K-Dense-AI/scientific-agent-skills

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https://github.com/K-Dense-AI/scientific-agent-skills · scanned 2026-05-14 23:07 UTC (3 weeks ago) · 10 languages

491 findings (392 legacy + 99 scanner) 52nd percentile · Python · medium (20-100K LoC) Scanner says 74 (lower by 12)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 3 weeks ago · v1 · 380 findings from 1 source. Findings combine the legacy security pipeline AND the multi-layer engine (atlas, wiring, flows, ranked) AND verified AI agent contributions.

JSON

Score breakdown â 2026-05-14-v3

Component	Sub-score	Weight	Contribution
`structure_score`	60.0	0.15	9.00
`security_score`	75.9	0.25	18.98
`testing_score`	38.0	0.20	7.60
`documentation_score`	74.6	0.15	11.19
`practices_score`	65.0	0.15	9.75
`code_quality`	50.0	0.10	5.00
Overall		1.00	61.5

Severity distribution — click a segment to filter

Active filters: excluding tests × Reset all

Severity: Critical 20 High 251 Medium 106 Low 3 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Legacy 380 9-layer 0 Crowd 0 Layer: Software 227 Quality 131 Security 22

Exclude dismissed / FP Exclude test files

All 3228 nodes from the latest scan, grouped by kind. Each node is a unit the engine identified (file, function, endpoint, table…). Most users won't need this view — it's primarily for debugging the engine's graph extraction or for AI agents that want to enumerate the project structure.

