{"id":37617639,"url":"https://github.com/bio-phys/hplusminus","last_synced_at":"2026-01-16T10:33:31.415Z","repository":{"id":57437597,"uuid":"317839327","full_name":"bio-phys/hplusminus","owner":"bio-phys","description":"Statistical tests to detect and quantify correlations in residuals when fitting models to one-dimensional data. ","archived":false,"fork":false,"pushed_at":"2021-01-25T10:39:31.000Z","size":1835,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-28T05:02:15.032Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/bio-phys.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-12-02T11:23:09.000Z","updated_at":"2021-04-28T12:21:19.000Z","dependencies_parsed_at":"2022-09-26T17:01:09.815Z","dependency_job_id":null,"html_url":"https://github.com/bio-phys/hplusminus","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/bio-phys/hplusminus","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fhplusminus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fhplusminus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fhplusminus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fhplusminus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio-phys","download_url":"https://codeload.github.com/bio-phys/hplusminus/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fhplusminus/sbom","scorecard":{"id":239056,"data":{"date":"2025-08-11","repo":{"name":"github.com/bio-phys/hplusminus","commit":"6a59333f91b7bada98872e041afe7cce1a6c5149"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":1.7,"checks":[{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Code-Review","score":0,"reason":"Found 0/23 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":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"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":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","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":"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":"Pinned-Dependencies","score":-1,"reason":"no dependencies found","details":null,"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":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Info: FSF or OSI recognized license: MIT License: LICENSE.txt:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'main'"],"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":"Vulnerabilities","score":0,"reason":"11 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2021-427 / GHSA-f865-m6cq-j9vx","Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52","Warn: Project is vulnerable to: PYSEC-2019-156 / GHSA-xp76-357g-9wqq","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 8 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"}}]},"last_synced_at":"2025-08-17T06:18:47.740Z","repository_id":57437597,"created_at":"2025-08-17T06:18:47.740Z","updated_at":"2025-08-17T06:18:47.740Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478050,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-16T10:33:30.781Z","updated_at":"2026-01-16T10:33:31.399Z","avatar_url":"https://github.com/bio-phys.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hplusminus\n\n![](img/overview.png)\n\n\u003cp align=\"center\"\u003e\n\u003ca href=\"https://pypi.org/project/hplusminus/\"\u003e\u003cimg alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/hplusminus\"\u003e\u003c/a\u003e\n\u003ca href=\"https://travis-ci.com/bio-phys/hplusminus\"\u003e\u003cimg alt=\"Build Status\" src=\"https://travis-ci.com/bio-phys/hplusminus.svg?branch=main\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\nCopyright (C) 2020 Juergen Koefinger, Max Planck Institute of Biophysics, Frankfurt am Main, Germany\n\nWith contributions from Klaus Reuter, Max Planck Computing and Data Facility, Garching, Germany.\n\nReleased under the MIT Licence, see the file LICENSE.txt.\n\n## Reference\n\n**Powerful statistical tests for ordered data** \\\nJuergen Koefinger and Gerhard Hummer \\\nPreprint: https://doi.org/10.26434/chemrxiv.13373351 (2020)\n\n## Requirements\n\n* Python 3\n* Jupyter (for Jupyter notebooks only)\n* Python modules (can be installed with `pip` or `conda`):\n  * numpy\n  * scipy\n  * mpmath\n  * matplotlib (for Jupyter notebooks only)\n\n## Installation\n\nThe **hplusminus** package can be installed in the following ways:\n\n### `pip` installation\n\nTo install via `pip` please run:\n\n```bash\npip install --user hplusminus\n```\n\n### Installation from source\n\nAfter downloading and unpacking the source tarball please run:\n\n```bash\npython setup.py install --user\n```\n\n## Python script\n\n### *hplusminus_tests.py*\n\nPython 3 script to evaluate test statistics for normalized residuals.\nThis script contains the central functionality.\n\nSee help for more information and usage:\n\n```bash\npython hplusminus_tests.py -h\n````\n\n#### Example for alternative model\n\n```bash\npython hplusminus_tests.py ./examples/alternative_model_normalized_residuals.txt\n```\n\n#### Example for true model\n\n```bash\npython hplusminus_tests.py ./examples/true_model_normalized_residuals.txt\n```\n\n## Jupyter notebooks\n\nNotebooks in the directory *./ipynb/* serve to explore the capabilties of our statistical tests.\nSee notebooks themselves for more details on purpose and usage.\n\n### *hplusminus_tests.ipynb*\n\nEvaluate statistical tests.\n\nAddtionally to the functionality of *hplusminus_tests.py*, the notebook provides\nplots of normalized residuals and signs and a bar-plot to visually compare the p-values of the various tests.\n\n### *hplusminus_statistical_power.ipynb*\n\nCalculate statistical power for all tests and given model\n\n### *generate_models_for_residuals.ipynb*\n\nGenerate models for residuals, which can be used with the Python script *hplusminus_tests.py* and the Jupyter notebooks *hplusminus_tests.ipyn* and *hplusminus_statistical_power.ipynb*.\n\n## Python package *hplusminus*\n\n### *tests.py*\n\nPython 3 module file containing functions for the convenient evaluation of the statistical tests.\n\n### *io.py*\n\nPython 3 module file for input and output.\n\n### *rld.py*\n\nPython 3 module file for the calculation of the Shannon information (neg. log-probabilities) of all test statistics (rld for Run-Length Distribution).\nRequired by Python script *hplusminus_tests.py* and Jupyter notebooks *hplusminus_tests.ipynb* and *hplusminus_statistical_power.ipynb*.\n\n### *sid.py*\n\nPython 3 module file for the calculation of p-values using the gamma distribution approximation\nof the cumulative Shannon information distributions (SID).\nRequired by Python script *hplusminus_tests.py* and Jupyter notebooks *hplusminus_tests.ipynb* and *hplusminus_statistical_power.ipynb*.\n\n\n### Directories\n\n#### *./hplusminus/*\n\nPython module hplusminus\n\n#### *./examples/*\n\nExamples for normalized residuals generated with *generate_models_for_residuals.ipynb*.\n\n#### *./hplusminus/gsp/*\n\nNumpy binary files containing B-spline parameters (knots and coefficients) for gamma distribution parameters for all tests.\nInformation is read from these files. No need for user interaction.\n\n#### *./ipynb*\n\nDirectory containing Jupyter notebooks.\n\n##### *./ipynb/data/*\n\nDirectory used by Jupyter notebooks for input/output.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fhplusminus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio-phys%2Fhplusminus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fhplusminus/lists"}