Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 175,000+ scientists worldwide. 163 ready-to-use validated skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.
This report presents the forensic synthetic code analysis of K-Dense-AI/scientific-agent-skills, a Python project with 36,452 GitHub stars. SynthScan v2.0 examined 617,887 lines of code across 2040 source files, recording 6215 pattern matches distributed across 20 syntactic categories. The overall adjusted score of 13.8 places this repository in the Low AI signal band.
The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).
This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.
Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.
This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.
The scanner identified 6215 distinct pattern matches across 20 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_skills.py | 338 | def cache_invalidation_reason(previous: dict | None, max_age_days: int) -> str | None: | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 96 | def test_collection_date_differs_between_instances(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 103 | def test_string_typed_date_is_rejected_not_guessed(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 110 | def test_submission_date_differs_between_instances(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 116 | def test_missing_date_field_raises_with_the_alternatives(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 121 | def test_supports_range_follows_declared_type(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 131 | def test_indexed_column_preferred(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 134 | def test_unindexed_instance_reports_no_index(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 137 | def test_qc_columns_are_not_lineage_columns(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 143 | def test_per_segment_columns_excluded(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 148 | def test_ha_clade_outranks_na_clade(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 155 | def test_no_lineage_column_raises(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 163 | def test_bare_name_stays_exact(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 166 | def test_sublineages_expand_on_an_indexed_column(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 170 | def test_sublineages_refused_without_an_index(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 177 | def test_trailing_star_refused_without_an_index(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 181 | def test_exact_query_still_allowed_without_an_index(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 186 | def test_zero_successes_has_nonzero_upper_bound(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 192 | def test_interval_stays_inside_the_unit_interval(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 198 | def test_interval_brackets_the_estimate(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 203 | def test_interval_narrows_with_n(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 208 | def test_empty_denominator_is_maximally_uncertain(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 224 | def test_rising_series_has_positive_slope(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 231 | def test_falling_series_has_negative_slope(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 237 | def test_flat_series_slope_near_zero(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 243 | def test_all_zero_observations_returns_no_fit(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 250 | def test_too_few_successes_returns_no_fit(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 254 | def test_too_few_nonzero_weeks_returns_no_fit(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 258 | def test_too_few_points_returns_no_fit(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 261 | def test_dispersion_never_shrinks_the_interval_below_binomial(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 271 | def test_overdispersion_widens_the_interval(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 280 | def test_empty_weeks_are_dropped_not_counted(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 289 | def test_iso_week_start_is_monday(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 294 | def test_partial_and_null_dates_are_unparseable(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 298 | def test_undated_rows_are_counted_separately(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 309 | def test_week_range_is_inclusive_and_gapless(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 317 | def test_recent_thin_weeks_are_flagged(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 327 | def test_steady_series_flags_nothing(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 346 | def test_unalias_expands_one_level(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 349 | def test_unalias_full_walks_to_a_fixed_point(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 352 | def test_unalias_stops_at_a_recombinant(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 356 | def test_unalias_leaves_root_lineages_alone(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 359 | def test_recombinant_parents_deduplicated(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 364 | def test_ordinary_lineage_has_no_recombinant_parents(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 367 | def test_unknown_prefix_is_returned_unchanged(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 380 | def test_parent_chain_walks_to_the_root(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 388 | def test_descendants_are_transitive(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 394 | def test_leaf_has_no_descendants(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 461 | def test_parses_status_and_strips_the_marker(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 469 | def test_header_and_blank_lines_ignored(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 474 | def test_redesignation_target_is_extracted(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 479 | def test_withdrawal_without_a_successor(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 484 | def test_blob_hashes_reported_per_file(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 514 | def test_non_json_body_does_not_raise(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 517 | def test_unknown_instance_lists_the_known_ones(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 522 | def test_base_url_overrides_the_registry(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 530 | def test_list_values_repeat_the_key(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 537 | def test_empty_string_preserved(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 543 | def test_valid_field_accepted(self): | CODE |
| LOW⚡ | tests/pathogen-variant-surveillance/test_scripts.py | 548 | def test_range_suffix_accepted(self): | CODE |
| 3632 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | tests/pathogen-variant-surveillance/test_scripts.py | 0 | load a bundled script as a module regardless of cwd. | STRING |
| HIGH | tests/analytical-method-validation/test_scripts.py | 0 | load a bundled script as a module regardless of cwd. | STRING |
| HIGH | tests/ontology-term-resolution/test_scripts.py | 0 | load a bundled script as a module regardless of cwd. | STRING |
| HIGH | tests/genomic-coordinates/test_scripts.py | 0 | load a bundled script as a module regardless of cwd. | STRING |
| HIGH | skills/scikit-survival/scripts/_common.py | 0 | return an argparse converter for a bounded integer. | STRING |
| HIGH | skills/pytdc/scripts/_common.py | 0 | return an argparse converter for a bounded integer. | STRING |