Label	Layer	Status	Path
`build_scanner`	software	healthy	`scan_skills.py:26`
`severity_badge`	software	healthy	`scan_skills.py:46`
`generate_report`	software	healthy	`scan_skills.py:58`
`scan_with_progress`	software	healthy	`scan_skills.py:125`
`main`	software	healthy	`scan_skills.py:205`
`_sev_str`	software	healthy	`scan_pr_skills.py:35`
`scan_skill_dirs`	software	healthy	`scan_pr_skills.py:42`
`_loc`	software	healthy	`scan_pr_skills.py:90`
`format_comment`	software	healthy	`scan_pr_skills.py:99`
`_should_block`	software	healthy	`scan_pr_skills.py:171`
`main`	software	healthy	`scan_pr_skills.py:182`
`main`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic.…`
`_load_env_file`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`__init__`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`_log`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`_make_request`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`_extract_image_from_response`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`_image_to_base64`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`generate_image`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`review_image`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`improve_prompt`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`generate_iterative`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`main`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`matches_filter`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`fetch`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`parse_markdown`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`finalize`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`render_entry`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`render_entries`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`cmd_topics`	software	dead	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`cmd_topic`	software	dead	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`cmd_all`	software	dead	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`cmd_search`	software	dead	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`cmd_raw`	software	dead	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`main`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`__init__`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`extract_dois`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`verify_doi`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`_get_crossref_metadata`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`_format_authors`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`_extract_year`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`verify_url`	software	dead	`scientific-skills/literature-review/scripts/verify_citation…`
`verify_citations_in_file`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`format_citation_apa`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`format_citation_nature`	software	dead	`scientific-skills/literature-review/scripts/verify_citation…`
`main`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`main`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`_load_env_file`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`__init__`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`_log`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`README.md`	software	healthy	`README.md`
`scan_skills.py`	software	healthy	`scan_skills.py`
`LICENSE.md`	software	healthy	`LICENSE.md`
`pyproject.toml`	software	healthy	`pyproject.toml`
`SECURITY.md`	software	healthy	`SECURITY.md`
`scan_pr_skills.py`	software	healthy	`scan_pr_skills.py`
`SKILL.md`	software	healthy	`scientific-skills/latex-posters/SKILL.md`
`review_poster.sh`	software	healthy	`scientific-skills/latex-posters/scripts/review_poster.sh`
`generate_schematic.py`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic.…`
`generate_schematic_ai.py`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`latex_poster_packages.md`	software	healthy	`scientific-skills/latex-posters/references/latex_poster_pac…`
`README.md`	software	healthy	`scientific-skills/latex-posters/references/README.md`
`poster_design_principles.md`	software	healthy	`scientific-skills/latex-posters/references/poster_design_pr…`
`poster_content_guide.md`	software	healthy	`scientific-skills/latex-posters/references/poster_content_g…`
`poster_layout_design.md`	software	healthy	`scientific-skills/latex-posters/references/poster_layout_de…`
`poster_quality_checklist.md`	software	healthy	`scientific-skills/latex-posters/assets/poster_quality_check…`
`SKILL.md`	software	healthy	`scientific-skills/dnanexus-integration/SKILL.md`
`app-development.md`	software	healthy	`scientific-skills/dnanexus-integration/references/app-devel…`
`job-execution.md`	software	healthy	`scientific-skills/dnanexus-integration/references/job-execu…`
`configuration.md`	software	healthy	`scientific-skills/dnanexus-integration/references/configura…`
`python-sdk.md`	software	healthy	`scientific-skills/dnanexus-integration/references/python-sd…`
`data-operations.md`	software	healthy	`scientific-skills/dnanexus-integration/references/data-oper…`
`SKILL.md`	software	healthy	`scientific-skills/parallel-web/SKILL.md`
`web-extract.md`	software	healthy	`scientific-skills/parallel-web/references/web-extract.md`
`deep-research.md`	software	healthy	`scientific-skills/parallel-web/references/deep-research.md`
`data-enrichment.md`	software	healthy	`scientific-skills/parallel-web/references/data-enrichment.md`
`web-search.md`	software	healthy	`scientific-skills/parallel-web/references/web-search.md`
`SKILL.md`	software	healthy	`scientific-skills/hugging-science/SKILL.md`
`fetch_catalog.py`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py`
`using-datasets.md`	software	healthy	`scientific-skills/hugging-science/references/using-datasets…`
`topics-and-slugs.md`	software	healthy	`scientific-skills/hugging-science/references/topics-and-slu…`
`using-spaces.md`	software	healthy	`scientific-skills/hugging-science/references/using-spaces.md`
`using-models.md`	software	healthy	`scientific-skills/hugging-science/references/using-models.md`
`flagship-resources.md`	software	healthy	`scientific-skills/hugging-science/references/flagship-resou…`
`SKILL.md`	software	healthy	`scientific-skills/literature-review/SKILL.md`
`verify_citations.py`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`generate_schematic.py`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`generate_schematic_ai.py`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`search_databases.py`	software	healthy	`scientific-skills/literature-review/scripts/search_database…`
`generate_pdf.py`	software	healthy	`scientific-skills/literature-review/scripts/generate_pdf.py`
`citation_styles.md`	software	healthy	`scientific-skills/literature-review/references/citation_sty…`
`database_strategies.md`	software	healthy	`scientific-skills/literature-review/references/database_str…`
`review_template.md`	software	healthy	`scientific-skills/literature-review/assets/review_template.…`
`SKILL.md`	software	healthy	`scientific-skills/anndata/SKILL.md`
`best_practices.md`	software	healthy	`scientific-skills/anndata/references/best_practices.md`
`concatenation.md`	software	healthy	`scientific-skills/anndata/references/concatenation.md`
`manipulation.md`	software	healthy	`scientific-skills/anndata/references/manipulation.md`
`io_operations.md`	software	healthy	`scientific-skills/anndata/references/io_operations.md`
`data_structure.md`	software	healthy	`scientific-skills/anndata/references/data_structure.md`
`SKILL.md`	software	healthy	`scientific-skills/esm/SKILL.md`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`scientific-skills`	software	healthy	`scientific-skills`
`latex-posters`	software	healthy	`scientific-skills/latex-posters`
`scripts`	software	healthy	`scientific-skills/latex-posters/scripts`
`references`	software	healthy	`scientific-skills/latex-posters/references`
`assets`	software	healthy	`scientific-skills/latex-posters/assets`
`dnanexus-integration`	software	healthy	`scientific-skills/dnanexus-integration`
`references`	software	healthy	`scientific-skills/dnanexus-integration/references`
`parallel-web`	software	healthy	`scientific-skills/parallel-web`
`references`	software	healthy	`scientific-skills/parallel-web/references`
`hugging-science`	software	healthy	`scientific-skills/hugging-science`
`scripts`	software	healthy	`scientific-skills/hugging-science/scripts`
`references`	software	healthy	`scientific-skills/hugging-science/references`
`literature-review`	software	healthy	`scientific-skills/literature-review`
`scripts`	software	healthy	`scientific-skills/literature-review/scripts`
`references`	software	healthy	`scientific-skills/literature-review/references`
`assets`	software	healthy	`scientific-skills/literature-review/assets`
`anndata`	software	healthy	`scientific-skills/anndata`
`references`	software	healthy	`scientific-skills/anndata/references`
`esm`	software	healthy	`scientific-skills/esm`
`references`	software	healthy	`scientific-skills/esm/references`
`pydeseq2`	software	healthy	`scientific-skills/pydeseq2`
`scripts`	software	healthy	`scientific-skills/pydeseq2/scripts`
`references`	software	healthy	`scientific-skills/pydeseq2/references`
`networkx`	software	healthy	`scientific-skills/networkx`
`references`	software	healthy	`scientific-skills/networkx/references`
`matplotlib`	software	healthy	`scientific-skills/matplotlib`
`scripts`	software	healthy	`scientific-skills/matplotlib/scripts`
`references`	software	healthy	`scientific-skills/matplotlib/references`
`dask`	software	healthy	`scientific-skills/dask`
`references`	software	healthy	`scientific-skills/dask/references`
`flowio`	software	healthy	`scientific-skills/flowio`
`references`	software	healthy	`scientific-skills/flowio/references`
`bgpt-paper-search`	software	healthy	`scientific-skills/bgpt-paper-search`
`treatment-plans`	software	healthy	`scientific-skills/treatment-plans`
`scripts`	software	healthy	`scientific-skills/treatment-plans/scripts`
`references`	software	healthy	`scientific-skills/treatment-plans/references`
`assets`	software	healthy	`scientific-skills/treatment-plans/assets`
`neuropixels-analysis`	software	healthy	`scientific-skills/neuropixels-analysis`
`scripts`	software	healthy	`scientific-skills/neuropixels-analysis/scripts`
`references`	software	healthy	`scientific-skills/neuropixels-analysis/references`
`assets`	software	healthy	`scientific-skills/neuropixels-analysis/assets`
`pptx-posters`	software	healthy	`scientific-skills/pptx-posters`
`scripts`	software	healthy	`scientific-skills/pptx-posters/scripts`
`references`	software	healthy	`scientific-skills/pptx-posters/references`
`assets`	software	healthy	`scientific-skills/pptx-posters/assets`
`gget`	software	healthy	`scientific-skills/gget`
`scripts`	software	healthy	`scientific-skills/gget/scripts`
`references`	software	healthy	`scientific-skills/gget/references`
`clinical-decision-support`	software	healthy	`scientific-skills/clinical-decision-support`
`scripts`	software	healthy	`scientific-skills/clinical-decision-support/scripts`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/latex-posters/scripts/generate_schematic_…`
`Entry`	software	healthy	`scientific-skills/hugging-science/scripts/fetch_catalog.py:…`
`CitationVerifier`	software	healthy	`scientific-skills/literature-review/scripts/verify_citation…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/literature-review/scripts/generate_schema…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/treatment-plans/scripts/generate_schemati…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/pptx-posters/scripts/generate_schematic_a…`
`DecisionNode`	software	healthy	`scientific-skills/clinical-decision-support/scripts/build_d…`
`ActionNode`	software	healthy	`scientific-skills/clinical-decision-support/scripts/build_d…`
`CDSValidator`	software	healthy	`scientific-skills/clinical-decision-support/scripts/validat…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/clinical-decision-support/scripts/generat…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/scientific-critical-thinking/scripts/gene…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/hypothesis-generation/scripts/generate_sc…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/scientific-writing/scripts/generate_schem…`
`TestSkillDirectoryStructure`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestSkillMdFrontmatter`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestSkillMdContent`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestReferenceFiles`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestExampleScripts`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestPyprojectToml`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`TestSkillMdApiEndpointCoverage`	software	healthy	`scientific-skills/open-notebook/scripts/test_open_notebook_…`
`GapAnalyzer`	software	healthy	`scientific-skills/iso-13485-certification/scripts/gap_analy…`
`BibTeXFormatter`	software	healthy	`scientific-skills/citation-management/scripts/format_bibtex…`
`MetadataExtractor`	software	healthy	`scientific-skills/citation-management/scripts/extract_metad…`
`CitationValidator`	software	healthy	`scientific-skills/citation-management/scripts/validate_cita…`
`GoogleScholarSearcher`	software	healthy	`scientific-skills/citation-management/scripts/search_google…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/citation-management/scripts/generate_sche…`
`PubMedSearcher`	software	healthy	`scientific-skills/citation-management/scripts/search_pubmed…`
`DOIConverter`	software	healthy	`scientific-skills/citation-management/scripts/doi_to_bibtex…`
`StubBackend`	software	healthy	`scientific-skills/autoskill/tests/test_run.py:40`
`_FakeLMStudioHandler`	software	healthy	`scientific-skills/autoskill/tests/test_e2e.py:100`
`StubBackend`	software	healthy	`scientific-skills/autoskill/tests/test_synthesize.py:8`
`ClaudeBackend`	software	healthy	`scientific-skills/autoskill/scripts/backends.py:6`
`LocalBackend`	software	healthy	`scientific-skills/autoskill/scripts/backends.py:31`
`SynthesisError`	software	healthy	`scientific-skills/autoskill/scripts/synthesize.py:7`
`PromoteError`	software	healthy	`scientific-skills/autoskill/scripts/promote.py:7`
`ScreenpipeUnreachable`	software	healthy	`scientific-skills/autoskill/scripts/run.py:13`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/scientific-schematics/scripts/generate_sc…`
`MyEnvironment`	software	healthy	`scientific-skills/pufferlib/scripts/env_template.py:14`
`MultiAgentEnvironment`	software	healthy	`scientific-skills/pufferlib/scripts/env_template.py:165`
`Policy`	software	healthy	`scientific-skills/pufferlib/scripts/train_template.py:18`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/markitdown/scripts/generate_schematic_ai.…`
`PresentationValidator`	software	healthy	`scientific-skills/scientific-slides/scripts/validate_presen…`
`SlideImageGenerator`	software	healthy	`scientific-skills/scientific-slides/scripts/generate_slide_…`
`PDFToImagesConverter`	software	healthy	`scientific-skills/scientific-slides/scripts/pdf_to_images.p…`
`ScientificSchematicGenerator`	software	healthy	`scientific-skills/scientific-slides/scripts/generate_schema…`
`CheckResult`	software	healthy	`scientific-skills/timesfm-forecasting/scripts/check_system.…`
`SystemReport`	software	healthy	`scientific-skills/timesfm-forecasting/scripts/check_system.…`
`MEMORYSTATUSEX`	software	healthy	`scientific-skills/timesfm-forecasting/scripts/check_system.…`
`ResearchLookup`	software	healthy	`scientific-skills/research-lookup/research_lookup.py:24`
`ResearchLookup`	software	healthy	`scientific-skills/research-lookup/scripts/research_lookup.p…`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`password_literal::scientific-skills/labarchive-integration/…`	security	healthy	`scientific-skills/labarchive-integration/scripts/setup_conf…`
`password_literal::scientific-skills/labarchive-integration/…`	security	healthy	`scientific-skills/labarchive-integration/scripts/setup_conf…`
`password_literal::scientific-skills/labarchive-integration/…`	security	healthy	`scientific-skills/labarchive-integration/scripts/setup_conf…`
`generic_api_key::scientific-skills/research-lookup/lookup.py`	security	healthy	`scientific-skills/research-lookup/lookup.py`

