{"id":1559,"name":"ViMMS 2.0","description":"ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics - Published in JOSS (2022)","url":"https://github.com/glasgowcompbio/vimms","last_synced_at":"2025-09-04T16:29:38.343Z","repository":{"id":37214451,"uuid":"276972989","full_name":"glasgowcompbio/vimms","owner":"glasgowcompbio","description":"A programmable and modular LC/MS simulator in Python","archived":false,"fork":false,"pushed_at":"2025-07-12T16:54:50.000Z","size":305879,"stargazers_count":23,"open_issues_count":14,"forks_count":7,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-28T00:14:35.032Z","etag":null,"topics":["dda","fragmentation","metabolomics","python","simulation"],"latest_commit_sha":null,"homepage":"https://glasgowcompbio.github.io/vimms/","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/glasgowcompbio.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,"zenodo":".zenodo.json"}},"created_at":"2020-07-03T19:25:39.000Z","updated_at":"2025-07-12T17:38:05.000Z","dependencies_parsed_at":"2023-02-16T18:45:28.446Z","dependency_job_id":"2a7d2cc2-acd2-41c8-a82f-14a9109803cf","html_url":"https://github.com/glasgowcompbio/vimms","commit_stats":{"total_commits":1032,"total_committers":10,"mean_commits":103.2,"dds":0.5726744186046512,"last_synced_commit":"c8be0baf2de031c78d0a3e986b544ba22bdbec15"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/glasgowcompbio/vimms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/sbom","scorecard":{"id":429278,"data":{"date":"2025-08-11","repo":{"name":"github.com/glasgowcompbio/vimms","commit":"03ac596fa5dd49ef4e41bf3a608fe767eb8036c9"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":4,"checks":[{"name":"Maintained","score":5,"reason":"7 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 5","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"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":"Code-Review","score":0,"reason":"Found 0/29 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":"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Info: topLevel 'contents' permission set to 'read': .github/workflows/docs.yml:15","Warn: no topLevel permission defined: .github/workflows/python-package-poetry.yml:1","Warn: no topLevel permission defined: .github/workflows/release-to-pypi.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":"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: MIT License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Packaging","score":10,"reason":"packaging workflow detected","details":["Info: Project packages its releases by way of GitHub Actions.: .github/workflows/release-to-pypi.yml:8"],"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":"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":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"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":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 2 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/docs.yml:27: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/docs.yml:30: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docs.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/docs.yml:43: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/docs.yml:59: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/docs.yml:73: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-package-poetry.yml:9: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/python-package-poetry.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-package-poetry.yml:11: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/python-package-poetry.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/release-to-pypi.yml:11: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/release-to-pypi.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/release-to-pypi.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/release-to-pypi.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/release-to-pypi.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/glasgowcompbio/vimms/release-to-pypi.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/python-package-poetry.yml:16","Warn: pipCommand not pinned by hash: .github/workflows/release-to-pypi.yml:18","Info:   0 out of   9 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   2 third-party GitHubAction dependencies pinned","Info:   0 out of   2 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":7,"reason":"3 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2025-61 / GHSA-xg8h-j46f-w952","Warn: Project is vulnerable to: GHSA-48p4-8xcf-vxj5","Warn: Project is vulnerable to: GHSA-pq67-6m6q-mj2v"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-19T02:56:32.154Z","repository_id":37214451,"created_at":"2025-08-19T02:56:32.154Z","updated_at":"2025-08-19T02:56:32.154Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273603086,"owners_count":25135598,"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":"glasgowcompbio","name":"glasgowcompbio","uuid":"47832966","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/47832966?v=4","repositories_count":11,"last_synced_at":"2023-03-04T12:09:27.112Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/glasgowcompbio","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-14T18:29:50.878Z","updated_at":"2023-03-04T12:09:27.123Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio/repositories"},"packages":[{"id":337748,"name":"vimms","ecosystem":"pypi","description":"A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics.","homepage":"https://github.com/glasgowcompbio/vimms","licenses":"MIT","normalized_licenses":["MIT"],"repository_url":"https://github.com/glasgowcompbio/vimms","keywords_array":["LC-MS","metabolomics","simulator","mass spectrometry"],"namespace":null,"versions_count":13,"first_release_published_at":"2021-08-11T13:40:35.000Z","latest_release_published_at":"2025-06-04T11:59:32.000Z","latest_release_number":"2.1.6","last_synced_at":"2025-09-04T11:41:55.593Z","created_at":"2022-04-06T12:49:43.789Z","updated_at":"2025-09-04T11:41:55.594Z","registry_url":"https://pypi.org/project/vimms/","install_command":"pip install vimms --index-url https://pypi.org/simple","documentation_url":"https://vimms.