{"id":161559,"name":null,"description":"Pyro models of SARS-CoV-2 variants","url":"https://github.com/broadinstitute/pyro-cov","last_synced_at":"2025-09-09T18:28:20.797Z","repository":{"id":37266058,"uuid":"292037402","full_name":"broadinstitute/pyro-cov","owner":"broadinstitute","description":"Pyro models of SARS-CoV-2 variants","archived":false,"fork":false,"pushed_at":"2024-07-26T14:29:47.000Z","size":444800,"stargazers_count":78,"open_issues_count":12,"forks_count":30,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-04-05T05:11:35.256Z","etag":null,"topics":["epidemiology","genetics","sars-cov-2"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/broadinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-09-01T15:34:42.000Z","updated_at":"2024-12-17T15:58:45.000Z","dependencies_parsed_at":"2023-02-08T14:30:30.843Z","dependency_job_id":"c03aa338-81ef-4b09-aba9-d2da0018ab45","html_url":"https://github.com/broadinstitute/pyro-cov","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/broadinstitute/pyro-cov","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/pyro-cov/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274340950,"owners_count":25267296,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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":"broadinstitute","name":"Broad Institute","uuid":"393552","kind":"organization","description":"Broad Institute of MIT and Harvard","email":null,"website":"http://www.broadinstitute.org/","location":"Cambridge, MA","twitter":"broadinstitute","company":null,"icon_url":"https://avatars.githubusercontent.com/u/393552?v=4","repositories_count":1083,"last_synced_at":"2023-04-09T09:48:11.262Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/broadinstitute","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-02T16:23:28.278Z","updated_at":"2023-04-09T09:48:11.836Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute/repositories"},"packages":[],"commits":{"id":8085215,"full_name":"broadinstitute/pyro-cov","default_branch":"master","committers":[{"name":"Fritz Obermeyer","email":"fritz.obermeyer@gmail.com","login":"fritzo","count":773},{"name":"barkasn","email":"nikolas.barkas@outlook.com","login":"barkasn","count":53},{"name":"nikolas.barkas@outlook.com","email":"nbarkas@broadinstitute.org","login":null,"count":37},{"name":"martin jankowiak","email":"jankowiak@gmail.com","login":"martinjankowiak","count":29},{"name":"bkotzen","email":"bkotzen@mgh.harvard.edu","login":"bkotzen","count":15},{"name":"jy17","email":"lemieux@broadinstitute.org","login":"JacobLemieux","count":7},{"name":"Cornelius Roemer","email":"cornelius.roemer@gmail.com","login":"corneliusroemer","count":2},{"name":"martin jankowiak","email":"mjankowi@broad.io","login":null,"count":1}],"total_commits":917,"total_committers":8,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":114.625,"dds":0.1570338058887677,"past_year_committers":[],"past_year_total_commits":0,"past_year_total_committers":0,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":0.0,"past_year_dds":0.0,"last_synced_at":"2025-01-29T04:50:30.428Z","last_synced_commit":"9f84acc3ddff9bcb55c8d1b77fd23204a4f54b8e","created_at":"2024-12-31T19:51:40.651Z","updated_at":"2025-01-29T04:51:04.676Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:17:06.873Z","repositories_count":5533016,"commits_count":871413133,"contributors_count":32103352,"owners_count":918325,"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":"broadinstitute/pyro-cov","html_url":"https://github.com/broadinstitute/pyro-cov","last_synced_at":"2025-01-29T10:13:06.839Z","status":null,"issues_count":32,"pull_requests_count":77,"avg_time_to_close_issue":3341145.5,"avg_time_to_close_pull_request":832462.7142857143,"issues_closed_count":18,"pull_requests_closed_count":77,"pull_request_authors_count":6,"issue_authors_count":19,"avg_comments_per_issue":3.625,"avg_comments_per_pull_request":0.22077922077922077,"merged_pull_requests_count":70,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":2,"past_year_pull_requests_count":15,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":314.93333333333334,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":15,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":0.0,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":15,"created_at":"2024-12-31T19:51:45.868Z","updated_at":"2025-09-02T00:23:05.836Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/issues","issue_labels_count":{"question":6,"enhancement":4,"bug":3,"help wanted":2,"invalid":1},"pull_request_labels_count":{"enhancement":1},"issue_author_associations_count":{"NONE":21,"CONTRIBUTOR":6},"pull_request_author_associations_count":{"CONTRIBUTOR":69,"COLLABORATOR":1},"issue_authors":{"smruti241":3,"fritzo":3,"corneliusroemer":2,"liamxg":2,"Shicheng-Guo":2,"omarcr":1,"Sanyukta2001":1,"lingxuan85511":1,"lucadesabato":1,"yzy990924":1,"cwhittaker1000":1,"sweety919":1,"ShaneSchroeder":1,"liyupeng111":1,"joicy":1,"Xiaofeiff":1,"ai4pharma":1,"rlaskar":1,"bkotzen":1,"zwallace425":1},"pull_request_authors":{"bkotzen":56,"barkasn":5,"fritzo":4,"martinjankowiak":2,"corneliusroemer":2,"JacobLemieux":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-03T00:00:08.273Z","repositories_count":10052430,"issues_count":30837503,"pull_requests_count":92378505,"authors_count":10524589,"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":"JacobLemieux","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/JacobLemieux"}],"active_maintainers":[]},"events":{"total":{"WatchEvent":1,"ForkEvent":2},"last_year":{"WatchEvent":1,"ForkEvent":2}},"keywords":["epidemiology","genetics","sars-cov-2"],"dependencies":[{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-07-12T05:00:57.293Z","updated_at":"2022-07-12T05:00:57.293Z","repository_link":"https://github.com/broadinstitute/pyro-cov/blob/master/setup.py","dependencies":[{"id":152675215,"package_name":"biopython","ecosystem":"pypi","requirements":"\u003e=1.54","direct":true,"kind":"runtime","optional":false},{"id":152675216,"package_name":"pyro-ppl","ecosystem":"pypi","requirements":"\u003e=1.7","direct":true,"kind":"runtime","optional":false},{"id":152675217,"package_name":"geopy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675218,"package_name":"gpytorch","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675219,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675220,"package_name":"umap-learn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675221,"package_name":"mappy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675222,"package_name":"protobuf","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675223,"package_name":"tqdm","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":152675224,"package_name":"colorcet","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2023-02-08T14:30:30.795Z","updated_at":"2023-02-08T14:30:30.795Z","repository_link":"https://github.com/broadinstitute/pyro-cov/blob/master/.github/workflows/ci.yml","dependencies":[{"id":7455883214,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7455883215,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]}],"score":6.579251212010101,"created_at":"2025-09-09T00:57:04.206Z","updated_at":"2025-10-07T08:38:37.914Z","avatar_url":"https://github.com/broadinstitute.png","language":"Jupyter Notebook","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["sequences"],"project_url":"https://science.ecosyste.ms/api/v1/projects/161559","html_url":"https://science.ecosyste.ms/projects/161559"}