{"version": "2.1.0", "$schema": "https://json.schemastore.org/sarif-2.1.0.json", "runs": [{"tool": {"driver": {"name": "Repobility", "informationUri": "https://repobility.com", "rules": [{"id": "scanner-4e126a321d831838", "name": "Possibly dead Python function: define_env", "shortDescription": {"text": "Possibly dead Python function: define_env"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-0187fc79a7e79d64", "name": "Possibly dead Python function: plot_timeseries_carpet", "shortDescription": {"text": "Possibly dead Python function: plot_timeseries_carpet"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-a16139f67fbd58bb", "name": "Possibly dead Python function: transform", "shortDescription": {"text": "Possibly dead Python function: transform"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-3155c5e89794bbcb", "name": "Possibly dead Python function: init_save_layout", "shortDescription": {"text": "Possibly dead Python function: init_save_layout"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-d794ef64a0ace2fb", "name": "Possibly dead Python function: save_caption", "shortDescription": {"text": "Possibly dead Python function: save_caption"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-7e083d16205d1fd6", "name": "Possibly dead Python function: load_matrices", "shortDescription": {"text": "Possibly dead Python function: load_matrices"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-e13e90cd8264eb3e", "name": "Possibly dead Python function: parse_session", "shortDescription": {"text": "Possibly dead Python function: parse_session"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-d4b841551b03a162", "name": "Possibly dead Python function: fit_edge", "shortDescription": {"text": "Possibly dead Python function: fit_edge"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-26a28b28a2fbb824", "name": "Possibly dead Python function: plot_heatmap_coordinate", "shortDescription": {"text": "Possibly dead Python function: plot_heatmap_coordinate"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-f0d294c5f86b32cf", "name": "Possibly dead Python function: iterencode", "shortDescription": {"text": "Possibly dead Python function: iterencode"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-f3feced09adf1c25", "name": "Possibly dead Python function: simulate_sc_length_bias", "shortDescription": {"text": "Possibly dead Python function: simulate_sc_length_bias"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-b6d3af71f1eb6d51", "name": "Possibly dead Python function: simulate_sc_noisy_copies", "shortDescription": {"text": "Possibly dead Python function: simulate_sc_noisy_copies"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-fa28272479f7196d", "name": "Possibly dead Python function: simulate_sc_no_bias", "shortDescription": {"text": "Possibly dead Python function: simulate_sc_no_bias"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-68d072893cb80df1", "name": "Possibly dead Python function: simulate_sc_fps", "shortDescription": {"text": "Possibly dead Python function: simulate_sc_fps"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-5d5b675f96ff9264", "name": "Possibly dead Python function: simulate_sc_fns", "shortDescription": {"text": "Possibly dead Python function: simulate_sc_fns"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-9e01b43e3b4b2c21", "name": "Possibly dead Python function: filter_dicom", "shortDescription": {"text": "Possibly dead Python function: filter_dicom"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-725cfaebcc3b42a9", "name": "Possibly dead Python function: filter_files", "shortDescription": {"text": "Possibly dead Python function: filter_files"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-0a23080d7a36df6f", "name": "Possibly dead Python function: infotodict", "shortDescription": {"text": "Possibly dead Python function: infotodict"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-0a8c35a9ec812c13", "name": "Possibly dead Python function: decode_string", "shortDescription": {"text": "Possibly dead Python function: decode_string"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-0fdca758fa5bd279", "name": "Privileged port 20 in use", "shortDescription": {"text": "Privileged port 20 in use"}, "fullDescription": {"text": "Port 20 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer."}, "properties": {"scanner": "scanner-primary", "layer": "network", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-9710c8d059e53154", "name": "No frontend routes/components detected", "shortDescription": {"text": "No frontend routes/components detected"}, "fullDescription": {"text": "No React/Vue/Next routes were found. This is fine for backend-only repos."}, "properties": {"scanner": "scanner-primary", "layer": "frontend", "severity": "info", "confidence": 1.0}}, {"id": "scanner-ba0e1434942ac224", "name": "Insecure pattern 'subprocess_shell_true' in code/bugfixes/fix_pe_fieldmaps.py:80", "shortDescription": {"text": "Insecure pattern 'subprocess_shell_true' in code/bugfixes/fix_pe_fieldmaps.py:80"}, "fullDescription": {"text": "Found a known-risky pattern (subprocess_shell_true). Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-6372cebde0220094", "name": "No auth library detected", "shortDescription": {"text": "No auth library detected"}, "fullDescription": {"text": "The scanner did not find any standard auth library (JWT, OAuth, NextAuth, Auth0, etc.). The repo has auth/admin/session surface indicators, so auth may live in custom code, in a separate service, or be missing."