{"id":69384,"name":"orthofisher","description":"a broadly applicable tool for automated gene identification and retrieval","url":"https://github.com/jlsteenwyk/orthofisher","last_synced_at":"2025-09-08T14:51:20.323Z","repository":{"id":40397664,"uuid":"329736506","full_name":"JLSteenwyk/orthofisher","owner":"JLSteenwyk","description":"a broadly applicable tool for automated gene identification and retrieval","archived":false,"fork":false,"pushed_at":"2024-12-06T00:10:19.000Z","size":85927,"stargazers_count":32,"open_issues_count":3,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-05T07:46:12.931Z","etag":null,"topics":["bioinformatics","evolution","evolutionary-biology","genomics","orthology","orthology-assignments","orthology-inference","phylogenetics","phylogenomics","python"],"latest_commit_sha":null,"homepage":"https://jlsteenwyk.com/orthofisher/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JLSteenwyk.png","metadata":{"files":{"readme":"README.md","changelog":"change_log.txt","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-01-14T21:16:30.000Z","updated_at":"2025-07-02T03:10:01.000Z","dependencies_parsed_at":"2023-01-29T19:46:07.537Z","dependency_job_id":"72c657c6-3663-4c64-8448-15f9d1a9a712","html_url":"https://github.com/JLSteenwyk/orthofisher","commit_stats":{"total_commits":105,"total_committers":3,"mean_commits":35.0,"dds":0.01904761904761909,"last_synced_commit":"af364fd05a19990c5f30c23b10475864ba96220f"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/JLSteenwyk/orthofisher","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/sbom","scorecard":{"id":69006,"data":{"date":"2025-08-11","repo":{"name":"github.com/JLSteenwyk/orthofisher","commit":"5624721902278680f5e8e31c3284c47db73e95fa"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.8,"checks":[{"name":"Code-Review","score":0,"reason":"Found 0/28 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":"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":"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/ci.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":"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":"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.md:0","Info: FSF or OSI recognized license: MIT License: LICENSE.md: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":-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":"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":"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"}},{"name":"Vulnerabilities","score":0,"reason":"12 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2024-230 / GHSA-248v-346w-9cwc","Warn: Project is vulnerable to: GHSA-vqfr-h8mv-ghfj","Warn: Project is vulnerable to: GHSA-cpwx-vrp4-4pq7","Warn: Project is vulnerable to: GHSA-gmj6-6f8f-6699","Warn: Project is vulnerable to: GHSA-q2x7-8rv6-6q7h","Warn: Project is vulnerable to: GHSA-9hjg-9r4m-mvj7","Warn: Project is vulnerable to: GHSA-2c2j-9gv5-cj73","Warn: Project is vulnerable to: GHSA-f96h-pmfr-66vw","Warn: Project is vulnerable to: GHSA-34jh-p97f-mpxf","Warn: Project is vulnerable to: GHSA-48p4-8xcf-vxj5","Warn: Project is vulnerable to: GHSA-pq67-6m6q-mj2v","Warn: Project is vulnerable to: GHSA-g7vv-2v7x-gj9p"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"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/ci.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:37: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:56: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:65: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:77: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:81: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:85: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:93: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:10: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:12: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:42","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:46","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:47","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:48","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:17","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:21","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:22","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:23","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   4 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"}}]},"last_synced_at":"2025-08-15T03:22:03.394Z","repository_id":40397664,"created_at":"2025-08-15T03:22:03.394Z","updated_at":"2025-08-15T03:22:03.394Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274202153,"owners_count":25240362,"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":"JLSteenwyk","name":"Jacob L. Steenwyk","uuid":"17225603","kind":"user","description":"Berkeley Science Fellow and Postdoctoral Scholar. Evolutionary