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12"],"normalized_name":"vimms","project_status":null},"repo_metadata":{"id":37214451,"uuid":"276972989","full_name":"glasgowcompbio/vimms","owner":"glasgowcompbio","description":"A programmable and modular LC/MS simulator in Python","archived":false,"fork":false,"pushed_at":"2025-07-12T16:54:50.000Z","size":305879,"stargazers_count":23,"open_issues_count":14,"forks_count":7,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-13T10:06:47.747Z","etag":null,"topics":["dda","fragmentation","metabolomics","python","simulation"],"latest_commit_sha":null,"homepage":"https://glasgowcompbio.github.io/vimms/","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/glasgowcompbio.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,"zenodo":".zenodo.json"}},"created_at":"2020-07-03T19:25:39.000Z","updated_at":"2025-07-12T17:38:05.000Z","dependencies_parsed_at":"2023-02-16T18:45:28.446Z","dependency_job_id":"2a7d2cc2-acd2-41c8-a82f-14a9109803cf","html_url":"https://github.com/glasgowcompbio/vimms","commit_stats":{"total_commits":1032,"total_committers":10,"mean_commits":103.2,"dds":0.5726744186046512,"last_synced_commit":"c8be0baf2de031c78d0a3e986b544ba22bdbec15"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/glasgowcompbio/vimms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270843626,"owners_count":24655424,"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":"2025-08-17T02:00:09.016Z","response_time":129,"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":"glasgowcompbio","name":"glasgowcompbio","uuid":"47832966","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/47832966?v=4","repositories_count":11,"last_synced_at":"2023-03-04T12:09:27.112Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/glasgowcompbio","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-14T18:29:50.878Z","updated_at":"2023-03-04T12:09:27.123Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glasgowcompbio/repositories"},"tags":[{"name":"V2.1.6","sha":"b8ccddded0302bfa3023c39378d5978e28610eb9","kind":"commit","published_at":"2025-06-04T11:57:28.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.1.6","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.1.6","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.1.6","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.6","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.6/manifests"},{"name":"V2.1.5","sha":"1f51b7619fba7a4b1a02a4779f6b33d0099ec837","kind":"tag","published_at":"2025-02-09T19:40:37.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.1.5","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.1.5","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.1.5","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.5","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.5/manifests"},{"name":"test","sha":"1f51b7619fba7a4b1a02a4779f6b33d0099ec837","kind":"commit","published_at":"2025-02-09T19:36:28.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/test","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/test","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@test","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/test","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/test/manifests"},{"name":"V2.1.4","sha":"3e34b18d9502b23fc4640d3d40f7038f84df234a","kind":"commit","published_at":"2023-10-02T23:10:24.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.1.4","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.1.4","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.1.4","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.4","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.4/manifests"},{"name":"V2.1.1","sha":"0f0e9ad44ad5250853cdff9819ba2ab9402bf7c1","kind":"commit","published_at":"2023-03-12T00:22:22.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.1.1","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.1.1","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.1.1","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.1/manifests"},{"name":"V2.1.0","sha":"25ca2402f693fcec8f55fca5fffc748c314922e5","kind":"commit","published_at":"2023-01-31T11:16:25.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.1.0","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.1.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.1.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.1.0/manifests"},{"name":"V2.0.9","sha":"718d7fbdfd3c72b08776c870f0c05f509b71a845","kind":"commit","published_at":"2022-12-21T15:07:55.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.0.9","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.0.9","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.0.9","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.9","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.9/manifests"},{"name":"V2.0.5","sha":"55394ca0b4d9ed05b486135a7722e9ce8a3fe25d","kind":"commit","published_at":"2022-03-29T20:30:04.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.0.5","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.0.5","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.0.5","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.5","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.5/manifests"},{"name":"V2.0.3","sha":"5cf8c8e25fbd43edf90e599dbfa2fa2f8492312c","kind":"commit","published_at":"2021-11-19T14:04:31.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.0.3","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.0.3","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.0.3","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.3","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.3/manifests"},{"name":"V2.0.0","sha":"69bc8e26b706e3acdeea75ef66694d86f8e3d15d","kind":"tag","published_at":"2021-04-12T13:46:10.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/V2.0.0","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/V2.0.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@V2.0.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/V2.0.0/manifests"},{"name":"v2.0","sha":"111a75ea11e7061a833d7c202c5815e1e454ccf2","kind":"commit","published_at":"2020-09-22T09:57:20.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/v2.0","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/v2.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@v2.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/v2.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/v2.0/manifests"},{"name":"2.0.0","sha":"111a75ea11e7061a833d7c202c5815e1e454ccf2","kind":"commit","published_at":"2020-09-22T09:57:20.000Z","download_url":"https://codeload.github.com/glasgowcompbio/vimms/tar.gz/2.0.0","html_url":"https://github.com/glasgowcompbio/vimms/releases/tag/2.0.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/glasgowcompbio/vimms@2.0.