{"id":4512,"name":"gtnet","description":"The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences","url":"https://github.com/lbl-cbg/gtnet","last_synced_at":"2025-09-04T17:25:39.959Z","repository":{"id":41830634,"uuid":"392503663","full_name":"lbl-cbg/gtnet","owner":"lbl-cbg","description":"The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences","archived":false,"fork":false,"pushed_at":"2024-03-05T01:10:43.000Z","size":61221,"stargazers_count":1,"open_issues_count":5,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-08-31T03:23:33.727Z","etag":null,"topics":["metagenomic-analysis","metagenomic-classification","metagenomics","microbial-taxonomy","neural-network","taxonomic-classification"],"latest_commit_sha":null,"homepage":"https://gtnet.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lbl-cbg.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"docs/CONTRIBUTING.rst","funding":null,"license":"license.txt","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-08-04T01:09:51.000Z","updated_at":"2024-12-05T18:14:25.000Z","dependencies_parsed_at":"2025-01-11T22:49:42.491Z","dependency_job_id":"eea3ee27-3e0f-4687-b5e3-ba890a3d543d","html_url":"https://github.com/lbl-cbg/gtnet","commit_stats":{"total_commits":42,"total_committers":3,"mean_commits":14.0,"dds":0.2142857142857143,"last_synced_commit":"adb23bffea26eeaa33fd51a85aee569e62c8cd25"},"previous_names":["exabiome/gtnet"],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/lbl-cbg/gtnet","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lbl-cbg","download_url":"https://codeload.github.com/lbl-cbg/gtnet/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273642884,"owners_count":25142491,"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":"lbl-cbg","name":"lbl-cbg","uuid":"146298223","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/146298223?v=4","repositories_count":1,"last_synced_at":"2024-01-13T14:06:11.468Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/lbl-cbg","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2024-01-13T14:06:11.471Z","updated_at":"2024-01-13T14:06:11.471Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lbl-cbg","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lbl-cbg/repositories"},"packages":[],"commits":{"id":8755430,"full_name":"lbl-cbg/gtnet","default_branch":"master","committers":null,"total_commits":null,"total_committers":null,"total_bot_commits":null,"total_bot_committers":null,"mean_commits":null,"dds":null,"past_year_committers":null,"past_year_total_commits":null,"past_year_total_committers":null,"past_year_total_bot_commits":null,"past_year_total_bot_committers":null,"past_year_mean_commits":null,"past_year_dds":null,"last_synced_at":null,"last_synced_commit":null,"created_at":"2025-02-14T11:31:49.254Z","updated_at":"2025-02-14T11:31:49.254Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.936Z","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":"lbl-cbg/gtnet","html_url":"https://github.com/lbl-cbg/gtnet","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-09-04T17:25:14.286Z","updated_at":"2025-09-04T17:25:14.286Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbl-cbg%2Fgtnet/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{},"issue_authors":{},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10079913,"issues_count":31291083,"pull_requests_count":96059117,"authors_count":10693123,"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":[],"active_maintainers":[]},"events":{"total":{},"last_year":{}},"keywords":["metagenomic-analysis","metagenomic-classification","metagenomics","microbial-taxonomy","neural-network","taxonomic-classification"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/codespell.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:33.799Z","updated_at":"2025-01-11T22:49:33.799Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/.github/workflows/codespell.yml","dependencies":[{"id":21446693282,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":21446693283,"package_name":"codespell-project/actions-codespell","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/deploy_release.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:34.084Z","updated_at":"2025-01-11T22:49:34.084Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/.github/workflows/deploy_release.yml","dependencies":[{"id":21446693284,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":21446693285,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ruff.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:34.140Z","updated_at":"2025-01-11T22:49:34.140Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/.github/workflows/ruff.yml","dependencies":[{"id":21446693286,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":21446693287,"package_name":"chartboost/ruff-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/run_coverage.