genomics and software development.","email":"","website":"https://jlsteenwyk.com","location":"Berkeley, CA","twitter":"JLSteenwyk","company":"University of California, Berkeley","icon_url":"https://avatars.githubusercontent.com/u/17225603?u=370657f310a69a5facb58b2d8e3a0ef1e7fdd1ac\u0026v=4","repositories_count":10,"last_synced_at":"2023-03-06T17:39:56.653Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/JLSteenwyk","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-16T19:18:26.309Z","updated_at":"2023-03-06T17:39:56.680Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk/repositories"},"packages":[{"id":2842247,"name":"orthofisher","ecosystem":"pypi","description":"orthofisher","homepage":"https://github.com/JLSteenwyk/orthofisher.git","licenses":"mit","normalized_licenses":["MIT"],"repository_url":"https://github.com/JLSteenwyk/orthofisher","keywords_array":[],"namespace":null,"versions_count":21,"first_release_published_at":"2021-01-17T16:36:37.000Z","latest_release_published_at":"2024-06-03T22:42:36.000Z","latest_release_number":"1.1.1","last_synced_at":"2025-09-05T07:44:14.703Z","created_at":"2022-04-10T11:58:07.514Z","updated_at":"2025-09-06T01:14:31.595Z","registry_url":"https://pypi.org/project/orthofisher/","install_command":"pip install orthofisher --index-url https://pypi.org/simple","documentation_url":"https://orthofisher.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["Intended Audience :: Science/Research","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.9","Topic :: Scientific/Engineering"],"normalized_name":"orthofisher","project_status":null},"repo_metadata":{"id":40397664,"uuid":"329736506","full_name":"JLSteenwyk/orthofisher","owner":"JLSteenwyk","description":"a broadly applicable tool for automated gene identification and retrieval","archived":false,"fork":false,"pushed_at":"2024-12-06T00:10:19.000Z","size":85927,"stargazers_count":32,"open_issues_count":3,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-05T07:46:12.931Z","etag":null,"topics":["bioinformatics","evolution","evolutionary-biology","genomics","orthology","orthology-assignments","orthology-inference","phylogenetics","phylogenomics","python"],"latest_commit_sha":null,"homepage":"https://jlsteenwyk.com/orthofisher/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JLSteenwyk.png","metadata":{"files":{"readme":"README.md","changelog":"change_log.txt","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-01-14T21:16:30.000Z","updated_at":"2025-07-02T03:10:01.000Z","dependencies_parsed_at":"2023-01-29T19:46:07.537Z","dependency_job_id":"72c657c6-3663-4c64-8448-15f9d1a9a712","html_url":"https://github.com/JLSteenwyk/orthofisher","commit_stats":{"total_commits":105,"total_committers":3,"mean_commits":35.0,"dds":0.01904761904761909,"last_synced_commit":"af364fd05a19990c5f30c23b10475864ba96220f"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/JLSteenwyk/orthofisher","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/sbom","scorecard":{"id":69006,"data":{"date":"2025-08-11","repo":{"name":"github.com/JLSteenwyk/orthofisher","commit":"5624721902278680f5e8e31c3284c47db73e95fa"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.8,"checks":[{"name":"Code-Review","score":0,"reason":"Found 0/28 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":"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":"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/ci.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":"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":"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.md:0","Info: FSF or OSI recognized license: MIT License: LICENSE.md: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":-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":"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":"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"}},{"name":"Vulnerabilities","score":0,"reason":"12 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2024-230 / GHSA-248v-346w-9cwc","Warn: Project is vulnerable to: GHSA-vqfr-h8mv-ghfj","Warn: Project is vulnerable to: GHSA-cpwx-vrp4-4pq7","Warn: Project is vulnerable to: GHSA-gmj6-6f8f-6699","Warn: Project is vulnerable to: GHSA-q2x7-8rv6-6q7h","Warn: Project is vulnerable to: GHSA-9hjg-9r4m-mvj7","Warn: Project is vulnerable to: GHSA-2c2j-9gv5-cj73","Warn: Project is vulnerable to: GHSA-f96h-pmfr-66vw","Warn: Project is vulnerable to: GHSA-34jh-p97f-mpxf","Warn: Project is vulnerable to: GHSA-48p4-8xcf-vxj5","Warn: Project is vulnerable to: GHSA-pq67-6m6q-mj2v","Warn: Project is vulnerable to: GHSA-g7vv-2v7x-gj9p"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"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/ci.