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gvmfhy/constitutional-seq

Principle-based canonical sequence retrieval for mRNA therapeutics. An AI-safety inspired approach to biological sequence selection.

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Python
★ 1
commit 8f8c546d3e20
scored 2026-11-14
scoring prov-5+qual-2+sec-2

unreviewed-ai-risk

AI provenance

76%

explicit

Confidence: 84%
Coverage: 100%

Estimated share of AI-generated code. Explicit attribution is a lower bound.

Code quality

52/100

weak

Confidence: 90%
Coverage: 100%

Complexity, duplication, lint density, tests, CI, docs and review process.

Security

77/100

adequate

Confidence: 85%
Coverage: 100%

Secrets, static analysis, vulnerable dependencies, CI and supply-chain posture.

Dispute or request a re-score Full report JSON

AI provenance

76% explicit

Explicit AI attribution on 76% of first-party code added; an estimated 76% including velocity signals.

How the score is built

Explicitly attributed share76%
Unattributed share in AI-pace bursts9%
Estimated AI-generated share76%
AI tool configuration files0
Work sessions at AI pace2
Releases at AI pacenot measured
Coding-style index (1.0+ means possible)0.97

Attributed AI tools

Tool	Commits	Lines added	First seen	Last seen
Claude Code	6	13,931	2025-07-22	2025-08-06

Lines added per month all AI-attributed share

2025-0712,863 · 100% AI
2025-085,511 · 19% AI
2026-090 · 0% AI

Findings in AI-attributed lines vs the rest

From git blame: 9,515 lines trace to AI-attributed commits, 2,374 to others. Reported, not scored.

Findings per 1,000 lines	AI-attributed	Other	Ratio
Code quality	3.78	2.11	1.80×
Security	0.32	0.00	—

Evidence by analyzer

Explicit AI attributionok7 items

Claude Code: 6 attributed commits, 13,931 lines added
Claude Code: trailer 'Co-Authored-By: Claude'
Claude Code: trailer 'Co-Authored-By: Claude'
Claude Code: trailer 'Co-Authored-By: Claude'
Claude Code: trailer 'Co-Authored-By: Claude'
Claude Code: trailer 'Co-Authored-By: Claude'
Claude Code: trailer 'Co-Authored-By: Claude'

attributed_commit_share: 10.9%
attributed_commits: 6
attributed_loc: 13,931
attributed_loc_share: 75.8%
commits: 55
effective_loc: 18,374
tools_detected: 1

AI tool configurationok

artifacts: 0
tools_configured: 0
workflow_agents: 0

Commit velocityok2 items

excluded_import_loc: 10,156
flagged_loc: 4,220
flagged_loc_share: 51.4%
flagged_units: 2
max_loc_per_hour: 822.01
measured_loc: 8,218
median_loc_per_hour: 242.57
pr_timed_units: 0
pre_ai_era_burst_loc: 0
pre_ai_era_bursts: 0
pre_ai_era_measured_loc: 0
work_units: 8

Release velocityskipped

Coding styleok3 items

count:assistant_voice: 0
count:emoji_in_code: 15
count:narrated_steps: 2
count:placeholder: 1
files:assistant_voice: 0
files:emoji_in_code: 6
files:narrated_steps: 2
files:placeholder: 1
index: 0.97
lines_scanned: 11,889
per_kloc:assistant_voice: 0
per_kloc:emoji_in_code: 1.26
per_kloc:narrated_steps: 0.17
per_kloc:placeholder: 0.08

Findings in AI-written linesok

ai_lines: 9,515
blame_failures: 0
files_blamed: 38
other_lines: 2,374
quality:ai_findings: 36
quality:ai_per_kloc: 3.78
quality:other_findings: 5
quality:other_per_kloc: 2.11
quality:ratio: 1.80
security:ai_findings: 3
security:ai_per_kloc: 0.32
security:other_findings: 0
security:other_per_kloc: 0

Code quality

52 weak

Code quality is weak: test-to-source ratio 0.42, no CI test run detected; 26% of function code in complex or long functions; 10% duplicated lines. Weakest area: lint.