| HIGH | skills/uncertainty-and-units/scripts/_common.py | 0 | return an argparse converter for a bounded integer. | STRING |
| HIGH | skills/scikit-survival/scripts/_common.py | 0 | return a bounded regular local file, rejecting urls and symlinks. | STRING |
| HIGH | skills/simpy/scripts/_common.py | 0 | return a bounded regular local file, rejecting urls and symlinks. | STRING |
| HIGH | skills/uncertainty-and-units/scripts/_common.py | 0 | return a bounded regular local file, rejecting urls and symlinks. | STRING |
| HIGH | skills/scikit-survival/scripts/_common.py | 0 | validate an explicit local output without following symlinks. | STRING |
| HIGH | skills/simpy/scripts/_common.py | 0 | validate an explicit local output without following symlinks. | STRING |
| HIGH | skills/uncertainty-and-units/scripts/_common.py | 0 | validate an explicit local output without following symlinks. | STRING |
| HIGH | skills/scikit-survival/scripts/_common.py | 0 | write bytes through a same-directory temporary file. | STRING |
| HIGH | skills/simpy/scripts/_common.py | 0 | write bytes through a same-directory temporary file. | STRING |
| HIGH | skills/uncertainty-and-units/scripts/_common.py | 0 | write bytes through a same-directory temporary file. | STRING |
| HIGH | skills/scientific-visualization/scripts/_common.py | 0 | write bytes through a same-directory temporary file. | STRING |
| HIGH | skills/exploratory-data-analysis/scripts/_common.py | 0 | run a cli body with concise expected-error handling. | STRING |
| HIGH | skills/neurokit2/scripts/_common.py | 0 | run a cli body with concise expected-error handling. | STRING |
| HIGH | skills/pathml/scripts/_common.py | 0 | run a cli body with concise expected-error handling. | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes - | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | strip markdown decoration so the rubric's fields can be found. | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric prompt | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | skills/generate-image/scripts/generate_image.py | 0 | resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directo | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine if | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine if | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine if | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine if | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine if | STRING |
| 124 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM⚡ | tests/onekgpd/test_scripts.py | 97 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/onekgpd/test_scripts.py | 99 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/onekgpd/test_scripts.py | 522 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/onekgpd/test_scripts.py | 524 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 62 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 64 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 197 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 199 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 383 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 385 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 490 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 492 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 600 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | tests/genomic-coordinates/test_scripts.py | 602 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 16 | # =============== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 24 | # ============== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 45 | # ========================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 55 | # ============ | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 71 | # ==================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 93 | # ============================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 103 | # ================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 115 | # ============================ | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 136 | # =============== | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 16 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 18 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 51 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 53 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 96 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 98 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 112 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 114 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 132 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 134 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 182 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 184 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 198 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 200 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 262 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 264 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 320 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 322 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 16 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 18 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 41 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 43 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 69 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 71 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 85 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 87 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 106 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 108 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 149 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 151 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 165 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 167 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 195 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 197 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 230 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 232 | # ============================================================================= | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 36 | # --------------------------------------------------------------------------- | COMMENT |
| 180 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 79 | except Exception as exc: # pragma: no cover - defensive | STRING |
| LOW | scan_pr_skills.py | 100 | except Exception as exc: # pragma: no cover - defensive | STRING |
| LOW | scan_skills.py | 443 | except Exception: # counted per skill below when it is scanned | CODE |
| LOW | scan_skills.py | 461 | except Exception as e: | CODE |
| LOW | scan_skills.py | 527 | except Exception as e: | CODE |
| LOW⚡ | tests/deepchem/test_scripts.py | 213 | except Exception: | CODE |
| LOW | tests/pytorch-lightning/test_scripts.py | 76 | except Exception as error: # noqa: BLE001 - the message is the assertion | CODE |
| LOW | …lls/benchling-integration/references/authentication.md | 328 | except Exception as e: | CODE |
| LOW | skills/lab-hardware-cad/scripts/gen.py | 65 | except Exception as exc: # noqa: BLE001 - the kernel raises assorted OCCT errors | CODE |
| LOW | skills/lab-hardware-cad/scripts/gen.py | 124 | except Exception as exc: # noqa: BLE001 - model code raises arbitrary errors | CODE |
| LOW | skills/lab-hardware-cad/scripts/_common.py | 383 | except Exception: # noqa: BLE001 - kernel raises assorted OCCT errors | CODE |
| LOW | skills/lab-hardware-cad/scripts/_common.py | 386 | except Exception as exc: # noqa: BLE001 | CODE |
| LOW | skills/lab-hardware-cad/scripts/snapshot.py | 125 | except Exception: # noqa: BLE001 - skip an edge the kernel cannot sample | CODE |
