{"id":34071118,"url":"https://github.com/specifysystems/lmpy","last_synced_at":"2025-12-30T16:18:08.811Z","repository":{"id":37919560,"uuid":"190765597","full_name":"specifysystems/lmpy","owner":"specifysystems","description":"A library of tools useful for Lifemapper and related computations","archived":true,"fork":false,"pushed_at":"2023-07-31T17:14:53.000Z","size":70934,"stargazers_count":2,"open_issues_count":18,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-09-09T18:19:15.167Z","etag":null,"topics":["dendropy","null-model","numpy-arrays","presence-absence-matrix","randomization"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/specifysystems.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null}},"created_at":"2019-06-07T15:18:47.000Z","updated_at":"2024-09-04T16:02:43.000Z","dependencies_parsed_at":"2023-02-14T12:02:54.040Z","dependency_job_id":null,"html_url":"https://github.com/specifysystems/lmpy","commit_stats":null,"previous_names":[],"tags_count":40,"template":false,"template_full_name":null,"purl":"pkg:github/specifysystems/lmpy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/specifysystems%2Flmpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/specifysystems%2Flmpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/specifysystems%2Flmpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/specifysystems%2Flmpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/specifysystems","download_url":"https://codeload.github.com/specifysystems/lmpy/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/specifysystems%2Flmpy/sbom","scorecard":{"id":840864,"data":{"date":"2025-08-11","repo":{"name":"github.com/specifysystems/lmpy","commit":"61e1a17681038c0f04facdc04e29bf77178c3128"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.9,"checks":[{"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Info: jobLevel 'contents' permission set to 'read': .github/workflows/docker.yml:13","Warn: no topLevel permission defined: .github/workflows/build_sphinx_docs.yml:1","Warn: no topLevel permission defined: .github/workflows/check_citation.yml:1","Warn: no topLevel permission defined: .github/workflows/docker.yml:1","Warn: no topLevel permission defined: .github/workflows/main.yml:1","Warn: no topLevel permission defined: .github/workflows/pre-commit.yml:1","Warn: no topLevel permission defined: .github/workflows/pre-release.yml:1","Warn: no topLevel permission defined: .github/workflows/publish_to_pypi.yml:1","Warn: no topLevel permission defined: .github/workflows/pytest-conda.yml:1","Warn: no topLevel permission defined: .github/workflows/pytest-installed.yml:1","Warn: no topLevel permission defined: .github/workflows/test_sphinx_docs.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":"Code-Review","score":0,"reason":"Found 0/3 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":"project is archived","details":["Warn: Repository is archived."],"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":"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":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: GNU General Public License v3.0: 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":"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":"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":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"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":"Signed-Releases","score":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact 3.1.21 not signed: https://api.github.com/repos/specifysystems/lmpy/releases/68481199","Warn: release artifact 3.1.20 not signed: https://api.github.com/repos/specifysystems/lmpy/releases/67831756","Warn: release artifact 3.1.19 not signed: https://api.github.com/repos/specifysystems/lmpy/releases/67557208","Warn: release artifact 3.1.21 does not have provenance: https://api.github.com/repos/specifysystems/lmpy/releases/68481199","Warn: release artifact 3.1.20 does not have provenance: https://api.github.com/repos/specifysystems/lmpy/releases/67831756","Warn: release artifact 3.1.19 does not have provenance: https://api.github.com/repos/specifysystems/lmpy/releases/67557208"],"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":0,"reason":"17 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2019-241","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","Warn: Project is vulnerable to: PYSEC-2014-14 / GHSA-652x-xj99-gmcc","Warn: Project is vulnerable to: GHSA-9hjg-9r4m-mvj7","Warn: Project is vulnerable to: GHSA-9wx4-h78v-vm56","Warn: Project is vulnerable to: PYSEC-2014-13 / GHSA-cfj3-7x9c-4p3h","Warn: Project is vulnerable to: PYSEC-2018-28 / GHSA-x84v-xcm2-53pg","Warn: Project is vulnerable to: PYSEC-2013-22 / GHSA-27x4-j476-jp5f","Warn: Project is vulnerable to: PYSEC-2025-49 / GHSA-5rjg-fvgr-3xxf","Warn: Project is vulnerable to: GHSA-cx63-2mw6-8hw5","Warn: Project is vulnerable to: PYSEC-2022-43012 / GHSA-r9hx-vwmv-q579"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"SAST","score":7,"reason":"SAST tool detected but not run on all commits","details":["Info: SAST configuration detected: CodeQL","Warn: 0 commits out of 30 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"}},{"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/build_sphinx_docs.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/build_sphinx_docs.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build_sphinx_docs.yml:39: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/build_sphinx_docs.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build_sphinx_docs.yml:43: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/build_sphinx_docs.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/check_citation.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/check_citation.