How the score is built

Complexity46
Duplication54
Lint and smells40
Tests and CI49
Documentation65
Type safety100
Review processnot measured

Evidence by analyzer

Complexity (lizard)ok10 items

complex_functions: 14
function_nloc: 6,834
functions: 350
long_functions: 6
many_param_functions: 7
mean_ccn: 4.34
p90_ccn: 9
risky_nloc_share: 25.9%

Duplication (jscpd)ok10 items

compared_lines: 8,880
duplicated_lines: 909
duplicated_share: 10.2%
files: 38

Lintok

category:best-practice: 36
category:maintainability: 5
findings: 41
scanned_lines: 11,889
weighted_findings: 43

Tests and CIok

check:ci_present: no
check:ci_runs_lint: no
check:ci_runs_tests: no
check:has_tests: yes
check:test_ratio: no
check:tests_cochange: no
ci_files: 0
cochange_commits: 31
cochange_share: 19.4%
source_lines: 11,889
test_lines: 5,019
test_ratio: 0.42

Documentationok2 items

README.md README.md
LICENSE LICENSE

check:changelog: no
check:contributing: no
check:license: yes
check:readme: yes
readme_lines: 183

Type safetyok1 item

Python strict type checking: pyproject.toml pyproject.toml

check:low_escape_density: yes
check:strict_config: yes
escapes: 47
escapes_per_kloc: 3.95

Security

77 adequate

Security posture is adequate: 20 known vulnerabilities in 5 dependencies; 1 high-severity SAST findings. Weakest area: posture.

How the score is built

Secrets100
Static analysis (SAST)97
Vulnerable dependencies66
CI workflowsnot measured
Security posture0
OpenSSF Scorecardnot measured

Evidence by analyzer

OpenSSF Scorecardskipped

no published OpenSSF Scorecard result for this repo

Package registriesok

checked: 16
declared: 16
lookup_errors: 0
missing: 0
recent: 0

Secrets (gitleaks)ok

secrets_current: 0
secrets_history: 0
secrets_low_confidence: 0
secrets_nonprod: 0

Static analysis (opengrep)ok

findings: 3
findings_high: 1
findings_low: 1
findings_medium: 1
parse_errors: 0
scanned_lines: 11,889
weighted_findings: 1.15

Dependencies (osv-scanner)ok

penalty: 25
vulnerabilities: 20
vulnerable_packages: 5
vulns_critical: 0
vulns_high: 9
vulns_low: 0
vulns_medium: 11
vulns_unknown: 0

CI workflows (zizmor)skipped

Security postureok

check:dependency_updates: no
check:lockfiles: yes
check:security_policy: no
check:signed_commits: no
signed_commit_share: 9.1%
unpinned_manifests: 0