| LOW | skills/deepspot-m/references/api.md | 174 | except Exception as exc: | CODE |
| MEDIUM | skills/deepspot-m/references/api.md | 167 | def load_deepspotm(source="scgpt"): | CODE |
| MEDIUM | skills/networkx/references/io.md | 447 | print(f"Error reading GraphML: {e}") | CODE |
| LOW | skills/scikit-survival/scripts/_common.py | 273 | except Exception as exc: | CODE |
| LOW | skills/qiskit/references/setup.md | 93 | except Exception: | CODE |
| LOW | skills/qiskit/scripts/check_environment.py | 49 | except Exception as error: # Report broken optional environments clearly. | CODE |
| LOW | skills/qiskit/scripts/check_environment.py | 149 | except Exception as error: | CODE |
| LOW | skills/qiskit/scripts/inspect_runtime.py | 205 | except Exception as error: | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 936 | except Exception as exc: | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 951 | except Exception as fallback_exc: | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 1167 | except Exception as exc: | STRING |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 1168 | print(f"Error: {exc}", file=sys.stderr) | STRING |
| LOW | skills/imaging-data-commons/scripts/check_version.py | 52 | except Exception: | CODE |
| LOW | skills/dask/references/futures.md | 499 | except Exception as e: | CODE |
| LOW | skills/dask/references/futures.md | 533 | except Exception: | CODE |
| LOW | skills/esm/references/forge-api.md | 363 | except Exception as e: | CODE |
| MEDIUM | skills/esm/references/forge-api.md | 364 | print(f"Error processing {i}: {e}") | CODE |
| LOW | skills/esm/references/forge-api.md | 404 | except Exception as e: | CODE |
| LOW | skills/esm/references/forge-api.md | 582 | except Exception as e: | CODE |
| LOW | skills/esm/references/forge-api.md | 641 | except Exception as e: | CODE |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 34 | print("Error: requests library not found. Install with: uv pip install requests") | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 383 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 486 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 649 | except Exception as e: | CODE |
| MEDIUM⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 908 | print("Error: OPENROUTER_API_KEY not found") | STRING |
| MEDIUM⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 917 | print("Error: Iterations must be between 1 and 2") | STRING |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 943 | except Exception as e: | STRING |
| MEDIUM⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 159 | print("Error: OPENROUTER_API_KEY not found") | STRING |
| MEDIUM⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 173 | print(f"Error: AI generation script not found: {ai_script}") | STRING |
| LOW | …ls/scientific-schematics/scripts/generate_schematic.py | 191 | except Exception as e: | STRING |
| MEDIUM | …ls/scientific-schematics/scripts/generate_schematic.py | 192 | print(f"Error executing AI generation: {e}") | STRING |
| LOW | skills/geopandas/scripts/crs_reprojection_plan.py | 205 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | skills/geopandas/scripts/geometry_validity_report.py | 222 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | …s/geopandas/scripts/sensitive_coordinates_checklist.py | 225 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | skills/geopandas/scripts/vector_inventory.py | 135 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | skills/geopandas/scripts/export_plan.py | 300 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | skills/geopandas/scripts/spatial_join_audit.py | 363 | except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundary | CODE |
| LOW | skills/pyzotero/references/files-attachments.md | 95 | except Exception as e: | CODE |
| LOW | skills/pyzotero/references/error-handling.md | 45 | except Exception as e: | CODE |
| LOW | skills/pyzotero/references/error-handling.md | 105 | except Exception as e: | CODE |
| LOW | skills/deeptools/scripts/validate_files.py | 72 | except Exception as e: | CODE |
| LOW | skills/protocolsio-integration/scripts/_common.py | 222 | except Exception: | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 23 | print(f"Error: Missing required package: {e}") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 50 | print(f"Error: Column '{smiles_column}' not found") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 65 | print(f"Error: Unsupported file format: {suffix}") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 237 | print("Error: Specify at least one filter (--rules, --query, --pains, --nibr, etc.)") | CODE |
| LOW | skills/pymatgen/scripts/mp_query.py | 277 | except Exception as exc: | CODE |
| 416 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/iso-standards-readiness/SKILL.md | 119 | ### Step 1: Declare the standard, purpose, and authorized owners | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 144 | ### Step 2: Freeze source/version evidence | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 155 | ### Step 3: Inventory controlled documents and records | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 169 | ### Step 4: Review process implementation | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 178 | ### Step 5: Run the focused checks that apply to the lane | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 210 | ### Step 6: Address lane-specific regulator evidence separately | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 230 | ### Step 7: Assemble a bounded readiness manifest | COMMENT |
| LOW | skills/iso-standards-readiness/SKILL.md | 262 | ### Step 8: Human review and controlled handoff | COMMENT |
| LOW⚡ | skills/imaging-data-commons/SKILL.md | 345 | # Step 1: Query for series UIDs | STRING |
| LOW⚡ | skills/imaging-data-commons/SKILL.md | 355 | # Step 2: Extract UIDs as a list from the DataFrame | STRING |
| LOW⚡ | skills/imaging-data-commons/SKILL.md | 358 | # Step 3: Pass the list to download_from_selection (NOT the DataFrame itself) | STRING |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 69 | ### Step 1: Fetch Clinical Index | COMMENT |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 81 | ### Step 2: Discover Available Clinical Data | COMMENT |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 93 | ### Step 3: Search for Specific Attributes | COMMENT |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 103 | ### Step 4: Load Clinical Table | COMMENT |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 114 | ### Step 5: Map Coded Values to Descriptions | COMMENT |
| LOW | …imaging-data-commons/references/clinical_data_guide.md | 141 | ### Step 6: Join with Imaging Data | COMMENT |
| LOW⚡ | skills/vaex/references/machine_learning.md | 388 | # Step 1: Encode categorical | COMMENT |
| LOW⚡ | skills/vaex/references/machine_learning.md | 392 | # Step 2: Scale features | COMMENT |
| LOW⚡ | skills/vaex/references/machine_learning.md | 396 | # Step 3: PCA | COMMENT |
| LOW | skills/onekgpd/SKILL.md | 214 | # Step 4: For that set of individuals, see the actual variants they carry. | COMMENT |
| LOW⚡ | skills/onekgpd/SKILL.md | 322 | # Step 1: resolve gene -> verified GRCh38 region (authoritative source). | COMMENT |
| LOW⚡ | skills/onekgpd/SKILL.md | 323 | # Step 2: count individuals carrying a qualifying variant in the region. | COMMENT |
| LOW⚡ | skills/onekgpd/SKILL.md | 328 | # Step 3: list those individuals. | COMMENT |
| LOW⚡ | skills/onekgpd/SKILL.md | 333 | # Step 4: for that set of individuals, see the actual variants they carry. | COMMENT |
| LOW⚡ | skills/dask/references/schedulers.md | 400 | # Step 1: Debug with synchronous scheduler | COMMENT |
| LOW⚡ | skills/dask/references/schedulers.md | 404 | # Step 2: Test with threads | COMMENT |