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/2.0.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/tags/2.0.0/manifests"}]},"repo_metadata_updated_at":"2025-08-17T14:51:45.287Z","dependent_packages_count":0,"downloads":33,"downloads_period":"last-month","dependent_repos_count":1,"rankings":{"downloads":25.256265265198675,"dependent_repos_count":21.534861440080295,"dependent_packages_count":10.125576461732065,"stargazers_count":15.637580065763215,"forks_count":13.34258370477376,"docker_downloads_count":null,"average":17.179373387509603},"purl":"pkg:pypi/vimms","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/vimms","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/pypi/vimms","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/vimms/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-08-17T12:03:36.571Z","issues_count":71,"pull_requests_count":76,"avg_time_to_close_issue":18244722.852459017,"avg_time_to_close_pull_request":2216994.301369863,"issues_closed_count":61,"pull_requests_closed_count":73,"pull_request_authors_count":4,"issue_authors_count":11,"avg_comments_per_issue":2.0422535211267605,"avg_comments_per_pull_request":0.4605263157894737,"merged_pull_requests_count":39,"bot_issues_count":0,"bot_pull_requests_count":34,"past_year_issues_count":1,"past_year_pull_requests_count":30,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":11422.925925925925,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":27,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":1.0,"past_year_avg_comments_per_pull_request":0.03333333333333333,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":3,"past_year_merged_pull_requests_count":22,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/issues","maintainers":[{"login":"joewandy","count":72,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joewandy"},{"login":"sdrogers","count":16,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/sdrogers"},{"login":"vinnydavies","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/vinnydavies"},{"login":"mcbrider5002","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mcbrider5002"},{"login":"RonanDaly","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RonanDaly"}],"active_maintainers":[{"login":"joewandy","count":27,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joewandy"}]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/vimms/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/vimms/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/vimms/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/vimms/related_packages","maintainers":[{"uuid":"joewandy","login":"joewandy","name":null,"email":null,"url":null,"packages_count":5,"html_url":"https://pypi.org/user/joewandy/","role":null,"created_at":"2023-02-23T15:16:12.940Z","updated_at":"2023-02-23T15:16:12.940Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/joewandy/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":724829,"maintainers_count":308209,"namespaces_count":0,"keywords_count":237984,"github":"pypi","metadata":{"funded_packages_count":50481},"icon_url":"https://github.com/pypi.png","created_at":"2022-04-04T15:19:23.364Z","updated_at":"2025-09-04T05:23:51.177Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/namespaces"}}],"commits":{"id":527827,"full_name":"glasgowcompbio/vimms","default_branch":"master","committers":[{"name":"Joe Wandy","email":"joewandy@gmail.com","login":"joewandy","count":469},{"name":"VinnyDavies","email":"vinny.davies@glasgow.ac.uk","login":"vinnydavies","count":210},{"name":"Simon Rogers","email":"simon.d.rogers@gmail.com","login":"sdrogers","count":190},{"name":"unknown","email":"mcbrider5002@gmail.com","login":"mcbrider5002","count":173},{"name":"Rónán Daly","email":"ronan.daly@glasgow.ac.uk","login":"RonanDaly","count":14},{"name":"Kei kuan To","email":"2498456t@student.gla.ac.uk","login":null,"count":9},{"name":"dependabot[bot]","email":"49699333+dependabot[bot]","login":"dependabot[bot]","count":3}],"total_commits":1068,"total_committers":7,"total_bot_commits":3,"total_bot_committers":1,"mean_commits":152.57142857142858,"dds":0.5608614232209738,"past_year_committers":[{"name":"Joe Wandy","email":"jwandy@metabolon.com","login":"joewandy","count":7},{"name":"unknown","email":"mcbrider5002@gmail.com","login":"mcbrider5002","count":1},{"name":"dependabot[bot]","email":"49699333+dependabot[bot]","login":"dependabot[bot]","count":1}],"past_year_total_commits":9,"past_year_total_committers":3,"past_year_total_bot_commits":1,"past_year_total_bot_committers":1,"past_year_mean_commits":3.0,"past_year_dds":0.2222222222222222,"last_synced_at":"2025-08-07T06:37:09.244Z","last_synced_commit":"03ac596fa5dd49ef4e41bf3a608fe767eb8036c9","created_at":"2023-03-09T03:38:14.055Z","updated_at":"2025-08-07T06:37:09.249Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-30T00:00:08.254Z","repositories_count":5479765,"commits_count":853310153,"contributors_count":31095234,"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":"glasgowcompbio/vimms","html_url":"https://github.com/glasgowcompbio/vimms","last_synced_at":"2025-08-31T08:47:17.176Z","status":null,"issues_count":73,"pull_requests_count":98,"avg_time_to_close_issue":17665527.222222224,"avg_time_to_close_pull_request":1819852.426966292,"issues_closed_count":63,"pull_requests_closed_count":89,"pull_request_authors_count":4,"issue_authors_count":11,"avg_comments_per_issue":1.9726027397260275,"avg_comments_per_pull_request":0.3673469387755102,"merged_pull_requests_count":51,"bot_issues_count":0,"bot_pull_requests_count":36,"past_year_issues_count":3,"past_year_pull_requests_count":52,"past_year_avg_time_to_close_issue":60.5,"past_year_avg_time_to_close_pull_request":10109.32558139535,"past_year_issues_closed_count":2,"past_year_pull_requests_closed_count":43,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":0.0,"past_year_avg_comments_per_pull_request":0.038461538461538464,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":5,"past_year_merged_pull_requests_count":34,"created_at":"2023-05-14T08:05:45.256Z","updated_at":"2025-09-01T05:28:44.327Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/glasgowcompbio%2Fvimms/issues","issue_labels_count":{"bug":22,"enhancement":22,"refactoring":8,"question":6,"discussion":3,"priority":2,"codex":2,"invalid":1,"documentation":1,"good first