lists"}