Release downloadsok

binary_assets: 0
signals: 0
suspicious: 0

Findings

11 high52 medium1 low

Severity	Rule	Location	Message	Tool
high	`opengrep/python.lang.best-practice.arbitrary-sleep`	src/genbank_tool/network_recovery.py:99	time.sleep() call; did you mean to leave this in?	Lint
high	`osv/GHSA-2xpw-w6gg-jr37`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1994, GHSA-2xpw-w6gg-jr37	Dependencies (osv-scanner)
high	`osv/GHSA-38jv-5279-wg99`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1996, GHSA-38jv-5279-wg99	Dependencies (osv-scanner)
high	`osv/GHSA-5wmx-573v-2qwq`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-89, GHSA-5wmx-573v-2qwq	Dependencies (osv-scanner)
high	`osv/GHSA-8988-9cw3-xx77`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-4175, GHSA-8988-9cw3-xx77	Dependencies (osv-scanner)
high	`osv/GHSA-gm62-xv2j-4w53`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1998, GHSA-gm62-xv2j-4w53	Dependencies (osv-scanner)
high	`osv/GHSA-q2q7-5pp4-w6pg`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2021-108, GHSA-q2q7-5pp4-w6pg	Dependencies (osv-scanner)
high	`osv/GHSA-qccp-gfcp-xxvc`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-141, GHSA-qccp-gfcp-xxvc	Dependencies (osv-scanner)
high	`osv/GHSA-v845-jxx5-vc9f`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2023-192, GHSA-v845-jxx5-vc9f	Dependencies (osv-scanner)
high	`osv/GHSA-vxq7-64xx-v4gw`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-4177, GHSA-vxq7-64xx-v4gw	Dependencies (osv-scanner)
high	`opengrep/python.lang.security.use-defused-xml`	src/genbank_tool/mane_selector.py:221	The Python documentation recommends using `defusedxml` instead of `xml` because the native Python `xml` library is vulnerable to XML External Entity (XXE) attacks. These attacks can leak confidential data and "XML bombs" can cause...	Static analysis (opengrep)
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/batch_processor.py:38	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/batch_processor.py:44	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/cache_manager.py:112	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/cache_manager.py:165	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/cache_manager.py:331	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/cache_manager.py:360	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.pass-body-fn`	src/genbank_tool/cli_enhanced.py:245	`pass` is the body of function progress_callback. Consider removing this or raise NotImplementedError() if this is a TODO	Lint
medium	`opengrep/python.lang.maintainability.is-function-without-parentheses`	src/genbank_tool/cli_old.py:171	Is "is_valid" a function or an attribute? If it is a function, you may have meant validation_result.is_valid() because validation_result.is_valid is always true.	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/cli_old.py:54	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/config.py:104	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/config.py:81	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.maintainability.is-function-without-parentheses`	src/genbank_tool/data_validator.py:447	Is "is_valid" a function or an attribute? If it is a function, you may have meant r.is_valid() because r.is_valid is always true.	Lint
medium	`opengrep/python.lang.maintainability.is-function-without-parentheses`	src/genbank_tool/data_validator.py:472	Is "is_valid" a function or an attribute? If it is a function, you may have meant r.is_valid() because r.is_valid is always true.	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/error_handler.py:440	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/error_handler.py:462	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/error_handler.py:495	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/error_handler.py:597	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/gene_resolver.py:152	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/gene_resolver.py:170	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/gui/main_window.py:676	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/hgnc_resolver.py:237	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/hgnc_resolver.py:267	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/input_parser.py:103	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/input_parser.py:215	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/input_parser.py:269	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/input_parser.py:280	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/input_parser.py:79	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.logging-error-without-handling`	src/genbank_tool/logging_config.py:296	Errors should only be logged when handled. The code logs the error and propogates the exception, consider reducing the level to warning or info.	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/mane_selector.py:452	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/mane_selector.py:473	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.requests.best-practice.use-raise-for-status`	src/genbank_tool/network_recovery.py:62	There's an HTTP request made with requests, but the raise_for_status() utility method isn't used. This can result in request errors going unnoticed and your code behaving in unexpected ways, such as if your authorization API returns a...	Lint
medium	`opengrep/python.lang.maintainability.is-function-without-parentheses`	src/genbank_tool/output_formatter.py:154	Is "is_valid" a function or an attribute? If it is a function, you may have meant validation.is_valid() because validation.is_valid is always true.	Lint
medium	`opengrep/python.lang.maintainability.is-function-without-parentheses`	src/genbank_tool/output_formatter.py:183	Is "is_valid" a function or an attribute? If it is a function, you may have meant validation.is_valid() because validation.is_valid is always true.	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/sequence_retriever.py:117	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/sequence_retriever.py:99	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/uniprot_canonical.py:271	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/uniprot_canonical.py:58	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/uniprot_downloader.py:186	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`opengrep/python.requests.best-practice.use-timeout`	src/genbank_tool/uniprot_downloader.py:57	Detected a 'requests' call without a timeout set. By default, 'requests' calls wait until the connection is closed. This means a 'requests' call without a timeout will hang the program if a response is never received. Consider setting a...	Lint
medium	`opengrep/python.lang.best-practice.unspecified-open-encoding`	src/genbank_tool/uniprot_downloader.py:89	Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").	Lint
medium	`osv/GHSA-34jh-p97f-mpxf`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1995, GHSA-34jh-p97f-mpxf	Dependencies (osv-scanner)
medium	`osv/GHSA-5phf-pp7p-vc2r`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2021-59, GHSA-5phf-pp7p-vc2r	Dependencies (osv-scanner)
medium	`osv/GHSA-6p56-wp2h-9hxr`	requirements.txt	[email protected] (PyPI) is affected by GHSA-6p56-wp2h-9hxr	Dependencies (osv-scanner)
medium	`osv/GHSA-9hjg-9r4m-mvj7`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1872, GHSA-9hjg-9r4m-mvj7	Dependencies (osv-scanner)
medium	`osv/GHSA-9wx4-h78v-vm56`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1873, GHSA-9wx4-h78v-vm56	Dependencies (osv-scanner)
medium	`osv/GHSA-fpfv-jqm9-f5jm`	requirements.txt	[email protected] (PyPI) is affected by GHSA-fpfv-jqm9-f5jm	Dependencies (osv-scanner)
medium	`osv/GHSA-g4mx-q9vg-27p4`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2023-212, GHSA-g4mx-q9vg-27p4	Dependencies (osv-scanner)
medium	`osv/GHSA-gc5v-m9x4-r6x2`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-2275, GHSA-gc5v-m9x4-r6x2	Dependencies (osv-scanner)
medium	`osv/GHSA-j8r2-6x86-q33q`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2023-74, GHSA-j8r2-6x86-q33q	Dependencies (osv-scanner)
medium	`osv/GHSA-pq67-6m6q-mj2v`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1999, GHSA-pq67-6m6q-mj2v	Dependencies (osv-scanner)
medium	`osv/GHSA-x3vf-39hj-gxr4`	requirements.txt	[email protected] (PyPI) is affected by PYSEC-2026-1221, GHSA-x3vf-39hj-gxr4	Dependencies (osv-scanner)
medium	`opengrep/python.lang.security.audit.dynamic-urllib-use-detected`	src/genbank_tool/mane_database.py:32	Detected a dynamic value being used with urllib. urllib supports 'file://' schemes, so a dynamic value controlled by a malicious actor may allow them to read arbitrary files. Audit uses of urllib calls to ensure user data cannot control...	Static analysis (opengrep)
low	`opengrep/python.lang.security.audit.insecure-transport.requests.request-session-with-http`	src/genbank_tool/network_recovery.py:142	Detected a request using 'http://'. This request will be unencrypted. Use 'https://' instead. [confidence medium]	Static analysis (opengrep)

Tools and coverage

Every analyzer that ran on this commit. A failed or skipped tool is a coverage gap: its share of the score is left out and the coverage figure drops.

Analyzer	Pillar	Status	Version	Findings	Note
AI tool configuration	AI provenance	ok	`signatures-v1`	0
Explicit AI attribution	AI provenance	ok	`signatures-v1`	0
Release velocity	AI provenance	skipped	`—`	0
Coding style	AI provenance	ok	`—`	0
Commit velocity	AI provenance	ok	`prov-4`	0
Findings in AI-written lines	AI provenance	ok	`git-blame`	0
Complexity (lizard)	Code quality	ok	`lizard 1.25.1`	0
Documentation	Code quality	ok	`—`	0
Duplication (jscpd)	Code quality	ok	`repotrust-dup-w6`	0
Lint	Code quality	ok	`opengrep 1.33.1; rules f1d2b562b414`	41
Tests and CI	Code quality	ok	`—`	0
Type safety	Code quality	ok	`—`	0
CI workflows (zizmor)	Security	skipped	`—`	0
Dependencies (osv-scanner)	Security	ok	`osv-scanner version: 2.7.1`	20
Release downloads	Security	ok	`—`	0
Security posture	Security	ok	`—`	0
Package registries	Security	ok	`—`	0
Static analysis (opengrep)	Security	ok	`opengrep 1.33.1; rules f1d2b562b414`	3
OpenSSF Scorecard	Security	skipped	`—`	0	no published OpenSSF Scorecard result for this repo
Secrets (gitleaks)	Security	ok	`gitleaks 8.30.1`	0

Score history

Scores from different scoring versions aren't directly comparable.

Scored	Commit	Scoring	AI provenance	Quality	Security
2026-11-14	`8f8c546d3e20`	`prov-5+qual-2+sec-2`	76%	52	77
2026-11-14	`8f8c546d3e20`	`prov-4+qual-2+sec-2`	76%	52	77

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Full text report

Repository: https://github.com/gvmfhy/constitutional-seq
Commit: 8f8c546d3e203911b879d30898bd4b4226187a9d
Generated: 2026-11-14T14:52:04+00:00
Scorer 0.1.0, scoring prov-5+qual-2+sec-2, report schema v2

Scores

Unreviewed AI code risk: a large share of this code is explicitly AI-attributed, and its tests or review process are weak while quality or security scores are low.

Pillar	Score	Signal	Confidence	Coverage
AI provenance (estimated AI-generated share)	76	explicit	84%	100%
Code quality	52	weak	90%	100%
Security	77	adequate	85%	100%

AI provenance

Explicit AI attribution on 76% of first-party code added; an estimated 76% including velocity signals.

Explicitly attributed share (lower bound): 75.8%
Unattributed share in AI-consistent velocity bursts: 9.4%
Estimated AI-generated share: 75.8%

AI tool	Attributed commits	Lines added
Claude Code	6	13,931

Current source lines last changed by AI-attributed commits: 9,515 of 11,889.

Findings per 1,000 lines	AI-attributed	Other	Ratio
Quality	3.783	2.106	1.8x
Security	0.315	0.0	n/a

Stylometry index: 0.97 per 1,000 lines (narrated steps 2, placeholders 1, assistant phrasing 0, emoji 15). Reported as a signal, not scored.

Month	Lines added	Attributed to AI
2025-07	12,863	100%
2025-08	5,511	19%

Evidence

Claude Code: trailer 'Co-Authored-By: Claude' (ff2bbd648624)
Claude Code: trailer 'Co-Authored-By: Claude' (48c6eec9b97e)
Claude Code: trailer 'Co-Authored-By: Claude' (cb2c828b616a)
Claude Code: trailer 'Co-Authored-By: Claude' (905724183361)
Claude Code: trailer 'Co-Authored-By: Claude' (0a072e0e80b5)
Claude Code: trailer 'Co-Authored-By: Claude' (c28d369d018c)
2,793 lines of first-party code in ~3.4h (822 lines/hour, 13 commit session) (5ac9b924af4c)
1,427 lines of first-party code in ~2.4h (598 lines/hour, 1 commit session) (cb2c828b616a)
step-by-step narration comment: # First, get gene ID (src/genbank_)
placeholder or demo-only phrasing: # This is a simplified version - would need proper GenBank parsing (src/genbank_)
step-by-step narration comment: # First, get the UniProt entry (src/genbank_)

AI provenance describes how code was produced; it is not a quality judgment. Unless attribution is explicit, these are signals consistent with AI generation, not proof. Squash/rebase workflows, imported code, and rewritten history reduce accuracy.

Code quality

Code quality is weak: test-to-source ratio 0.42, no CI test run detected; 26% of function code in complex or long functions; 10% duplicated lines. Weakest area: lint.

Area	Score
Complexity (lizard)	46
Duplication	54
Code smells (Opengrep)	40
Tests and CI	49
Documentation	65
Type safety	100
Process (Scorecard review/maintenance)	n/a

Functions: 350; mean complexity 4.3, 90th percentile 9; 14 complex and 6 long functions
Duplicated lines: 10.2% of 8,880 compared
Tests: 5,019 test lines for 11,889 source lines (ratio 0.42); CI test commands: none detected; 19% of recent source commits also change tests
Docs missing or thin: contributing, changelog

Most complex functions:

Security

Security posture is adequate: 20 known vulnerabilities in 5 dependencies; 1 high-severity SAST findings. Weakest area: posture.

Area	Score
Secrets (gitleaks, tree + history)	100
Static analysis (Opengrep)	97
Vulnerable dependencies (OSV)	66
CI workflows (zizmor)	n/a
Posture (policy, updates, signing, lockfiles)	0
OpenSSF Scorecard	n/a

Known vulnerabilities: 20 in 5 packages (critical 0, high 9, medium 11, low 0)
Posture checks passed: lockfiles; missing: security policy, dependency updates, signed commits

Top findings

Severity	Finding	Location
high	`opengrep/python.lang.security.use-defused-xml`: The Python documentation recommends using `defusedxml` instead of `xml` because the native Python `xml` library is vulnerable to XML External Entity (XXE) attacks. These attacks can leak confidential data and "XML bombs" can cause denial of service. [confidence low]	src/genbank_tool/mane_selector.py:221
high	`osv/GHSA-5wmx-573v-2qwq`: [email protected] (PyPI) is affected by PYSEC-2026-89, GHSA-5wmx-573v-2qwq	requirements.txt
high	`osv/GHSA-q2q7-5pp4-w6pg`: [email protected] (PyPI) is affected by PYSEC-2021-108, GHSA-q2q7-5pp4-w6pg	requirements.txt
high	`osv/GHSA-v845-jxx5-vc9f`: [email protected] (PyPI) is affected by PYSEC-2023-192, GHSA-v845-jxx5-vc9f	requirements.txt
high	`osv/GHSA-qccp-gfcp-xxvc`: [email protected] (PyPI) is affected by PYSEC-2026-141, GHSA-qccp-gfcp-xxvc	requirements.txt
high	`osv/GHSA-2xpw-w6gg-jr37`: [email protected] (PyPI) is affected by PYSEC-2026-1994, GHSA-2xpw-w6gg-jr37	requirements.txt
high	`osv/GHSA-38jv-5279-wg99`: [email protected] (PyPI) is affected by PYSEC-2026-1996, GHSA-38jv-5279-wg99	requirements.txt
high	`osv/GHSA-gm62-xv2j-4w53`: [email protected] (PyPI) is affected by PYSEC-2026-1998, GHSA-gm62-xv2j-4w53	requirements.txt
high	`osv/GHSA-8988-9cw3-xx77`: [email protected] (PyPI) is affected by PYSEC-2026-4175, GHSA-8988-9cw3-xx77	requirements.txt
high	`osv/GHSA-vxq7-64xx-v4gw`: [email protected] (PyPI) is affected by PYSEC-2026-4177, GHSA-vxq7-64xx-v4gw	requirements.txt
medium	`opengrep/python.lang.security.audit.dynamic-urllib-use-detected`: Detected a dynamic value being used with urllib. urllib supports 'file://' schemes, so a dynamic value controlled by a malicious actor may allow them to read arbitrary files. Audit uses of urllib calls to ensure user data cannot control the URLs, or consider using the 'requests' library instead. [confidence low]	src/genbank_tool/mane_database.py:32
medium	`osv/GHSA-x3vf-39hj-gxr4`: [email protected] (PyPI) is affected by PYSEC-2026-1221, GHSA-x3vf-39hj-gxr4	requirements.txt
medium	`osv/GHSA-6p56-wp2h-9hxr`: [email protected] (PyPI) is affected by GHSA-6p56-wp2h-9hxr	requirements.txt
medium	`osv/GHSA-fpfv-jqm9-f5jm`: [email protected] (PyPI) is affected by GHSA-fpfv-jqm9-f5jm	requirements.txt
medium	`osv/GHSA-j8r2-6x86-q33q`: [email protected] (PyPI) is affected by PYSEC-2023-74, GHSA-j8r2-6x86-q33q	requirements.txt
medium	`osv/GHSA-9hjg-9r4m-mvj7`: [email protected] (PyPI) is affected by PYSEC-2026-1872, GHSA-9hjg-9r4m-mvj7	requirements.txt
medium	`osv/GHSA-9wx4-h78v-vm56`: [email protected] (PyPI) is affected by PYSEC-2026-1873, GHSA-9wx4-h78v-vm56	requirements.txt
medium	`osv/GHSA-gc5v-m9x4-r6x2`: [email protected] (PyPI) is affected by PYSEC-2026-2275, GHSA-gc5v-m9x4-r6x2	requirements.txt
medium	`osv/GHSA-5phf-pp7p-vc2r`: [email protected] (PyPI) is affected by PYSEC-2021-59, GHSA-5phf-pp7p-vc2r	requirements.txt
medium	`osv/GHSA-g4mx-q9vg-27p4`: [email protected] (PyPI) is affected by PYSEC-2023-212, GHSA-g4mx-q9vg-27p4	requirements.txt
medium	`osv/GHSA-34jh-p97f-mpxf`: [email protected] (PyPI) is affected by PYSEC-2026-1995, GHSA-34jh-p97f-mpxf	requirements.txt
medium	`osv/GHSA-pq67-6m6q-mj2v`: [email protected] (PyPI) is affected by PYSEC-2026-1999, GHSA-pq67-6m6q-mj2v	requirements.txt
low	`opengrep/python.lang.security.audit.insecure-transport.requests.request-session-with-http`: Detected a request using 'http://'. This request will be unencrypted. Use 'https://' instead. [confidence medium]	src/genbank_tool/network_recovery.py:142

Static signals only: the scorer never runs the project's code. Secret findings are pattern matches that were not verified, and secret values are never stored.

Repository profile

Source lines: 11,889; test lines: 5,019

Language	Lines
Python	16,908