{"id":33175272,"url":"https://github.com/SUNCAT-Center/CatKit","last_synced_at":"2025-11-20T20:02:27.737Z","repository":{"id":25842643,"uuid":"106468332","full_name":"SUNCAT-Center/CatKit","owner":"SUNCAT-Center","description":"General purpose tools for high-throughput catalysis","archived":false,"fork":false,"pushed_at":"2025-05-20T20:58:33.000Z","size":26124,"stargazers_count":96,"open_issues_count":14,"forks_count":57,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-10-27T13:58:16.854Z","etag":null,"topics":["catalysis-informatics","catalyst","chemical-engineering","chemical-kinetics","chemical-reaction-networks","combinatorics","computational-chemistry","materials-informatics","materials-science"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SUNCAT-Center.png","metadata":{"files":{"readme":"readme.org","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":"docs/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-10-10T20:34:23.000Z","updated_at":"2025-09-08T05:43:36.000Z","dependencies_parsed_at":"2023-02-10T12:45:43.425Z","dependency_job_id":"f3a882d0-f93e-4062-a611-4af0170eca7d","html_url":"https://github.com/SUNCAT-Center/CatKit","commit_stats":{"total_commits":206,"total_committers":8,"mean_commits":25.75,"dds":"0.46601941747572817","last_synced_commit":"79e7b5fb3e560a8d8654c65e103fb95cf5ecf590"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/SUNCAT-Center/CatKit","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SUNCAT-Center%2FCatKit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SUNCAT-Center%2FCatKit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SUNCAT-Center%2FCatKit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SUNCAT-Center%2FCatKit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SUNCAT-Center","download_url":"https://codeload.github.com/SUNCAT-Center/CatKit/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SUNCAT-Center%2FCatKit/sbom","scorecard":{"id":124574,"data":{"date":"2025-08-11","repo":{"name":"github.com/SUNCAT-Center/CatKit","commit":"38ca0c8dc87c4be67b34e03a74e57ad29c85b902"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.6,"checks":[{"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":"Code-Review","score":4,"reason":"Found 10/21 approved changesets -- score normalized to 4","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":"Maintained","score":0,"reason":"1 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":"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":"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":"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:0","Info: FSF or OSI recognized license: GNU General Public License v3.0: 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":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"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":"Vulnerabilities","score":0,"reason":"11 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2022-42991 / GHSA-v3c5-jqr6-7qm8","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: GHSA-6p56-wp2h-9hxr","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","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-2019-156 / GHSA-xp76-357g-9wqq","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114","Warn: Project is vulnerable to: PYSEC-2019-124 / GHSA-38fc-9xqv-7f7q","Warn: Project is vulnerable to: PYSEC-2019-123 / GHSA-887w-45rq-vxgf"],"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 28 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":"2025-08-16T03:26:33.736Z","repository_id":25842643,"created_at":"2025-08-16T03:26:33.736Z","updated_at":"2025-08-16T03:26:33.736Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":285503668,"owners_count":27182913,"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":"2025-11-20T02:00:05.334Z","response_time":54,"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"}},"keywords":["catalysis-informatics","catalyst","chemical-engineering","chemical-kinetics","chemical-reaction-networks","combinatorics","computational-chemistry","materials-informatics","materials-science"],"created_at":"2025-11-16T02:00:37.344Z","updated_at":"2025-11-20T20:02:27.727Z","avatar_url":"https://github.com/SUNCAT-Center.png","language":"Python","funding_links":[],"categories":["Simulations"],"sub_categories":[],"readme":"#+Title: CatKit: Catalysis Kit\n#+Author: SUNCAT Method Development Team\n#+OPTIONS: toc:nil\n#+LATEX_HEADER: \\setlength{\\parindent}{0em}\n\n#+BEGIN_HTML\n\u003ca href='https://travis-ci.org/SUNCAT-Center/CatKit.svg?branch=master'\u003e\u003cimg src='https://travis-ci.org/SUNCAT-Center/CatKit.svg?branch=master'/\u003e\u003c/a\u003e\n\u003ca href='https://coveralls.io/github/SUNCAT-Center/CatKit?branch=master'\u003e\u003cimg src='https://coveralls.io/repos/github/SUNCAT-Center/CatKit/badge.svg?branch=master' alt='Coverage Status' /\u003e\u003c/a\u003e\n\u003ca href='http://catkit.readthedocs.io/en/latest/?badge=latest'\u003e\u003cimg src='https://readthedocs.org/projects/catkit/badge/?version=latest' alt='Documentation Status' /\u003e\u003c/a\u003e\n#+END_HTML\n\nWelcome to CatKit! A staging ground for computational tools which are generally useful for catalysis research. The goal of the project is to provide a communal location for those interested in hosting such tools under a common banner. In doing so, we hope to provide the infrastructure to produce more advanced functionality based on modular components of individual contributors.\n\nYou can find our [[http://catkit.readthedocs.io/en/latest/?badge=latest][full documentation here]].\n\n* Installation\n** Pip installation\nCatKit is most easily installed with pip using:\n\n#+BEGIN_SRC sh\npip install git+https://github.com/SUNCAT-Center/CatKit.git\n#+END_SRC\n\nFor usage on high-performance computers, installation will need to be performed locally which can be done using:\n\n#+BEGIN_SRC sh\npip install --user git+https://github.com/SUNCAT-Center/CatKit.git\n#+END_SRC\n\nThese commands will install all of the necessary dependencies for you.\n\n** Source installation\nAlternatively, clone the git repo to your home directory.\n\n#+BEGIN_SRC sh\ngit clone https://github.com/SUNCAT-Center/CatKit.git catkit\n#+END_SRC\n\nThen, add =~/catkit/bin= and =~/catkit= to your =PATH= and =PYTHONPATH= environment variables by adding the following line to your =~/.bashrc= file.\n\n#+BEGIN_SRC sh\nexport PYTHONPATH=~/catkit:$PYTHONPATH\nexport PATH=~/catkit/bin:$PATH\n#+END_SRC\n\nAnd install the package:\n#+BEGIN_SRC sh\ncd catkit/\npython setup.py install\n#+END_SRC\n\n* CatGen: Catalysis Generator\nCatGen is an enumeration module designed to construct various catalytic structures.\n\n- [X] Gas phase molecules\n- [ ] Bulk structures\n- [X] Surfaces structures\n- [X] Adsorption sites\n- [X] Catalytic structures\n\nIt also has functionality for enumeration of other systems relevant to the field of catalysis.\n\n- [X] Reaction mechanisms\n- [X] Reaction routes\n\nFor additional details regarding how the generator operates, including example usage, see the [[https://catkit-jboes.readthedocs.io/en/latest/_static/frontmatter/catgen.html][CatGen documentation]].\n\n* CatFlow: Catalysis Workflow\nCatFlow is currently a staging ground for Workflow code and techniques. These functions are meant to be used in conjunction with the other modules inside CatKit to help automate these tasks.\n\nCurrently, CatFlow's functionality utilizes [[https://materialsproject.github.io/fireworks/][Fireworks]] and many of the functions are also specifically tailored to work on the high-performance computers which are available to the [[http://suncat.stanford.edu/][SUNCAT]] group as Stanford.\n\nFor additional detail see the [[https://catkit-jboes.readthedocs.io/en/latest/_static/frontmatter/catflow.html][CatFlow documentation]].\n\n* Dependencies\nCatKit attempts to make use of basic functionalities implemented by existing softwares when possible to extend its capabilities.\n\nA full list of required packaged can be found in [[./requirements.txt][the requirements]].\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSUNCAT-Center%2FCatKit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FSUNCAT-Center%2FCatKit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSUNCAT-Center%2FCatKit/lists"}