| LOW⚡ | skills/dask/references/schedulers.md | 408 | # Step 3: Scale with distributed | COMMENT |
| LOW⚡ | skills/esm/SKILL.md | 180 | # Step 1: Generate initial structure | COMMENT |
| LOW⚡ | skills/esm/SKILL.md | 184 | # Step 2: Refine sequence based on structure | COMMENT |
| LOW⚡ | skills/esm/SKILL.md | 188 | # Step 3: Predict function | COMMENT |
| LOW | skills/esm/references/workflows.md | 25 | # Step 1: Define target properties | COMMENT |
| LOW | skills/esm/references/workflows.md | 41 | # Step 2: Generate initial sequence with function conditioning | COMMENT |
| LOW | skills/esm/references/workflows.md | 52 | # Step 3: Predict structure | COMMENT |
| LOW | skills/esm/references/workflows.md | 62 | # Step 4: Refine sequence based on structure | COMMENT |
| LOW | skills/esm/references/workflows.md | 84 | # Step 5: Final validation | COMMENT |
| LOW | skills/esm/references/workflows.md | 160 | # Step 1: Generate variant library | COMMENT |
| LOW | skills/esm/references/workflows.md | 195 | # Step 2: Predict structures for variants | COMMENT |
| LOW | skills/esm/references/workflows.md | 213 | # Step 3: Analyze variant diversity | COMMENT |
| LOW | skills/esm/references/workflows.md | 225 | # Step 4: Get embeddings for clustering | COMMENT |
| LOW | skills/esm/references/workflows.md | 241 | # Step 5: Cluster variants | COMMENT |
| LOW | skills/esm/references/workflows.md | 259 | # Step 6: Select diverse representatives | COMMENT |
| LOW | skills/esm/references/workflows.md | 316 | # Step 1: Generate multiple sequence designs | COMMENT |
| LOW | skills/esm/references/workflows.md | 343 | # Step 2: Validate structural compatibility | COMMENT |
| LOW | skills/esm/references/workflows.md | 366 | # Step 3: Analyze sequence properties | COMMENT |
| LOW | skills/esm/references/workflows.md | 409 | # Step 4: Rank designs | COMMENT |
| LOW | skills/esm/references/workflows.md | 433 | # Step 5: Save results | COMMENT |
| LOW | skills/esm/references/workflows.md | 559 | # Step 1: Generate embeddings | COMMENT |
| LOW | skills/esm/references/workflows.md | 578 | # Step 2: Dimensionality reduction for visualization | COMMENT |
| LOW | skills/esm/references/workflows.md | 590 | # Step 3: Clustering | COMMENT |
| LOW | skills/esm/references/workflows.md | 603 | # Step 4: Visualize | COMMENT |
| LOW | skills/esm/references/workflows.md | 621 | # Step 5: Analyze clusters | COMMENT |
| LOW⚡ | skills/esm/references/esm3-api.md | 260 | # Step 1: Complete sequence | COMMENT |
| LOW⚡ | skills/esm/references/esm3-api.md | 266 | # Step 2: Predict structure for completed sequence | COMMENT |
| LOW⚡ | skills/esm/references/esm3-api.md | 272 | # Step 3: Predict function | COMMENT |
| LOW⚡ | skills/arboreto/references/distributed_computing.md | 106 | ### Step 1: Set Up Dask Scheduler (on cluster head node) | COMMENT |
| LOW⚡ | skills/arboreto/references/distributed_computing.md | 112 | ### Step 2: Start Dask Workers (on cluster compute nodes) | COMMENT |
| LOW⚡ | skills/arboreto/references/distributed_computing.md | 117 | ### Step 3: Connect from Client | COMMENT |
| LOW | skills/bids/references/conversion_tools.md | 72 | #### Step 1: Reconnaissance — Discover DICOM series | COMMENT |
| LOW | skills/bids/references/conversion_tools.md | 92 | #### Step 2: Write a heuristic file | COMMENT |
| 315 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 15 | CODE | |
| LOW | tests/conftest.py | 21 | CODE | |
| LOW | tests/run_all.py | 32 | CODE | |
| LOW | tests/pathogen-variant-surveillance/test_scripts.py | 10 | CODE | |
| LOW | tests/lab-hardware-cad/test_scripts.py | 8 | CODE | |
| LOW | tests/iso-standards-readiness/test_scripts.py | 1 | CODE | |
| LOW | tests/scikit-survival/test_scripts.py | 4 | CODE | |
| LOW | tests/qiskit/test_scripts.py | 17 | CODE | |
| LOW | tests/scientific-brainstorming/test_scripts.py | 3 | CODE | |
| LOW | tests/pymc/test_scripts.py | 20 | CODE | |
| LOW | tests/pymc/test_scripts.py | 30 | CODE | |
| LOW | tests/pkpd-modeling/test_scripts.py | 20 | CODE | |
| LOW | tests/research-lookup/test_research_lookup.py | 3 | CODE | |
| LOW | tests/shap/test_scripts.py | 17 | CODE | |
| LOW | tests/onekgpd/test_scripts.py | 21 | CODE | |
| LOW | tests/onekgpd/test_scripts.py | 33 | CODE | |
| LOW | tests/get-available-resources/test_scripts.py | 3 | CODE | |
| LOW | tests/exploratory-data-analysis/test_static.py | 4 | CODE | |
| LOW | tests/exploratory-data-analysis/test_scripts.py | 4 | CODE | |
| LOW | tests/exploratory-data-analysis/test_scripts.py | 268 | CODE | |
| LOW | tests/experimental-design/test_scripts.py | 15 | CODE | |
| LOW | tests/scientific-schematics/test_scripts.py | 9 | CODE | |
| LOW | tests/arboreto/test_scripts.py | 14 | CODE | |
| LOW | tests/bids/test_scripts.py | 14 | CODE | |
| LOW | tests/geniml/test_scripts.py | 3 | CODE | |
| LOW | tests/geopandas/test_static.py | 3 | CODE | |
| LOW | tests/geopandas/test_scripts.py | 3 | CODE | |
| LOW | tests/deeptools/test_scripts.py | 13 | CODE | |
| LOW | tests/protocolsio-integration/test_scripts.py | 3 | CODE | |
| LOW | tests/analytical-method-validation/test_scripts.py | 10 | CODE | |
| LOW | tests/medchem/test_scripts.py | 19 | CODE | |
| LOW | tests/fluidsim/test_static.py | 3 | CODE | |
| LOW | tests/fluidsim/test_scripts.py | 3 | CODE | |
| LOW | tests/pymatgen/test_static.py | 3 | CODE | |
| LOW | tests/pymatgen/test_scripts.py | 3 | CODE | |
| LOW | tests/pathway-enrichment/test_scripts.py | 11 | CODE | |
| LOW | tests/citation-management/test_scripts.py | 12 | CODE | |
| LOW | tests/pydicom/test_static.py | 3 | CODE | |
| LOW | tests/pydicom/test_scripts.py | 3 | CODE | |
| LOW | tests/markitdown/test_scripts.py | 17 | CODE | |
| LOW | tests/openpiv/test_scripts.py | 19 | CODE | |
| LOW | tests/pytdc/test_scripts.py | 4 | CODE | |
| LOW | tests/xlsx/test_scripts.py | 14 | CODE | |
| LOW | tests/pdf/test_scripts.py | 14 | CODE | |
| LOW | tests/pdf/test_scripts.py | 19 | CODE | |
| LOW | tests/pdf/test_scripts.py | 25 | CODE | |
| LOW | tests/exa-search/test_exa_search.py | 12 | CODE | |
| LOW | tests/autoskill/test_e2e.py | 9 | CODE | |
| LOW | tests/ncats-arax/test_scripts.py | 1 | CODE | |
| LOW | tests/ncats-arax/test_scripts.py | 9 | CODE | |
| LOW | tests/timesfm-forecasting/test_scripts.py | 27 | CODE | |
| LOW | tests/opentrons-integration/test_scripts.py | 30 | CODE | |
| LOW | tests/opentrons-integration/test_scripts.py | 36 | CODE | |
| LOW | tests/infographics/test_scripts.py | 15 | CODE | |
| LOW | tests/_meta/test_repo_contract.py | 15 | CODE | |
| LOW | tests/_contract/office.py | 15 | CODE | |
| LOW | tests/_contract/__init__.py | 34 | CODE | |
| LOW | tests/_contract/__init__.py | 36 | CODE | |
| LOW | tests/_contract/__init__.py | 36 | CODE | |
| LOW | tests/_contract/__init__.py | 36 | CODE | |
| 508 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 115 | CODE | |
| LOW | scan_skills.py | 127 | CODE | |
| LOW | scan_skills.py | 373 | CODE | |
| LOW | tests/run_all.py | 108 | CODE | |
| LOW | tests/pkpd-modeling/test_scripts.py | 96 | CODE | |
| LOW | tests/geniml/test_scripts.py | 55 | CODE | |
| LOW | tests/geopandas/test_static.py | 78 | CODE | |
| LOW | tests/geopandas/test_static.py | 111 | CODE | |
| LOW | tests/fluidsim/test_static.py | 60 | CODE | |
| LOW | tests/pymatgen/test_static.py | 60 | CODE | |
| LOW | tests/pymatgen/test_static.py | 95 | CODE | |
| LOW | tests/pydicom/test_static.py | 87 | CODE | |
| LOW | tests/openpiv/test_scripts.py | 251 | CODE | |
| LOW | tests/ncats-arax/test_scripts.py | 373 | CODE | |
| LOW | tests/ncats-arax/test_scripts.py | 1131 | CODE | |
| LOW | tests/ncats-arax/test_scripts.py | 1514 | CODE | |
| LOW | tests/opentrons-integration/test_scripts.py | 150 | CODE | |
| LOW | tests/_contract/office.py | 107 | CODE | |
| LOW | tests/_contract/office.py | 277 | CODE | |
| LOW | tests/_contract/cli.py | 102 | CODE | |
| LOW | tests/_contract/cli.py | 158 | CODE | |
