Repository Analysis

K-Dense-AI/scientific-agent-skills

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.

13.8 Low AI signal View on GitHub

Analysis Overview

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).

13.8
Adjusted Score
13.8
Raw Score
100%
Time Factor
2026-08-24
Last Push
36.5K
Stars
Python
Language
617.9K
Lines of Code
2.0K
Files
6.2K
Pattern Hits
2026-08-29
Scan Date
0.14
HC Hit Rate

What These Metrics Mean

Adjusted Score
Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score
The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor
The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits
Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate
High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files
Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

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.

Severity Breakdown

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.

CRITICAL 0HIGH 295MEDIUM 504LOW 5416

Directory Score Breakdown

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.

Pattern Findings

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.

Hyper-Verbose Identifiers3692 hits · 3744 pts
SeverityFileLineSnippetContext
LOWscan_skills.py338def cache_invalidation_reason(previous: dict | None, max_age_days: int) -> str | None:CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py96 def test_collection_date_differs_between_instances(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py103 def test_string_typed_date_is_rejected_not_guessed(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py110 def test_submission_date_differs_between_instances(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py116 def test_missing_date_field_raises_with_the_alternatives(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py121 def test_supports_range_follows_declared_type(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py131 def test_indexed_column_preferred(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py134 def test_unindexed_instance_reports_no_index(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py137 def test_qc_columns_are_not_lineage_columns(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py143 def test_per_segment_columns_excluded(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py148 def test_ha_clade_outranks_na_clade(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py155 def test_no_lineage_column_raises(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py163 def test_bare_name_stays_exact(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py166 def test_sublineages_expand_on_an_indexed_column(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py170 def test_sublineages_refused_without_an_index(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py177 def test_trailing_star_refused_without_an_index(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py181 def test_exact_query_still_allowed_without_an_index(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py186 def test_zero_successes_has_nonzero_upper_bound(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py192 def test_interval_stays_inside_the_unit_interval(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py198 def test_interval_brackets_the_estimate(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py203 def test_interval_narrows_with_n(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py208 def test_empty_denominator_is_maximally_uncertain(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py224 def test_rising_series_has_positive_slope(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py231 def test_falling_series_has_negative_slope(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py237 def test_flat_series_slope_near_zero(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py243 def test_all_zero_observations_returns_no_fit(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py250 def test_too_few_successes_returns_no_fit(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py254 def test_too_few_nonzero_weeks_returns_no_fit(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py258 def test_too_few_points_returns_no_fit(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py261 def test_dispersion_never_shrinks_the_interval_below_binomial(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py271 def test_overdispersion_widens_the_interval(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py280 def test_empty_weeks_are_dropped_not_counted(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py289 def test_iso_week_start_is_monday(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py294 def test_partial_and_null_dates_are_unparseable(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py298 def test_undated_rows_are_counted_separately(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py309 def test_week_range_is_inclusive_and_gapless(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py317 def test_recent_thin_weeks_are_flagged(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py327 def test_steady_series_flags_nothing(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py346 def test_unalias_expands_one_level(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py349 def test_unalias_full_walks_to_a_fixed_point(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py352 def test_unalias_stops_at_a_recombinant(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py356 def test_unalias_leaves_root_lineages_alone(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py359 def test_recombinant_parents_deduplicated(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py364 def test_ordinary_lineage_has_no_recombinant_parents(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py367 def test_unknown_prefix_is_returned_unchanged(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py380 def test_parent_chain_walks_to_the_root(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py388 def test_descendants_are_transitive(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py394 def test_leaf_has_no_descendants(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py461 def test_parses_status_and_strips_the_marker(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py469 def test_header_and_blank_lines_ignored(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py474 def test_redesignation_target_is_extracted(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py479 def test_withdrawal_without_a_successor(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py484 def test_blob_hashes_reported_per_file(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py514 def test_non_json_body_does_not_raise(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py517 def test_unknown_instance_lists_the_known_ones(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py522 def test_base_url_overrides_the_registry(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py530 def test_list_values_repeat_the_key(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py537 def test_empty_string_preserved(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py543 def test_valid_field_accepted(self):CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py548 def test_range_suffix_accepted(self):CODE
3632 more matches not shown…
Cross-File Repetition184 hits · 920 pts
SeverityFileLineSnippetContext
HIGHtests/pathogen-variant-surveillance/test_scripts.py0load a bundled script as a module regardless of cwd.STRING
HIGHtests/analytical-method-validation/test_scripts.py0load a bundled script as a module regardless of cwd.STRING