Label	Layer	Status	Path
`port:09`	network	healthy	`scientific-skills/autoskill/references/screenpipe-config.ya…`
`port:19`	network	healthy	`scientific-skills/autoskill/references/screenpipe-config.ya…`
`port:6832`	network	healthy	`scientific-skills/hypogenic/references/config_template.yaml`

Label	Layer	Status	Path
`gha::security-scan`	cicd	healthy	`.github/workflows/security-scan.yml`
`gha::pr-skill-scan`	cicd	healthy	`.github/workflows/pr-skill-scan.yml`
`gha::release`	cicd	healthy	`.github/workflows/release.yml`

Label	Layer	Status	Path
`scan`	cicd	healthy	`.github/workflows/security-scan.yml`
`scan`	cicd	healthy	`.github/workflows/pr-skill-scan.yml`
`release`	cicd	healthy	`.github/workflows/release.yml`

Label	Layer	Status	Path
`vps::aws`	hardware	healthy	`scientific-skills/diffdock/scripts/setup_check.py`
`vps::gcp`	hardware	healthy	`scientific-skills/clinical-reports/scripts/compliance_check…`

Label	Layer	Status	Path
`auth::scientific-skills/autoskill/scripts/redact.py`	security	healthy	`scientific-skills/autoskill/scripts/redact.py`
`auth::scientific-skills/autoskill/tests/test_redact.py`	security	healthy	`scientific-skills/autoskill/tests/test_redact.py`

Label	Layer	Status	Path
`SKILL_SCANNER_LLM_API_KEY`	cicd	healthy	`—`
`GITHUB_TOKEN`	cicd	healthy	`—`

Label	Layer	Status	Path
`repobility-clone-izw8m2ei`	software	healthy	`/tmp/repobility-clone-izw8m2ei`

Label	Layer	Status	Path
`redis`	data	healthy	`scientific-skills/hypogenic/references/config_template.yaml`

Label	Layer	Status	Path
`caddy`	network	healthy	`scientific-skills/autoskill/config.yaml`

Label	Layer	Status	Path
`gpu (detected)`	hardware	healthy	`scientific-skills/citation-management/scripts/extract_metad…`

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K-Dense-AI/scientific-agent-skills

Complete repo analysis

function 50+

file 50+

directory 50+

class 50+

secret 4

port 3

pipeline 3

job 3

vps 2

auth 2

env_var 2

repo 1

database 1

load_balancer 1

gpu 1