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-28c4a04bd807da0c", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/setup-python@v5 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-1a50467f36b413ec", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-6893a6c8b0861585", "name": "Very low test-to-source ratio", "shortDescription": {"text": "Very low test-to-source ratio"}, "fullDescription": {"text": "3 test file(s) for 38 source file(s) (ratio 0.08). Consider adding integration or unit tests for critical paths."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-3ab5d313dda8e5f9", "name": "Debug logging residue appears in source files", "shortDescription": {"text": "Debug logging residue appears in source files"}, "fullDescription": {"text": "Found 91 console/debugger/print-style debug statements in non-test source. This is a common fast-generation residue before production cleanup."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-2d0c7b7ab8f8aacf", "name": "Critical user flow still appears backed by mock or placeholder data", "shortDescription": {"text": "Critical user flow still appears backed by mock or placeholder data"}, "fullDescription": {"text": "A payment/auth/admin/order/billing-style flow contains mock, fake, TODO, dummy, or placeholder markers in runtime source. In the Fable corpus this is a high-leverage completeness smell: the app can look finished while the money, identity, or tenant flow is still scaffolded."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-ea8f3013f588db25", "name": "Shallow git history limits provenance confidence", "shortDescription": {"text": "Shallow git history limits provenance confidence"}, "fullDescription": {"text": "The repository is a shallow clone. Origin/evolution analysis cannot distinguish fresh generation, imported legacy code, or long-lived human code with high confidence."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-8424db9c75e04ba4", "name": "Very short observed git history", "shortDescription": {"text": "Very short observed git history"}, "fullDescription": {"text": "The repo has multiple source files but two or fewer visible commits. This is not a failure by itself, but it lowers confidence in evolution-based diagnosis."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "info", "confidence": 1.0}}, {"id": "scanner-9f44986169fcadfa", "name": "Commented-code block (11 lines) in code/fmri/nilearn_patcher.py:48", "shortDescription": {"text": "Commented-code block (11 lines) in code/fmri/nilearn_patcher.py:48"}, "fullDescription": {"text": "A long run of `//` or `#` lines usually means abandoned code. Delete or move to git history. Keeps the canvas + dead-code detection honest."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "info", "confidence": 1.0}}, {"id": "scanner-4888e89f51f33d6a", "name": "Network/subprocess call without timeout or try/except \u2014 code/confounds/parse_mood_quest.py:216", "shortDescription": {"text": "Network/subprocess call without timeout or try/except \u2014 code/confounds/parse_mood_quest.py:216"}, "fullDescription": {"text": "`requests.get(...)` here lacks both a `timeout=` arg and an enclosing try/except. This is exactly the class of bug that took down our git-clone earlier (HTTP/2 stream cancel surfaced as a fatal). Add a `timeout=` and wrap in try/except, or use a wrapper that retries."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-94dcc93c6056e7a2", "name": "Commented-code block (8 lines) in code/heudiconv/reproin.py:87", "shortDescription": {"text": "Commented-code block (8 lines) in code/heudiconv/reproin.py:87"}, "fullDescription": {"text": "A long run of `//` or `#` lines usually means abandoned code. Delete or move to git history. Keeps the canvas + dead-code detection honest."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "info", "confidence": 1.0}}, {"id": "scanner-2c04133e54348533", "name": "Near-duplicate function bodies in 2 places", "shortDescription": {"text": "Near-duplicate function bodies in 2 places"}, "fullDescription": {"text": "Functions with the same first-5-line body hash:\ncode/fmri/reports.py:group_reportlet_censoring, code/fmri/reports.py:group_report\n\nThis is *the* AI-coder failure mode (4\u00d7 more duplication in vibe-coded repos \u2014 see https://jw.hn/ai-code-hygiene). Consolidate or document why they're separate."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}]}}, "automationDetails": {"id": "repobility/21082"}, "properties": {"repository": "TheAxonLab/hcph-sops", "repoUrl": "https://github.com/TheAxonLab/hcph-sops", "branch": "main"}, "results": [{"ruleId": "scanner-4e126a321d831838", "level": "note", "message": {"text": "Possibly dead Python function: define_env"}, "properties": {"repobilityId": "9690c14e4773d99b", "scanner": "scanner-primary", "fingerprint": "4e126a321d831838", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "main.py:26"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-0187fc79a7e79d64", "level": "note", "message": {"text": "Possibly dead Python function: plot_timeseries_carpet"}, "properties": {"repobilityId": "38c474fabbcf0564", "scanner": "scanner-primary", "fingerprint": "0187fc79a7e79d64", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/fmri/reports.py:68"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-a16139f67fbd58bb", "level": "note", "message": {"text": "Possibly