HIGHtests/ontology-term-resolution/test_scripts.py0load a bundled script as a module regardless of cwd.STRING
HIGHtests/genomic-coordinates/test_scripts.py0load a bundled script as a module regardless of cwd.STRING
HIGHskills/scikit-survival/scripts/_common.py0return an argparse converter for a bounded integer.STRING
HIGHskills/pytdc/scripts/_common.py0return an argparse converter for a bounded integer.STRING
HIGHskills/uncertainty-and-units/scripts/_common.py0return an argparse converter for a bounded integer.STRING
HIGHskills/scikit-survival/scripts/_common.py0return a bounded regular local file, rejecting urls and symlinks.STRING
HIGHskills/simpy/scripts/_common.py0return a bounded regular local file, rejecting urls and symlinks.STRING
HIGHskills/uncertainty-and-units/scripts/_common.py0return a bounded regular local file, rejecting urls and symlinks.STRING
HIGHskills/scikit-survival/scripts/_common.py0validate an explicit local output without following symlinks.STRING
HIGHskills/simpy/scripts/_common.py0validate an explicit local output without following symlinks.STRING
HIGHskills/uncertainty-and-units/scripts/_common.py0validate an explicit local output without following symlinks.STRING
HIGHskills/scikit-survival/scripts/_common.py0write bytes through a same-directory temporary file.STRING
HIGHskills/simpy/scripts/_common.py0write bytes through a same-directory temporary file.STRING
HIGHskills/uncertainty-and-units/scripts/_common.py0write bytes through a same-directory temporary file.STRING
HIGHskills/scientific-visualization/scripts/_common.py0write bytes through a same-directory temporary file.STRING
HIGHskills/exploratory-data-analysis/scripts/_common.py0run a cli body with concise expected-error handling.STRING
HIGHskills/neurokit2/scripts/_common.py0run a cli body with concise expected-error handling.STRING
HIGHskills/pathml/scripts/_common.py0run a cli body with concise expected-error handling.STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0ai-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.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0ai-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.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0the 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.py0the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes -STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0the 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.py0the outcome of one quality review. a named tuple rather than a bare tuple because the review has several failure modes -STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0the 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.py0the 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.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py0strip markdown decoration so the rubric's fields can be found.STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0return 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.py0return the reviewer's 0-10 score, or none when there isn't a usable one. none rather than a default: a fabricated score STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0return 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.py0return 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.py0return 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.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py0return acceptable / needs_improvement from the verdict line, or none. anchored to the start of a line. the rubric promptSTRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGHskills/generate-image/scripts/generate_image.py0resolve the api key from --api-key, the environment, then any .env file. the .env scan walks up from the working directoSTRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine ifSTRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py0generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine ifSTRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine ifSTRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py0generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine ifSTRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0generate infographics using ai with smart iterative refinement. uses gemini 3.6 flash for quality review to determine ifSTRING
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Decorative Section Separators240 hits · 742 pts
SeverityFileLineSnippetContext
MEDIUMtests/onekgpd/test_scripts.py97# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/onekgpd/test_scripts.py99# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/onekgpd/test_scripts.py522# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/onekgpd/test_scripts.py524# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py62# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py64# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py197# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py199# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py383# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py385# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py490# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py492# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py600# ---------------------------------------------------------------------------COMMENT
MEDIUMtests/genomic-coordinates/test_scripts.py602# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/pymc/references/workflows.md16# ===============COMMENT
MEDIUMskills/pymc/references/workflows.md24# ==============COMMENT
MEDIUMskills/pymc/references/workflows.md45# ==========================COMMENT
MEDIUMskills/pymc/references/workflows.md55# ============COMMENT
MEDIUMskills/pymc/references/workflows.md71# ====================COMMENT
MEDIUMskills/pymc/references/workflows.md93# ==============================COMMENT
MEDIUMskills/pymc/references/workflows.md103# ==================COMMENT
MEDIUMskills/pymc/references/workflows.md115# ============================COMMENT
MEDIUMskills/pymc/references/workflows.md136# ===============COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py16# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py18# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py51# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py53# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py96# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py98# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py112# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py114# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py132# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py134# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py182# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py184# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py198# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py200# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py262# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py264# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py320# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py322# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py16# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py18# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py41# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py43# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py69# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py71# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py85# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py87# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py106# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py108# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py149# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py151# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py165# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py167# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py195# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py197# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py230# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py232# =============================================================================COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py36# ---------------------------------------------------------------------------COMMENT
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Excessive Try-Catch Wrapping476 hits · 668 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py79 except Exception as exc: # pragma: no cover - defensiveSTRING
LOWscan_pr_skills.py100 except Exception as exc: # pragma: no cover - defensiveSTRING
LOWscan_skills.py443 except Exception: # counted per skill below when it is scannedCODE
LOWscan_skills.py461 except Exception as e:CODE
LOWscan_skills.py527 except Exception as e:CODE
LOWtests/deepchem/test_scripts.py213 except Exception:CODE
LOWtests/pytorch-lightning/test_scripts.py76 except Exception as error: # noqa: BLE001 - the message is the assertionCODE
LOW…lls/benchling-integration/references/authentication.md328except Exception as e:CODE
LOWskills/lab-hardware-cad/scripts/gen.py65 except Exception as exc: # noqa: BLE001 - the kernel raises assorted OCCT errorsCODE
LOWskills/lab-hardware-cad/scripts/gen.py124 except Exception as exc: # noqa: BLE001 - model code raises arbitrary errorsCODE
LOWskills/lab-hardware-cad/scripts/_common.py383 except Exception: # noqa: BLE001 - kernel raises assorted OCCT errorsCODE
LOWskills/lab-hardware-cad/scripts/_common.py386 except Exception as exc: # noqa: BLE001CODE
LOWskills/lab-hardware-cad/scripts/snapshot.py125 except Exception: # noqa: BLE001 - skip an edge the kernel cannot sampleCODE
LOWskills/deepspot-m/references/api.md174 except Exception as exc:CODE
MEDIUMskills/deepspot-m/references/api.md167def load_deepspotm(source="scgpt"):CODE
MEDIUMskills/networkx/references/io.md447 print(f"Error reading GraphML: {e}")CODE
LOWskills/scikit-survival/scripts/_common.py273 except Exception as exc:CODE
LOWskills/qiskit/references/setup.md93 except Exception:CODE
LOWskills/qiskit/scripts/check_environment.py49 except Exception as error: # Report broken optional environments clearly.CODE
LOWskills/qiskit/scripts/check_environment.py149 except Exception as error:CODE
LOWskills/qiskit/scripts/inspect_runtime.py205 except Exception as error:CODE
LOWskills/research-lookup/scripts/research_lookup.py936 except Exception as exc:CODE
LOWskills/research-lookup/scripts/research_lookup.py951 except Exception as fallback_exc:CODE
LOWskills/research-lookup/scripts/research_lookup.py1167 except Exception as exc:STRING
MEDIUMskills/research-lookup/scripts/research_lookup.py1168 print(f"Error: {exc}", file=sys.stderr)STRING
LOWskills/imaging-data-commons/scripts/check_version.py52 except Exception:CODE
LOWskills/dask/references/futures.md499 except Exception as e:CODE
LOWskills/dask/references/futures.md533except Exception:CODE
LOWskills/esm/references/forge-api.md363 except Exception as e:CODE
MEDIUMskills/esm/references/forge-api.md364 print(f"Error processing {i}: {e}")CODE
LOWskills/esm/references/forge-api.md404 except Exception as e:CODE
LOWskills/esm/references/forge-api.md582 except Exception as e:CODE
LOWskills/esm/references/forge-api.md641except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py34 print("Error: requests library not found. Install with: uv pip install requests")CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py383 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py486 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py649 except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py908 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py917 print("Error: Iterations must be between 1 and 2")STRING
LOW…scientific-schematics/scripts/generate_schematic_ai.py943 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py159 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py173 print(f"Error: AI generation script not found: {ai_script}")STRING
LOW…ls/scientific-schematics/scripts/generate_schematic.py191 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py192 print(f"Error executing AI generation: {e}")STRING
LOWskills/geopandas/scripts/crs_reprojection_plan.py205 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOWskills/geopandas/scripts/geometry_validity_report.py222 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOW…s/geopandas/scripts/sensitive_coordinates_checklist.py225 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOWskills/geopandas/scripts/vector_inventory.py135 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOWskills/geopandas/scripts/export_plan.py300 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOWskills/geopandas/scripts/spatial_join_audit.py363 except Exception as exc: # noqa: BLE001 - errors are redacted at CLI boundaryCODE
LOWskills/pyzotero/references/files-attachments.md95 except Exception as e:CODE
LOWskills/pyzotero/references/error-handling.md45except Exception as e:CODE
LOWskills/pyzotero/references/error-handling.md105except Exception as e:CODE
LOWskills/deeptools/scripts/validate_files.py72 except Exception as e:CODE
LOWskills/protocolsio-integration/scripts/_common.py222 except Exception:CODE
MEDIUMskills/medchem/scripts/filter_molecules.py23 print(f"Error: Missing required package: {e}")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py50 print(f"Error: Column '{smiles_column}' not found")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py65 print(f"Error: Unsupported file format: {suffix}")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py237 print("Error: Specify at least one filter (--rules, --query, --pains, --nibr, etc.)")CODE
LOWskills/pymatgen/scripts/mp_query.py277 except Exception as exc:CODE
416 more matches not shown…
Structural Annotation Overuse375 hits · 609 pts
SeverityFileLineSnippetContext
LOWskills/iso-standards-readiness/SKILL.md119### Step 1: Declare the standard, purpose, and authorized ownersCOMMENT
LOWskills/iso-standards-readiness/SKILL.md144### Step 2: Freeze source/version evidenceCOMMENT
LOWskills/iso-standards-readiness/SKILL.md155### Step 3: Inventory controlled documents and recordsCOMMENT
LOWskills/iso-standards-readiness/SKILL.md169### Step 4: Review process implementationCOMMENT
LOWskills/iso-standards-readiness/SKILL.md178### Step 5: Run the focused checks that apply to the laneCOMMENT
LOWskills/iso-standards-readiness/SKILL.md210### Step 6: Address lane-specific regulator evidence separatelyCOMMENT
LOWskills/iso-standards-readiness/SKILL.md230### Step 7: Assemble a bounded readiness manifestCOMMENT
LOWskills/iso-standards-readiness/SKILL.md262### Step 8: Human review and controlled handoffCOMMENT
LOWskills/imaging-data-commons/SKILL.md345# Step 1: Query for series UIDsSTRING
LOWskills/imaging-data-commons/SKILL.md355# Step 2: Extract UIDs as a list from the DataFrameSTRING
LOWskills/imaging-data-commons/SKILL.md358# Step 3: Pass the list to download_from_selection (NOT the DataFrame itself)STRING
LOW…imaging-data-commons/references/clinical_data_guide.md69### Step 1: Fetch Clinical IndexCOMMENT
LOW…imaging-data-commons/references/clinical_data_guide.md81### Step 2: Discover Available Clinical DataCOMMENT
LOW…imaging-data-commons/references/clinical_data_guide.md93### Step 3: Search for Specific AttributesCOMMENT
LOW…imaging-data-commons/references/clinical_data_guide.md103### Step 4: Load Clinical TableCOMMENT
LOW…imaging-data-commons/references/clinical_data_guide.md114### Step 5: Map Coded Values to DescriptionsCOMMENT
LOW…imaging-data-commons/references/clinical_data_guide.md141### Step 6: Join with Imaging DataCOMMENT
LOWskills/vaex/references/machine_learning.md388# Step 1: Encode categoricalCOMMENT
LOWskills/vaex/references/machine_learning.md392# Step 2: Scale featuresCOMMENT
LOWskills/vaex/references/machine_learning.md396# Step 3: PCACOMMENT
LOWskills/onekgpd/SKILL.md214# Step 4: For that set of individuals, see the actual variants they carry.COMMENT
LOWskills/onekgpd/SKILL.md322# Step 1: resolve gene -> verified GRCh38 region (authoritative source).COMMENT
LOWskills/onekgpd/SKILL.md323# Step 2: count individuals carrying a qualifying variant in the region.COMMENT
LOWskills/onekgpd/SKILL.md328# Step 3: list those individuals.COMMENT
LOWskills/onekgpd/SKILL.md333# Step 4: for that set of individuals, see the actual variants they carry.COMMENT
LOWskills/dask/references/schedulers.md400# Step 1: Debug with synchronous schedulerCOMMENT
LOWskills/dask/references/schedulers.md404# Step 2: Test with threadsCOMMENT
LOWskills/dask/references/schedulers.md408# Step 3: Scale with distributedCOMMENT
LOWskills/esm/SKILL.md180# Step 1: Generate initial structureCOMMENT
LOWskills/esm/SKILL.md184# Step 2: Refine sequence based on structureCOMMENT
LOWskills/esm/SKILL.md188# Step 3: Predict functionCOMMENT
LOWskills/esm/references/workflows.md25# Step 1: Define target propertiesCOMMENT
LOWskills/esm/references/workflows.md41# Step 2: Generate initial sequence with function conditioningCOMMENT
LOWskills/esm/references/workflows.md52# Step 3: Predict structureCOMMENT
LOWskills/esm/references/workflows.md62# Step 4: Refine sequence based on structureCOMMENT
LOWskills/esm/references/workflows.md84# Step 5: Final validationCOMMENT
LOWskills/esm/references/workflows.md160# Step 1: Generate variant libraryCOMMENT
LOWskills/esm/references/workflows.md195# Step 2: Predict structures for variantsCOMMENT
LOWskills/esm/references/workflows.md213# Step 3: Analyze variant diversityCOMMENT
LOWskills/esm/references/workflows.md225# Step 4: Get embeddings for clusteringCOMMENT
LOWskills/esm/references/workflows.md241# Step 5: Cluster variantsCOMMENT
LOWskills/esm/references/workflows.md259# Step 6: Select diverse representativesCOMMENT
LOWskills/esm/references/workflows.md316# Step 1: Generate multiple sequence designsCOMMENT
LOWskills/esm/references/workflows.md343# Step 2: Validate structural compatibilityCOMMENT
LOWskills/esm/references/workflows.md366# Step 3: Analyze sequence propertiesCOMMENT
LOWskills/esm/references/workflows.md409# Step 4: Rank designsCOMMENT
LOWskills/esm/references/workflows.md433# Step 5: Save resultsCOMMENT
LOWskills/esm/references/workflows.md559# Step 1: Generate embeddingsCOMMENT
LOWskills/esm/references/workflows.md578# Step 2: Dimensionality reduction for visualizationCOMMENT
LOWskills/esm/references/workflows.md590# Step 3: ClusteringCOMMENT
LOWskills/esm/references/workflows.md603# Step 4: VisualizeCOMMENT
LOWskills/esm/references/workflows.md621# Step 5: Analyze clustersCOMMENT
LOWskills/esm/references/esm3-api.md260# Step 1: Complete sequenceCOMMENT
LOWskills/esm/references/esm3-api.md266# Step 2: Predict structure for completed sequenceCOMMENT
LOWskills/esm/references/esm3-api.md272# Step 3: Predict functionCOMMENT
LOWskills/arboreto/references/distributed_computing.md106### Step 1: Set Up Dask Scheduler (on cluster head node)COMMENT
LOWskills/arboreto/references/distributed_computing.md112### Step 2: Start Dask Workers (on cluster compute nodes)COMMENT
LOWskills/arboreto/references/distributed_computing.md117### Step 3: Connect from ClientCOMMENT
LOWskills/bids/references/conversion_tools.md72#### Step 1: Reconnaissance — Discover DICOM seriesCOMMENT
LOWskills/bids/references/conversion_tools.md92#### Step 2: Write a heuristic fileCOMMENT
315 more matches not shown…
Unused Imports568 hits · 530 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py15CODE
LOWtests/conftest.py21CODE
LOWtests/run_all.py32CODE
LOWtests/pathogen-variant-surveillance/test_scripts.py10CODE
LOWtests/lab-hardware-cad/test_scripts.py8CODE
LOWtests/iso-standards-readiness/test_scripts.py1CODE
LOWtests/scikit-survival/test_scripts.py4CODE
LOWtests/qiskit/test_scripts.py17CODE
LOWtests/scientific-brainstorming/test_scripts.py3CODE
LOWtests/pymc/test_scripts.py20CODE
LOWtests/pymc/test_scripts.py30CODE
LOWtests/pkpd-modeling/test_scripts.py20CODE
LOWtests/research-lookup/test_research_lookup.py3CODE
LOWtests/shap/test_scripts.py17CODE
LOWtests/onekgpd/test_scripts.py21CODE
LOWtests/onekgpd/test_scripts.py33CODE
LOWtests/get-available-resources/test_scripts.py3CODE
LOWtests/exploratory-data-analysis/test_static.py4CODE
LOWtests/exploratory-data-analysis/test_scripts.py4CODE
LOWtests/exploratory-data-analysis/test_scripts.py268CODE
LOWtests/experimental-design/test_scripts.py15CODE
LOWtests/scientific-schematics/test_scripts.py9CODE
LOWtests/arboreto/test_scripts.py14CODE
LOWtests/bids/test_scripts.py14CODE
LOWtests/geniml/test_scripts.py3CODE
LOWtests/geopandas/test_static.py3CODE
LOWtests/geopandas/test_scripts.py3CODE
LOWtests/deeptools/test_scripts.py13CODE
LOWtests/protocolsio-integration/test_scripts.py3CODE
LOWtests/analytical-method-validation/test_scripts.py10CODE
LOWtests/medchem/test_scripts.py19CODE
LOWtests/fluidsim/test_static.py3CODE
LOWtests/fluidsim/test_scripts.py3CODE
LOWtests/pymatgen/test_static.py3CODE
LOWtests/pymatgen/test_scripts.py3CODE
LOWtests/pathway-enrichment/test_scripts.py11CODE
LOWtests/citation-management/test_scripts.py12CODE
LOWtests/pydicom/test_static.py3CODE
LOWtests/pydicom/test_scripts.py3CODE
LOWtests/markitdown/test_scripts.py17CODE
LOWtests/openpiv/test_scripts.py19CODE
LOWtests/pytdc/test_scripts.py4CODE
LOWtests/xlsx/test_scripts.py14CODE
LOWtests/pdf/test_scripts.py14CODE
LOWtests/pdf/test_scripts.py19CODE
LOWtests/pdf/test_scripts.py25CODE
LOWtests/exa-search/test_exa_search.py12CODE
LOWtests/autoskill/test_e2e.py9CODE
LOWtests/ncats-arax/test_scripts.py1CODE
LOWtests/ncats-arax/test_scripts.py9CODE
LOWtests/timesfm-forecasting/test_scripts.py27CODE
LOWtests/opentrons-integration/test_scripts.py30CODE
LOWtests/opentrons-integration/test_scripts.py36CODE
LOWtests/infographics/test_scripts.py15CODE
LOWtests/_meta/test_repo_contract.py15CODE
LOWtests/_contract/office.py15CODE
LOWtests/_contract/__init__.py34CODE
LOWtests/_contract/__init__.py36CODE
LOWtests/_contract/__init__.py36CODE
LOWtests/_contract/__init__.py36CODE
508 more matches not shown…
Deep Nesting378 hits · 364 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py115CODE
LOWscan_skills.py127CODE
LOWscan_skills.py373CODE
LOWtests/run_all.py108CODE
LOWtests/pkpd-modeling/test_scripts.py96CODE
LOWtests/geniml/test_scripts.py55CODE
LOWtests/geopandas/test_static.py78CODE
LOWtests/geopandas/test_static.py111CODE
LOWtests/fluidsim/test_static.py60CODE
LOWtests/pymatgen/test_static.py60CODE
LOWtests/pymatgen/test_static.py95CODE
LOWtests/pydicom/test_static.py87CODE
LOWtests/openpiv/test_scripts.py251CODE
LOWtests/ncats-arax/test_scripts.py373CODE
LOWtests/ncats-arax/test_scripts.py1131CODE
LOWtests/ncats-arax/test_scripts.py1514CODE
LOWtests/opentrons-integration/test_scripts.py150CODE
LOWtests/_contract/office.py107CODE
LOWtests/_contract/office.py277CODE
LOWtests/_contract/cli.py102CODE
LOWtests/_contract/cli.py158CODE
LOWtests/_contract/cli.py118CODE
LOWtests/_contract/cli.py177CODE
LOWtests/_contract/structure.py263CODE
LOWtests/_contract/structure.py369CODE
LOWtests/gtars/test_static.py18CODE
LOWtests/pptx-posters/test_static.py127CODE
LOWtests/pptx-posters/test_static.py148CODE
LOWtests/pptx-posters/test_static.py162CODE
LOWtests/scientific-writing/test_static.py45CODE
LOWtests/qutip/test_static.py104CODE
LOWtests/qutip/test_static.py128CODE
LOWtests/deepchem/test_scripts.py119CODE
LOWtests/matlab/test_static.py131CODE
LOWtests/matlab/test_static.py159CODE
LOWtests/hypothesis-generation/test_scripts.py318CODE
LOWtests/labarchive-integration/test_scripts.py356CODE
LOWtests/peer-review/test_scripts.py320CODE
LOWtests/hugging-science/test_scripts.py251CODE
LOW…hogen-variant-surveillance/scripts/mutation_profile.py92CODE
LOW…thogen-variant-surveillance/scripts/resolve_lineage.py83CODE
LOW…gen-variant-surveillance/scripts/lineage_prevalence.py120CODE
LOWskills/lab-hardware-cad/scripts/_common.py486CODE
LOW…ndards-readiness/scripts/validate_evidence_manifest.py87CODE
LOWskills/iso-standards-readiness/scripts/_common.py99CODE
LOWskills/iso-standards-readiness/scripts/gap_analyzer.py44CODE
LOW…o-standards-readiness/scripts/validate_scope_intake.py57CODE
LOWskills/iso-standards-readiness/scripts/check_capa.py52CODE
LOWskills/scikit-survival/scripts/train_survival_model.py82CODE
LOWskills/qiskit/scripts/check_environment.py63CODE
LOW…/scientific-brainstorming/scripts/validate_register.py150CODE
LOW…ls/scientific-brainstorming/scripts/evaluate_matrix.py138CODE
LOWskills/pymc/scripts/model_comparison.py32CODE
LOWskills/pymc/scripts/model_comparison.py138CODE
LOWskills/pkpd-modeling/scripts/simulate_regimen.py117CODE
LOWskills/pkpd-modeling/scripts/allometry_and_fih.py161CODE
LOWskills/pkpd-modeling/scripts/_common.py234CODE
LOWskills/pkpd-modeling/scripts/ddi_static.py182CODE
LOWskills/pkpd-modeling/scripts/check_popk_dataset.py84CODE
LOWskills/pkpd-modeling/scripts/fit_compartmental.py395CODE
318 more matches not shown…
Cross-Language Confusion55 hits · 321 pts
SeverityFileLineSnippetContext
HIGHtests/exploratory-data-analysis/test_scripts.py207 '{"secret_field": [{"value": "secret-value"}, null]}',CODE
HIGHtests/geopandas/test_scripts.py201 self.assertTrue(arrow_roundtrip.crs.equals(coverage.crs))CODE
HIGHtests/pydeseq2/test_scripts.py138 self.assertTrue(counts.index.equals(metadata.index))CODE
HIGHtests/pydeseq2/test_scripts.py147 self.assertTrue(counts.index.equals(metadata.index))CODE
HIGHtests/pydeseq2/test_scripts.py205 self.assertTrue(counts.index.equals(metadata.index))CODE
HIGHtests/pyopenms/test_scripts.py272 peptide.toString()CODE
HIGHskills/research-lookup/scripts/research_lookup.py126 "Find conflicting, contradictory, null, negative, replication, and limitation "CODE
HIGHskills/geopandas/scripts/export_plan.py134 "Legacy multi-file output has field-name, null, type, encoding, geometry, and size limitations.",CODE
HIGHskills/geopandas/scripts/export_plan.py276 "null, empty, invalid, geometry type, and dimensionality counts",CODE
HIGHskills/xlsx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/xlsx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH…recasting/examples/global-temperature/generate_html.py403 ...Array(nActual).fill(null),CODE
HIGH…recasting/examples/global-temperature/generate_html.py411 dataUsed.push(step.historical_values[i]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py413 dataUsed.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py413 dataUsed.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py427 if (forecastIdx >= 0 && forecastIdx < nForecast) {{CODE
HIGH…recasting/examples/global-temperature/generate_html.py428 q90Lower.push(step.q10[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py429 q90Upper.push(step.q90[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py430 q80Lower.push(step.q20[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py431 q80Upper.push(step.q80[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py433 q90Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py433 q90Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py434 q90Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py434 q90Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py435 q80Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py435 q80Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py436 q80Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py436 q80Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py448 if (forecastIdx >= 0 && forecastIdx < nForecast) {{CODE
HIGH…recasting/examples/global-temperature/generate_html.py449 forecastData.push(step.point_forecast[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py451 forecastData.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py451 forecastData.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py227 let chart = null;CODE
HIGH…recasting/examples/global-temperature/generate_html.py229 let playInterval = null;CODE
HIGH…recasting/examples/global-temperature/generate_html.py275 data: [...Array(animationData.actual_data.dates.length).fill(null), ...finalStep.point_forecCODE
HIGHskills/pydeseq2/scripts/run_deseq2_analysis.py53 if not counts_df.index.equals(metadata.index):CODE
HIGHskills/paper-lookup/scripts/paginate.py15 than sending null; bioRxiv just returns an empty collection)STRING
HIGHskills/pptx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/pptx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGHskills/relsa-severity-assessment/scripts/_common.py186 undefined, which is what ``score_to_percent`` exists to avoid.STRING
HIGHskills/pacsomatic/scripts/run_pacsomatic.py449 documented shape, e.g. "module purge && module load nextflow/23.10.0".STRING
HIGHskills/pyopenms/scripts/theoretical_spectrum.py49 print(f"Peptide: {seq.toString()} ({len(spec)} fragment peaks)")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py69 print(f"Peptide: {seq.toString()}")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py70 print(f"Formula: {formula.toString()}")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py81 print(f"\nFormula: {formula.toString()}")CODE
HIGHskills/pyopenms/scripts/digest_protein.py74 pep_str = pep.toString()CODE
HIGHskills/flowio/scripts/inspect_fcs.py110 "PnN label to classify as null; repeat for multiple labels. "CODE
HIGHskills/docx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/docx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
Magic Placeholder Names54 hits · 248 pts
SeverityFileLineSnippetContext
HIGHdocs/security-report.md666 > Several reference documents contain example snippets that embed credentials directly in code: `SentinelAPI('user', 'CODE
HIGHdocs/security-report.md2294 > A reference file shows an IonQ device instantiation with an inline `api_key='your_api_key'` parameter. This is an obCODE
HIGH…lls/benchling-integration/references/authentication.md301 -u "your_api_key:" \CODE
HIGH…lls/benchling-integration/references/authentication.md321 auth_method=ApiKeyAuth("your_api_key")CODE
HIGH…lls/benchling-integration/references/authentication.md381 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGH…ills/benchling-integration/references/api_endpoints.md26 -u "your_api_key:"CODE
HIGH…ills/benchling-integration/references/sdk_reference.md571 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGH…ills/benchling-integration/references/sdk_reference.md578 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGHskills/geomaster/references/data-sources.md179 'key': YOUR_API_KEYSTRING
HIGHskills/geomaster/references/data-sources.md208 'appid': YOUR_API_KEYSTRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py910 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py911 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py163 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py164 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/pyzotero/SKILL.md40ZOTERO_API_KEY=your_api_keyCODE
HIGHskills/database-lookup/references/bea.md13- Pass as query parameter: `&UserID=YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/lincs-l1000.md13- Pass via header: `user_key: YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/lincs-l1000.md36curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md40curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md44curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md48curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/omim.md10- Pass as query parameter: `?apiKey=YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/addgene.md10Pass as: `Authorization: Token <your_api_key>`CODE
HIGHskills/citation-management/references/pubmed_search.md385 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md418 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md442 api_key=YOUR_API_KEYCODE
HIGHskills/infographics/scripts/generate_infographic_ai.py1411 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py1412 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/infographics/scripts/generate_infographic.py241 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic.py242 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/paper-lookup/references/core.md15- **Header:** `Authorization: Bearer YOUR_API_KEY`CODE
HIGHskills/paper-lookup/references/core.md16- **Query param:** `?api_key=YOUR_API_KEY`CODE
HIGH…lls/literature-review/scripts/generate_schematic_ai.py910 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py911 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/literature-review/scripts/generate_schematic.py163 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/literature-review/scripts/generate_schematic.py164 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/cirq/references/hardware.md173# export IONQ_API_KEY=your_api_keyCOMMENT
HIGHskills/cirq/references/hardware.md493export IONQ_API_KEY=your_api_keyCODE
HIGHskills/latex-posters/scripts/generate_schematic_ai.py910 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py911 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/latex-posters/scripts/generate_schematic.py163 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/latex-posters/scripts/generate_schematic.py164 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/adaptyv/SKILL.md52ADAPTYV_API_KEY=your_api_keyCODE
HIGHskills/pytorch-lightning/references/logging.md103 api_key="YOUR_API_KEY",CODE
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py910 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py911 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py839 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py840 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/scientific-slides/scripts/generate_schematic.py163 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/scientific-slides/scripts/generate_schematic.py164 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ills/scientific-slides/scripts/generate_slide_image.py155 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/scientific-slides/scripts/generate_slide_image.py156 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/tamarind/SKILL.md59export TAMARIND_API_KEY="your_api_key"CODE
HIGHskills/pennylane/references/devices_backends.md220 api_key='your_api_key'CODE
Modern AI Meta-Vocabulary41 hits · 123 pts
SeverityFileLineSnippetContext
MEDIUMREADME.md673- **[Agentic Data Scientist: An Open Source AI That Actually Does the Analysis](https://www.k-dense.ai/blog/agentic-dataCODE
MEDIUMREADME.md674- **[Karpathy: An Open Source Agentic Machine Learning Engineer](https://www.k-dense.ai/blog/karpathy-agentic-ml-engineeCODE
MEDIUMtests/timesfm-forecasting/test_scripts.py608 # A NaN passed through would poison the whole context window.COMMENT
MEDIUMskills/exploratory-data-analysis/SKILL.md233### 5. Create the report scaffoldCOMMENT
MEDIUMskills/molfeat/references/choosing_a_featurizer.md17# MACCS - Fast, good for scaffold hoppingCOMMENT
MEDIUMskills/molfeat/references/choosing_a_featurizer.md72# MACCS - Fast, scaffold-based similarityCOMMENT
MEDIUMskills/markitdown/references/workflows.md129## 5. RAG IngestionCOMMENT
MEDIUMskills/nextflow/references/developing.md27│ └── mypipeline.nf # the primary workflow (orchestrates subworkflows)CODE
MEDIUMskills/nextflow/references/testing.md23nf-test init # creates nf-test.config + tests/ scaffolding in a projectCODE
MEDIUMskills/nextflow/references/nf-core-tools.md120nf-core pipelines create # scaffoldCODE
MEDIUM…ls/timesfm-forecasting/references/output_and_config.md72 max_context=1024, # Max context window (truncates longer series)CODE
MEDIUMskills/datamol/references/fragments_scaffolds.md3## Scaffolds Module (`datamol.scaffold`)COMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md28# Count scaffold frequencyCOMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md36#### `dm.scaffold.fuzzy_scaffolding(mol, ...)`COMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md45# Group compounds by scaffoldCOMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md58# Group by scaffold and analyze activityCOMMENT
MEDIUMskills/datamol/references/core_workflows.md236# Get Bemis-Murcko scaffold (core structure)COMMENT
MEDIUMskills/datamol/references/core_workflows.md243# Group compounds by scaffoldCOMMENT
MEDIUMskills/datamol/references/core_workflows.md249# Count scaffold frequencyCOMMENT
MEDIUMskills/datamol/references/core_workflows.md253# Create scaffold-to-molecules mappingCOMMENT
MEDIUMskills/datamol/references/workflow_patterns.md55# Group by scaffoldCOMMENT
MEDIUMskills/datamol/references/workflow_patterns.md66# Analyze each scaffold seriesCOMMENT
MEDIUMskills/scholar-evaluation/references/local_tooling.md191## 7. Report scaffoldCOMMENT
MEDIUMskills/market-research-reports/SKILL.md140#### Measurement guardrailsCOMMENT
MEDIUMskills/venue-templates/SKILL.md143### Poster scaffoldCOMMENT
MEDIUMskills/venue-templates/SKILL.md209### Copy and customize a scaffoldCOMMENT
MEDIUM…ills/venue-templates/references/grants_requirements.md98### Bundled NSF scaffoldCOMMENT
MEDIUMskills/scientific-visualization/SKILL.md16## Non-negotiable guardrailsCOMMENT
MEDIUM…lls/hypothesis-generation/references/tool_reference.md210## 7. Preregistration scaffold generatorCOMMENT
MEDIUM…generation/assets/preregistration_scaffold_template.md1# Preregistration scaffold: {{PROJECT_ID}}COMMENT
MEDIUMskills/markdown-mermaid-writing/templates/kanban.md127| [Work item] | [Person] | [Person] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.mCODE
MEDIUMskills/markdown-mermaid-writing/templates/kanban.md138| [Work item] | [Person] | [Date] | [N days] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-mCODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md60| **Resolved in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) orCODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md163**Fixed in:** [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md)CODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md208| **Shipped in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or N/ACODE
MEDIUM…lls/markdown-mermaid-writing/templates/pull_request.md49| **Related issues** | [#ISSUE](../../docs/project/issues/issue-00000001-agentic-documentation-system.md), [#ISSUE2](..CODE
MEDIUMskills/rdkit/references/core_capabilities.md567# Generate Murcko scaffold hashCOMMENT
MEDIUMskills/pylabrobot/references/material-handling.md180## Multi-device orchestrationCOMMENT
MEDIUMskills/optimize-for-gpu/references/cuvs.md430### End-to-End RAG Pipeline ExampleCOMMENT
MEDIUMskills/liteparse/references/output_formats.md141## Layout-aware RAG patternsCOMMENT
MEDIUMskills/peer-review/references/tool_reference.md182## Review scaffold generatorCOMMENT
Verbosity Indicators49 hits · 81 pts
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LOWskills/deeptools/scripts/workflow_generator.py127# Step 2: Coverage assessmentCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py135# Step 3: Fragment size (for paired-end data)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py142# Step 4: ChIP signal strengthCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py368# Step 2: Generate coverage trackCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py378# Step 3: Fragment size analysisCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py385# Step 4: Compute matrix at peaks (if peaks provided)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py106# Step 1: Correlation analysisCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py185# Step 1: Generate normalized coverage tracksCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py208# Step 2: Create log2 ratio trackCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py221# Step 3: Compute matrix around TSSCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py235# Step 4: Generate heatmapCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py248# Step 5: Generate profile plotCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py260# Step 6: Enrichment at peaks (if peaks provided)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py355# Step 1: Shift reads for Tn5 correctionCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh26# Step 1: Preflight checkCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh34# Step 2: Run forecastCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh40# Step 3: Generate visualizationCOMMENT
LOWskills/bioservices/scripts/compound_cross_reference.py346 # Step 1: Search KEGGSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py352 # Step 2: Get KEGG detailsSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py355 # Step 3: Map to ChEMBLSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py358 # Step 4: Get ChEBI detailsSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py363 # Step 5: Get ChEMBL detailsSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py400 # Step 1: Search proteinSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py406 # Step 2: Retrieve sequenceSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py411 # Step 3: BLAST searchSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py416 # Step 4: Pathway discoverySTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py420 # Step 5: Interaction mappingSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py423 # Step 6: GO annotationsSTRING
LOWskills/gget/scripts/batch_sequence_analysis.py67 # Step 1: BLAST each sequenceCOMMENT
LOWskills/gget/scripts/batch_sequence_analysis.py90 # Step 2: Multiple sequence alignmentCOMMENT
LOWskills/gget/scripts/batch_sequence_analysis.py106 # Step 3: Structure prediction (optional)COMMENT
LOWskills/gget/scripts/gene_analysis.py41 # Step 1: Search for the geneCOMMENT
LOWskills/gget/scripts/gene_analysis.py53 # Step 2: Get detailed informationCOMMENT
LOWskills/gget/scripts/gene_analysis.py64 # Step 3: Get sequencesCOMMENT
LOWskills/gget/scripts/gene_analysis.py77 # Step 4: Get tissue expressionCOMMENT
LOWskills/gget/scripts/gene_analysis.py92 # Step 5: Find correlated genesCOMMENT
LOWskills/gget/scripts/gene_analysis.py106 # Step 6: Get disease associationsCOMMENT
LOWskills/gget/scripts/gene_analysis.py119 # Step 7: Get drug associationsCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py63 # Step 1: High-pass filterCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py67 # Step 2: Detect bad channelsCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py75 # Step 3: Phase shift (for Neuropixels 1.0)COMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py80 # Step 4: Common median referenceCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py138 # Step 1: Run optimizationCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py141 # Step 2: Find extreme solutionsCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py144 # Step 3: Compare different preference weightsCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py147 # Step 4: Visualize selections with petal diagramCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py236 # Step 1: Multiple Sequence AlignmentCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py245 # Step 2: Tree InferenceCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py258 # Step 3: VisualizationCOMMENT
Redundant / Tautological Comments27 hits · 36 pts
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LOW…scientific-schematics/scripts/generate_schematic_ai.py792 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/deeptools/scripts/validate_files.py61 # Check if start and end are integersCOMMENT
LOWskills/deeptools/scripts/validate_files.py168 # Check if any files were providedSTRING
LOWskills/deeptools/scripts/validate_files.py180 # Print resultsSTRING
LOWskills/deeptools/scripts/workflow_generator.py478 # Check if workflow was specifiedSTRING
LOWskills/citation-management/scripts/extract_metadata.py55 # Check if URLCOMMENT
LOWskills/timesfm-forecasting/scripts/check_system.py388 # Check if GPU is availableCOMMENT
LOWskills/infographics/scripts/generate_infographic_ai.py1259 # Check if quality is acceptableSTRING
LOW…ills/statistical-analysis/scripts/assumption_checks.py566 # Check if grouped dataCOMMENT
LOWskills/diffdock/scripts/analyze_results.py36 # Check if this is a single complex or batch resultsCOMMENT
LOWskills/diffdock/scripts/prepare_batch_csv.py133 # Check if it's a file path or SMILESCOMMENT
LOWskills/bioservices/scripts/protein_analysis_workflow.py84 # Display resultsCOMMENT
LOW…lls/literature-review/scripts/generate_schematic_ai.py792 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/literature-review/scripts/generate_pdf.py44 # Check if pandoc is installedCOMMENT
LOWskills/deepchem/scripts/predict_solubility.py149 # Display resultsCOMMENT
LOWskills/latex-posters/scripts/generate_schematic_ai.py792 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh13# Check if file argument providedCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh22# Check if file existsCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh93 # Check if file is too large for emailCOMMENT
LOW…lls/scientific-slides/scripts/validate_presentation.py392 # Print resultsSTRING
LOW…lls/scientific-slides/scripts/generate_schematic_ai.py792 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/rdkit/scripts/similarity_search.py288 # Output resultsSTRING
LOWskills/rdkit/scripts/molecular_properties.py131 # Output resultsCOMMENT
LOWskills/stable-baselines3/scripts/custom_env_template.py135 # Check if goal is reachedCOMMENT
LOWskills/pymoo/scripts/many_objective_example.py46 # Print results summaryCOMMENT
LOWskills/pymoo/scripts/single_objective_example.py45 # Print resultsCOMMENT
LOWskills/pymoo/scripts/multi_objective_example.py36 # Print results summaryCOMMENT
AI Slop Vocabulary10 hits · 24 pts
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MEDIUMskills/exploratory-data-analysis/scripts/_tabular.py583 """Compare robust/classical summaries without deleting or transforming data."""STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py173 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…ills/statistical-analysis/scripts/assumption_checks.py186 # Levene's test (robust to non-normality)COMMENT
MEDIUM…ills/statistical-analysis/scripts/assumption_checks.py646 # Run comprehensive checkCOMMENT
MEDIUM…lls/literature-review/scripts/generate_schematic_ai.py173 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/latex-posters/scripts/generate_schematic_ai.py173 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/pyopenms/scripts/accurate_mass_search.py94 # Re-read the mzTab text for a robust flat dump of the SML tableCOMMENT
MEDIUMskills/matplotlib/scripts/plot_template.py322 """Create a comprehensive figure with multiple subplots."""STRING
MEDIUM…lls/scientific-slides/scripts/generate_schematic_ai.py173 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/rdkit/scripts/molecular_properties.py26 """Calculate comprehensive molecular properties."""STRING
Over-Commented Block22 hits · 22 pts
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LOWpyproject.toml21# Required: in prepend/append mode pytest puts tests/ on sys.path, which turnsCOMMENT
LOWtests/skill-requirements.toml1# Per-skill test environments.COMMENT
LOWskills/anndata/references/best_practices.md261 gene_expr = adata.raw[:, 'GENE_NAME'].XCOMMENT
LOWskills/bids/references/conversion_tools.md361#### Step 4: ConvertCOMMENT
LOWskills/bids/references/beps.yml1---COMMENT
LOWskills/autoskill/config.yaml1# autoskill configurationCOMMENT
LOWskills/autoskill/references/screenpipe-config.yaml1# Starter screenpipe configuration for autoskill users.COMMENT
LOW…forecasting/examples/global-temperature/run_example.sh1#!/bin/bashCOMMENT
LOWskills/diffdock/assets/custom_inference_config.yaml61# samples_per_complex: 30COMMENT
LOWskills/diffdock/assets/custom_inference_config.yaml81# PRESET 4: Rigid Ligands (more focused predictions)COMMENT
LOWskills/gget/references/workflows.md561COMMENT
LOWskills/literature-review/references/example_workflow.md41# - Use parallel-cli extract to fetch full content from promising URLsCOMMENT
LOW…ls/literature-review/references/database_strategies.md421# 2. Search bioRxivCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md281# Drug discovery workflow - HIGH-LEVEL ONLY, 3 stagesCOMMENT
LOWskills/pytorch-lightning/scripts/template_datamodule.py321 print(f"Train batches: {len(train_loader)}")COMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py201 # Example 1: Evaluate a trained modelCOMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py221 # watch_agent(COMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py241 # model_path="./models/best_model/best_model.zip",COMMENT
LOWskills/stable-baselines3/scripts/train_rl_agent.py141 algorithm=PPO,COMMENT
LOWskills/stable-baselines3/scripts/train_rl_agent.py161 # algorithm=DQN,COMMENT
LOWskills/stable-baselines3/scripts/custom_env_template.py61 # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...])COMMENT
LOWskills/optimize-for-gpu/references/installation.md21COMMENT
Self-Referential Comments7 hits · 21 pts
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MEDIUMskills/open-notebook/scripts/chat_interaction.py140 # Create a notebook with some content firstCOMMENT
MEDIUMskills/open-notebook/scripts/chat_interaction.py162 # Create a chat sessionCOMMENT
MEDIUMskills/open-notebook/scripts/source_ingestion.py124 # Create a notebook firstCOMMENT
MEDIUMskills/hypogenic/assets/task_config.example.yaml3# This file contains no provider choice, credential, budget, or execution approval.COMMENT
MEDIUMskills/pymoo/scripts/many_objective_example.py19 # Define the problem - DTLZ2 with 5 objectivesCOMMENT
MEDIUMskills/pymoo/scripts/single_objective_example.py21 # Define the problem - Sphere function (sum of squares)COMMENT
MEDIUMskills/pymoo/scripts/multi_objective_example.py18 # Define the problem - ZDT1 (bi-objective)COMMENT
Fake / Example Data10 hits · 11 pts
SeverityFileLineSnippetContext
LOWtests/citation-management/test_scripts.py625 "authorships": [{"author": {"display_name": "Jane Doe"}}],CODE
LOWtests/citation-management/test_scripts.py631 self.assertEqual(record["authors"], "Jane Doe")CODE
LOWtests/citation-management/test_scripts.py641 "type": "preprint", "authors": "Jane Doe", "title": "A Preprint",CODE
LOWtests/pptx-posters/test_scripts.py113 with self.assertRaisesRegex(CliError, "placeholder"):STRING
LOWskills/pptx-posters/references/poster_content_guide.md158The validator rejects common placeholder forms such as TODO, TBD, Lorem ipsum,CODE
LOWskills/scientific-writing/scripts/lint_manuscript.py24 re.compile(r"\blorem ipsum\b", re.IGNORECASE),CODE
LOW…-posters/references/compilation_and_quality_control.md270- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOWskills/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOWskills/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOWskills/dnanexus-integration/scripts/validate_dxapp.py61 "placeholder",CODE
Example Usage Blocks8 hits · 11 pts
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LOWskills/pymc/scripts/model_comparison.py380# Example usageSTRING
LOWskills/pymc/scripts/model_diagnostics.py306# Example usageCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh9# Usage:COMMENT
LOW…ills/statistical-analysis/scripts/assumption_checks.py634 # Example usageCOMMENT
LOWskills/pytorch-lightning/scripts/template_datamodule.py301# Example usageCOMMENT
LOW…pytorch-lightning/scripts/template_lightning_module.py198# Example usageCOMMENT
LOWskills/scikit-learn/scripts/clustering_analysis.py338# Example usageCOMMENT
LOWskills/scikit-learn/scripts/classification_pipeline.py230# Example usageCOMMENT
Synthetic Comment Markers2 hits · 10 pts
SeverityFileLineSnippetContext
HIGHskills/scientific-brainstorming/references/sources.md267bibliographic citations generated by ChatGPT,” *Scientific Reports* 13.CODE
HIGH…ls/latex-posters/references/ai_graphics_for_posters.md80The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE
AI Structural Patterns9 hits · 9 pts
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LOWskills/pkpd-modeling/scripts/ddi_static.py77CODE
LOWskills/research-lookup/scripts/research_lookup.py143CODE
LOWskills/openpiv/scripts/runner.py22CODE
LOWskills/infographics/scripts/generate_infographic_ai.py1102CODE
LOW…ills/scientific-visualization/scripts/figure_export.py149CODE
LOW…ills/scientific-visualization/scripts/figure_export.py323CODE
LOW…lls/scientific-visualization/scripts/image_metadata.py468CODE
LOW…s/neuropixels-analysis/scripts/preprocess_recording.py15CODE
LOWskills/stable-baselines3/scripts/train_rl_agent.py24CODE
Modern Structural Boilerplate8 hits · 8 pts
SeverityFileLineSnippetContext
LOWtests/_contract/__init__.py38__all__ = ["cli", "office", "schematic", "structure"]CODE
LOWskills/pkpd-modeling/scripts/_common.py311__all__ = [CODE
LOWskills/pkpd-modeling/scripts/_models.py654__all__ = [CODE
LOWskills/xlsx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWskills/pptx/scripts/clean.py233def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None:CODE
LOWskills/pptx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWskills/docx/scripts/accept_changes.py14logger = logging.getLogger(__name__)CODE
LOWskills/docx/scripts/office/validators/__init__.py10__all__ = [CODE