{"id":63487,"name":"cogent","description":"PyCogent: Official repository for software and unit tests","url":"https://github.com/pycogent/pycogent","last_synced_at":"2025-09-08T12:57:52.699Z","repository":{"id":6021932,"uuid":"7245628","full_name":"pycogent/pycogent","owner":"pycogent","description":"PyCogent: Official repository for software and unit tests","archived":false,"fork":false,"pushed_at":"2021-03-24T01:34:33.000Z","size":9681,"stargazers_count":91,"open_issues_count":0,"forks_count":51,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-08-27T15:54:17.716Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.pycogent.org/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pycogent.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2012-12-19T18:55:02.000Z","updated_at":"2025-01-11T19:05:43.000Z","dependencies_parsed_at":"2022-08-26T20:00:54.652Z","dependency_job_id":null,"html_url":"https://github.com/pycogent/pycogent","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/pycogent/pycogent","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/sbom","scorecard":{"id":751196,"data":{"date":"2025-08-11","repo":{"name":"github.com/pycogent/pycogent","commit":"f720cc3753429d130f9e9bc0756b8878c3d50ef2"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.6,"checks":[{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Code-Review","score":0,"reason":"Found 1/27 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"License","score":0,"reason":"license file not detected","details":["Warn: project does not have a license file"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Pinned-Dependencies","score":-1,"reason":"no dependencies found","details":null,"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 4 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-22T20:26:31.425Z","repository_id":6021932,"created_at":"2025-08-22T20:26:31.425Z","updated_at":"2025-08-22T20:26:31.425Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274188922,"owners_count":25237853,"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":"2025-09-08T02:00:09.813Z","response_time":121,"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"}},"owner":{"login":"pycogent","name":"pycogent","uuid":"3082578","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/3082578?v=4","repositories_count":3,"last_synced_at":"2024-03-26T22:26:31.720Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/pycogent","funding_links":[],"total_stars":87,"followers":1,"following":0,"created_at":"2022-11-04T14:53:17.391Z","updated_at":"2024-03-26T22:26:31.730Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent/repositories"},"packages":[{"id":2675215,"name":"cogent","ecosystem":"pypi","description":"COmparative GENomics Toolkit","homepage":"http://github.com/pycogent/pycogent","licenses":"GPL","normalized_licenses":["GPL-2.0+"],"repository_url":"https://github.com/pycogent/pycogent","keywords_array":["biology","genomics","statistics","phylogeny","evolution","bioinformatics"],"namespace":null,"versions_count":12,"first_release_published_at":"2007-08-15T06:38:32.000Z","latest_release_published_at":"2012-09-15T08:02:06.000Z","latest_release_number":"1.5.3","last_synced_at":"2025-08-27T08:34:34.190Z","created_at":"2022-04-10T10:24:03.775Z","updated_at":"2025-08-27T08:42:32.278Z","registry_url":"https://pypi.org/project/cogent/","install_command":"pip install cogent --index-url https://pypi.org/simple","documentation_url":"https://cogent.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["Development Status :: 5 - Production/Stable","Intended Audience :: Science/Research","License :: OSI Approved :: GNU General Public License (GPL)","Operating System :: OS Independent","Topic :: Scientific/Engineering :: Bio-Informatics","Topic :: Software Development :: Libraries :: Python Modules"],"normalized_name":"cogent","project_status":null},"repo_metadata":{"id":6021932,"uuid":"7245628","full_name":"pycogent/pycogent","owner":"pycogent","description":"PyCogent: Official repository for software and unit tests","archived":false,"fork":false,"pushed_at":"2021-03-24T01:34:33.000Z","size":9681,"stargazers_count":91,"open_issues_count":0,"forks_count":51,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-07-26T04:24:29.641Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.pycogent.org/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pycogent.