{"id":2825,"name":"SuchTree","description":"SuchTree: Fast, thread-safe computations with phylogenetic trees - Published in JOSS (2018)","url":"https://github.com/ryneches/suchtree","last_synced_at":"2025-09-04T16:53:42.668Z","repository":{"id":8344734,"uuid":"58027217","full_name":"ryneches/SuchTree","owner":"ryneches","description":"A Python library for fast, thread-safe computations on phylogenetic trees","archived":false,"fork":false,"pushed_at":"2025-02-05T03:05:14.000Z","size":21247,"stargazers_count":28,"open_issues_count":8,"forks_count":6,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-08-29T19:51:29.137Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ryneches.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2016-05-04T06:09:27.000Z","updated_at":"2025-03-17T16:15:00.000Z","dependencies_parsed_at":"2025-04-12T17:59:30.845Z","dependency_job_id":null,"html_url":"https://github.com/ryneches/SuchTree","commit_stats":{"total_commits":267,"total_committers":6,"mean_commits":44.5,"dds":"0.38951310861423216","last_synced_commit":"1fbb0992055f74225e57b8f97d2bf7cb6f4a8d4d"},"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/ryneches/SuchTree","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/sbom","scorecard":{"id":792965,"data":{"date":"2025-08-11","repo":{"name":"github.com/ryneches/SuchTree","commit":"7eb66165335cb7ce64c0b8ff7de6da9ad9d4484d"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.5,"checks":[{"name":"Code-Review","score":0,"reason":"Found 0/30 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":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","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":"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/codecov.yml:1","Warn: no topLevel permission defined: .github/workflows/package.yml:1","Info: no jobLevel write permissions found"],"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":"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":"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":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"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":"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":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: BSD 3-Clause \"New\" or \"Revised\" License: LICENSE:0"],"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":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact v1.2 not signed: https://api.github.com/repos/ryneches/SuchTree/releases/187188020","Warn: release artifact v1.1 not signed: https://api.github.com/repos/ryneches/SuchTree/releases/156212592","Warn: release artifact v1.0 not signed: https://api.github.com/repos/ryneches/SuchTree/releases/69806390","Warn: release artifact v1.2 does not have provenance: https://api.github.com/repos/ryneches/SuchTree/releases/187188020","Warn: release artifact v1.1 does not have provenance: https://api.github.com/repos/ryneches/SuchTree/releases/156212592","Warn: release artifact v1.0 does not have provenance: https://api.github.com/repos/ryneches/SuchTree/releases/69806390"],"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"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":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codecov.yml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/codecov.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codecov.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/codecov.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/codecov.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/codecov.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/codecov.yml:40: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/codecov.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:17: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:43: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:77: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/package.yml:84: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/package.yml:89: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/package.yml:97: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/package.yml:105: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:112: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yml:122: update your workflow using https://app.stepsecurity.io/secureworkflow/ryneches/SuchTree/package.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/codecov.yml:24","Warn: pipCommand not pinned by hash: .github/workflows/codecov.yml:25","Warn: pipCommand not pinned by hash: .github/workflows/codecov.yml:26","Warn: pipCommand not pinned by hash: .github/workflows/codecov.yml:29","Warn: pipCommand not pinned by hash: .github/workflows/package.yml:22","Warn: pipCommand not pinned by hash: .github/workflows/package.yml:24","Warn: pipCommand not pinned by hash: .github/workflows/package.yml:25","Warn: pipCommand not pinned by hash: .github/workflows/package.yml:26","Info:   0 out of   8 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   6 third-party GitHubAction dependencies pinned","Info:   0 out of   8 pipCommand dependencies pinned"],"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":"Vulnerabilities","score":3,"reason":"7 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-23T08:05:17.021Z","repository_id":8344734,"created_at":"2025-08-23T08:05:17.021Z","updated_at":"2025-08-23T08:05:17.021Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273611447,"owners_count":25136972,"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":"2025-09-04T02:00:08.968Z","response_time":61,"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":"ryneches","name":"Russell Neches","uuid":"440383","kind":"user","description":"Assistant professor at Kyoto University: Evolution \u0026 ecology of viruses \u0026 microbes with a side of graph theory \u0026 machine learning. Open( Access, Science, Data )","email":"","website":"http://vort.org","location":"京都府","twitter":null,"company":"Kyoto University","icon_url":"https://avatars.githubusercontent.com/u/440383?u=84888b5902bec02262cd72e4b96a71b2831d9d61\u0026v=4","repositories_count":95,"last_synced_at":"2025-08-31T00:24:57.175Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/ryneches","funding_links":[],"total_stars":99,"followers":81,"following":57,"created_at":"2022-11-02T22:49:09.604Z","updated_at":"2025-08-31T00:24:57.175Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches/repositories"},"packages":[{"id":2935533,"name":"suchtree","ecosystem":"pypi","description":"A python library for doing fast, thread-safe computations on phylogenetic trees","homepage":"https://github.com/ryneches/SuchTree","licenses":"BSD","normalized_licenses":["BSD-3-Clause"],"repository_url":"https://github.com/ryneches/SuchTree","keywords_array":["biology","bio","phylogenetics","phylogeny","tree"],"namespace":null,"versions_count":9,"first_release_published_at":"2017-04-01T00:44:31.000Z","latest_release_published_at":"2024-11-20T09:07:11.000Z","latest_release_number":"1.2","last_synced_at":"2025-09-03T21:42:53.923Z","created_at":"2022-04-10T12:44:43.906Z","updated_at":"2025-09-03T21:42:53.923Z","registry_url":"https://pypi.org/project/suchtree/","install_command":"pip install suchtree --index-url https://pypi.org/simple","documentation_url":"https://suchtree.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["License :: OSI Approved :: BSD License","Programming Language :: Python :: 3"],"normalized_name":"suchtree","project_status":null},"repo_metadata":{"uuid":"58027217","full_name":"ryneches/SuchTree","owner":"ryneches","description":"A Python library for fast, thread-safe computations on phylogenetic trees","archived":false,"fork":false,"pushed_at":"2023-07-19T05:46:33.000Z","size":19810,"stargazers_count":26,"open_issues_count":8,"forks_count":5,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-01-02T04:36:36.514Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ryneches.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-05-04T06:09:27.000Z","updated_at":"2023-04-26T05:51:02.000Z","dependencies_parsed_at":"2023-11-09T13:14:22.578Z","dependency_job_id":null,"html_url":"https://github.com/ryneches/SuchTree","commit_stats":{"total_commits":267,"total_committers":6,"mean_commits":44.5,"dds":"0.38951310861423216","last_synced_commit":"1fbb0992055f74225e57b8f97d2bf7cb6f4a8d4d"},"previous_names":[],"tags_count":7,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":178766185,"owners_count":10723682,"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"},"owner_record":{"login":"ryneches","name":"Russell Neches","uuid":"440383","kind":"user","description":"JSPS Fellow at Kyoto University: Evolution \u0026 ecology of viruses \u0026 microbes with a side of graph theory and machine learning. Open( Access, Science, Data ).","email":"","website":"http://vort.org","location":"京都, 日本","twitter":"ryneches","company":"Kyoto University","icon_url":"https://avatars.githubusercontent.com/u/440383?v=4","repositories_count":38,"last_synced_at":"2023-03-11T10:10:48.285Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/ryneches","created_at":"2022-11-02T22:49:09.604Z","updated_at":"2023-03-11T10:10:48.306Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryneches/repositories"},"tags":[{"name":"v1.0","sha":"7594bc4b9b32e36a54e0d837d3ea0a4ce352d4d0","kind":"commit","published_at":"2022-06-17T09:30:49.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/v1.0","html_url":"https://github.com/ryneches/SuchTree/releases/tag/v1.0","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/v1.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/v1.0/manifests"},{"name":"0.8","sha":"8cd01d5cff97f03e42aaaa311f93e23c817430be","kind":"commit","published_at":"2022-06-15T12:11:04.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.8","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.8","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.8","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.8/manifests"},{"name":"0.7","sha":"275b3c75622e80a0cede19bba73158d824014d5b","kind":"commit","published_at":"2018-06-20T23:43:19.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.7","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.7","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.7","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.7/manifests"},{"name":"0.6","sha":"ed0a599c6083c3c96f4eb4ceef07cb6297d00afb","kind":"commit","published_at":"2018-04-04T20:38:58.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.6","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.6","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.6","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.6/manifests"},{"name":"0.3","sha":"a21ffc8a519b5bdd9b052dc4581ce9c76642bceb","kind":"commit","published_at":"2018-03-03T03:11:19.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.3","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.3","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.3","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.3/manifests"},{"name":"0.2","sha":"6fd877785487e4f100a8a96fc2e604dccccfd383","kind":"tag","published_at":"2017-04-01T00:43:19.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.2","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.2","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.2","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.2/manifests"},{"name":"0.1","sha":"7f6ab986fb8b83def2fd3f659a95d6ce7db3a1cf","kind":"tag","published_at":"2017-04-01T00:33:17.000Z","download_url":"https://codeload.github.com/ryneches/SuchTree/tar.gz/0.1","html_url":"https://github.com/ryneches/SuchTree/releases/tag/0.1","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/tags/0.1/manifests"}]},"repo_metadata_updated_at":"2024-01-02T04:36:49.556Z","dependent_packages_count":0,"downloads":110,"downloads_period":"last-month","dependent_repos_count":1,"rankings":{"downloads":21.23400009502542,"dependent_repos_count":21.525853977374208,"dependent_packages_count":10.141135697755281,"stargazers_count":12.06924381365089,"forks_count":14.234498848670462,"docker_downloads_count":null,"average":15.840946486495252},"purl":"pkg:pypi/suchtree","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/suchtree","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/pypi/suchtree","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/suchtree/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2023-12-28T00:39:42.575Z","issues_count":18,"pull_requests_count":7,"avg_time_to_close_issue":107249023.3,"avg_time_to_close_pull_request":476995.5714285714,"issues_closed_count":10,"pull_requests_closed_count":7,"pull_request_authors_count":4,"issue_authors_count":6,"avg_comments_per_issue":0.5,"avg_comments_per_pull_request":0.5714285714285714,"merged_pull_requests_count":7,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":2,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":710062.0,"past_year_avg_time_to_close_pull_request":710272.0,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":0.5,"past_year_avg_comments_per_pull_request":1.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":1,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/issues"},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/suchtree/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/suchtree/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/suchtree/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/suchtree/related_packages","maintainers":[{"uuid":"ryneches","login":"ryneches","name":null,"email":null,"url":null,"packages_count":3,"html_url":"https://pypi.org/user/ryneches/","role":null,"created_at":"2023-02-25T13:59:07.682Z","updated_at":"2023-02-25T13:59:07.682Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/ryneches/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":724747,"maintainers_count":308195,"namespaces_count":0,"keywords_count":237984,"github":"pypi","metadata":{"funded_packages_count":50481},"icon_url":"https://github.com/pypi.png","created_at":"2022-04-04T15:19:23.364Z","updated_at":"2025-09-04T05:23:51.177Z","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":666855,"full_name":"ryneches/SuchTree","default_branch":"master","committers":[{"name":"Russell Neches","email":"russell@vort.org","login":null,"count":224},{"name":"Russell Neches","email":"git@vort.org","login":"ryneches","count":96},{"name":"Camille Scott","email":"camille.scott.w@gmail.com","login":"camillescott","count":4},{"name":"James Gerity","email":"snoopjedi@gmail.com","login":"SnoopJ","count":2},{"name":"Matthew Andres Moreno","email":"mmore500.login@gmail.com","login":"mmore500","count":1},{"name":"Arfon Smith","email":"arfon","login":"arfon","count":1}],"total_commits":328,"total_committers":6,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":54.666666666666664,"dds":0.31707317073170727,"past_year_committers":[{"name":"Russell Neches","email":"russell@vort.org","login":null,"count":20}],"past_year_total_commits":20,"past_year_total_committers":1,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":20.0,"past_year_dds":0.0,"last_synced_at":"2025-08-07T07:23:43.058Z","last_synced_commit":"7eb66165335cb7ce64c0b8ff7de6da9ad9d4484d","created_at":"2023-03-09T10:18:12.717Z","updated_at":"2025-08-07T07:23:43.062Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-08T00:00:12.331Z","repositories_count":5415193,"commits_count":848608369,"contributors_count":30915594,"owners_count":904139,"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":"ryneches/SuchTree","html_url":"https://github.com/ryneches/SuchTree","last_synced_at":"2025-08-31T20:09:01.324Z","status":"error","issues_count":19,"pull_requests_count":8,"avg_time_to_close_issue":97502451.18181819,"avg_time_to_close_pull_request":421024.75,"issues_closed_count":11,"pull_requests_closed_count":8,"pull_request_authors_count":5,"issue_authors_count":6,"avg_comments_per_issue":0.47368421052631576,"avg_comments_per_pull_request":0.5,"merged_pull_requests_count":8,"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":"2023-05-15T00:54:10.652Z","updated_at":"2025-09-01T14:42:55.469Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryneches%2FSuchTree/issues","issue_labels_count":{"enhancement":4,"build":1,"question":1},"pull_request_labels_count":{},"issue_author_associations_count":{"OWNER":14,"NONE":4,"CONTRIBUTOR":1},"pull_request_author_associations_count":{"CONTRIBUTOR":4,"COLLABORATOR":3,"OWNER":2},"issue_authors":{"ryneches":14,"apcamargo":1,"cboettig":1,"Mass23":1,"weirdlobster":1,"mmore500":1},"pull_request_authors":{"camillescott":3,"SnoopJ":2,"ryneches":2,"arfon":1,"mmore500":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-01T00:00:07.725Z","repositories_count":9946380,"issues_count":29473096,"pull_requests_count":85381310,"authors_count":9367128,"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":"ryneches","count":16,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ryneches"},{"login":"camillescott","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/camillescott"}],"active_maintainers":[]},"events":{"total":{"ReleaseEvent":1,"WatchEvent":2,"PushEvent":11,"CreateEvent":1},"last_year":{"ReleaseEvent":1,"WatchEvent":2,"PushEvent":11,"CreateEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-08-07T03:00:34.846Z","updated_at":"2022-08-07T03:00:34.846Z","repository_link":"https://github.com/ryneches/SuchTree/blob/master/requirements.txt","dependencies":[{"id":587007768,"package_name":"cython","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":587007769,"package_name":"numpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":587007770,"package_name":"dendropy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-11-09T13:14:22.325Z","updated_at":"2023-11-09T13:14:22.325Z","repository_link":"https://github.com/ryneches/SuchTree/blob/master/pyproject.toml","dependencies":[]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2023-11-09T13:14:22.468Z","updated_at":"2023-11-09T13:14:22.468Z","repository_link":"https://github.com/ryneches/SuchTree/blob/master/setup.py","dependencies":[]},{"ecosystem":"actions","filepath":".github/workflows/package.yml","sha":null,"kind":"manifest","created_at":"2024-09-14T18:25:52.058Z","updated_at":"2024-09-14T18:25:52.058Z","repository_link":"https://github.com/ryneches/SuchTree/blob/master/.github/workflows/package.yml","dependencies":[{"id":20140382339,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":20140382340,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v5","direct":true,"kind":"composite","optional":false},{"id":20140382341,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":20140382342,"package_name":"actions/download-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":20140382343,"package_name":"docker/setup-qemu-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":20140382344,"package_name":"pypa/cibuildwheel","ecosystem":"actions","requirements":"v2.18.0","direct":true,"kind":"composite","optional":false},{"id":20140382345,"package_name":"actions/upload-artifact/merge","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/codecov.yml","sha":null,"kind":"manifest","created_at":"2024-11-27T07:28:34.532Z","updated_at":"2024-11-27T07:28:34.532Z","repository_link":"https://github.com/ryneches/SuchTree/blob/master/.github/workflows/codecov.yml","dependencies":[{"id":20922009952,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":20922009953,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":20922009954,"package_name":"codecov/codecov-action","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":20922009955,"package_name":"codecov/test-results-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]}],"score":10.093777278979259,"created_at":"2025-09-04T09:18:06.563Z","updated_at":"2025-10-07T08:04:42.376Z","avatar_url":"https://github.com/ryneches.png","language":"Jupyter Notebook","category":"Scientific Software","sub_category":"Peer-reviewed","monthly_downloads":110,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioinformatics","genomics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/2825","html_url":"https://science.ecosyste.ms/projects/2825","bibtex_url":"https://science.ecosyste.ms/projects/2825/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/2825/export.apalike"}