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:37: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:56: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:65: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:77: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:81: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:85: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/ci.yml:93: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:10: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/ci.yml:12: update your workflow using https://app.stepsecurity.io/secureworkflow/JLSteenwyk/orthofisher/ci.yml/main?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:42","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:46","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:47","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:48","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:17","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:21","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:22","Warn: pipCommand not pinned by hash: .github/workflows/ci.yml:23","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   4 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"}}]},"last_synced_at":"2025-08-15T03:22:03.394Z","repository_id":40397664,"created_at":"2025-08-15T03:22:03.394Z","updated_at":"2025-08-15T03:22:03.394Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273766926,"owners_count":25164459,"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":"2025-09-05T02:00:09.113Z","response_time":402,"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":"JLSteenwyk","name":"Jacob L. Steenwyk","uuid":"17225603","kind":"user","description":"Berkeley Science Fellow and Postdoctoral Scholar. Evolutionary genomics and software development.","email":"","website":"https://jlsteenwyk.com","location":"Berkeley, CA","twitter":"JLSteenwyk","company":"University of California, Berkeley","icon_url":"https://avatars.githubusercontent.com/u/17225603?u=370657f310a69a5facb58b2d8e3a0ef1e7fdd1ac\u0026v=4","repositories_count":10,"last_synced_at":"2023-03-06T17:39:56.653Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/JLSteenwyk","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-16T19:18:26.309Z","updated_at":"2023-03-06T17:39:56.680Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JLSteenwyk/repositories"},"tags":[{"name":"v1.1.1","sha":"af364fd05a19990c5f30c23b10475864ba96220f","kind":"commit","published_at":"2024-06-03T22:39:28.000Z","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/v1.1.1","html_url":"https://github.com/JLSteenwyk/orthofisher/releases/tag/v1.1.1","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/JLSteenwyk/orthofisher@v1.1.1","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.1.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.1.1/manifests"},{"name":"v1.1.0","sha":"5231165e3c3ce831f050328844fb3043cf559ff1","kind":"commit","published_at":"2023-10-24T22:39:20.000Z","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/v1.1.0","html_url":"https://github.com/JLSteenwyk/orthofisher/releases/tag/v1.1.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/JLSteenwyk/orthofisher@v1.1.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.1.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.1.0/manifests"},{"name":"v1.0.2","sha":"e3a4d0ab78e15bbc0b744f7db5a320c5d40b7273","kind":"commit","published_at":"2021-10-28T20:07:52.000Z","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/v1.0.2","html_url":"https://github.com/JLSteenwyk/orthofisher/releases/tag/v1.0.2","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/JLSteenwyk/orthofisher@v1.0.2","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.0.2","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v1.0.2/manifests"},{"name":"v0.2.1","sha":"9ecd1954bff11c01fe29db2967e1521a53006a5a","kind":"commit","published_at":"2021-10-17T18:19:05.000Z","download_url":"https://codeload.github.com/JLSteenwyk/orthofisher/tar.gz/v0.2.1","html_url":"https://github.com/JLSteenwyk/orthofisher/releases/tag/v0.2.1","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/JLSteenwyk/orthofisher@v0.2.1","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v0.2.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/tags/v0.2.1/manifests"}]},"repo_metadata_updated_at":"2025-09-06T01:14:31.594Z","dependent_packages_count":0,"downloads":260,"downloads_period":"last-month","dependent_repos_count":1,"rankings":{"downloads":35.97544208073941,"dependent_repos_count":21.627614287651376,"dependent_packages_count":10.069287946036377,"stargazers_count":12.629074634161244,"forks_count":22.614941540906088,"docker_downloads_count":null,"average":20.5832720978989},"purl":"pkg:pypi/orthofisher","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/orthofisher","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/pypi/orthofisher","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/orthofisher/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