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2012-12-19T18:55:02.000Z","updated_at":"2025-01-11T19:05:43.000Z","dependencies_parsed_at":"2022-08-26T20:00:54.652Z","dependency_job_id":null,"html_url":"https://github.com/pycogent/pycogent","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/pycogent/pycogent","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/sbom","scorecard":{"id":751196,"data":{"date":"2025-08-11","repo":{"name":"github.com/pycogent/pycogent","commit":"f720cc3753429d130f9e9bc0756b8878c3d50ef2"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.6,"checks":[{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Code-Review","score":0,"reason":"Found 1/27 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"License","score":0,"reason":"license file not detected","details":["Warn: project does not have a license file"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Pinned-Dependencies","score":-1,"reason":"no dependencies found","details":null,"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 4 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-22T20:26:31.425Z","repository_id":6021932,"created_at":"2025-08-22T20:26:31.425Z","updated_at":"2025-08-22T20:26:31.425Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272310762,"owners_count":24911657,"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":"2025-08-27T02:00:09.397Z","response_time":76,"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"},"owner_record":{"login":"pycogent","name":"pycogent","uuid":"3082578","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/3082578?v=4","repositories_count":3,"last_synced_at":"2024-03-26T22:26:31.720Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/pycogent","funding_links":[],"total_stars":87,"followers":1,"following":0,"created_at":"2022-11-04T14:53:17.391Z","updated_at":"2024-03-26T22:26:31.730Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pycogent/repositories"},"tags":[{"name":"1.9","sha":"8bd7b7b23715b6a329fd4e6b765a707d718d2b45","kind":"commit","published_at":"2016-06-15T03:12:56.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.9","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.9","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.9","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.9","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.9/manifests"},{"name":"1.5.3-release","sha":"c77e75ebf42c4a6379693cb792034efb9acd5891","kind":"tag","published_at":"2012-09-14T19:36:13.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.5.3-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.5.3-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.5.3-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.3-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.3-release/manifests"},{"name":"1.5.2rc2-release","sha":"51177575db65b8e9b4c9c509655f1563a32ae4bf","kind":"tag","published_at":"2012-09-07T22:12:55.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.5.2rc2-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.5.2rc2-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.5.2rc2-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.2rc2-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.2rc2-release/manifests"},{"name":"1.5.2-release","sha":"d9e69a361a31388aca689a6ad02d5da1c2f44a59","kind":"tag","published_at":"2012-09-07T18:33:11.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.5.2-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.5.2-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.5.2-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.2-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.2-release/manifests"},{"name":"1.5.1-release","sha":"ddd31466ce1e46d0251e7b5651412cb6a1603034","kind":"tag","published_at":"2011-06-07T00:47:52.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.5.1-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.5.1-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.5.1-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.1-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5.1-release/manifests"},{"name":"1.5-release","sha":"22d8b32829c9bf01d372865513972220489ddfb1","kind":"tag","published_at":"2010-11-09T01:32:17.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.5-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.5-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.5-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.5-release/manifests"},{"name":"1.4.1-release","sha":"d0b8ae5d790bd474489fc352ef7f49fc6a0a8a94","kind":"tag","published_at":"2010-04-08T04:09:41.