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:34.474Z","updated_at":"2025-01-11T22:49:34.474Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/.github/workflows/run_coverage.yml","dependencies":[{"id":21446693288,"package_name":"styfle/cancel-workflow-action","ecosystem":"actions","requirements":"0.11.0","direct":true,"kind":"composite","optional":false},{"id":21446693289,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":21446693290,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":21446693291,"package_name":"codecov/codecov-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/run_tests.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:34.715Z","updated_at":"2025-01-11T22:49:34.715Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/.github/workflows/run_tests.yml","dependencies":[{"id":21446693292,"package_name":"styfle/cancel-workflow-action","ecosystem":"actions","requirements":"0.11.0","direct":true,"kind":"composite","optional":false},{"id":21446693293,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":21446693294,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"pypi","filepath":"environment.yml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:41.863Z","updated_at":"2025-01-11T22:49:41.863Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/environment.yml","dependencies":[{"id":21446693447,"package_name":"fonttools","ecosystem":"pypi","requirements":"==4.39.3","direct":true,"kind":"runtime","optional":false},{"id":21446693448,"package_name":"mpmath","ecosystem":"pypi","requirements":"==1.2.1","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:41.920Z","updated_at":"2025-01-11T22:49:41.920Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/pyproject.toml","dependencies":[{"id":21446693449,"package_name":"numpy","ecosystem":"pypi","requirements":"\u003e=1.24.3","direct":true,"kind":"runtime","optional":false},{"id":21446693450,"package_name":"pandas","ecosystem":"pypi","requirements":"\u003e=2.0.1","direct":true,"kind":"runtime","optional":false},{"id":21446693451,"package_name":"torch","ecosystem":"pypi","requirements":"\u003e=2.0.1","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"requirements-dev.txt","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:41.977Z","updated_at":"2025-01-11T22:49:41.977Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/requirements-dev.txt","dependencies":[{"id":21446693452,"package_name":"black","ecosystem":"pypi","requirements":"==23.3.0","direct":true,"kind":"development","optional":false},{"id":21446693453,"package_name":"codespell","ecosystem":"pypi","requirements":"==2.2.4","direct":true,"kind":"development","optional":false},{"id":21446693454,"package_name":"coverage","ecosystem":"pypi","requirements":"==7.2.5","direct":true,"kind":"development","optional":false},{"id":21446693455,"package_name":"pre-commit","ecosystem":"pypi","requirements":"==3.3.1","direct":true,"kind":"development","optional":false},{"id":21446693456,"package_name":"pre-commit","ecosystem":"pypi","requirements":"==2.21.0","direct":true,"kind":"development","optional":false},{"id":21446693457,"package_name":"pytest","ecosystem":"pypi","requirements":"==7.3.1","direct":true,"kind":"development","optional":false},{"id":21446693458,"package_name":"pytest-cov","ecosystem":"pypi","requirements":"==4.0.0","direct":true,"kind":"development","optional":false},{"id":21446693459,"package_name":"ruff","ecosystem":"pypi","requirements":"==0.0.265","direct":true,"kind":"development","optional":false}]},{"ecosystem":"pypi","filepath":"requirements-doc.txt","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:42.310Z","updated_at":"2025-01-11T22:49:42.310Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/requirements-doc.txt","dependencies":[{"id":21446693460,"package_name":"sphinx","ecosystem":"pypi","requirements":"\u003e=4","direct":true,"kind":"runtime","optional":false},{"id":21446693461,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"\u003e=1","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2025-01-11T22:49:42.367Z","updated_at":"2025-01-11T22:49:42.367Z","repository_link":"https://github.com/lbl-cbg/gtnet/blob/main/requirements.txt","dependencies":[{"id":21446693462,"package_name":"numpy","ecosystem":"pypi","requirements":"\u003e=1.24.3","direct":true,"kind":"runtime","optional":false},{"id":21446693463,"package_name":"pandas","ecosystem":"pypi","requirements":"\u003e=2.0.1","direct":true,"kind":"runtime","optional":false},{"id":21446693464,"package_name":"torch","ecosystem":"pypi","requirements":"\u003e=2.0.1","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:50:11.798Z","updated_at":"2025-10-07T08:05:05.156Z","avatar_url":"https://github.com/lbl-cbg.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/4512","html_url":"https://science.ecosyste.ms/projects/4512","bibtex_url":"https://science.ecosyste.ms/projects/4512/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/4512/export.apalike"}