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/check_citation.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/check_citation.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/check_citation.yml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/check_citation.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/docker.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:21: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:24: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:27: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:33: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:41: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker.yml:52: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/docker.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/main.yml:39: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/main.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/main.yml:43: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/main.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/main.yml:54: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/main.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/main.yml:68: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/main.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre-commit.yml:11: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-commit.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre-commit.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-commit.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pre-commit.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-commit.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre-release.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-release.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre-release.yml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-release.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pre-release.yml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pre-release.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/publish_to_pypi.yml:14: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/publish_to_pypi.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/publish_to_pypi.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/publish_to_pypi.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/publish_to_pypi.yml:33: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/publish_to_pypi.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/publish_to_pypi.yml:39: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/publish_to_pypi.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pytest-conda.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pytest-conda.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pytest-conda.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pytest-conda.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pytest-installed.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pytest-installed.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pytest-installed.yml:21: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/pytest-installed.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/test_sphinx_docs.yml:9: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/test_sphinx_docs.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_sphinx_docs.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/specifysystems/lmpy/test_sphinx_docs.yml/main?enable=pin","Warn: containerImage not pinned by hash: Dockerfile:1","Warn: pipCommand not pinned by hash: Dockerfile:27","Warn: pipCommand not pinned by hash: .github/workflows/build_sphinx_docs.yml:19","Warn: pipCommand not pinned by hash: .github/workflows/build_sphinx_docs.yml:25","Warn: pipCommand not pinned by hash: .github/workflows/build_sphinx_docs.yml:28","Warn: pipCommand not pinned by hash: .github/workflows/build_sphinx_docs.yml:34","Warn: pipCommand not pinned by hash: .github/workflows/check_citation.yml:24","Warn: pipCommand not pinned by hash: .github/workflows/check_citation.yml:25","Warn: pipCommand not pinned by hash: .github/workflows/pre-release.yml:20","Warn: pipCommand not pinned by hash: .github/workflows/pre-release.yml:21","Warn: pipCommand not pinned by hash: .github/workflows/publish_to_pypi.yml:21","Warn: pipCommand not pinned by hash: .github/workflows/pytest-conda.yml:56","Warn: pipCommand not pinned by hash: .github/workflows/test_sphinx_docs.yml:15","Warn: pipCommand not pinned by hash: .github/workflows/test_sphinx_docs.yml:21","Warn: pipCommand not pinned by hash: .github/workflows/test_sphinx_docs.yml:24","Warn: pipCommand not pinned by hash: .github/workflows/test_sphinx_docs.yml:30","Info:   0 out of  17 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of  16 third-party GitHubAction dependencies pinned","Info:   0 out of   1 containerImage dependencies pinned","Info:   0 out of  15 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"}}]},"last_synced_at":"2025-08-23T20:26:45.092Z","repository_id":37919560,"created_at":"2025-08-23T20:26:45.092Z","updated_at":"2025-08-23T20:26:45.092Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27722332,"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":"2025-12-14T02:00:11.348Z","response_time":56,"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":["dendropy","null-model","numpy-arrays","presence-absence-matrix","randomization"],"created_at":"2025-12-14T07:54:41.104Z","updated_at":"2025-12-14T07:54:41.970Z","avatar_url":"https://github.com/specifysystems.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":null,"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fspecifysystems%2Flmpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fspecifysystems%2Flmpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fspecifysystems%2Flmpy/lists"}