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.4.1-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.4.1-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.4.1-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.4.1-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.4.1-release/manifests"},{"name":"1.4-release","sha":"fae854e9c3d66ab17fea2391ef655061d3f77f2f","kind":"tag","published_at":"2009-12-16T17:10:55.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.4-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.4-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.4-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.4-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.4-release/manifests"},{"name":"1.3.1-release","sha":"0df9489ca8e33c339ec9a322c6cdff281e93a270","kind":"tag","published_at":"2009-06-19T16:23:42.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.3.1-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.3.1-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.3.1-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.3.1-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.3.1-release/manifests"},{"name":"1.3-release","sha":"ee096458578244aad37b12e37cce6a89866fcf90","kind":"tag","published_at":"2009-06-19T00:38:57.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.3-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.3-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.3-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.3-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.3-release/manifests"},{"name":"1.2-release","sha":"3ee3d3d3d5fe0c05b776b3111dee6692f0d8f214","kind":"tag","published_at":"2008-12-19T00:53:48.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.2-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.2-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.2-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.2-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.2-release/manifests"},{"name":"1.1-release","sha":"d962e171f7cf8efd3f71a00db33451cd515682e8","kind":"tag","published_at":"2008-08-07T02:47:43.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/1.1-release","html_url":"https://github.com/pycogent/pycogent/releases/tag/1.1-release","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@1.1-release","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.1-release","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/1.1-release/manifests"},{"name":"presprint-1.1","sha":"af395d1492716644601f61cf683f34d43da0df3c","kind":"tag","published_at":"2007-12-14T21:24:21.000Z","download_url":"https://codeload.github.com/pycogent/pycogent/tar.gz/presprint-1.1","html_url":"https://github.com/pycogent/pycogent/releases/tag/presprint-1.1","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/pycogent/pycogent@presprint-1.1","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/presprint-1.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/tags/presprint-1.1/manifests"}]},"repo_metadata_updated_at":"2025-08-27T08:42:32.278Z","dependent_packages_count":0,"downloads":420,"downloads_period":"last-month","dependent_repos_count":24,"rankings":{"downloads":13.815334273711091,"dependent_repos_count":2.9623203250106056,"dependent_packages_count":10.051680376746889,"stargazers_count":7.552932452113284,"forks_count":5.626898105764508,"docker_downloads_count":1.4395650163730223,"average":6.908121758286566},"purl":"pkg:pypi/cogent","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/cogent","docker_dependents_count":3,"docker_downloads_count":220,"usage_url":"https://repos.ecosyste.ms/usage/pypi/cogent","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/cogent/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-07-26T00:00:17.174Z","issues_count":72,"pull_requests_count":28,"avg_time_to_close_issue":90670437.09722222,"avg_time_to_close_pull_request":80468235.82142857,"issues_closed_count":72,"pull_requests_closed_count":28,"pull_request_authors_count":16,"issue_authors_count":44,"avg_comments_per_issue":2.055555555555556,"avg_comments_per_pull_request":4.642857142857143,"merged_pull_requests_count":14,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":0,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":0,"past_year_pull_request_authors_count":0,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/issues","maintainers":[{"login":"gregcaporaso","count":12,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/gregcaporaso"},{"login":"jairideout","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jairideout"},{"login":"mikerobeson","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikerobeson"},{"login":"GavinHuttley","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/GavinHuttley"}],"active_maintainers":[]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/cogent/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/cogent/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/cogent/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/cogent/related_packages","maintainers":[{"uuid":"mcdonald","login":"mcdonald","name":null,"email":null,"url":null,"packages_count":13,"html_url":"https://pypi.org/user/mcdonald/","role":null,"created_at":"2023-02-23T20:29:44.919Z","updated_at":"2023-02-23T20:29:44.919Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/mcdonald/packages"},{"uuid":"GavinHuttley","login":"GavinHuttley","name":null,"email":null,"url":null,"packages_count":10,"html_url":"https://pypi.org/user/GavinHuttley/","role":null,"created_at":"2023-02-23T20:29:44.876Z","updated_at":"2023-02-23T20:29:44.876Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/GavinHuttley/packages"},{"uuid":"hamady","login":"hamady","name":null,"email":null,"url":null,"packages_count":1,"html_url":"https://pypi.org/user/hamady/","role":null,"created_at":"2023-02-23T20:29:44.893Z","updated_at":"2023-02-23T20:29:44.893Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/hamady/packages"},{"uuid":"rdknight","login":"rdknight","name":null,"email":null,"url":null,"packages_count":1,"html_url":"https://pypi.org/user/rdknight/","role":null,"created_at":"2023-02-23T20:29:44.931Z","updated_at":"2023-02-23T20:29:44.931Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/rdknight/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":726136,"maintainers_count":308800,"namespaces_count":0,"keywords_count":238245,"github":"pypi","metadata":{"funded_packages_count":50579},"icon_url":"https://github.com/pypi.png","created_at":"2022-04-04T15:19:23.364Z","updated_at":"2025-09-08T05:32:36.857Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/namespaces"}}],"commits":{"id":550743,"full_name":"pycogent/pycogent","default_branch":"master","committers":[{"name":"Gavin Huttley","email":"gavin.huttley@anu.edu.au","login":null,"count":381},{"name":"Daniel McDonald","email":"mcdonadt@colorado.edu","login":null,"count":122},{"name":"Peter Maxwell","email":"pm67nz@gmail.com","login":null,"count":122},{"name":"Greg Caporaso","email":"gregcaporaso@gmail.com","login":null,"count":110},{"name":"mikerobeson","email":"soilbdelloid@gmail.com","login":null,"count":98},{"name":"Gavin Huttley","email":"Gavin.Huttley@anu.edu.au","login":null,"count":79},{"name":"Jai Ram Rideout","email":"jai.rideout@gmail.com","login":null,"count":51},{"name":"Justin Kuczynski","email":"justinak@gmail.com","login":null,"count":46},{"name":"Jeremy Widmann","email":"jeremy.widmann@colorado.edu","login":null,"count":45},{"name":"Kyle Bittinger","email":"kylebittinger@gmail.com","login":null,"count":41},{"name":"Rob Knight","email":"rob.knight@colorado.edu","login":null,"count":32},{"name":"Jesse Stombaugh","email":"jistombaugh@gmail.com","login":null,"count":20},{"name":"Micah Hamady","email":"hamady@colorado.edu","login":null,"count":18},{"name":"Sandra Smit","email":"S.Smit@few.vu.nl","login":null,"count":18},{"name":"Jesse Zaneveld","email":"zaneveld@gmail.com","login":null,"count":16},{"name":"Catherine Lozupone","email":"lozupone@colorado.edu","login":null,"count":15},{"name":"Antonio Gonzalez","email":"antgonza@gmail.com","login":null,"count":14},{"name":"Marcin Cieślik","email":"marcin.cieslik@gmail.com","login":null,"count":11},{"name":"Jens Reeder","email":"jens.reeder@gmail.com","login":null,"count":10},{"name":"Dan Knights","email":"dknights@umn.edu","login":null,"count":9},{"name":"Mike Robeson","email":"mike.robeson@colorado.edu","login":null,"count":9},{"name":"Tony Walters","email":"william.a.walters@gmail.com","login":null,"count":8},{"name":"Kristian Rother","email":"krother@rubor.de","login":null,"count":7},{"name":"gawbul","email":"gawbul@gmail.com","login":null,"count":5},{"name":"Zongzhi Liu","email":"zongzhi.liu@gmail.com","login":null,"count":3},{"name":"Shinya SUZUKI","email":"minasitawakou@gmail.com","login":null,"count":2},{"name":"Skyler Sun","email":"skyler@acm.org","login":null,"count":2},{"name":"Hua Ying","email":"hua.ying@anu.edu.au","login":null,"count":2},{"name":"Jose Carlos Clemente Litran","email":"jose.clemente@gmail.com","login":null,"count":2},{"name":"Meg Pirrung","email":"meganap@gmail.com","login":null,"count":2},{"name":"Julia Goodrich","email":"jkg59@cornell.edu","login":null,"count":2},{"name":"Matthew Wakefield","email":"wakefield@wehi.edu.au","login":null,"count":2},{"name":"zech","email":"not.to.miss@gmail.com","login":null,"count":2},{"name":"Doug Wendel","email":"douginator2000@gmail.com","login":null,"count":1},{"name":"Adam Robbins-Pianka","email":"adam.robbinspianka@colorado.edu","login":null,"count":1},{"name":"Robeson","email":"msr@mac92855.ornl.gov","login":null,"count":1},{"name":"Daniel McDonald","email":"wasade@gmail.com","login":null,"count":1},{"name":"Jonatan Nilsson","email":"jonatan.nilsson@atlasantibodies.com","login":null,"count":1},{"name":"mikerobeson","email":"mike@little-beast.gateway.2wire.net","login":null,"count":1}],"total_commits":1312,"total_committers":39,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":33.64102564102564,"dds":0.7096036585365854,"past_year_committers":[],"past_year_total_commits":0,"past_year_total_committers":0,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":0.0,"past_year_dds":0.0,"last_synced_at":"2024-01-25T02:37:45.335Z","last_synced_commit":"f720cc3753429d130f9e9bc0756b8878c3d50ef2","created_at":"2023-03-09T04:38:46.204Z","updated_at":"2024-01-25T02:37:45.336Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5483322,"commits_count":854270774,"contributors_count":31138750,"owners_count":908526,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"pycogent/pycogent","html_url":"https://github.com/pycogent/pycogent","last_synced_at":"2025-08-27T08:43:09.339Z","status":"error","issues_count":72,"pull_requests_count":28,"avg_time_to_close_issue":90670437.09722222,"avg_time_to_close_pull_request":80468235.82142857,"issues_closed_count":72,"pull_requests_closed_count":28,"pull_request_authors_count":16,"issue_authors_count":44,"avg_comments_per_issue":2.055555555555556,"avg_comments_per_pull_request":4.642857142857143,"merged_pull_requests_count":14,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":0,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":0,"past_year_pull_request_authors_count":0,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"created_at":"2023-05-14T10:49:47.174Z","updated_at":"2025-08-27T08:43:09.339Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/pycogent%2Fpycogent/issues","issue_labels_count":{"bug":5,"question":4,"enhancement":3},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":55,"MEMBER":13,"CONTRIBUTOR":3},"pull_request_author_associations_count":{"MEMBER":10,"CONTRIBUTOR":10,"NONE":8},"issue_authors":{"gregcaporaso":7,"tillea":5,"jairideout":5,"guillermomarco":4,"boxiangliu":3,"jergosh":3,"mbiokyle29":2,"finswimmer":2,"RNAer":2,"vladie0":2,"BenKaehler":2,"nieder":2,"ropermpv":1,"wasade":1,"JensTimmerman":1,"gawbul":1,"kulkarnik":1,"krcurtis":1,"fizwit":1,"zz2liu":1,"santiagoha":1,"GavinHuttley":1,"lassancejm":1,"riemannzetagambit":1,"ghost":1,"campenr":1,"skylersun":1,"Gaby1212":1,"josenavas":1,"alanwilter":1,"sulsj":1,"yarden":1,"sarahparks":1,"MarijkeVM":1,"miklou":1,"raonyguimaraes":1,"adamrp":1,"chirrie":1,"mlynekg3":1,"evolvedmicrobe":1,"merenlin":1,"yuharasatoshi":1,"yvancouver":1,"lczech":1},"pull_request_authors":{"gregcaporaso":5,"mikerobeson":5,"wasade":3,"ctSkennerton":2,"adamrp":2,"gawbul":1,"ggonnella":1,"skylersun":1,"jonatanfan":1,"blankenberg":1,"TaskeHAMANO":1,"davidsoergel":1,"zachcp":1,"pm67nz":1,"grandynguyen":1,"kylebittinger":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-30T00:00:08.204Z","repositories_count":8430842,"issues_count":20140335,"pull_requests_count":49421580,"authors_count":7006763,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{},"past_year_pull_request_authors":{},"maintainers":[{"login":"gregcaporaso","count":12,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/gregcaporaso"},{"login":"jairideout","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jairideout"},{"login":"mikerobeson","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikerobeson"},{"login":"GavinHuttley","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/GavinHuttley"}],"active_maintainers":[]},"events":{"total":{"WatchEvent":2},"last_year":{"WatchEvent":2}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-08-26T20:00:54.399Z","updated_at":"2022-08-26T20:00:54.399Z","repository_link":"https://github.com/pycogent/pycogent/blob/master/setup.py","dependencies":[{"id":2850343044,"package_name":"numpy","ecosystem":"pypi","requirements":"\u003e=1.3.0","direct":true,"kind":"runtime","optional":false}]}],"score":14.683190289618178,"created_at":"2025-09-08T11:18:30.025Z","updated_at":"2025-10-07T08:24:34.416Z","avatar_url":"https://github.com/pycogent.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":420,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/63487","html_url":"https://science.ecosyste.ms/projects/63487"}