issue":1},"pull_request_labels_count":{"codex":44,"dependencies":36,"python":5,"enhancement":1},"issue_author_associations_count":{"MEMBER":42,"COLLABORATOR":24,"NONE":6},"pull_request_author_associations_count":{"MEMBER":53,"CONTRIBUTOR":36,"COLLABORATOR":9},"issue_authors":{"joewandy":40,"sdrogers":9,"vinnydavies":8,"mcbrider5002":7,"RonanDaly":2,"samsonjm":1,"NitTza":1,"pisistrato":1,"MKoesters":1,"oolonek":1,"jspaezp":1},"pull_request_authors":{"joewandy":53,"dependabot[bot]":36,"sdrogers":7,"vinnydavies":2},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-01T00:00:07.725Z","repositories_count":9946380,"issues_count":29473096,"pull_requests_count":85381310,"authors_count":9367128,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{"codex":2},"past_year_pull_request_labels_count":{"codex":44,"dependencies":5,"python":5},"past_year_issue_author_associations_count":{"MEMBER":2,"NONE":1},"past_year_pull_request_author_associations_count":{"MEMBER":47,"CONTRIBUTOR":5},"past_year_issue_authors":{"joewandy":2,"NitTza":1},"past_year_pull_request_authors":{"joewandy":47,"dependabot[bot]":5},"maintainers":[{"login":"joewandy","count":93,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joewandy"},{"login":"sdrogers","count":16,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/sdrogers"},{"login":"vinnydavies","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/vinnydavies"},{"login":"mcbrider5002","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mcbrider5002"},{"login":"RonanDaly","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RonanDaly"}],"active_maintainers":[{"login":"joewandy","count":49,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joewandy"}]},"events":{"total":{"CreateEvent":23,"ReleaseEvent":3,"IssuesEvent":1,"WatchEvent":3,"DeleteEvent":19,"IssueCommentEvent":2,"PushEvent":47,"PullRequestEvent":39,"ForkEvent":1},"last_year":{"CreateEvent":23,"ReleaseEvent":3,"IssuesEvent":1,"WatchEvent":3,"DeleteEvent":19,"IssueCommentEvent":2,"PushEvent":47,"PullRequestEvent":39,"ForkEvent":1}},"keywords":["dda","fragmentation","metabolomics","python","simulation"],"dependencies":[{"ecosystem":"pypi","filepath":"Pipfile","sha":null,"kind":"manifest","created_at":"2022-06-22T14:11:37.408Z","updated_at":"2022-06-22T14:11:37.408Z","repository_link":"https://github.com/glasgowcompbio/vimms/blob/master/Pipfile","dependencies":[{"id":5900353,"package_name":"numpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900354,"package_name":"pandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900355,"package_name":"scipy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900356,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900357,"package_name":"seaborn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900358,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900359,"package_name":"pymzml","ecosystem":"pypi","requirements":"==2.4.7","direct":true,"kind":"runtime","optional":false},{"id":5900360,"package_name":"psims","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900361,"package_name":"events","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900362,"package_name":"tqdm","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900363,"package_name":"joblib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900364,"package_name":"ipyparallel","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900365,"package_name":"requests","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900366,"package_name":"loguru","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900367,"package_name":"networkx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900368,"package_name":"jsonpickle","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900369,"package_name":"statsmodels","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900370,"package_name":"mass-spec-utils","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900371,"package_name":"tabulate","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900372,"package_name":"pysmiles","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900373,"package_name":"pipenv-setup","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900374,"package_name":"flake8","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900375,"package_name":"autopep8","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900376,"package_name":"pytest","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900377,"package_name":"pytest-cov","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900378,"package_name":"intervaltree","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900379,"package_name":"jupyterlab","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900380,"package_name":"ipywidgets","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900381,"package_name":"gpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5900382,"package_name":"twine","ecosystem":"pypi","requirements":"*","direct":true,"kind":"develop","optional":false},{"id":5900383,"package_name":"build","ecosystem":"pypi","requirements":"*","direct":true,"kind":"develop","optional":false},{"id":5900384,"package_name":"mkdocs","ecosystem":"pypi","requirements":"*","direct":true,"kind":"develop","optional":false},{"id":5900385,"package_name":"mkdocstrings","ecosystem":"pypi","requirements":"*","direct":true,"kind":"develop","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-06-22T14:11:39.881Z","updated_at":"2022-06-22T14:11:39.881Z","repository_link":"https://github.com/glasgowcompbio/vimms/blob/master/requirements.txt","dependencies":[{"id":5902045,"package_name":"anyio","ecosystem":"pypi","requirements":"==3.3.1","direct":true,"kind":"runtime","optional":false},{"id":5902046,"package_name":"appdirs","ecosystem":"pypi","requirements":"==1.4.4","direct":true,"kind":"runtime","optional":false},{"id":5902047,"package_name":"argon2-cffi","ecosystem":"pypi","requirements":"==21.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902048,"package_name":"astunparse","ecosystem":"pypi","requirements":"==1.6.3","direct":true,"kind":"runtime","optional":false},{"id":5902049,"package_name":"async-generator","ecosystem":"pypi","requirements":"==1.10","direct":true,"kind":"runtime","optional":false},{"id":5902050,"package_name":"attrs","ecosystem":"pypi","requirements":"==21.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902051,"package_name":"Babel","ecosystem":"pypi","requirements":"==2.9.1","direct":true,"kind":"runtime","optional":false},{"id":5902052,"package_name":"backcall","ecosystem":"pypi","requirements":"==0.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902053,"package_name":"black","ecosystem":"pypi","requirements":"==19.10b0","direct":true,"kind":"runtime","optional":false},{"id":5902054,"package_name":"bleach","ecosystem":"pypi","requirements":"==4.