| LOW | tests/_contract/cli.py | 118 | CODE | |
| LOW | tests/_contract/cli.py | 177 | CODE | |
| LOW | tests/_contract/structure.py | 263 | CODE | |
| LOW | tests/_contract/structure.py | 369 | CODE | |
| LOW | tests/gtars/test_static.py | 18 | CODE | |
| LOW | tests/pptx-posters/test_static.py | 127 | CODE | |
| LOW | tests/pptx-posters/test_static.py | 148 | CODE | |
| LOW | tests/pptx-posters/test_static.py | 162 | CODE | |
| LOW | tests/scientific-writing/test_static.py | 45 | CODE | |
| LOW | tests/qutip/test_static.py | 104 | CODE | |
| LOW | tests/qutip/test_static.py | 128 | CODE | |
| LOW | tests/deepchem/test_scripts.py | 119 | CODE | |
| LOW | tests/matlab/test_static.py | 131 | CODE | |
| LOW | tests/matlab/test_static.py | 159 | CODE | |
| LOW | tests/hypothesis-generation/test_scripts.py | 318 | CODE | |
| LOW | tests/labarchive-integration/test_scripts.py | 356 | CODE | |
| LOW | tests/peer-review/test_scripts.py | 320 | CODE | |
| LOW | tests/hugging-science/test_scripts.py | 251 | CODE | |
| LOW | …hogen-variant-surveillance/scripts/mutation_profile.py | 92 | CODE | |
| LOW | …thogen-variant-surveillance/scripts/resolve_lineage.py | 83 | CODE | |
| LOW | …gen-variant-surveillance/scripts/lineage_prevalence.py | 120 | CODE | |
| LOW | skills/lab-hardware-cad/scripts/_common.py | 486 | CODE | |
| LOW | …ndards-readiness/scripts/validate_evidence_manifest.py | 87 | CODE | |
| LOW | skills/iso-standards-readiness/scripts/_common.py | 99 | CODE | |
| LOW | skills/iso-standards-readiness/scripts/gap_analyzer.py | 44 | CODE | |
| LOW | …o-standards-readiness/scripts/validate_scope_intake.py | 57 | CODE | |
| LOW | skills/iso-standards-readiness/scripts/check_capa.py | 52 | CODE | |
| LOW | skills/scikit-survival/scripts/train_survival_model.py | 82 | CODE | |
| LOW | skills/qiskit/scripts/check_environment.py | 63 | CODE | |
| LOW | …/scientific-brainstorming/scripts/validate_register.py | 150 | CODE | |
| LOW | …ls/scientific-brainstorming/scripts/evaluate_matrix.py | 138 | CODE | |
| LOW | skills/pymc/scripts/model_comparison.py | 32 | CODE | |
| LOW | skills/pymc/scripts/model_comparison.py | 138 | CODE | |
| LOW | skills/pkpd-modeling/scripts/simulate_regimen.py | 117 | CODE | |
| LOW | skills/pkpd-modeling/scripts/allometry_and_fih.py | 161 | CODE | |
| LOW | skills/pkpd-modeling/scripts/_common.py | 234 | CODE | |
| LOW | skills/pkpd-modeling/scripts/ddi_static.py | 182 | CODE | |
| LOW | skills/pkpd-modeling/scripts/check_popk_dataset.py | 84 | CODE | |
| LOW | skills/pkpd-modeling/scripts/fit_compartmental.py | 395 | CODE | |
| 318 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH⚡ | tests/exploratory-data-analysis/test_scripts.py | 207 | '{"secret_field": [{"value": "secret-value"}, null]}', | CODE |
| HIGH | tests/geopandas/test_scripts.py | 201 | self.assertTrue(arrow_roundtrip.crs.equals(coverage.crs)) | CODE |
| HIGH⚡ | tests/pydeseq2/test_scripts.py | 138 | self.assertTrue(counts.index.equals(metadata.index)) | CODE |
| HIGH⚡ | tests/pydeseq2/test_scripts.py | 147 | self.assertTrue(counts.index.equals(metadata.index)) | CODE |
| HIGH⚡ | tests/pydeseq2/test_scripts.py | 205 | self.assertTrue(counts.index.equals(metadata.index)) | CODE |
| HIGH⚡ | tests/pyopenms/test_scripts.py | 272 | peptide.toString() | CODE |
| HIGH | skills/research-lookup/scripts/research_lookup.py | 126 | "Find conflicting, contradictory, null, negative, replication, and limitation " | CODE |
| HIGH | skills/geopandas/scripts/export_plan.py | 134 | "Legacy multi-file output has field-name, null, type, encoding, geometry, and size limitations.", | CODE |
| HIGH | skills/geopandas/scripts/export_plan.py | 276 | "null, empty, invalid, geometry type, and dimensionality counts", | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 403 | ...Array(nActual).fill(null), | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 411 | dataUsed.push(step.historical_values[i]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 427 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 428 | q90Lower.push(step.q10[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 429 | q90Upper.push(step.q90[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 430 | q80Lower.push(step.q20[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 431 | q80Upper.push(step.q80[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 448 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 449 | forecastData.push(step.point_forecast[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 227 | let chart = null; | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 229 | let playInterval = null; | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 275 | data: [...Array(animationData.actual_data.dates.length).fill(null), ...finalStep.point_forec | CODE |
| HIGH | skills/pydeseq2/scripts/run_deseq2_analysis.py | 53 | if not counts_df.index.equals(metadata.index): | CODE |
| HIGH | skills/paper-lookup/scripts/paginate.py | 15 | than sending null; bioRxiv just returns an empty collection) | STRING |
| HIGH | skills/pptx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH | skills/relsa-severity-assessment/scripts/_common.py | 186 | undefined, which is what ``score_to_percent`` exists to avoid. | STRING |
| HIGH | skills/pacsomatic/scripts/run_pacsomatic.py | 449 | documented shape, e.g. "module purge && module load nextflow/23.10.0". | STRING |
| HIGH | skills/pyopenms/scripts/theoretical_spectrum.py | 49 | print(f"Peptide: {seq.toString()} ({len(spec)} fragment peaks)") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 69 | print(f"Peptide: {seq.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 70 | print(f"Formula: {formula.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 81 | print(f"\nFormula: {formula.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/digest_protein.py | 74 | pep_str = pep.toString() | CODE |
| HIGH | skills/flowio/scripts/inspect_fcs.py | 110 | "PnN label to classify as null; repeat for multiple labels. " | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | docs/security-report.md | 666 | > Several reference documents contain example snippets that embed credentials directly in code: `SentinelAPI('user', ' | CODE |
| HIGH | docs/security-report.md | 2294 | > A reference file shows an IonQ device instantiation with an inline `api_key='your_api_key'` parameter. This is an ob | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 301 | -u "your_api_key:" \ | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 321 | auth_method=ApiKeyAuth("your_api_key") | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 381 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | …ills/benchling-integration/references/api_endpoints.md | 26 | -u "your_api_key:" | CODE |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 571 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 578 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | skills/geomaster/references/data-sources.md | 179 | 'key': YOUR_API_KEY | STRING |
| HIGH | skills/geomaster/references/data-sources.md | 208 | 'appid': YOUR_API_KEY | STRING |
| HIGH⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 910 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 911 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 163 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 164 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH | skills/pyzotero/SKILL.md | 40 | ZOTERO_API_KEY=your_api_key | CODE |
| HIGH | skills/database-lookup/references/bea.md | 13 | - Pass as query parameter: `&UserID=YOUR_API_KEY` | CODE |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 13 | - Pass via header: `user_key: YOUR_API_KEY` | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 36 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 40 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 44 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 48 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH | skills/database-lookup/references/omim.md | 10 | - Pass as query parameter: `?apiKey=YOUR_API_KEY` | CODE |