dead Python function: transform"}, "properties": {"repobilityId": "001ae182079c9116", "scanner": "scanner-primary", "fingerprint": "a16139f67fbd58bb", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/fmri/nilearn_patcher.py:250"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-3155c5e89794bbcb", "level": "note", "message": {"text": "Possibly dead Python function: init_save_layout"}, "properties": {"repobilityId": "efa788c6e3d91f45", "scanner": "scanner-primary", "fingerprint": "3155c5e89794bbcb", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/data_loader/load_save.py:583"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-d794ef64a0ace2fb", "level": "note", "message": {"text": "Possibly dead Python function: save_caption"}, "properties": {"repobilityId": "7999e739e4efaa52", "scanner": "scanner-primary", "fingerprint": "d794ef64a0ace2fb", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/data_loader/load_save.py:600"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-7e083d16205d1fd6", "level": "note", "message": {"text": "Possibly dead Python function: load_matrices"}, "properties": {"repobilityId": "9ee1d021ed757492", "scanner": "scanner-primary", "fingerprint": "7e083d16205d1fd6", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/data_loader/load_save.py:618"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-e13e90cd8264eb3e", "level": "note", "message": {"text": "Possibly dead Python function: parse_session"}, "properties": {"repobilityId": "552654129ce47d2f", "scanner": "scanner-primary", "fingerprint": "e13e90cd8264eb3e", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/physioconv/splitruns.py:210"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-d4b841551b03a162", "level": "note", "message": {"text": "Possibly dead Python function: fit_edge"}, "properties": {"repobilityId": "cf77520e7fdf0ef0", "scanner": "scanner-primary", "fingerprint": "d4b841551b03a162", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/analysis/run_bayesian_sc.py:39"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-26a28b28a2fbb824", "level": "note", "message": {"text": "Possibly dead Python function: plot_heatmap_coordinate"}, "properties": {"repobilityId": "0a450d495ac4f068", "scanner": "scanner-primary", "fingerprint": "26a28b28a2fbb824", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/eyetracking/plot.py:39"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-f0d294c5f86b32cf", "level": "note", "message": {"text": "Possibly dead Python function: iterencode"}, "properties": {"repobilityId": "44f4f9372687f746", "scanner": "scanner-primary", "fingerprint": "f0d294c5f86b32cf", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/eyetracking/ppjson.py:104"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-f3feced09adf1c25", "level": "note", "message": {"text": "Possibly dead Python function: simulate_sc_length_bias"}, "properties": {"repobilityId": "c120662536dfec55", "scanner": "scanner-primary", "fingerprint": "f3feced09adf1c25", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/dmri/simulate_sc.py:172"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-b6d3af71f1eb6d51", "level": "note", "message": {"text": "Possibly dead Python function: simulate_sc_noisy_copies"}, "properties": {"repobilityId": "5eda228c4e838d8d", "scanner": "scanner-primary", "fingerprint": "b6d3af71f1eb6d51", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/dmri/simulate_sc.py:249"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-fa28272479f7196d", "level": "note", "message": {"text": "Possibly dead Python function: simulate_sc_no_bias"}, "properties": {"repobilityId": "45976dd1eea9a7ed", "scanner": "scanner-primary", "fingerprint": "fa28272479f7196d", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/dmri/simulate_sc.py:299"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-68d072893cb80df1", "level": "note", "message": {"text": "Possibly dead Python function: simulate_sc_fps"}, "properties": {"repobilityId": "e36c34246b6825f8", "scanner": "scanner-primary", "fingerprint": "68d072893cb80df1", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/dmri/simulate_sc.py:339"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-5d5b675f96ff9264", "level": "note", "message": {"text": "Possibly dead Python function: simulate_sc_fns"}, "properties": {"repobilityId": "669da21124ea6ca9", "scanner": "scanner-primary", "fingerprint": "5d5b675f96ff9264", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/dmri/simulate_sc.py:408"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-9e01b43e3b4b2c21", "level": "note", "message": {"text": "Possibly dead Python function: filter_dicom"}, "properties": {"repobilityId": "c3b838e34ce7bd6c", "scanner": "scanner-primary", "fingerprint": "9e01b43e3b4b2c21", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "code/heudiconv/reproin.py:196"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-725cfaebcc3b42a9", "level": "note", "message": {"text": "Possibly dead Python function: filter_files"}, "properties": {"repobilityId": "052b767479509c8c", "scanner": "scanner-primary", "fingerprint": "725cfaebcc3b42a9", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": 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