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902055,"package_name":"build","ecosystem":"pypi","requirements":"==0.7.0","direct":true,"kind":"runtime","optional":false},{"id":5902056,"package_name":"cached-property","ecosystem":"pypi","requirements":"==1.5.2","direct":true,"kind":"runtime","optional":false},{"id":5902057,"package_name":"Cerberus","ecosystem":"pypi","requirements":"==1.3.4","direct":true,"kind":"runtime","optional":false},{"id":5902058,"package_name":"certifi","ecosystem":"pypi","requirements":"==2021.5.30","direct":true,"kind":"runtime","optional":false},{"id":5902059,"package_name":"cffi","ecosystem":"pypi","requirements":"==1.14.6","direct":true,"kind":"runtime","optional":false},{"id":5902060,"package_name":"chardet","ecosystem":"pypi","requirements":"==3.0.4","direct":true,"kind":"runtime","optional":false},{"id":5902061,"package_name":"charset-normalizer","ecosystem":"pypi","requirements":"==2.0.6","direct":true,"kind":"runtime","optional":false},{"id":5902062,"package_name":"click","ecosystem":"pypi","requirements":"==8.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902063,"package_name":"colorama","ecosystem":"pypi","requirements":"==0.4.4","direct":true,"kind":"runtime","optional":false},{"id":5902064,"package_name":"cryptography","ecosystem":"pypi","requirements":"==3.4.8","direct":true,"kind":"runtime","optional":false},{"id":5902065,"package_name":"cycler","ecosystem":"pypi","requirements":"==0.10.0","direct":true,"kind":"runtime","optional":false},{"id":5902066,"package_name":"Cython","ecosystem":"pypi","requirements":"==0.29.24","direct":true,"kind":"runtime","optional":false},{"id":5902067,"package_name":"debugpy","ecosystem":"pypi","requirements":"==1.4.3","direct":true,"kind":"runtime","optional":false},{"id":5902068,"package_name":"decorator","ecosystem":"pypi","requirements":"==5.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902069,"package_name":"defusedxml","ecosystem":"pypi","requirements":"==0.7.1","direct":true,"kind":"runtime","optional":false},{"id":5902070,"package_name":"distlib","ecosystem":"pypi","requirements":"==0.3.2","direct":true,"kind":"runtime","optional":false},{"id":5902071,"package_name":"docutils","ecosystem":"pypi","requirements":"==0.17.1","direct":true,"kind":"runtime","optional":false},{"id":5902072,"package_name":"entrypoints","ecosystem":"pypi","requirements":"==0.3","direct":true,"kind":"runtime","optional":false},{"id":5902073,"package_name":"Events","ecosystem":"pypi","requirements":"==0.4","direct":true,"kind":"runtime","optional":false},{"id":5902074,"package_name":"flake8","ecosystem":"pypi","requirements":"==3.9.2","direct":true,"kind":"runtime","optional":false},{"id":5902075,"package_name":"ghp-import","ecosystem":"pypi","requirements":"==2.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902076,"package_name":"GPy","ecosystem":"pypi","requirements":"==1.10.0","direct":true,"kind":"runtime","optional":false},{"id":5902077,"package_name":"greenlet","ecosystem":"pypi","requirements":"==1.1.1","direct":true,"kind":"runtime","optional":false},{"id":5902078,"package_name":"idna","ecosystem":"pypi","requirements":"==3.2","direct":true,"kind":"runtime","optional":false},{"id":5902079,"package_name":"importlib-metadata","ecosystem":"pypi","requirements":"==4.8.1","direct":true,"kind":"runtime","optional":false},{"id":5902080,"package_name":"iniconfig","ecosystem":"pypi","requirements":"==1.1.1","direct":true,"kind":"runtime","optional":false},{"id":5902081,"package_name":"intervaltree","ecosystem":"pypi","requirements":"==3.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902082,"package_name":"ipykernel","ecosystem":"pypi","requirements":"==6.4.1","direct":true,"kind":"runtime","optional":false},{"id":5902083,"package_name":"ipyparallel","ecosystem":"pypi","requirements":"==7.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902084,"package_name":"ipython","ecosystem":"pypi","requirements":"==7.27.0","direct":true,"kind":"runtime","optional":false},{"id":5902085,"package_name":"ipython-genutils","ecosystem":"pypi","requirements":"==0.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902086,"package_name":"ipywidgets","ecosystem":"pypi","requirements":"==7.5.1","direct":true,"kind":"runtime","optional":false},{"id":5902087,"package_name":"jedi","ecosystem":"pypi","requirements":"==0.18.0","direct":true,"kind":"runtime","optional":false},{"id":5902088,"package_name":"jeepney","ecosystem":"pypi","requirements":"==0.7.1","direct":true,"kind":"runtime","optional":false},{"id":5902089,"package_name":"Jinja2","ecosystem":"pypi","requirements":"==3.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902090,"package_name":"joblib","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902091,"package_name":"json5","ecosystem":"pypi","requirements":"==0.9.6","direct":true,"kind":"runtime","optional":false},{"id":5902092,"package_name":"jsonpickle","ecosystem":"pypi","requirements":"==2.0.0","direct":true,"kind":"runtime","optional":false},{"id":5902093,"package_name":"jsonschema","ecosystem":"pypi","requirements":"==3.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902094,"package_name":"jupyter","ecosystem":"pypi","requirements":"==1.0.0","direct":true,"kind":"runtime","optional":false},{"id":5902095,"package_name":"jupyter-client","ecosystem":"pypi","requirements":"==7.0.3","direct":true,"kind":"runtime","optional":false},{"id":5902096,"package_name":"jupyter-console","ecosystem":"pypi","requirements":"==6.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902097,"package_name":"jupyter-core","ecosystem":"pypi","requirements":"==4.8.1","direct":true,"kind":"runtime","optional":false},{"id":5902098,"package_name":"jupyter-server","ecosystem":"pypi","requirements":"==1.11.0","direct":true,"kind":"runtime","optional":false},{"id":5902099,"package_name":"jupyterlab","ecosystem":"pypi","requirements":"==3.1.12","direct":true,"kind":"runtime","optional":false},{"id":5902100,"package_name":"jupyterlab-pygments","ecosystem":"pypi","requirements":"==0.1.2","direct":true,"kind":"runtime","optional":false},{"id":5902101,"package_name":"jupyterlab-server","ecosystem":"pypi","requirements":"==2.8.1","direct":true,"kind":"runtime","optional":false},{"id":5902102,"package_name":"keyring","ecosystem":"pypi","requirements":"==23.2.1","direct":true,"kind":"runtime","optional":false},{"id":5902103,"package_name":"kiwisolver","ecosystem":"pypi","requirements":"==1.3.2","direct":true,"kind":"runtime","optional":false},{"id":5902104,"package_name":"loguru","ecosystem":"pypi","requirements":"==0.5.3","direct":true,"kind":"runtime","optional":false},{"id":5902105,"package_name":"lxml","ecosystem":"pypi","requirements":"==4.6.3","direct":true,"kind":"runtime","optional":false},{"id":5902106,"package_name":"Markdown","ecosystem":"pypi","requirements":"==3.3.4","direct":true,"kind":"runtime","optional":false},{"id":5902107,"package_name":"MarkupSafe","ecosystem":"pypi","requirements":"==2.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902108,"package_name":"mass-spec-utils","ecosystem":"pypi","requirements":"==0.0.12","direct":true,"kind":"runtime","optional":false},{"id":5902109,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.4.3","direct":true,"kind":"runtime","optional":false},{"id":5902110,"package_name":"matplotlib-inline","ecosystem":"pypi","requirements":"==0.1.3","direct":true,"kind":"runtime","optional":false},{"id":5902111,"package_name":"mccabe","ecosystem":"pypi","requirements":"==0.6.1","direct":true,"kind":"runtime","optional":false},{"id":5902112,"package_name":"mergedeep","ecosystem":"pypi","requirements":"==1.3.4","direct":true,"kind":"runtime","optional":false},{"id":5902113,"package_name":"mistune","ecosystem":"pypi","requirements":"==0.8.4","direct":true,"kind":"runtime","optional":false},{"id":5902114,"package_name":"mkdocs","ecosystem":"pypi","requirements":"==1.2.2","direct":true,"kind":"runtime","optional":false},{"id":5902115,"package_name":"mkdocs-autorefs","ecosystem":"pypi","requirements":"==0.2.1","direct":true,"kind":"runtime","optional":false},{"id":5902116,"package_name":"mkdocstrings","ecosystem":"pypi","requirements":"==0.15.2","direct":true,"kind":"runtime","optional":false},{"id":5902117,"package_name":"molmass","ecosystem":"pypi","requirements":"==2021.6.18","direct":true,"kind":"runtime","optional":false},{"id":5902118,"package_name":"more-itertools","ecosystem":"pypi","requirements":"==8.4.0","direct":true,"kind":"runtime","optional":false},{"id":5902119,"package_name":"nbclassic","ecosystem":"pypi","requirements":"==0.3.2","direct":true,"kind":"runtime","optional":false},{"id":5902120,"package_name":"nbclient","ecosystem":"pypi","requirements":"==0.5.4","direct":true,"kind":"runtime","optional":false},{"id":5902121,"package_name":"nbconvert","ecosystem":"pypi","requirements":"==6.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902122,"package_name":"nbformat","ecosystem":"pypi","requirements":"==5.1.3","direct":true,"kind":"runtime","optional":false},{"id":5902123,"package_name":"nest-asyncio","ecosystem":"pypi","requirements":"==1.5.1","direct":true,"kind":"runtime","optional":false},{"id":5902124,"package_name":"networkx","ecosystem":"pypi","requirements":"==2.6.3","direct":true,"kind":"runtime","optional":false},{"id":5902125,"package_name":"notebook","ecosystem":"pypi","requirements":"==6.4.4","direct":true,"kind":"runtime","optional":false},{"id":5902126,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.21.2","direct":true,"kind":"runtime","optional":false},{"id":5902127,"package_name":"orderedmultidict","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902128,"package_name":"outcome","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902129,"package_name":"packaging","ecosystem":"pypi","requirements":"==20.9","direct":true,"kind":"runtime","optional":false},{"id":5902130,"package_name":"pandas","ecosystem":"pypi","requirements":"==1.3.3","direct":true,"kind":"runtime","optional":false},{"id":5902131,"package_name":"pandocfilters","ecosystem":"pypi","requirements":"==1.5.0","direct":true,"kind":"runtime","optional":false},{"id":5902132,"package_name":"paramz","ecosystem":"pypi","requirements":"==0.9.5","direct":true,"kind":"runtime","optional":false},{"id":5902133,"package_name":"parso","ecosystem":"pypi","requirements":"==0.8.2","direct":true,"kind":"runtime","optional":false},{"id":5902134,"package_name":"pathspec","ecosystem":"pypi","requirements":"==0.9.0","direct":true,"kind":"runtime","optional":false},{"id":5902135,"package_name":"patsy","ecosystem":"pypi","requirements":"==0.5.1","direct":true,"kind":"runtime","optional":false},{"id":5902136,"package_name":"pbr","ecosystem":"pypi","requirements":"==5.6.0","direct":true,"kind":"runtime","optional":false},{"id":5902137,"package_name":"pep517","ecosystem":"pypi","requirements":"==0.11.0","direct":true,"kind":"runtime","optional":false},{"id":5902138,"package_name":"pexpect","ecosystem":"pypi","requirements":"==4.8.0","direct":true,"kind":"runtime","optional":false},{"id":5902139,"package_name":"pickleshare","ecosystem":"pypi","requirements":"==0.7.5","direct":true,"kind":"runtime","optional":false},{"id":5902140,"package_name":"Pillow","ecosystem":"pypi","requirements":"==8.3.2","direct":true,"kind":"runtime","optional":false},{"id":5902141,"package_name":"pip-shims","ecosystem":"pypi","requirements":"==0.5.3","direct":true,"kind":"runtime","optional":false},{"id":5902142,"package_name":"pipenv-setup","ecosystem":"pypi","requirements":"==3.1.1","direct":true,"kind":"runtime","optional":false},{"id":5902143,"package_name":"pipfile","ecosystem":"pypi","requirements":"==0.0.2","direct":true,"kind":"runtime","optional":false},{"id":5902144,"package_name":"pkginfo","ecosystem":"pypi","requirements":"==1.7.1","direct":true,"kind":"runtime","optional":false},{"id":5902145,"package_name":"plette","ecosystem":"pypi","requirements":"==0.2.3","direct":true,"kind":"runtime","optional":false},{"id":5902146,"package_name":"pluggy","ecosystem":"pypi","requirements":"==1.0.0","direct":true,"kind":"runtime","optional":false},{"id":5902147,"package_name":"prometheus-client","ecosystem":"pypi","requirements":"==0.11.0","direct":true,"kind":"runtime","optional":false},{"id":5902148,"package_name":"prompt-toolkit","ecosystem":"pypi","requirements":"==3.0.20","direct":true,"kind":"runtime","optional":false},{"id":5902149,"package_name":"psims","ecosystem":"pypi","requirements":"==0.1.43","direct":true,"kind":"runtime","optional":false},{"id":5902150,"package_name":"psutil","ecosystem":"pypi","requirements":"==5.8.0","direct":true,"kind":"runtime","optional":false},{"id":5902151,"package_name":"ptyprocess","ecosystem":"pypi","requirements":"==0.7.0","direct":true,"kind":"runtime","optional":false},{"id":5902152,"package_name":"py","ecosystem":"pypi","requirements":"==1.10.0","direct":true,"kind":"runtime","optional":false},{"id":5902153,"package_name":"pycodestyle","ecosystem":"pypi","requirements":"==2.7.0","direct":true,"kind":"runtime","optional":false},{"id":5902154,"package_name":"pycparser","ecosystem":"pypi","requirements":"==2.20","direct":true,"kind":"runtime","optional":false},{"id":5902155,"package_name":"pyDOE","ecosystem":"pypi","requirements":"==0.3.8","direct":true,"kind":"runtime","optional":false},{"id":5902156,"package_name":"pyflakes","ecosystem":"pypi","requirements":"==2.3.1","direct":true,"kind":"runtime","optional":false},{"id":5902157,"package_name":"Pygments","ecosystem":"pypi","requirements":"==2.10.0","direct":true,"kind":"runtime","optional":false},{"id":5902158,"package_name":"pymdown-extensions","ecosystem":"pypi","requirements":"==8.2","direct":true,"kind":"runtime","optional":false},{"id":5902159,"package_name":"pymzml","ecosystem":"pypi","requirements":"==2.4.7","direct":true,"kind":"runtime","optional":false},{"id":5902160,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==2.4.7","direct":true,"kind":"runtime","optional":false},{"id":5902161,"package_name":"pyrsistent","ecosystem":"pypi","requirements":"==0.18.0","direct":true,"kind":"runtime","optional":false},{"id":5902162,"package_name":"pysmiles","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":5902163,"package_name":"pytest","ecosystem":"pypi","requirements":"==6.2.5","direct":true,"kind":"runtime","optional":false},{"id":5902164,"package_name":"pytest-cov","ecosystem":"pypi","requirements":"==2.12.1","direct":true,"kind":"runtime","optional":false},{"id":5902165,"package_name":"python-dateutil","ecosystem":"pypi","requirements":"==2.8.2","direct":true,"kind":"runtime","optional":false},{"id":5902166,"package_name":"pytkdocs","ecosystem":"pypi","requirements":"==0.11.1","direct":true,"kind":"runtime","optional":false},{"id":5902167,"package_name":"pytz","ecosystem":"pypi","requirements":"==2021.1","direct":true,"kind":"runtime","optional":false},{"id":5902168,"package_name":"PyYAML","ecosystem":"pypi","requirements":"==5.4.1","direct":true,"kind":"runtime","optional":false},{"id":5902169,"package_name":"pyyaml-env-tag","ecosystem":"pypi","requirements":"==0.1","direct":true,"kind":"runtime","optional":false},{"id":5902170,"package_name":"pyzmq","ecosystem":"pypi","requirements":"==22.3.0","direct":true,"kind":"runtime","optional":false},{"id":5902171,"package_name":"qtconsole","ecosystem":"pypi","requirements":"==4.7.5","direct":true,"kind":"runtime","optional":false},{"id":5902172,"package_name":"QtPy","ecosystem":"pypi","requirements":"==1.9.0","direct":true,"kind":"runtime","optional":false},{"id":5902173,"package_name":"readme-renderer","ecosystem":"pypi","requirements":"==29.0","direct":true,"kind":"runtime","optional":false},{"id":5902174,"package_name":"regex","ecosystem":"pypi","requirements":"==2021.8.28","direct":true,"kind":"runtime","optional":false},{"id":5902175,"package_name":"requests","ecosystem":"pypi","requirements":"==2.26.0","direct":true,"kind":"runtime","optional":false},{"id":5902176,"package_name":"requests-toolbelt","ecosystem":"pypi","requirements":"==0.9.1","direct":true,"kind":"runtime","optional":false},{"id":5902177,"package_name":"requests-unixsocket","ecosystem":"pypi","requirements":"==0.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902178,"package_name":"requirementslib","ecosystem":"pypi","requirements":"==1.5.16","direct":true,"kind":"runtime","optional":false},{"id":5902179,"package_name":"rfc3986","ecosystem":"pypi","requirements":"==1.5.0","direct":true,"kind":"runtime","optional":false},{"id":5902180,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"==0.24.2","direct":true,"kind":"runtime","optional":false},{"id":5902181,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.4.1","direct":true,"kind":"runtime","optional":false},{"id":5902182,"package_name":"seaborn","ecosystem":"pypi","requirements":"==0.11.2","direct":true,"kind":"runtime","optional":false},{"id":5902183,"package_name":"SecretStorage","ecosystem":"pypi","requirements":"==3.3.1","direct":true,"kind":"runtime","optional":false},{"id":5902184,"package_name":"Send2Trash","ecosystem":"pypi","requirements":"==1.8.0","direct":true,"kind":"runtime","optional":false},{"id":5902185,"package_name":"six","ecosystem":"pypi","requirements":"==1.16.0","direct":true,"kind":"runtime","optional":false},{"id":5902186,"package_name":"sniffio","ecosystem":"pypi","requirements":"==1.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902187,"package_name":"sortedcontainers","ecosystem":"pypi","requirements":"==2.4.0","direct":true,"kind":"runtime","optional":false},{"id":5902188,"package_name":"SQLAlchemy","ecosystem":"pypi","requirements":"==1.4.23","direct":true,"kind":"runtime","optional":false},{"id":5902189,"package_name":"statsmodels","ecosystem":"pypi","requirements":"==0.12.2","direct":true,"kind":"runtime","optional":false},{"id":5902190,"package_name":"tabulate","ecosystem":"pypi","requirements":"==0.8.9","direct":true,"kind":"runtime","optional":false},{"id":5902191,"package_name":"terminado","ecosystem":"pypi","requirements":"==0.12.1","direct":true,"kind":"runtime","optional":false},{"id":5902192,"package_name":"testpath","ecosystem":"pypi","requirements":"==0.5.0","direct":true,"kind":"runtime","optional":false},{"id":5902193,"package_name":"threadpoolctl","ecosystem":"pypi","requirements":"==2.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902194,"package_name":"toml","ecosystem":"pypi","requirements":"==0.10.2","direct":true,"kind":"runtime","optional":false},{"id":5902195,"package_name":"tomli","ecosystem":"pypi","requirements":"==1.2.1","direct":true,"kind":"runtime","optional":false},{"id":5902196,"package_name":"tomlkit","ecosystem":"pypi","requirements":"==0.7.2","direct":true,"kind":"runtime","optional":false},{"id":5902197,"package_name":"tornado","ecosystem":"pypi","requirements":"==6.1","direct":true,"kind":"runtime","optional":false},{"id":5902198,"package_name":"tqdm","ecosystem":"pypi","requirements":"==4.62.2","direct":true,"kind":"runtime","optional":false},{"id":5902199,"package_name":"traitlets","ecosystem":"pypi","requirements":"==5.1.0","direct":true,"kind":"runtime","optional":false},{"id":5902200,"package_name":"trio","ecosystem":"pypi","requirements":"==0.16.0","direct":true,"kind":"runtime","optional":false},{"id":5902201,"package_name":"twine","ecosystem":"pypi","requirements":"==3.4.2","direct":true,"kind":"runtime","optional":false},{"id":5902202,"package_name":"typed-ast","ecosystem":"pypi","requirements":"==1.4.3","direct":true,"kind":"runtime","optional":false},{"id":5902203,"package_name":"urllib3","ecosystem":"pypi","requirements":"==1.26.6","direct":true,"kind":"runtime","optional":false},{"id":5902204,"package_name":"vistir","ecosystem":"pypi","requirements":"==0.5.2","direct":true,"kind":"runtime","optional":false},{"id":5902205,"package_name":"watchdog","ecosystem":"pypi","requirements":"==2.1.5","direct":true,"kind":"runtime","optional":false},{"id":5902206,"package_name":"wcwidth","ecosystem":"pypi","requirements":"==0.2.5","direct":true,"kind":"runtime","optional":false},{"id":5902207,"package_name":"webencodings","ecosystem":"pypi","requirements":"==0.5.1","direct":true,"kind":"runtime","optional":false},{"id":5902208,"package_name":"websocket-client","ecosystem":"pypi","requirements":"==1.2.1","direct":true,"kind":"runtime","optional":false},{"id":5902209,"package_name":"widgetsnbextension","ecosystem":"pypi","requirements":"==3.5.1","direct":true,"kind":"runtime","optional":false},{"id":5902210,"package_name":"xlrd","ecosystem":"pypi","requirements":"==1.2.0","direct":true,"kind":"runtime","optional":false},{"id":5902211,"package_name":"zipp","ecosystem":"pypi","requirements":"==3.5.0","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-06-22T14:11:41.219Z","updated_at":"2022-06-22T14:11:41.219Z","repository_link":"https://github.com/glasgowcompbio/vimms/blob/master/setup.py","dependencies":[{"id":5902505,"package_name":"numpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902506,"package_name":"pandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902507,"package_name":"scipy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902508,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902509,"package_name":"seaborn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902510,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902511,"package_name":"pymzml","ecosystem":"pypi","requirements":"==2.4.7","direct":true,"kind":"runtime","optional":false},{"id":5902512,"package_name":"psims","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902513,"package_name":"events","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902514,"package_name":"tqdm","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902515,"package_name":"joblib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902516,"package_name":"ipyparallel","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902517,"package_name":"requests","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902518,"package_name":"loguru","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902519,"package_name":"networkx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902520,"package_name":"jsonpickle","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902521,"package_name":"statsmodels","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902522,"package_name":"mass-spec-utils","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902523,"package_name":"tabulate","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902524,"package_name":"pysmiles","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902525,"package_name":"intervaltree","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":5902526,"package_name":"gpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/python-package.yml","sha":null,"kind":"manifest","created_at":"2023-02-16T18:45:28.010Z","updated_at":"2023-02-16T18:45:28.010Z","repository_link":"https://github.com/glasgowcompbio/vimms/blob/master/.github/workflows/python-package.yml","dependencies":[{"id":7721121612,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7721121619,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"conda","filepath":"environment.yml","sha":null,"kind":"manifest","created_at":"2023-02-16T18:45:28.207Z","updated_at":"2023-02-16T18:45:28.207Z","repository_link":"https://github.com/glasgowcompbio/vimms/blob/master/environment.yml","dependencies":[{"id":7721121991,"package_name":"autopep8","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122019,"package_name":"flake8","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122028,"package_name":"intervaltree","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122035,"package_name":"ipyparallel","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122061,"package_name":"ipywidgets","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122065,"package_name":"joblib","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122076,"package_name":"jsonpickle","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122085,"package_name":"jupyterlab","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122093,"package_name":"loguru","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122111,"package_name":"matplotlib","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122144,"package_name":"networkx","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122198,"package_name":"numba","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122199,"package_name":"numpy","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122202,"package_name":"pandas","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122203,"package_name":"pip","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122204,"package_name":"plotly","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122205,"package_name":"pytest","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122206,"package_name":"pytest-cov","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122207,"package_name":"requests","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122208,"package_name":"scikit-learn","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122209,"package_name":"scipy","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122210,"package_name":"seaborn","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122211,"package_name":"statsmodels","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122212,"package_name":"tabulate","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":7721122213,"package_name":"tqdm","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false}]}],"score":9.11217612318895,"created_at":"2025-09-04T09:17:49.608Z","updated_at":"2025-10-07T08:04:33.111Z","avatar_url":"https://github.com/glasgowcompbio.png","language":"Python","category":"Scientific Software","sub_category":"Peer-reviewed","monthly_downloads":33,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["mesh"],"project_url":"https://science.ecosyste.ms/api/v1/projects/1559","html_url":"https://science.ecosyste.ms/projects/1559"}