| HIGH | skills/database-lookup/references/addgene.md | 10 | Pass as: `Authorization: Token <your_api_key>` | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 385 | api_key=YOUR_API_KEY | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 418 | api_key=YOUR_API_KEY | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 442 | api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | skills/infographics/scripts/generate_infographic_ai.py | 1411 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/infographics/scripts/generate_infographic_ai.py | 1412 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | skills/infographics/scripts/generate_infographic.py | 241 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/infographics/scripts/generate_infographic.py | 242 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH | skills/paper-lookup/references/core.md | 15 | - **Header:** `Authorization: Bearer YOUR_API_KEY` | CODE |
| HIGH | skills/paper-lookup/references/core.md | 16 | - **Query param:** `?api_key=YOUR_API_KEY` | CODE |
| HIGH⚡ | …lls/literature-review/scripts/generate_schematic_ai.py | 910 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …lls/literature-review/scripts/generate_schematic_ai.py | 911 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | skills/literature-review/scripts/generate_schematic.py | 163 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/literature-review/scripts/generate_schematic.py | 164 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH | skills/cirq/references/hardware.md | 173 | # export IONQ_API_KEY=your_api_key | COMMENT |
| HIGH | skills/cirq/references/hardware.md | 493 | export IONQ_API_KEY=your_api_key | CODE |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic_ai.py | 910 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic_ai.py | 911 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic.py | 163 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic.py | 164 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH | skills/adaptyv/SKILL.md | 52 | ADAPTYV_API_KEY=your_api_key | CODE |
| HIGH | skills/pytorch-lightning/references/logging.md | 103 | api_key="YOUR_API_KEY", | CODE |
| HIGH⚡ | …lls/scientific-slides/scripts/generate_schematic_ai.py | 910 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …lls/scientific-slides/scripts/generate_schematic_ai.py | 911 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | …s/scientific-slides/scripts/generate_slide_image_ai.py | 839 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …s/scientific-slides/scripts/generate_slide_image_ai.py | 840 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | skills/scientific-slides/scripts/generate_schematic.py | 163 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/scientific-slides/scripts/generate_schematic.py | 164 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH⚡ | …ills/scientific-slides/scripts/generate_slide_image.py | 155 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ills/scientific-slides/scripts/generate_slide_image.py | 156 | print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file") | STRING |
| HIGH | skills/tamarind/SKILL.md | 59 | export TAMARIND_API_KEY="your_api_key" | CODE |
| HIGH | skills/pennylane/references/devices_backends.md | 220 | api_key='your_api_key' | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | README.md | 673 | - **[Agentic Data Scientist: An Open Source AI That Actually Does the Analysis](https://www.k-dense.ai/blog/agentic-data | CODE |
| MEDIUM | README.md | 674 | - **[Karpathy: An Open Source Agentic Machine Learning Engineer](https://www.k-dense.ai/blog/karpathy-agentic-ml-enginee | CODE |
| MEDIUM⚡ | tests/timesfm-forecasting/test_scripts.py | 608 | # A NaN passed through would poison the whole context window. | COMMENT |
| MEDIUM | skills/exploratory-data-analysis/SKILL.md | 233 | ### 5. Create the report scaffold | COMMENT |
| MEDIUM | skills/molfeat/references/choosing_a_featurizer.md | 17 | # MACCS - Fast, good for scaffold hopping | COMMENT |
| MEDIUM | skills/molfeat/references/choosing_a_featurizer.md | 72 | # MACCS - Fast, scaffold-based similarity | COMMENT |
| MEDIUM | skills/markitdown/references/workflows.md | 129 | ## 5. RAG Ingestion | COMMENT |
| MEDIUM | skills/nextflow/references/developing.md | 27 | │ └── mypipeline.nf # the primary workflow (orchestrates subworkflows) | CODE |
| MEDIUM | skills/nextflow/references/testing.md | 23 | nf-test init # creates nf-test.config + tests/ scaffolding in a project | CODE |
| MEDIUM | skills/nextflow/references/nf-core-tools.md | 120 | nf-core pipelines create # scaffold | CODE |
| MEDIUM | …ls/timesfm-forecasting/references/output_and_config.md | 72 | max_context=1024, # Max context window (truncates longer series) | CODE |
| MEDIUM | skills/datamol/references/fragments_scaffolds.md | 3 | ## Scaffolds Module (`datamol.scaffold`) | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 28 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 36 | #### `dm.scaffold.fuzzy_scaffolding(mol, ...)` | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 45 | # Group compounds by scaffold | COMMENT |
| MEDIUM | skills/datamol/references/fragments_scaffolds.md | 58 | # Group by scaffold and analyze activity | COMMENT |
| MEDIUM⚡ | skills/datamol/references/core_workflows.md | 236 | # Get Bemis-Murcko scaffold (core structure) | COMMENT |
| MEDIUM⚡ | skills/datamol/references/core_workflows.md | 243 | # Group compounds by scaffold | COMMENT |
| MEDIUM⚡ | skills/datamol/references/core_workflows.md | 249 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | skills/datamol/references/core_workflows.md | 253 | # Create scaffold-to-molecules mapping | COMMENT |
| MEDIUM | skills/datamol/references/workflow_patterns.md | 55 | # Group by scaffold | COMMENT |
| MEDIUM | skills/datamol/references/workflow_patterns.md | 66 | # Analyze each scaffold series | COMMENT |
| MEDIUM | skills/scholar-evaluation/references/local_tooling.md | 191 | ## 7. Report scaffold | COMMENT |
| MEDIUM | skills/market-research-reports/SKILL.md | 140 | #### Measurement guardrails | COMMENT |
| MEDIUM | skills/venue-templates/SKILL.md | 143 | ### Poster scaffold | COMMENT |
| MEDIUM | skills/venue-templates/SKILL.md | 209 | ### Copy and customize a scaffold | COMMENT |
| MEDIUM | …ills/venue-templates/references/grants_requirements.md | 98 | ### Bundled NSF scaffold | COMMENT |
| MEDIUM | skills/scientific-visualization/SKILL.md | 16 | ## Non-negotiable guardrails | COMMENT |
| MEDIUM | …lls/hypothesis-generation/references/tool_reference.md | 210 | ## 7. Preregistration scaffold generator | COMMENT |
| MEDIUM | …generation/assets/preregistration_scaffold_template.md | 1 | # Preregistration scaffold: {{PROJECT_ID}} | COMMENT |
| MEDIUM | skills/markdown-mermaid-writing/templates/kanban.md | 127 | | [Work item] | [Person] | [Person] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.m | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/kanban.md | 138 | | [Work item] | [Person] | [Date] | [N days] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-m | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 60 | | **Resolved in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 163 | **Fixed in:** [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 208 | | **Shipped in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or N/A | CODE |
| MEDIUM | …lls/markdown-mermaid-writing/templates/pull_request.md | 49 | | **Related issues** | [#ISSUE](../../docs/project/issues/issue-00000001-agentic-documentation-system.md), [#ISSUE2](.. | CODE |