-07-27T15:19:10.201Z","issues_count":2,"pull_requests_count":13,"avg_time_to_close_issue":15352.0,"avg_time_to_close_pull_request":11172641.3,"issues_closed_count":2,"pull_requests_closed_count":10,"pull_request_authors_count":2,"issue_authors_count":2,"avg_comments_per_issue":2.0,"avg_comments_per_pull_request":0.5384615384615384,"merged_pull_requests_count":3,"bot_issues_count":0,"bot_pull_requests_count":11,"past_year_issues_count":0,"past_year_pull_requests_count":1,"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":1,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":1,"past_year_merged_pull_requests_count":0,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/issues","maintainers":[{"login":"JLSteenwyk","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/JLSteenwyk"}],"active_maintainers":[]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/orthofisher/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/orthofisher/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/orthofisher/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/orthofisher/related_packages","maintainers":[{"uuid":"JLSteenwyk","login":"JLSteenwyk","name":null,"email":null,"url":null,"packages_count":7,"html_url":"https://pypi.org/user/JLSteenwyk/","role":null,"created_at":"2023-02-24T23:08:29.213Z","updated_at":"2023-02-24T23:08:29.213Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/JLSteenwyk/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":726167,"maintainers_count":308802,"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":623887,"full_name":"JLSteenwyk/orthofisher","default_branch":"main","committers":[{"name":"Jacob L. Steenwyk","email":"jlsteenwyk@gmail.com","login":"JLSteenwyk","count":104},{"name":"dependabot[bot]","email":"49699333+dependabot[bot]","login":"dependabot[bot]","count":1},{"name":"Jacob L Steenwyk","email":"jacoblsteenwyk@Jacobs-MacBook-Pro.local","login":null,"count":1}],"total_commits":106,"total_committers":3,"total_bot_commits":1,"total_bot_committers":1,"mean_commits":35.333333333333336,"dds":0.018867924528301883,"past_year_committers":[{"name":"Jacob L. Steenwyk","email":"jlsteenwyk@gmail.com","login":"JLSteenwyk","count":1}],"past_year_total_commits":1,"past_year_total_committers":1,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":1.0,"past_year_dds":0.0,"last_synced_at":"2025-07-27T15:10:05.385Z","last_synced_commit":"5624721902278680f5e8e31c3284c47db73e95fa","created_at":"2023-03-09T08:05:44.849Z","updated_at":"2025-07-27T15:10:05.493Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-03T00:00:08.276Z","repositories_count":5480019,"commits_count":853389012,"contributors_count":31098138,"owners_count":906558,"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":"JLSteenwyk/orthofisher","html_url":"https://github.com/JLSteenwyk/orthofisher","last_synced_at":"2025-07-27T15:19:10.201Z","status":"error","issues_count":2,"pull_requests_count":13,"avg_time_to_close_issue":15352.0,"avg_time_to_close_pull_request":11172641.3,"issues_closed_count":2,"pull_requests_closed_count":10,"pull_request_authors_count":2,"issue_authors_count":2,"avg_comments_per_issue":2.0,"avg_comments_per_pull_request":0.5384615384615384,"merged_pull_requests_count":3,"bot_issues_count":0,"bot_pull_requests_count":11,"past_year_issues_count":0,"past_year_pull_requests_count":1,"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":1,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":1,"past_year_merged_pull_requests_count":0,"created_at":"2023-05-14T19:39:09.174Z","updated_at":"2025-09-01T21:41:54.992Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/JLSteenwyk%2Forthofisher/issues","issue_labels_count":{},"pull_request_labels_count":{"dependencies":13},"issue_author_associations_count":{"NONE":2},"pull_request_author_associations_count":{"CONTRIBUTOR":13,"OWNER":3},"issue_authors":{"Ptero64":1,"sumanthmutte":1},"pull_request_authors":{"dependabot[bot]":13,"JLSteenwyk":3},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10092753,"issues_count":31358816,"pull_requests_count":96899754,"authors_count":10699020,"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":"JLSteenwyk","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/JLSteenwyk"}],"active_maintainers":[]},"events":{"total":{"WatchEvent":4,"PushEvent":1},"last_year":{"WatchEvent":4,"PushEvent":1}},"keywords":["bioinformatics","evolution","evolutionary-biology","genomics","orthology","orthology-assignments","orthology-inference","phylogenetics","phylogenomics","python"],"dependencies":[{"ecosystem":"pypi","filepath":"docs/Pipfile","sha":null,"kind":"manifest","created_at":"2022-08-09T19:20:11.013Z","updated_at":"2022-08-09T19:20:11.013Z","repository_link":"https://github.com/JLSteenwyk/orthofisher/blob/main/docs/Pipfile","dependencies":[{"id":945780367,"package_name":"Pygments","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":945780368,"package_name":"Sphinx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":945780369,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":945780370,"package_name":"sphinx-autobuild","ecosystem":"pypi","requirements":"*","direct":true,"kind":"develop","optional":false}]},{"ecosystem":"pypi","filepath":"docs/Pipfile.lock","sha":null,"kind":"lockfile","created_at":"2022-08-09T19:20:11.548Z","updated_at":"2022-08-09T19:20:11.548Z","repository_link":"https://github.com/JLSteenwyk/orthofisher/blob/main/docs/Pipfile.lock","dependencies":[{"id":945790161,"package_name":"alabaster","ecosystem":"pypi","requirements":"==0.7.12","direct":false,"kind":"runtime","optional":false},{"id":945790167,"package_name":"babel","ecosystem":"pypi","requirements":"==2.9.0","direct":false,"kind":"runtime","optional":false},{"id":945790169,"package_name":"certifi","ecosystem":"pypi","requirements":"==2020.12.5","direct":false,"kind":"runtime","optional":false},{"id":945790171,"package_name":"chardet","ecosystem":"pypi","requirements":"==4.0.0","direct":false,"kind":"runtime","optional":false},{"id":945790173,"package_name":"docutils","ecosystem":"pypi","requirements":"==0.16","direct":false,"kind":"runtime","optional":false},{"id":945790175,"package_name":"idna","ecosystem":"pypi","requirements":"==2.10","direct":false,"kind":"runtime","optional":false},{"id":945790178,"package_name":"imagesize","ecosystem":"pypi","requirements":"==1.2.0","direct":false,"kind":"runtime","optional":false},{"id":945790180,"package_name":"jinja2","ecosystem":"pypi","requirements":"==2.11.3","direct":false,"kind":"runtime","optional":false},{"id":945790183,"package_name":"markupsafe","ecosystem":"pypi","requirements":"==1.1.1","direct":false,"kind":"runtime","optional":false},{"id":945790186,"package_name":"packaging","ecosystem":"pypi","requirements":"==20.9","direct":false,"kind":"runtime","optional":false},{"id":945790189,"package_name":"pygments","ecosystem":"pypi","requirements":"==2.7.2","direct":false,"kind":"runtime","optional":false},{"id":945790192,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==2.4.7","direct":false,"kind":"runtime","optional":false},{"id":945790195,"package_name":"pytz","ecosystem":"pypi","requirements":"==2021.1","direct":false,"kind":"runtime","optional":false},{"id":945790198,"package_name":"requests","ecosystem":"pypi","requirements":"==2.25.1","direct":false,"kind":"runtime","optional":false},{"id":945790201,"package_name":"snowballstemmer","ecosystem":"pypi","requirements":"==2.1.0","direct":false,"kind":"runtime","optional":false},{"id":945790202,"package_name":"sphinx","ecosystem":"pypi","requirements":"==3.2.1","direct":false,"kind":"runtime","optional":false},{"id":945790203,"package_name":"sphinx-rtd-theme","ecosystem":"pypi","requirements":"==0.5.0","direct":false,"kind":"runtime","optional":false},{"id":945790204,"package_name":"sphinxcontrib-applehelp","ecosystem":"pypi","requirements":"==1.0.2","direct":false,"kind":"runtime","optional":false},{"id":945790205,"package_name":"sphinxcontrib-devhelp","ecosystem":"pypi","requirements":"==1.0.2","direct":false,"kind":"runtime","optional":false},{"id":945790206,"package_name":"sphinxcontrib-htmlhelp","ecosystem":"pypi","requirements":"==1.0.3","direct":false,"kind":"runtime","optional":false},{"id":945790207,"package_name":"sphinxcontrib-jsmath","ecosystem":"pypi","requirements":"==1.0.1","direct":false,"kind":"runtime","optional":false},{"id":945790208,"package_name":"sphinxcontrib-qthelp","ecosystem":"pypi","requirements":"==1.0.3","direct":false,"kind":"runtime","optional":false},{"id":945790210,"package_name":"sphinxcontrib-serializinghtml","ecosystem":"pypi","requirements":"==1.1.4","direct":false,"kind":"runtime","optional":false},{"id":945790211,"package_name":"urllib3","ecosystem":"pypi","requirements":"==1.26.4","direct":false,"kind":"runtime","optional":false},{"id":945790212,"package_name":"alabaster","ecosystem":"pypi","requirements":"==0.7.12","direct":false,"kind":"develop","optional":false},{"id":945790213,"package_name":"babel","ecosystem":"pypi","requirements":"==2.9.0","direct":false,"kind":"develop","optional":false},{"id":945790214,"package_name":"certifi","ecosystem":"pypi","requirements":"==2020.12.5","direct":false,"kind":"develop","optional":false},{"id":945790215,"package_name":"chardet","ecosystem":"pypi","requirements":"==4.0.0","direct":false,"kind":"develop","optional":false},{"id":945790216,"package_name":"docutils","ecosystem":"pypi","requirements":"==0.16","direct":false,"kind":"develop","optional":false},{"id":945790217,"package_name":"idna","ecosystem":"pypi","requirements":"==2.10","direct":false,"kind":"develop","optional":false},{"id":945790218,"package_name":"imagesize","ecosystem":"pypi","requirements":"==1.2.0","direct":false,"kind":"develop","optional":false},{"id":945790219,"package_name":"jinja2","ecosystem":"pypi","requirements":"==2.11.3","direct":false,"kind":"develop","optional":false},{"id":945790220,"package_name":"livereload","ecosystem":"pypi","requirements":"==2.6.3","direct":false,"kind":"develop","optional":false},{"id":945790221,"package_name":"markupsafe","ecosystem":"pypi","requirements":"==1.1.1","direct":false,"kind":"develop","optional":false},{"id":945790222,"package_name":"packaging","ecosystem":"pypi","requirements":"==20.9","direct":false,"kind":"develop","optional":false},{"id":945790223,"package_name":"pygments","ecosystem":"pypi","requirements":"==2.7.2","direct":false,"kind":"develop","optional":false},{"id":945790224,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==2.4.7","direct":false,"kind":"develop","optional":false},{"id":945790225,"package_name":"pytz","ecosystem":"pypi","requirements":"==2021.1","direct":false,"kind":"develop","optional":false},{"id":945790226,"package_name":"requests","ecosystem":"pypi","requirements":"==2.25.1","direct":false,"kind":"develop","optional":false},{"id":945790227,"package_name":"six","ecosystem":"pypi","requirements":"==1.15.0","direct":false,"kind":"develop","optional":false},{"id":945790228,"package_name":"snowballstemmer","ecosystem":"pypi","requirements":"==2.1.0","direct":false,"kind":"develop","optional":false},{"id":945790229,"package_name":"sphinx","ecosystem":"pypi","requirements":"==3.2.1","direct":false,"kind":"develop","optional":false},{"id":945790230,"package_name":"sphinx-autobuild","ecosystem":"pypi","requirements":"==2020.9.1","direct":false,"kind":"develop","optional":false},{"id":945790231,"package_name":"sphinxcontrib-applehelp","ecosystem":"pypi","requirements":"==1.0.2","direct":false,"kind":"develop","optional":false},{"id":945790232,"package_name":"sphinxcontrib-devhelp","ecosystem":"pypi","requirements":"==1.0.2","direct":false,"kind":"develop","optional":false},{"id":945790233,"package_name":"sphinxcontrib-htmlhelp","ecosystem":"pypi","requirements":"==1.0.3","direct":false,"kind":"develop","optional":false},{"id":945790234,"package_name":"sphinxcontrib-jsmath","ecosystem":"pypi","requirements":"==1.0.1","direct":false,"kind":"develop","optional":false},{"id":945790235,"package_name":"sphinxcontrib-qthelp","ecosystem":"pypi","requirements":"==1.0.3","direct":false,"kind":"develop","optional":false},{"id":945790236,"package_name":"sphinxcontrib-serializinghtml","ecosystem":"pypi","requirements":"==1.1.4","direct":false,"kind":"develop","optional":false},{"id":945790237,"package_name":"tornado","ecosystem":"pypi","requirements":"==6.1","direct":false,"kind":"develop","optional":false},{"id":945790239,"package_name":"urllib3","ecosystem":"pypi","requirements":"==1.26.4","direct":false,"kind":"develop","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-08-09T19:20:12.105Z","updated_at":"2022-08-09T19:20:12.105Z","repository_link":"https://github.com/JLSteenwyk/orthofisher/blob/main/requirements.txt","dependencies":[{"id":945795424,"package_name":"biopython","ecosystem":"pypi","requirements":"\u003e=1.79","direct":true,"kind":"runtime","optional":false},{"id":945795425,"package_name":"numpy","ecosystem":"pypi","requirements":"\u003e=1.19.5","direct":true,"kind":"runtime","optional":false},{"id":945795426,"package_name":"tqdm","ecosystem":"pypi","requirements":"\u003e=4.56.0","direct":true,"kind":"runtime","optional":false},{"id":945795427,"package_name":"cython","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2023-01-29T19:46:07.477Z","updated_at":"2023-01-29T19:46:07.477Z","repository_link":"https://github.com/JLSteenwyk/orthofisher/blob/main/.github/workflows/ci.yml","dependencies":[{"id":7230450842,"package_name":"actions/checkout","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":7230450843,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":7230450844,"package_name":"codecov/codecov-action","ecosystem":"actions","requirements":"v1.0.7","direct":true,"kind":"composite","optional":false},{"id":7230450845,"package_name":"dschep/install-pipenv-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7230450846,"package_name":"JamesIves/github-pages-deploy-action","ecosystem":"actions","requirements":"releases/v3","direct":true,"kind":"composite","optional":false}]}],"score":10.22230485391862,"created_at":"2025-09-08T11:19:01.560Z","updated_at":"2025-10-07T08:25:45.622Z","avatar_url":"https://github.com/JLSteenwyk.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":260,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["interactive","serializer","cycles","packaging","network-simulation","shellcodes","hacking","autograding","observability","embedded"],"project_url":"https://science.ecosyste.ms/api/v1/projects/69384","html_url":"https://science.ecosyste.ms/projects/69384"}