| MEDIUM | skills/rdkit/references/core_capabilities.md | 567 | # Generate Murcko scaffold hash | COMMENT |
| MEDIUM | skills/pylabrobot/references/material-handling.md | 180 | ## Multi-device orchestration | COMMENT |
| MEDIUM | skills/optimize-for-gpu/references/cuvs.md | 430 | ### End-to-End RAG Pipeline Example | COMMENT |
| MEDIUM | skills/liteparse/references/output_formats.md | 141 | ## Layout-aware RAG patterns | COMMENT |
| MEDIUM | skills/peer-review/references/tool_reference.md | 182 | ## Review scaffold generator | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 127 | # Step 2: Coverage assessment | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 135 | # Step 3: Fragment size (for paired-end data) | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 142 | # Step 4: ChIP signal strength | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 368 | # Step 2: Generate coverage track | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 378 | # Step 3: Fragment size analysis | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 385 | # Step 4: Compute matrix at peaks (if peaks provided) | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 106 | # Step 1: Correlation analysis | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 185 | # Step 1: Generate normalized coverage tracks | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 208 | # Step 2: Create log2 ratio track | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 221 | # Step 3: Compute matrix around TSS | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 235 | # Step 4: Generate heatmap | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 248 | # Step 5: Generate profile plot | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 260 | # Step 6: Enrichment at peaks (if peaks provided) | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 355 | # Step 1: Shift reads for Tn5 correction | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 26 | # Step 1: Preflight check | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 34 | # Step 2: Run forecast | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 40 | # Step 3: Generate visualization | COMMENT |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 346 | # Step 1: Search KEGG | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 352 | # Step 2: Get KEGG details | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 355 | # Step 3: Map to ChEMBL | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 358 | # Step 4: Get ChEBI details | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 363 | # Step 5: Get ChEMBL details | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 400 | # Step 1: Search protein | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 406 | # Step 2: Retrieve sequence | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 411 | # Step 3: BLAST search | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 416 | # Step 4: Pathway discovery | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 420 | # Step 5: Interaction mapping | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 423 | # Step 6: GO annotations | STRING |
| LOW | skills/gget/scripts/batch_sequence_analysis.py | 67 | # Step 1: BLAST each sequence | COMMENT |
| LOW⚡ | skills/gget/scripts/batch_sequence_analysis.py | 90 | # Step 2: Multiple sequence alignment | COMMENT |
| LOW⚡ | skills/gget/scripts/batch_sequence_analysis.py | 106 | # Step 3: Structure prediction (optional) | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 41 | # Step 1: Search for the gene | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 53 | # Step 2: Get detailed information | COMMENT |
| LOW | skills/gget/scripts/gene_analysis.py | 64 | # Step 3: Get sequences | COMMENT |
| LOW | skills/gget/scripts/gene_analysis.py | 77 | # Step 4: Get tissue expression | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 92 | # Step 5: Find correlated genes | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 106 | # Step 6: Get disease associations | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 119 | # Step 7: Get drug associations | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 63 | # Step 1: High-pass filter | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 67 | # Step 2: Detect bad channels | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 75 | # Step 3: Phase shift (for Neuropixels 1.0) | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 80 | # Step 4: Common median reference | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 138 | # Step 1: Run optimization | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 141 | # Step 2: Find extreme solutions | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 144 | # Step 3: Compare different preference weights | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 147 | # Step 4: Visualize selections with petal diagram | COMMENT |
| LOW⚡ | skills/phylogenetics/scripts/phylogenetic_analysis.py | 236 | # Step 1: Multiple Sequence Alignment | COMMENT |
| LOW⚡ | skills/phylogenetics/scripts/phylogenetic_analysis.py | 245 | # Step 2: Tree Inference | COMMENT |
| LOW | skills/phylogenetics/scripts/phylogenetic_analysis.py | 258 | # Step 3: Visualization | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 792 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/deeptools/scripts/validate_files.py | 61 | # Check if start and end are integers | COMMENT |
| LOW | skills/deeptools/scripts/validate_files.py | 168 | # Check if any files were provided | STRING |
| LOW | skills/deeptools/scripts/validate_files.py | 180 | # Print results | STRING |
| LOW | skills/deeptools/scripts/workflow_generator.py | 478 | # Check if workflow was specified | STRING |
| LOW | skills/citation-management/scripts/extract_metadata.py | 55 | # Check if URL | COMMENT |
| LOW⚡ | skills/timesfm-forecasting/scripts/check_system.py | 388 | # Check if GPU is available | COMMENT |
| LOW | skills/infographics/scripts/generate_infographic_ai.py | 1259 | # Check if quality is acceptable | STRING |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 566 | # Check if grouped data | COMMENT |
| LOW | skills/diffdock/scripts/analyze_results.py | 36 | # Check if this is a single complex or batch results | COMMENT |
| LOW | skills/diffdock/scripts/prepare_batch_csv.py | 133 | # Check if it's a file path or SMILES | COMMENT |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 84 | # Display results | COMMENT |
| LOW | …lls/literature-review/scripts/generate_schematic_ai.py | 792 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW⚡ | skills/literature-review/scripts/generate_pdf.py | 44 | # Check if pandoc is installed | COMMENT |
| LOW | skills/deepchem/scripts/predict_solubility.py | 149 | # Display results | COMMENT |
| LOW | skills/latex-posters/scripts/generate_schematic_ai.py | 792 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 13 | # Check if file argument provided | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 22 | # Check if file exists | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 93 | # Check if file is too large for email | COMMENT |
| LOW | …lls/scientific-slides/scripts/validate_presentation.py | 392 | # Print results | STRING |
| LOW | …lls/scientific-slides/scripts/generate_schematic_ai.py | 792 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/rdkit/scripts/similarity_search.py | 288 | # Output results | STRING |
| LOW | skills/rdkit/scripts/molecular_properties.py | 131 | # Output results | COMMENT |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 135 | # Check if goal is reached | COMMENT |
| LOW | skills/pymoo/scripts/many_objective_example.py | 46 | # Print results summary | COMMENT |
| LOW | skills/pymoo/scripts/single_objective_example.py | 45 | # Print results | COMMENT |
| LOW | skills/pymoo/scripts/multi_objective_example.py | 36 | # Print results summary | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/exploratory-data-analysis/scripts/_tabular.py | 583 | """Compare robust/classical summaries without deleting or transforming data.""" | STRING |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 173 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 186 | # Levene's test (robust to non-normality) | COMMENT |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 646 | # Run comprehensive check | COMMENT |
| MEDIUM | …lls/literature-review/scripts/generate_schematic_ai.py | 173 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/latex-posters/scripts/generate_schematic_ai.py | 173 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/pyopenms/scripts/accurate_mass_search.py | 94 | # Re-read the mzTab text for a robust flat dump of the SML table | COMMENT |
| MEDIUM | skills/matplotlib/scripts/plot_template.py | 322 | """Create a comprehensive figure with multiple subplots.""" | STRING |
| MEDIUM | …lls/scientific-slides/scripts/generate_schematic_ai.py | 173 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/rdkit/scripts/molecular_properties.py | 26 | """Calculate comprehensive molecular properties.""" | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | pyproject.toml | 21 | # Required: in prepend/append mode pytest puts tests/ on sys.path, which turns | COMMENT |
| LOW | tests/skill-requirements.toml | 1 | # Per-skill test environments. | COMMENT |
| LOW | skills/anndata/references/best_practices.md | 261 | gene_expr = adata.raw[:, 'GENE_NAME'].X | COMMENT |
| LOW | skills/bids/references/conversion_tools.md | 361 | #### Step 4: Convert | COMMENT |
| LOW | skills/bids/references/beps.yml | 1 | --- | COMMENT |
| LOW | skills/autoskill/config.yaml | 1 | # autoskill configuration | COMMENT |
| LOW | skills/autoskill/references/screenpipe-config.yaml | 1 | # Starter screenpipe configuration for autoskill users. | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 1 | #!/bin/bash | COMMENT |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 61 | # samples_per_complex: 30 | COMMENT |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 81 | # PRESET 4: Rigid Ligands (more focused predictions) | COMMENT |
| LOW | skills/gget/references/workflows.md | 561 | COMMENT | |
| LOW | skills/literature-review/references/example_workflow.md | 41 | # - Use parallel-cli extract to fetch full content from promising URLs | COMMENT |
| LOW | …ls/literature-review/references/database_strategies.md | 421 | # 2. Search bioRxiv | COMMENT |
| LOW | …ls/latex-posters/references/ai_graphics_for_posters.md | 281 | # Drug discovery workflow - HIGH-LEVEL ONLY, 3 stages | COMMENT |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 321 | print(f"Train batches: {len(train_loader)}") | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 201 | # Example 1: Evaluate a trained model | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 221 | # watch_agent( | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 241 | # model_path="./models/best_model/best_model.zip", | COMMENT |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 141 | algorithm=PPO, | COMMENT |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 161 | # algorithm=DQN, | COMMENT |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 61 | # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...]) | COMMENT |
| LOW | skills/optimize-for-gpu/references/installation.md | 21 | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 140 | # Create a notebook with some content first | COMMENT |
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 162 | # Create a chat session | COMMENT |
| MEDIUM | skills/open-notebook/scripts/source_ingestion.py | 124 | # Create a notebook first | COMMENT |
| MEDIUM | skills/hypogenic/assets/task_config.example.yaml | 3 | # This file contains no provider choice, credential, budget, or execution approval. | COMMENT |
| MEDIUM | skills/pymoo/scripts/many_objective_example.py | 19 | # Define the problem - DTLZ2 with 5 objectives | COMMENT |
| MEDIUM | skills/pymoo/scripts/single_objective_example.py | 21 | # Define the problem - Sphere function (sum of squares) | COMMENT |
| MEDIUM | skills/pymoo/scripts/multi_objective_example.py | 18 | # Define the problem - ZDT1 (bi-objective) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | tests/citation-management/test_scripts.py | 625 | "authorships": [{"author": {"display_name": "Jane Doe"}}], | CODE |
| LOW⚡ | tests/citation-management/test_scripts.py | 631 | self.assertEqual(record["authors"], "Jane Doe") | CODE |
| LOW⚡ | tests/citation-management/test_scripts.py | 641 | "type": "preprint", "authors": "Jane Doe", "title": "A Preprint", | CODE |
| LOW⚡ | tests/pptx-posters/test_scripts.py | 113 | with self.assertRaisesRegex(CliError, "placeholder"): | STRING |
| LOW | skills/pptx-posters/references/poster_content_guide.md | 158 | The validator rejects common placeholder forms such as TODO, TBD, Lorem ipsum, | CODE |
| LOW | skills/scientific-writing/scripts/lint_manuscript.py | 24 | re.compile(r"\blorem ipsum\b", re.IGNORECASE), | CODE |
| LOW | …-posters/references/compilation_and_quality_control.md | 270 | - [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.) | CODE |
| LOW | skills/latex-posters/scripts/review_poster.sh | 179 | echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)" | CODE |
| LOW | skills/latex-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | skills/dnanexus-integration/scripts/validate_dxapp.py | 61 | "placeholder", | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/pymc/scripts/model_comparison.py | 380 | # Example usage | STRING |
| LOW | skills/pymc/scripts/model_diagnostics.py | 306 | # Example usage | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 9 | # Usage: | COMMENT |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 634 | # Example usage | COMMENT |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 301 | # Example usage | COMMENT |
| LOW | …pytorch-lightning/scripts/template_lightning_module.py | 198 | # Example usage | COMMENT |
| LOW | skills/scikit-learn/scripts/clustering_analysis.py | 338 | # Example usage | COMMENT |
| LOW | skills/scikit-learn/scripts/classification_pipeline.py | 230 | # Example usage | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | skills/scientific-brainstorming/references/sources.md | 267 | bibliographic citations generated by ChatGPT,” *Scientific Reports* 13. | CODE |
| HIGH | …ls/latex-posters/references/ai_graphics_for_posters.md | 80 | The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/pkpd-modeling/scripts/ddi_static.py | 77 | CODE | |
| LOW | skills/research-lookup/scripts/research_lookup.py | 143 | CODE | |
| LOW | skills/openpiv/scripts/runner.py | 22 | CODE | |
| LOW | skills/infographics/scripts/generate_infographic_ai.py | 1102 | CODE | |
| LOW | …ills/scientific-visualization/scripts/figure_export.py | 149 | CODE | |
| LOW | …ills/scientific-visualization/scripts/figure_export.py | 323 | CODE | |
| LOW | …lls/scientific-visualization/scripts/image_metadata.py | 468 | CODE | |
| LOW | …s/neuropixels-analysis/scripts/preprocess_recording.py | 15 | CODE | |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 24 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/_contract/__init__.py | 38 | __all__ = ["cli", "office", "schematic", "structure"] | CODE |
| LOW | skills/pkpd-modeling/scripts/_common.py | 311 | __all__ = [ | CODE |
| LOW | skills/pkpd-modeling/scripts/_models.py | 654 | __all__ = [ | CODE |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | skills/pptx/scripts/clean.py | 233 | def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None: | CODE |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | skills/docx/scripts/accept_changes.py | 14 | logger = logging.getLogger(__name__) | CODE |
| LOW | skills/docx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |