The open-source AI workbench for scientific research
This report summarizes scanner evidence for synthetic-sciences/openscience, a TypeScript project with 3,968 GitHub stars. SynthScan examined 1,299,283 lines of code across 4317 source files, recording 4694 pattern matches distributed across 27 syntactic categories. The legacy adjusted pattern signal is 6.9 (Moderate pattern signal); it is not an authorship estimate.
Use the findings to ask whether maintainers can explain intent, verify dependencies, simplify unnecessary scaffolding, and focus review effort. Risk Payload v1 adds ownership, supply-chain, over-engineering, and review-effort vectors when available. These are prompts for human verification, not probabilities, security findings, or measured maintenance costs.
Use each vector to guide manual verification of the underlying findings.
Can maintainers explain intent, assumptions, and trade-offs? 2331 finding(s).
Are imports declared and package/API names verified? 563 finding(s).
Are wrappers, guards, and repeated structures necessary? 2496 finding(s).
Which changes need focused human review? 4694 finding(s).
This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.
Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.
This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.
The scanner identified 4694 distinct pattern matches across 27 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. 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 configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | frontend/workspace/src/science/renderers/index.ts | 19 | // ── renderer registrations ───────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/science/renderers/index.ts | 29 | // ──────────────────────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/components/settings/_shared.tsx | 200 | // ── Toolbar pieces ────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/components/settings/registry.ts | 4 | // ── Panel contract ────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 36 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 38 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 53 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 55 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 90 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 92 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 156 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 158 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 196 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 198 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 426 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 428 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 47 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 49 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 60 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 62 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 113 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 115 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 221 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 223 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 318 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 320 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 656 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 658 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 18 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 20 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 148 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 151 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 343 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 347 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 428 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …istry/analytical-method-validation/scripts/_catalog.py | 430 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 25 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 27 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 43 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 45 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 210 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 212 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 256 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 258 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 451 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 453 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 551 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 553 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 787 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …mistry/analytical-method-validation/scripts/_common.py | 789 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …/chemistry/molecular-docking/scripts/prepare_target.py | 350 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …/chemistry/molecular-docking/scripts/prepare_target.py | 352 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 23 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 25 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 57 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 59 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 70 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 72 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 99 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 101 | # --------------------------------------------------------------------------- | COMMENT |
| 681 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | backend/cli/test/agent/harness-contract.test.ts | 116 | expect(skill).not.toContain("### Step 5: Save Report") | CODE |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 7 | ### Step 1: Choose tokenization algorithm | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 14 | ### Step 2: Prepare training data | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 37 | ### Step 3: Initialize tokenizer | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 94 | ### Step 4: Train | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 114 | ### Step 5: Add post-processing | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 138 | ### Step 6: Save | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 7 | ### Step 1: Prepare corpus | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 19 | ### Step 2: Train model | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 45 | ### Step 3: Load and use | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 9 | ### Step 1: Load and Preprocess Data | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 36 | ### Step 2: Load Model | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 47 | ### Step 3: Define Metrics | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 61 | ### Step 4: Configure Training | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 82 | ### Step 5: Create Trainer and Train | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 103 | ### Step 6: Save Model | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 488 | # Step 1: 2k → 8k | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 491 | # Step 2: 8k → 16k | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 494 | # Step 3: 16k → 32k | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 220 | # Step 1: Find gene ID by name | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 223 | # Step 2: Link gene to pathways | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 226 | # Step 3: Get detailed pathway information | COMMENT |
| LOW | backend/cli/skills/databases/kegg-database/SKILL.md | 241 | # Step 1: List all human pathways | COMMENT |
| LOW | backend/cli/skills/databases/kegg-database/SKILL.md | 244 | # Step 2: For each pathway, get associated genes | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 259 | # Step 1: Search for compound | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 262 | # Step 2: Link compound to reactions | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 265 | # Step 3: Link reactions to pathways | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 268 | # Step 4: Get pathway details | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 279 | # Step 1: Convert KEGG gene IDs to external database IDs | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 283 | # Step 2: Parse conversion results | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 289 | # Step 3: Get sequences using KEGG | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 300 | # Step 1: List pathways for multiple organisms | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 305 | # Step 2: Get reference pathway for comparison | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 308 | # Step 3: Get organism-specific versions | COMMENT |
| LOW | backend/cli/skills/databases/onekgpd/SKILL.md | 221 | # Step 4: For that set of individuals, see the actual variants they carry. | COMMENT |
| LOW⚡ | backend/cli/skills/databases/onekgpd/SKILL.md | 329 | # Step 1: resolve gene -> verified GRCh38 region (authoritative source). | COMMENT |
| LOW⚡ | backend/cli/skills/databases/onekgpd/SKILL.md | 330 | # Step 2: count individuals carrying a qualifying variant in the region. | COMMENT |
| LOW⚡ | backend/cli/skills/databases/onekgpd/SKILL.md | 335 | # Step 3: list those individuals. | COMMENT |
| LOW⚡ | backend/cli/skills/databases/onekgpd/SKILL.md | 340 | # Step 4: for that set of individuals, see the actual variants they carry. | COMMENT |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 64 | # Step 1: Get the download URL | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 91 | # Step 2: Download the file | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 99 | # Step 3: Write to disk | COMMENT |
| LOW | …skills/databases/fred-economic-data/references/tags.md | 411 | # Step 1: Find tags matching the topic | COMMENT |
| LOW | …skills/databases/fred-economic-data/references/tags.md | 428 | # Step 2: Find related tags | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 267 | # Step 1: Search for GEO entries | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 280 | # Step 2: Fetch summaries | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 289 | # Step 3: Fetch full records | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 121 | # Step 1: Search for variants | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 124 | # Step 2: Parse IDs from search results | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 127 | # Step 3: Retrieve summaries | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 130 | # Step 4: Fetch full records if needed | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 154 | # Step 1: Submit similarity search | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 161 | # Step 2: Check status | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 164 | # Step 3: Poll until ready (with timeout) | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 165 | # Step 4: Retrieve results from the same URL | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 307 | # Step 1: Find assays for the target | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 314 | # Step 2: Get active compounds from these assays | COMMENT |
| LOW⚡ | backend/cli/skills/databases/string-database/SKILL.md | 287 | # Step 1: Map gene names to STRING IDs | COMMENT |
| LOW⚡ | backend/cli/skills/databases/string-database/SKILL.md | 291 | # Step 2: Get interaction network | COMMENT |
| LOW⚡ | backend/cli/skills/databases/string-database/SKILL.md | 294 | # Step 3: Test if network is enriched | COMMENT |
| 699 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …et-research-reports/scripts/generate_market_visuals.py | 359 | except Exception as e: | CODE |
| LOW | …s/research/statistical-power/scripts/simulate_power.py | 137 | except Exception: | CODE |
| LOW | …s/research/statistical-power/scripts/simulate_power.py | 171 | except Exception: | CODE |
| LOW | …s/research/statistical-power/scripts/simulate_power.py | 198 | except Exception: | CODE |
| MEDIUM | …ualization/protein-diagram/scripts/draw_contact_map.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …ualization/protein-diagram/scripts/draw_contact_map.py | 75 | print(f"Error: No C-alpha atoms found for chain {args.chain}.", file=sys.stderr) | CODE |
| MEDIUM | …isualization/protein-diagram/scripts/draw_alignment.py | 20 | print("Error: pyMSAviz is required. Install with: pip install pymsaviz", file=sys.stderr) | CODE |
| MEDIUM | …on/protein-diagram/scripts/draw_secondary_structure.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| LOW⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 55 | except Exception: | CODE |
| LOW⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 58 | except Exception as e: | CODE |
| MEDIUM⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 59 | print(f"Error running DSSP: {e}", file=sys.stderr) | CODE |
| MEDIUM | …on/protein-diagram/scripts/draw_secondary_structure.py | 78 | print("Error: No residues found for specified chain.", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 52 | print(f"Error fetching UniProt data for {uniprot_id}: {e}", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 92 | print(f"Error: Cannot parse features from '{features_arg}'.", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 123 | print("Error: Provide either --uniprot or --features.", file=sys.stderr) | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 41 | print(f"Error fetching InterPro data for {uniprot_id}: {e}", file=sys.stderr) | CODE |
| LOW | …sualization/protein-diagram/scripts/draw_domain_map.py | 51 | except Exception: | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 84 | print(f"Error: Cannot parse domains from '{domains_arg}'. Provide a JSON file or inline JSON array.", | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 171 | print("Error: Could not determine protein length. Provide --length.", file=sys.stderr) | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 181 | print("Error: Provide either --uniprot or --domains.", file=sys.stderr) | CODE |
| MEDIUM | …alization/protein-diagram/scripts/draw_ramachandran.py | 22 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …alization/protein-diagram/scripts/draw_ramachandran.py | 95 | print("Error: No phi/psi angles found. Check PDB file and chain ID.", file=sys.stderr) | CODE |
| MEDIUM | …zation/infographics/scripts/generate_infographic_ai.py | 35 | print("Error: requests library not found. Install with: pip install requests") | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 486 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 560 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 688 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 790 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 941 | except Exception as e: | CODE |
| MEDIUM | …zation/infographics/scripts/generate_infographic_ai.py | 1264 | print("Error: OPENROUTER_API_KEY environment variable not set") | STRING |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 1293 | except Exception as e: | STRING |
| MEDIUM⚡ | …alization/infographics/scripts/generate_infographic.py | 178 | print("Error: OPENROUTER_API_KEY environment variable not set") | STRING |
| MEDIUM⚡ | …alization/infographics/scripts/generate_infographic.py | 191 | print(f"Error: AI generation script not found: {ai_script}") | STRING |
| LOW | …alization/infographics/scripts/generate_infographic.py | 228 | except Exception as e: | STRING |
| MEDIUM | …alization/infographics/scripts/generate_infographic.py | 229 | print(f"Error executing AI generation: {e}") | STRING |
| MEDIUM | …sualization/dna-visualization/scripts/draw_gene_map.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …sualization/dna-visualization/scripts/draw_gene_map.py | 26 | print("Error: dna_features_viewer is required. Install with: pip install dna_features_viewer", file=sys.stderr) | CODE |
| MEDIUM | …tion/dna-visualization/scripts/draw_restriction_map.py | 22 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …isualization/dna-visualization/scripts/draw_plasmid.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …isualization/dna-visualization/scripts/draw_plasmid.py | 26 | print("Error: dna_features_viewer is required. Install with: pip install dna_features_viewer", file=sys.stderr) | CODE |
| MEDIUM | …alization/dna-visualization/scripts/draw_gc_content.py | 21 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …alization/dna-visualization/scripts/draw_gc_content.py | 72 | print(f"Error: Sequence length ({seq_len}) is shorter than window size ({args.window}).", | CODE |
| MEDIUM | …zation/dna-visualization/scripts/draw_sequence_logo.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …zation/dna-visualization/scripts/draw_sequence_logo.py | 26 | print("Error: logomaker is required. Install with: pip install logomaker", file=sys.stderr) | CODE |
| LOW | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 497 | except Exception as e: | CODE |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 499 | print(f"Error processing {input}: {e}") | CODE |
| LOW | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 520 | except Exception as e: | CODE |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 493 | def forward(self, input): | CODE |
| MEDIUM | …ugging-face-tool-builder/references/baseline_hf_api.py | 43 | print("Error: limit must be a number", file=sys.stderr) | CODE |
| LOW | backend/cli/skills/llm-tools/crewai/SKILL.md | 252 | except Exception as e: | CODE |
| LOW | backend/cli/skills/llm-tools/crewai/references/flows.md | 288 | except Exception as e: | CODE |
| MEDIUM | backend/cli/skills/llm-tools/crewai/references/flows.md | 283 | def risky_operation(self): | CODE |
| LOW | …/skills/llm-tools/crewai/references/troubleshooting.md | 352 | except Exception as e: | STRING |
| LOW | backend/cli/skills/llm-tools/crewai/references/tools.md | 299 | except Exception as e: | CODE |
| LOW | backend/cli/skills/llm-tools/crewai/references/tools.md | 350 | except Exception as e: | CODE |
| LOW | …ills/llm-tools/langsmith/references/troubleshooting.md | 137 | except Exception as e: | CODE |
| LOW | …ills/llm-tools/langsmith/references/troubleshooting.md | 234 | except Exception as e: | CODE |
| LOW | …ills/llm-tools/langsmith/references/troubleshooting.md | 353 | except Exception as e: | CODE |
| LOW | …ills/llm-tools/langsmith/references/troubleshooting.md | 501 | except Exception as e: | CODE |
| MEDIUM | …ills/llm-tools/langsmith/references/troubleshooting.md | 223 | def safe_evaluator(run, example): | CODE |
| LOW | backend/cli/skills/llm-tools/langchain/SKILL.md | 334 | except Exception as e: | CODE |
| 846 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/harbor/openscience_harbor/agent.py | 344 | def populate_context_post_run(self, context: AgentContext) -> None: | CODE |
| LOW⚡ | tooling/harbor/tests/test_agent.py | 422 | def test_process_failure_is_not_hidden_by_tee(tmp_path, monkeypatch): | CODE |
| LOW⚡ | tooling/harbor/tests/test_agent.py | 431 | def test_reported_version_and_changed_local_binary_fail(tmp_path, monkeypatch): | CODE |
| LOW⚡ | tooling/harbor/tests/test_agent.py | 440 | def test_config_skills_and_explicit_cwd_execute(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 121 | def test_real_harbor_contract(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 132 | def test_delegation_flags_are_validated_and_rendered(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 168 | def test_invalid_delegation_flags_fail_before_setup(tmp_path, kwargs): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 173 | def test_headless_config_and_env(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 215 | def test_skills_none_disables_bundled_catalog(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 222 | def test_trusted_title_override_does_not_mutate_headless_defaults(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 244 | def test_invalid_identity_and_cwd_fail_before_setup(tmp_path, kwargs): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 251 | def test_local_binary_digest_pin(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 263 | def test_native_workdir_remote_log_and_identity(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 296 | def test_delegated_run_writes_child_trajectories_and_counts_their_usage( | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 356 | def test_incomplete_delegated_run_still_counts_child_usage(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 376 | def test_unsupported_workspace_fails_before_agent_execution(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 394 | def test_remote_incomplete_or_failed_events_cannot_use_stale_success( | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 405 | def test_failed_trial_still_reports_spent_usage(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 459 | def test_native_resume_flag_is_scoped_to_resume_call(tmp_path, monkeypatch): | CODE |
| LOW | tooling/harbor/tests/test_agent.py | 471 | def test_release_install_uses_tagged_script_and_forces_checksum(tmp_path): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 27 | def test_parse_skips_stderr_noise_and_blank_lines() -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 32 | def test_fixture_is_the_documented_event_sequence(events: list[dict]) -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 50 | def test_convert_groups_steps_and_keeps_tool_observations(events: list[dict]) -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 127 | def test_failed_tool_calls_are_observed_with_their_error() -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 183 | def test_error_events_and_empty_streams() -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 216 | def test_trajectory_validates_against_harbor(events: list[dict]) -> None: | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 229 | def test_cache_writes_are_prompt_tokens_and_zero_remains_reported_zero(events): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 242 | def test_incomplete_step_keeps_tool_and_reasoning_without_fabricated_totals(events): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 257 | def test_missing_usage_and_mismatched_totals_are_not_reported_as_zero(events): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 271 | def test_repeated_tool_updates_do_not_duplicate_calls_and_unmatched_task_keeps_totals( | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 298 | def test_child_sessions_become_referenced_trajectories_with_rolled_up_usage( | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 406 | def test_child_usage_is_cross_checked_against_the_roll_up(delegated): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 461 | def test_child_matched_from_task_envelope_and_nested_dispatch(delegated): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 581 | def test_child_streams_must_be_balanced_and_tagged(delegated): | CODE |
| LOW | tooling/harbor/tests/test_trajectory.py | 634 | def test_success_requires_valid_terminal_and_root_stream(events, mutate): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 108 | def test_session_workspace_is_explicit_and_validated(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 125 | def test_http_methods_rich_prompt_and_scoping(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 183 | def test_mutation_errors_are_never_retried(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 194 | def test_cursor_errors_are_explicit_for_replay_and_stream(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 210 | def test_sse_reconnect_deduplicates_and_advances_header(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 231 | def test_sse_gap_wrong_session_and_content_type_fail(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 259 | def test_redirects_do_not_forward_credentials(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 270 | def test_capabilities_and_response_limits(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 281 | def test_sse_parser_newlines_identity_and_partial_eof(self): | CODE |
| LOW | tooling/sdk/python/tests/test_client.py | 298 | def test_invalid_inputs_fail_without_network(self): | CODE |
| LOW | tooling/repo/npm-release.ts | 143 | export function nativeReleasePackageNames() { | CODE |
| LOW | tooling/repo/npm-release.ts | 225 | export function createCompiledPackageManifest( | CODE |
| LOW | tooling/repo/npm-release.ts | 387 | export async function verifyPackedModuleExports( | CODE |
| LOW | tooling/repo/npm-release.ts | 548 | export async function verifyPublishedPackageIntegrities(inputs: PackedPackage[], options: NpmCommandOptions = {}) { | CODE |
| LOW | tooling/repo/npm-release.ts | 615 | export async function assertReleaseVersionUnoccupied(version: string, options: NpmCommandOptions = {}) { | CODE |
| LOW | tooling/repo/npm-release.ts | 637 | export async function verifyReleaseOptionalDependencies(artifacts: PackedPackage[], options: NpmCommandOptions = {}) { | CODE |
| LOW | evals/science-harness/prepare.py | 77 | def drugdiscovery_rubrics_populated(clone_dir: Path) -> dict[str, Any]: | CODE |
| LOW | evals/cadence-harness/tree-metrics.ts | 116 | export function aggregateCapturedSessionTree( | CODE |
| LOW | frontend/ui/src/context/marked.tsx | 380 | export function registerOpenScienceDiffTheme(diffs: Pick<DiffsModule, "registerCustomTheme">) { | CODE |
| LOW | frontend/ui/src/components/dropdown-menu.tsx | 182 | function DropdownMenuItemDescription(props: ParentProps<DropdownMenuItemDescriptionProps>) { | CODE |
| LOW | frontend/ui/src/components/dropdown-menu.tsx | 198 | function DropdownMenuItemIndicator(props: ParentProps<DropdownMenuItemIndicatorProps>) { | CODE |
| LOW | frontend/ui/src/theme/resolve.ts | 305 | function generateNeutralAlphaScale(neutralScale: HexColor[], isDark: boolean): HexColor[] { | CODE |
| LOW | frontend/workspace/script/e2e-mode.ts | 62 | export function externalRunnerEnvironment(env: Environment, packaged = false): Record<string, string> { | CODE |
| LOW | frontend/workspace/src/manuscript/publication-review.ts | 221 | export function normalizePublicationReview(format: string, value: unknown): PublicationReviewState { | CODE |
| LOW | frontend/workspace/src/artifacts/bytes.ts | 13 | export function storedArtifactPreviewKind(version: StoredArtifactVersion): StoredArtifactPreview["kind"] | undefined { | CODE |
| 615 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …nd/cli/skills/research/paper-lookup/references/core.md | 15 | - **Header:** `Authorization: Bearer YOUR_API_KEY` | CODE |
| HIGH | …nd/cli/skills/research/paper-lookup/references/core.md | 16 | - **Query param:** `?api_key=YOUR_API_KEY` | CODE |
| HIGH | …zation/infographics/scripts/generate_infographic_ai.py | 1266 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …alization/infographics/scripts/generate_infographic.py | 182 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | backend/cli/skills/llm-tools/dspy/SKILL.md | 301 | api_key="your-api-key", # Or set ANTHROPIC_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/dspy/SKILL.md | 313 | api_key="your-api-key", | CODE |
| HIGH | backend/cli/skills/llm-tools/langsmith/SKILL.md | 54 | export LANGSMITH_API_KEY="your-api-key" | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 45 | export LANGSMITH_API_KEY="your-api-key" | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 48 | LANGSMITH_API_KEY=your-api-key | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 55 | client = Client(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/langchain/SKILL.md | 348 | os.environ["LANGCHAIN_API_KEY"] = "your-api-key" | CODE |
| HIGH | …i/skills/llm-tools/langchain/references/integration.md | 40 | pinecone.init(api_key="your-api-key", environment="us-west1-gcp") | CODE |
| HIGH | backend/cli/skills/llm-tools/guidance/SKILL.md | 281 | api_key="your-api-key" # Or set ANTHROPIC_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/guidance/SKILL.md | 290 | api_key="your-api-key" # Or set OPENAI_API_KEY env var | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 28 | api_key="your-api-key-here" | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 53 | api_key="your-api-key", | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 95 | api_key="your-api-key-here" | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 120 | api_key="your-api-key", | CODE |
| HIGH | backend/cli/skills/llm-tools/pinecone/SKILL.md | 59 | pc = Pinecone(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/qdrant/SKILL.md | 427 | api_key="your-api-key" | CODE |
| HIGH | …/skills/llm-tools/qdrant/references/troubleshooting.md | 117 | api_key="your-api-key" | CODE |
| HIGH | backend/cli/skills/llm-tools/outlines/SKILL.md | 233 | api_key="your-api-key" | CODE |
| HIGH | …d/cli/skills/llm-tools/outlines/references/backends.md | 381 | model = outlines.models.openai("gpt-4o-mini", api_key="your-api-key") | CODE |
| HIGH | …d/cli/skills/llm-tools/outlines/references/backends.md | 393 | api_key="your-api-key", # Or set OPENAI_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/instructor/SKILL.md | 350 | Anthropic(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/instructor/SKILL.md | 368 | OpenAI(api_key="your-api-key") | CODE |
| HIGH | …li/skills/llm-tools/instructor/references/providers.md | 16 | Anthropic(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/databases/uspto-database/SKILL.md | 162 | "X-Api-Key": "YOUR_API_KEY", | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 26 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 123 | data = get_trademark_status("87654321", "YOUR_API_KEY") | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 147 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 240 | xml_data = search_trademark_assignments("5678901", "YOUR_API_KEY") | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 14 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 177 | -H "X-Api-Key: YOUR_API_KEY" \ | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 199 | "X-Api-Key": "YOUR_API_KEY", | CODE |
| HIGH | …ls/databases/gene-database/references/api_reference.md | 191 | api-key: YOUR_API_KEY | CODE |
| HIGH | …cli/skills/databases/database-lookup/references/bea.md | 13 | - Pass as query parameter: `&UserID=YOUR_API_KEY` | CODE |
| HIGH | …ls/databases/database-lookup/references/lincs-l1000.md | 13 | - Pass via header: `user_key: YOUR_API_KEY` | CODE |
| HIGH⚡ | …ls/databases/database-lookup/references/lincs-l1000.md | 36 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | …ls/databases/database-lookup/references/lincs-l1000.md | 40 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | …ls/databases/database-lookup/references/lincs-l1000.md | 44 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | …ls/databases/database-lookup/references/lincs-l1000.md | 48 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH | …li/skills/databases/database-lookup/references/omim.md | 10 | - Pass as query parameter: `?apiKey=YOUR_API_KEY` | CODE |
| HIGH | …skills/databases/database-lookup/references/addgene.md | 10 | Pass as: `Authorization: Token <your_api_key>` | CODE |
| HIGH | backend/cli/skills/databases/fda-database/SKILL.md | 51 | fda = FDAQuery(api_key="YOUR_API_KEY") | CODE |
| HIGH | …databases/fda-database/references/animal_veterinary.md | 93 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …li/skills/databases/fda-database/references/devices.md | 53 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/foods.md | 54 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/drugs.md | 39 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/other.md | 81 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …cli/skills/databases/fda-database/scripts/fda_query.py | 11 | fda = FDAQuery(api_key="YOUR_API_KEY") | STRING |
| HIGH⚡ | backend/cli/skills/databases/pubmed-database/SKILL.md | 142 | "api_key": "YOUR_API_KEY" # Optional but recommended | CODE |
| HIGH⚡ | backend/cli/skills/databases/pubmed-database/SKILL.md | 154 | "api_key": "YOUR_API_KEY" | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 17 | esearch.fcgi?db=pubmed&term=cancer&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 51 | esearch.fcgi?db=pubmed&term=breast+cancer&retmax=100&retmode=json&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 80 | efetch.fcgi?db=pubmed&id=123456,234567&rettype=abstract&retmode=text&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 105 | esummary.fcgi?db=pubmed&id=123456,234567&retmode=json&version=2.0&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 129 | epost.fcgi?db=pubmed&id=123456,234567,345678&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 154 | elink.fcgi?dbfrom=pubmed&db=pubmed&id=123456&cmd=neighbor&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 175 | einfo.fcgi?db=pubmed&retmode=json&api_key=YOUR_API_KEY | CODE |
| 37 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | tooling/sdk/python/tests/test_client.py | 92 | except (BrokenPipeError, ConnectionResetError): | CODE |
| HIGH | backend/cli/test/skill/fixture/database_helpers.py | 234 | except (BrokenPipeError, ConnectionResetError): | CODE |
| HIGH | backend/cli/test/skill/fixture/database_helpers.py | 222 | except (BrokenPipeError, ConnectionResetError): | CODE |
| HIGH | …visualization/protein-diagram/scripts/draw_features.py | 87 | except (FileNotFoundError, IsADirectoryError): | CODE |
| HIGH | …sualization/protein-diagram/scripts/draw_domain_map.py | 77 | except (FileNotFoundError, IsADirectoryError): | CODE |
| HIGH | …cli/skills/databases/ncats-arax/scripts/arax_client.py | 1569 | except OSError: | CODE |
| HIGH | …cli/skills/databases/ncats-arax/scripts/arax_client.py | 1593 | except OSError: | CODE |
| HIGH | …cli/skills/databases/ncats-arax/scripts/arax_client.py | 1588 | except OSError: | CODE |
| HIGH | …core/scientific-visualization/scripts/figure_export.py | 131 | except FileNotFoundError: | CODE |
| HIGH | …kills/core/scientific-visualization/scripts/_common.py | 93 | except FileNotFoundError: | CODE |
| HIGH | …/chemistry/molecular-docking/scripts/prepare_target.py | 264 | except Exception: | CODE |
| HIGH | …chemistry/molecular-docking/scripts/prepare_ligands.py | 146 | except Exception: | CODE |
| HIGH | …chemistry/molecular-docking/scripts/prepare_ligands.py | 126 | except Exception: | CODE |
| HIGH | …chemistry/molecular-docking/scripts/prepare_ligands.py | 297 | except Exception: | CODE |
| HIGH | …chemistry/molecular-docking/scripts/prepare_ligands.py | 178 | except Exception: | CODE |
| HIGH | …chemistry/molecular-docking/scripts/prepare_ligands.py | 291 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 48 | except ImportError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 56 | except ImportError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 68 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 154 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 454 | except OSError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 288 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 440 | except OSError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 500 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 800 | except OSError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 693 | except OSError: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 475 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 273 | except Exception: | CODE |
| HIGH | …li/skills/chemistry/molecular-docking/scripts/score.py | 46 | except ImportError: | CODE |
| HIGH | …li/skills/chemistry/molecular-docking/scripts/score.py | 55 | except ImportError: | CODE |
| HIGH | …ills/chemistry/structure-prediction/scripts/predict.py | 181 | except (ValueError, IndexError): | CODE |
| HIGH | …hemistry/structure-prediction/scripts/predict_batch.py | 134 | except (ValueError, IndexError): | CODE |
| HIGH | …ills/chemistry/structure-prediction/scripts/compare.py | 210 | except (ValueError, IndexError): | CODE |
| HIGH | …ills/chemistry/structure-prediction/scripts/compare.py | 194 | except (ValueError, IndexError): | CODE |
| HIGH | …ills/chemistry/structure-prediction/scripts/compare.py | 199 | except (ValueError, IndexError): | CODE |
| HIGH | …i/skills/chemistry/diffdock/scripts/analyze_results.py | 114 | except Exception: | CODE |
| HIGH | …i/skills/chemistry/diffdock/scripts/analyze_results.py | 103 | except Exception: | CODE |
| HIGH | …cli/skills/chemistry/binding-affinity/scripts/batch.py | 56 | except ImportError: | CODE |
| HIGH | …i/skills/chemistry/binding-affinity/scripts/predict.py | 47 | except ImportError: | CODE |
| HIGH | …skills/chemistry/binding-affinity/scripts/consensus.py | 83 | except ValueError: | CODE |
| HIGH | …skills/chemistry/binding-affinity/scripts/consensus.py | 91 | except ValueError: | CODE |
| HIGH | …nmr-compound-inference/scripts/nmr_candidate_report.py | 110 | except Exception: | CODE |
| HIGH | …/chemistry/molecule-visualization/scripts/render_3d.py | 75 | except Exception: | CODE |
| HIGH | …/chemistry/molecule-visualization/scripts/draw_grid.py | 35 | except ImportError: | CODE |
| HIGH | …ls/chemistry/molecule-visualization/scripts/draw_2d.py | 94 | except Exception: | CODE |
| HIGH | …mistry/molecule-visualization/scripts/draw_scaffold.py | 282 | except Exception: | CODE |
| HIGH | …/chemistry/denovo-design/scripts/generate_fragments.py | 355 | except Exception: | CODE |
| HIGH | …/chemistry/denovo-design/scripts/generate_fragments.py | 353 | except Exception: | CODE |
| HIGH | …/chemistry/denovo-design/scripts/generate_fragments.py | 341 | except Exception: | CODE |
| HIGH | …li/skills/chemistry/pocket-detection/scripts/detect.py | 479 | except Exception: | CODE |
| HIGH | …li/skills/chemistry/pocket-detection/scripts/detect.py | 585 | except Exception: | CODE |
| HIGH | …li/skills/chemistry/pocket-detection/scripts/detect.py | 304 | except Exception: | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 39 | except Exception: | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 110 | except (subprocess.TimeoutExpired, FileNotFoundError, Exception): | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 143 | except (subprocess.TimeoutExpired, FileNotFoundError, Exception): | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 198 | except Exception: | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 194 | except Exception: | CODE |
| HIGH | …er/get-available-resources/scripts/detect_resources.py | 192 | except: | CODE |
| HIGH | …her/labarchive-integration/scripts/entry_operations.py | 104 | except: | CODE |
| HIGH | …lls/coding/timesfm-forecasting/scripts/forecast_csv.py | 164 | except Exception: | CODE |
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| LOW | tooling/harbor/openscience_harbor/trajectory.py | 88 | CODE | |
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| LOW | tooling/harbor/openscience_harbor/trajectory.py | 305 | CODE | |
| LOW | tooling/sdk/python/openscience/client.py | 113 | CODE | |
| LOW | tooling/sdk/python/openscience/client.py | 431 | CODE | |
| LOW | evals/science-harness/campaign.py | 58 | CODE | |
| LOW | …visualization/protein-diagram/scripts/draw_features.py | 96 | CODE | |
| LOW | …sualization/protein-diagram/scripts/draw_domain_map.py | 34 | CODE | |
| LOW | …alization/protein-diagram/scripts/draw_ramachandran.py | 31 | CODE | |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 380 | CODE | |
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| LOW | …ills/databases/uspto-database/scripts/patent_search.py | 252 | CODE | |
| LOW | …s/databases/uspto-database/scripts/trademark_client.py | 226 | CODE | |
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| LOW | …skills/databases/uspto-database/scripts/peds_client.py | 214 | CODE | |
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| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 30 | CODE | |
| LOW | …s/databases/gene-database/scripts/batch_gene_lookup.py | 96 | CODE | |
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| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 301 | CODE | |
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| LOW | …databases/drugbank-database/scripts/drugbank_helper.py | 298 | CODE | |
| LOW | …cli/skills/databases/ncats-arax/scripts/arax_client.py | 609 | CODE | |
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| LOW | …cli/skills/databases/ncats-arax/scripts/arax_client.py | 1187 | CODE | |
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| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 188 | CODE | |
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| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 477 | CODE | |
| LOW | …/skills/databases/fda-database/scripts/fda_examples.py | 144 | CODE | |
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| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 108 | CODE | |
| LOW | …ls/databases/ensembl-database/scripts/ensembl_query.py | 314 | CODE | |
| LOW | …ls/databases/ensembl-database/scripts/ensembl_query.py | 50 | CODE | |
| LOW | …ls/databases/clinpgx-database/scripts/query_clinpgx.py | 41 | CODE | |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 233 | CODE | |
| LOW | …/databases/reactome-database/scripts/reactome_query.py | 241 | CODE | |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 44 | CODE | |
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| LOW | tooling/harbor/openscience_harbor/trajectory.py | 11 | CODE | |
| LOW | tooling/harbor/openscience_harbor/agent.py | 3 | CODE | |
| LOW | tooling/harbor/tests/test_agent.py | 7 | CODE | |
| LOW | tooling/harbor/tests/test_trajectory.py | 4 | CODE | |
| LOW | tooling/harbor/native-smoke/run.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/client.py | 8 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/openscience/__init__.py | 3 | CODE | |
| LOW | tooling/sdk/python/tests/server_conformance.py | 10 | CODE | |
| LOW | tooling/sdk/python/tests/test_client.py | 3 | CODE | |
| LOW | evals/science-harness/run.py | 8 | CODE | |
| LOW | evals/science-harness/campaign.py | 9 | CODE | |
| LOW | evals/science-harness/prepare.py | 8 | CODE | |
| LOW | evals/science-harness/adapters/bixbench3.py | 10 | CODE | |
| LOW | evals/science-harness/adapters/bixbench3.py | 14 | CODE | |
| LOW | evals/science-harness/adapters/researchclaw.py | 15 | CODE | |
| LOW | backend/cli/test/skill/fixture/scientific_integrity.py | 2 | CODE | |
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| LOW | …d/cli/skills/research/paper-lookup/scripts/paginate.py | 28 | CODE | |
| LOW | …cli/skills/research/paper-lookup/scripts/arxiv_atom.py | 21 | CODE | |
| LOW | …nd/cli/skills/research/paper-lookup/scripts/_common.py | 23 | CODE | |
| LOW | …i/skills/research/paper-lookup/scripts/jats_to_text.py | 23 | CODE | |
| LOW | …lls/research/paper-lookup/scripts/openalex_abstract.py | 18 | CODE | |
| LOW | …s/research/statistical-power/scripts/simulate_power.py | 18 | CODE | |
| LOW | …cli/skills/research/statistical-power/scripts/power.py | 27 | CODE | |
| LOW | …cli/skills/research/statistical-power/scripts/power.py | 30 | CODE | |
| LOW | …alization/protein-diagram/scripts/draw_ramachandran.py | 28 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 28 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 29 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 19 | CODE | |
| LOW | …visualization/matplotlib/scripts/style_configurator.py | 20 | CODE | |
| LOW | …ills/visualization/matplotlib/scripts/plot_template.py | 286 | CODE | |
| LOW | …ugging-face-tool-builder/references/baseline_hf_api.py | 9 | CODE | |
| LOW | …ills/databases/uspto-database/scripts/patent_search.py | 20 | CODE | |
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| LOW | …d/cli/skills/databases/onekgpd/scripts/onekgpd_meta.py | 25 | CODE | |
| LOW | …nd/cli/skills/databases/onekgpd/scripts/onekgpd_api.py | 28 | CODE | |
| LOW | …i/skills/databases/gene-database/scripts/query_gene.py | 16 | CODE | |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 14 | CODE | |
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| LOW | …/databases/fred-economic-data/scripts/fred_examples.py | 9 | CODE | |
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| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | backend/cli/AGENTS.md | 28 | ### RAG & Retrieval | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/dspy/SKILL.md | 260 | #### RAG System with Optimization | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 12 | ## RAG Systems | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 14 | ### Basic RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 40 | # Use RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 46 | ### Optimized RAG | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 65 | # Optimize RAG | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 69 | # Optimized RAG performs better on similar questions | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 73 | ### Multi-Hop RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 105 | # Use multi-hop RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 112 | ### RAG with Reranking | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 225 | # Use multi-agent system | COMMENT |
| MEDIUM | …end/cli/skills/llm-tools/dspy/references/optimizers.md | 71 | # Now optimized_qa has learned few-shot examples! | COMMENT |
| MEDIUM | …end/cli/skills/llm-tools/dspy/references/optimizers.md | 433 | # Stage 1: Bootstrap few-shot | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/nemo-guardrails/SKILL.md | 293 | - Docs: https://docs.nvidia.com/nemo/guardrails/ | STRING |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 61 | ### 5-line RAG example | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 202 | ### RAG agent (document search + tools) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 227 | ## Advanced RAG patterns | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 430 | ## Multi-modal RAG | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 469 | # Evaluate faithfulness (no hallucination) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 496 | # Complete RAG pipeline | COMMENT |
| MEDIUM | …kills/llm-tools/llamaindex/references/query_engines.md | 34 | # Combines chunks that fit in context window | COMMENT |
| MEDIUM | …kills/llm-tools/llamaindex/references/query_engines.md | 297 | # 2. context - Simple RAG | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/llamaindex/references/agents.md | 25 | ## RAG agent | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/llamaindex/references/agents.md | 39 | # Agent with RAG + calculator | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/crewai/SKILL.md | 383 | ## Flows - Event-driven orchestration | COMMENT |
| MEDIUM | …/skills/llm-tools/blip-2/references/troubleshooting.md | 354 | ### VQA hallucinations | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 20 | # LangChain - Build LLM Applications with Agents & RAG | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 192 | ## RAG (Retrieval-Augmented Generation) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 194 | ### Basic RAG pipeline | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 236 | ### Conversational RAG with memory | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 241 | # RAG with conversation memory | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 251 | # Multi-turn RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 1 | # LangChain RAG Guide | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 5 | ## What is RAG? | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 17 | ## RAG pipeline components | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 194 | ## Advanced RAG patterns | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 196 | ### Conversational RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 209 | # Conversational RAG chain | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 341 | ## RAG with agents | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 343 | ### Agent-based RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 582 | # Async RAG for concurrent queries | COMMENT |
| MEDIUM | …nd/cli/skills/llm-tools/langchain/references/agents.md | 160 | ### 2. ReAct agent (reasoning trace) | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/guidance/references/backends.md | 415 | # - Avoid large few-shot examples | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 238 | ## RAG integration | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 273 | # RAG retrieval | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 283 | # Use in RAG pipeline | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/whisper/SKILL.md | 252 | # Use transcription in RAG | COMMENT |
| MEDIUM | …kend/cli/skills/core/scientific-visualization/SKILL.md | 26 | ## Non-negotiable guardrails | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/molfeat/SKILL.md | 160 | # MACCS - Fast, good for scaffold hopping | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/molfeat/SKILL.md | 215 | # MACCS - Fast, scaffold-based similarity | COMMENT |
| MEDIUM | …/skills/chemistry/pytdc/scripts/load_and_split_data.py | 196 | # Example 1: Single prediction with scaffold split | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 269 | # Get Bemis-Murcko scaffold (core structure) | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 276 | # Group compounds by scaffold | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 282 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 286 | # Create scaffold-to-molecules mapping | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/datamol/SKILL.md | 551 | # Group by scaffold | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/datamol/SKILL.md | 562 | # Analyze each scaffold series | COMMENT |
| MEDIUM | …ls/chemistry/datamol/references/fragments_scaffolds.md | 3 | ## Scaffolds Module (`datamol.scaffold`) | COMMENT |
| MEDIUM⚡ | …ls/chemistry/datamol/references/fragments_scaffolds.md | 28 | # Count scaffold frequency | COMMENT |
| 44 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …zation/infographics/scripts/generate_infographic_ai.py | 0 | return only a user-owned openrouter key, never a retired product token. | STRING |
| HIGH | …i/skills/core/generate-image/scripts/generate_image.py | 0 | return only a user-owned openrouter key, never a retired product token. | STRING |
| HIGH | …kills/core/schematics/scripts/generate_schematic_ai.py | 0 | return only a user-owned openrouter key, never a retired product token. | STRING |
| HIGH | …g/scientific-slides/scripts/generate_slide_image_ai.py | 0 | return only a user-owned openrouter key, never a retired product token. | STRING |
| HIGH | …ls/chemistry/admet-prediction/scripts/drug_likeness.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …chemistry/admet-prediction/scripts/predict_toxicity.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …ls/chemistry/admet-prediction/scripts/compare_drugs.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …-face-datasets/tests/test_dataset_manager_templates.py | 0 | behavioral tests for bundled dataset helpers; no hub requests. | STRING |
| HIGH | …eering/hugging-face-datasets/tests/test_sql_manager.py | 0 | behavioral tests for bundled dataset helpers; no hub requests. | STRING |
| HIGH | …gging-face-datasets/tests/test_dataset_manager_init.py | 0 | behavioral tests for bundled dataset helpers; no hub requests. | STRING |
| HIGH | …ng/hugging-face-datasets/tests/test_dataset_manager.py | 0 | behavioral tests for bundled dataset helpers; no hub requests. | STRING |
| HIGH | …kills/document-parsing/xlsx/scripts/office/validate.py | 0 | command line tool to validate office document xml files against xsd schemas and tracked changes. usage: python validate. | STRING |
| HIGH | …kills/document-parsing/pptx/scripts/office/validate.py | 0 | command line tool to validate office document xml files against xsd schemas and tracked changes. usage: python validate. | STRING |
| HIGH | …kills/document-parsing/docx/scripts/office/validate.py | 0 | command line tool to validate office document xml files against xsd schemas and tracked changes. usage: python validate. | STRING |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 0 | helper for running libreoffice (soffice) in environments where af_unix sockets may be blocked (e.g., sandboxed vms). det | STRING |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 0 | helper for running libreoffice (soffice) in environments where af_unix sockets may be blocked (e.g., sandboxed vms). det | STRING |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 0 | helper for running libreoffice (soffice) in environments where af_unix sockets may be blocked (e.g., sandboxed vms). det | STRING |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 0 | return a minimal environment for a soffice subprocess. assembled from forwarded_env_vars instead of inheriting the paren | STRING |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 0 | return a minimal environment for a soffice subprocess. assembled from forwarded_env_vars instead of inheriting the paren | STRING |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 0 | return a minimal environment for a soffice subprocess. assembled from forwarded_env_vars instead of inheriting the paren | STRING |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 0 | #define _gnu_source #include <dlfcn.h> #include <errno.h> #include <signal.h> #include <stdio.h> #include <stdlib.h> #in | STRING |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 0 | #define _gnu_source #include <dlfcn.h> #include <errno.h> #include <signal.h> #include <stdio.h> #include <stdlib.h> #in | STRING |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 0 | #define _gnu_source #include <dlfcn.h> #include <errno.h> #include <signal.h> #include <stdio.h> #include <stdlib.h> #in | STRING |
| HIGH | …ocument-parsing/xlsx/scripts/office/validators/docx.py | 0 | validator for word document xml files against xsd schemas. | STRING |
| HIGH | …ocument-parsing/pptx/scripts/office/validators/docx.py | 0 | validator for word document xml files against xsd schemas. | STRING |
| HIGH | …ocument-parsing/docx/scripts/office/validators/docx.py | 0 | validator for word document xml files against xsd schemas. | STRING |
| HIGH | …nt-parsing/xlsx/scripts/office/validators/redlining.py | 0 | validator for tracked changes in word documents. detects untracked edits in word/document.xml: text that differs from th | STRING |
| HIGH | …nt-parsing/pptx/scripts/office/validators/redlining.py | 0 | validator for tracked changes in word documents. detects untracked edits in word/document.xml: text that differs from th | STRING |
| HIGH | …nt-parsing/docx/scripts/office/validators/redlining.py | 0 | validator for tracked changes in word documents. detects untracked edits in word/document.xml: text that differs from th | STRING |
| HIGH | …ocument-parsing/xlsx/scripts/office/validators/pptx.py | 0 | validator for powerpoint presentation xml files against xsd schemas. | STRING |
| HIGH | …ocument-parsing/pptx/scripts/office/validators/pptx.py | 0 | validator for powerpoint presentation xml files against xsd schemas. | STRING |
| HIGH | …ocument-parsing/docx/scripts/office/validators/pptx.py | 0 | validator for powerpoint presentation xml files against xsd schemas. | STRING |
| HIGH | …ocument-parsing/xlsx/scripts/office/validators/base.py | 0 | base validator with common validation logic for document files. | STRING |
| HIGH | …ocument-parsing/pptx/scripts/office/validators/base.py | 0 | base validator with common validation logic for document files. | STRING |
| HIGH | …ocument-parsing/docx/scripts/office/validators/base.py | 0 | base validator with common validation logic for document files. | STRING |
| HIGH | …ment-parsing/xlsx/scripts/office/helpers/pptx_chart.py | 0 | find chart xml that powerpoint refuses but the schema accepts. detection only: for either fault more than one repair is | STRING |
| HIGH | …ment-parsing/pptx/scripts/office/helpers/pptx_chart.py | 0 | find chart xml that powerpoint refuses but the schema accepts. detection only: for either fault more than one repair is | STRING |
| HIGH | …ment-parsing/docx/scripts/office/helpers/pptx_chart.py | 0 | find chart xml that powerpoint refuses but the schema accepts. detection only: for either fault more than one repair is | STRING |
| HIGH | …ment-parsing/xlsx/scripts/office/helpers/pptx_chart.py | 0 | \s*<c:axid\b[^>]*?\bval=["'](-?\d+)["']\s*(?:/>|>\s*</c:axid\s*>) | STRING |
| HIGH | …ment-parsing/pptx/scripts/office/helpers/pptx_chart.py | 0 | \s*<c:axid\b[^>]*?\bval=["'](-?\d+)["']\s*(?:/>|>\s*</c:axid\s*>) | STRING |
| HIGH | …ment-parsing/docx/scripts/office/helpers/pptx_chart.py | 0 | \s*<c:axid\b[^>]*?\bval=["'](-?\d+)["']\s*(?:/>|>\s*</c:axid\s*>) | STRING |
| HIGH | …ment-parsing/xlsx/scripts/office/helpers/pptx_chart.py | 0 | <c:(catax|valax|serax|dateax)\b[^>]*(?<!/)>\s*<c:axid\b[^>]*?\bval=["'](-?\d+)["'] | STRING |
| HIGH | …ment-parsing/pptx/scripts/office/helpers/pptx_chart.py | 0 | <c:(catax|valax|serax|dateax)\b[^>]*(?<!/)>\s*<c:axid\b[^>]*?\bval=["'](-?\d+)["'] | STRING |
| HIGH | …ment-parsing/docx/scripts/office/helpers/pptx_chart.py | 0 | <c:(catax|valax|serax|dateax)\b[^>]*(?<!/)>\s*<c:axid\b[^>]*?\bval=["'](-?\d+)["'] | STRING |
| HIGH | …ment-parsing/xlsx/scripts/office/helpers/pptx_slide.py | 0 | pick the slide-xml schema errors powerpoint refuses the file over. a denylist over lxml's messages, so an unrecognised e | STRING |
| HIGH | …ment-parsing/pptx/scripts/office/helpers/pptx_slide.py | 0 | pick the slide-xml schema errors powerpoint refuses the file over. a denylist over lxml's messages, so an unrecognised e | STRING |
| HIGH | …ment-parsing/docx/scripts/office/helpers/pptx_slide.py | 0 | pick the slide-xml schema errors powerpoint refuses the file over. a denylist over lxml's messages, so an unrecognised e | STRING |
| HIGH | …ment-parsing/xlsx/scripts/office/helpers/pptx_theme.py | 0 | find masters sharing a theme part in the way powerpoint refuses to open. reports only; the fix is to move <p:notesmaster | STRING |
| HIGH | …ment-parsing/pptx/scripts/office/helpers/pptx_theme.py | 0 | find masters sharing a theme part in the way powerpoint refuses to open. reports only; the fix is to move <p:notesmaster | STRING |
| HIGH | …ment-parsing/docx/scripts/office/helpers/pptx_theme.py | 0 | find masters sharing a theme part in the way powerpoint refuses to open. reports only; the fix is to move <p:notesmaster | STRING |
| HIGH | …iology/molecular-cloning/scripts/restriction_digest.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …ills/biology/molecular-cloning/scripts/simulate_pcr.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …lls/biology/molecular-cloning/scripts/design_crispr.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …ls/biology/molecular-cloning/scripts/design_primers.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | tooling/harbor/tests/test_agent.py | 484 | 'test "$1" = --version && test "$2" = 2.0.70 && test "$3" = --no-modify-path\n' | CODE |
| HIGH | …d/cli/skills/research/paper-lookup/scripts/paginate.py | 15 | than sending null; bioRxiv just returns an empty collection) | STRING |
| 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 | …ing/hugging-face-evaluation/scripts/test_extraction.py | 15 | Run from the scripts/ directory: cd scripts && uv run test_extraction.py | STRING |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 70 | print(" macOS: xcode-select --install && brew install cmake") | CODE |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 27 | - Ubuntu/Debian: sudo apt-get update && sudo apt-get install -y build-essential cmake | STRING |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 29 | - macOS: xcode-select --install && brew install cmake | STRING |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/xlsx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/pptx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 165 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 184 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 193 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | …skills/document-parsing/docx/scripts/office/soffice.py | 207 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH | …/biology/treatment-plans/scripts/check_completeness.py | 265 | python check_completeness.py plan.tex && echo "Complete" | CODE |
| HIGH | …ogy/treatment-plans/scripts/validate_treatment_plan.py | 316 | python validate_treatment_plan.py plan.tex && echo "Quality check passed" | CODE |
| HIGH | …s/biology/relsa-severity-assessment/scripts/_common.py | 186 | undefined, which is what ``score_to_percent`` exists to avoid. | STRING |
| HIGH | …li/skills/biology/pacsomatic/scripts/run_pacsomatic.py | 449 | documented shape, e.g. "module purge && module load nextflow/23.10.0". | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …nd/cli/test/skill/image-generation-entrypoints.test.ts | 39 | print(json.dumps({ | CODE |
| HIGH | …nd/cli/test/skill/image-generation-entrypoints.test.ts | 81 | print(json.dumps(errors)) | CODE |
| HIGH | backend/cli/src/file/science.ts | 51 | print(json.dumps({"error": "h5py is not available", "detail": str(exc)})) | CODE |
| HIGH | backend/cli/src/file/science.ts | 172 | print(json.dumps(result)) | CODE |
| HIGH⚡ | backend/cli/src/experiments/sdk.ts | 131 | elif record.get("t") == "finish": | CODE |
| HIGH | backend/cli/src/experiments/sdk.ts | 177 | return None | CODE |
| HIGH | backend/cli/src/experiments/sdk.ts | 179 | return None | CODE |
| HIGH | backend/cli/src/experiments/sdk.ts | 260 | return None | CODE |
| HIGH | backend/cli/src/experiments/sdk.ts | 264 | return True | CODE |
| HIGH | backend/cli/src/cli/ui.ts | 61 | print(...message) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 313 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 319 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 321 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 359 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 362 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 363 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 708 | return None | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 713 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 723 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 726 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 763 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 765 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 767 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 774 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 782 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 920 | elif value["scheduler"] == "pbs": | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1166 | elif action == "submit": submit(token) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1167 | elif action == "status": status(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1168 | elif action == "cancel": cancel(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1169 | elif action == "log": logs(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1170 | elif action == "harvest": harvest(token) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1171 | elif action == "release": release(token) | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 229 | return None | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 260 | return None | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 475 | return False | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 477 | return True | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1036 | elif identifier.startswith("pbs:"): | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1056 | elif not scope_empty(value): | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1233 | print(json.dumps({"staged": True, "files": len(manifest["files"])})) | CODE |
| HIGH | backend/cli/src/tool/biology/notebook.ts | 77 | print(repr(result)) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 44 | List entry identifiers and associated names. Args: database: KEGG database name or specific entry (e.g | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 72 | Search for entries by keywords or molecular properties. Args: database: Database to search ('genes', ' | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 111 | Retrieve full database entries or specific data formats. Args: entries: Single entry ID or list of ent | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 158 | Convert identifiers between KEGG and external databases. Args: target_db: Target database (e.g., 'ncbi | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 187 | Find related entries across KEGG databases. Args: target_db: Target database (e.g., 'pathway', 'enzyme | STRING |
| HIGH | …ls/databases/ensembl-database/scripts/ensembl_query.py | 58 | Make an API request with error handling and retries. Args: endpoint: API endpoint path | STRING |
| HIGH | …skills/databases/string-database/scripts/string_api.py | 29 | Map protein names, synonyms, and identifiers to STRING IDs. Args: identifiers: Single protein identifi | STRING |
| HIGH | …skills/databases/string-database/scripts/string_api.py | 78 | Get protein-protein interaction network data. Args: identifiers: Protein identifier(s) - use STRING ID | STRING |
| HIGH | …ases/opentargets-database/scripts/query_opentargets.py | 22 | Execute a GraphQL query against the Open Targets Platform API. Args: query: GraphQL query string | STRING |
| HIGH | …gineering/hugging-face-datasets/scripts/sql_manager.py | 132 | Execute SQL query on a Hugging Face dataset. Args: dataset_id: Dataset ID (e.g., "cais/mml | STRING |
| HIGH | …gineering/hugging-face-datasets/scripts/sql_manager.py | 350 | Filter and transform dataset with SQL clauses. Args: dataset_id: Dataset ID se | STRING |
| HIGH | …d/cli/skills/ml-training/adaptyv/reference/examples.md | 505 | Request a custom antigen not in the standard catalog Args: target_name: Name of the target protein | STRING |
| HIGH | …d/cli/skills/ml-training/adaptyv/reference/examples.md | 758 | Make API request with retry logic and error handling Args: method: HTTP method (GET, POST, etc.) | STRING |
| HIGH | …kills/biology/clinical-imaging/scripts/hemodynamics.py | 37 | Load blood pressure waveform data from CSV. Accepts CSV with columns 'time' and 'pressure', or just 'pressure' | STRING |
| HIGH | …kills/biology/clinical-imaging/scripts/ciliary_beat.py | 39 | Load video frames as grayscale numpy array. Args: video_path: Path to video file. fps_override | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 46 | Load diffusion-weighted NIfTI image. Args: dwi_path: Path to 4D NIfTI DWI file. Returns: | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 75 | Load binary brain mask NIfTI image. Args: mask_path: Path to 3D NIfTI mask file. Returns: | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 104 | Parse comma-separated b-value string into sorted numpy array. Args: bvalues_str: Comma-separated b-val | STRING |
| HIGH | …ls/biology/clinical-imaging/scripts/amyloid_plaques.py | 46 | Load microscopy image from file. Args: image_path: Path to image file (TIFF, PNG, JPEG, etc.). Re | STRING |
| HIGH | …ls/biology/clinical-imaging/scripts/amyloid_plaques.py | 105 | Threshold grayscale image to produce binary mask. Args: gray: 2D uint8 grayscale image (already smooth | STRING |
| HIGH | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 41 | Load time-series data from CSV. Expected columns: 'time' (hours) and 'value' (measurement). Args: | STRING |
| HIGH | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 99 | Fit cosinor model to data using least-squares optimization. Args: time: 1D array of time points (hours | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/colocalization.py | 38 | Load a single fluorescence channel image as a 2D grayscale array. Args: image_path: Path to the channel ima | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/colocalization.py | 82 | Apply a thresholding method to create a binary mask of signal pixels. Args: image: 2D float array of channe | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/count_colonies.py | 39 | Load an image from disk using OpenCV. Args: image_path: Path to the image file. Returns: numpy | STRING |
| HIGH | …iology/bioimage-analysis/scripts/analyze_morphology.py | 39 | Load a microscopy image from file. Args: image_path: Path to the image file. Returns: numpy.nd | STRING |
| HIGH | …iology/bioimage-analysis/scripts/analyze_morphology.py | 75 | Load a pre-segmented integer label mask. Args: mask_path: Path to the mask image file. Returns: | STRING |
| HIGH | …kills/biology/bioimage-analysis/scripts/track_cells.py | 39 | Load time-lapse frames from a directory of images or a multi-frame TIFF. Args: image_source: Path to a dire | STRING |
| HIGH | …lls/biology/bioimage-analysis/scripts/segment_cells.py | 38 | Load a microscopy image from file. Supports TIFF (via tifffile), PNG, JPEG, and other formats via skimage. Arg | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | backend/cli/test/agent/harness-contract.test.ts | 116 | expect(skill).not.toContain("### Step 5: Save Report") | CODE |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 64 | # Step 1: Get the download URL | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 91 | # Step 2: Download the file | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 99 | # Step 3: Write to disk | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 307 | # Step 1: Find assays for the target | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 314 | # Step 2: Get active compounds from these assays | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 164 | # Step 1: Submit job | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 177 | # Step 2: Poll for completion | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 190 | # Step 3: Retrieve results | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 28 | # Step 1: Find author ID | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 43 | # Step 2: Get works by author | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 74 | # Step 1: Find institution ID | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 89 | # Step 2: Get works from institution | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 234 | # Step 1: Find entity | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 246 | # Step 2: Get statistics | 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/coding/pymoo/scripts/decision_making_example.py | 138 | # Step 1: Run optimization | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 141 | # Step 2: Find extreme solutions | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 144 | # Step 3: Compare different preference weights | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 147 | # Step 4: Visualize selections with petal diagram | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 158 | # Step 2: Save merged model temporarily | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 169 | # Step 3: Install llama.cpp for conversion | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 281 | # Step 6: Upload to Hub | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 121 | # Step 1: Load base model and adapter | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 199 | # Step 4: Convert to GGUF (FP16) | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 223 | # Step 5: Quantize to different formats | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 450 | # Step 1: Replace with optimal codons | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 460 | # Step 2: Remove restriction sites | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 463 | # Step 3: Fix GC content | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 466 | # Step 4: Remove homopolymer runs | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 72 | # Step 2: Coverage assessment | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 80 | # Step 3: Fragment size (for paired-end data) | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 87 | # Step 4: ChIP signal strength | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 307 | # Step 2: Generate coverage track | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 317 | # Step 3: Fragment size analysis | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 324 | # Step 4: Compute matrix at peaks (if peaks provided) | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 51 | # Step 1: Correlation analysis | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 128 | # Step 1: Generate normalized coverage tracks | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 151 | # Step 2: Create log2 ratio track | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 164 | # Step 3: Compute matrix around TSS | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 178 | # Step 4: Generate heatmap | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 191 | # Step 5: Generate profile plot | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 203 | # Step 6: Enrichment at peaks (if peaks provided) | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 294 | # Step 1: Shift reads for Tn5 correction | COMMENT |
| LOW⚡ | …gy/opentrons-integration/scripts/pcr_setup_template.py | 80 | # Step 1: Distribute master mix | COMMENT |
| LOW⚡ | …gy/opentrons-integration/scripts/pcr_setup_template.py | 90 | # Step 2: Add template DNA | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 65 | # Step 1: Add diluent to all wells except first column | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 75 | # Step 2: Add stock solution to first column | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 84 | # Step 3: Perform serial dilution | COMMENT |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 337 | # Step 1: Search KEGG | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 343 | # Step 2: Get KEGG details | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 346 | # Step 3: Map to ChEMBL | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 349 | # Step 4: Get ChEBI details | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 354 | # Step 5: Get ChEMBL details | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 368 | # Step 1: Search protein | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 374 | # Step 2: Retrieve sequence | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 379 | # Step 3: BLAST search | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 383 | # Step 4: Pathway discovery | STRING |
| 19 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/repo/test-shards.ts | 1 | #!/usr/bin/env bun | COMMENT |
| LOW | frontend/workspace/vite.config.ts | 61 | // Molstar has circular re-exports throughout its package. Its three | COMMENT |
| LOW | frontend/workspace/e2e/loading-states.spec.ts | 101 | // itself: the only resource anywhere under it is FdaBanner's own probe, | COMMENT |
| LOW | frontend/workspace/src/utils/persist.ts | 21 | // cache becomes the only store. A single value the quota cannot hold is not | COMMENT |
| LOW | frontend/workspace/src/components/terminal-error.ts | 1 | // When a pty socket dies, WebKit dispatches a bare `error` Event (no detail) | COMMENT |
| LOW | …kspace/src/components/settings/settings-labels.test.ts | 21 | server.ssrLoadModule("solid-js/web") as Promise<typeof import("solid-js/web")>, | COMMENT |
| LOW | frontend/workspace/src/components/settings/registry.ts | 1 | import { lazy, type Component } from "solid-js" | COMMENT |
| LOW | frontend/workspace/src/atlas/poll-identity.ts | 1 | // A polling surface has to name itself to the server. Both compute samplers | COMMENT |
| LOW | frontend/workspace/src/atlas/HostStrip.test.ts | 241 | // which suspends the whole pane until the request resolves. Reading | COMMENT |
| LOW | backend/cli/bunfig.toml | 1 | [test] | COMMENT |
| LOW | backend/cli/test/preload.ts | 61 | COMMENT | |
| LOW | backend/cli/test/config/config.test.ts | 1781 | process.env["OPENSCIENCE_CONFIG_DIR"] = originalConfigDir | COMMENT |
| LOW | backend/cli/test/science/kernel/metrics.test.ts | 461 | COMMENT | |
| LOW | backend/cli/test/science/kernel/metrics.test.ts | 801 | // The grandchild alone holds 64MB the leader never touches, so the | COMMENT |
| LOW | backend/cli/test/tool/question.test.ts | 181 | // intentionally removed the zod validation due to tool call errors, hoping prompting is gonna be good enough | COMMENT |
| LOW | backend/cli/test/tool/question.test.ts | 201 | // test("should throw an Error for label exceeding 30 characters", async () => { | COMMENT |
| LOW | backend/cli/test/session/compaction-edge.test.ts | 761 | expect(await layout(history("m09"))).toEqual(["m03", "m04", "m05", "m06", "m07", "m08", "m09"]) | COMMENT |
| LOW | …d/cli/skills/llm-tools/outlines/references/backends.md | 221 | # - Speed: Slightly slower than Q4 | COMMENT |
| LOW | …databases/drugbank-database/references/drug-queries.md | 181 | # Common properties to extract: | COMMENT |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 41 | COMMENT | |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 61 | # temp_sampling_tor: 6.5 | COMMENT |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 81 | # temp_sampling_rot: 2.0 | COMMENT |
| LOW | …skills/ml-inference/vllm/references/troubleshooting.md | 441 | COMMENT | |
| LOW | …skills/ml-inference/tensorrt-llm/references/serving.md | 161 | curl http://localhost:9090/metrics | COMMENT |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 1 | # /// script | COMMENT |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 1 | # /// script | COMMENT |
| LOW | …d/cli/skills/coding/exploratory-data-analysis/SKILL.md | 321 | # - Data structure | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 1 | #!/bin/bash | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 41 | ### Execute Full Pipeline | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 61 | # - Computed trend: +0.18°C per decade | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 81 | # climate_research/ | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 421 | # - ROC curves | COMMENT |
| LOW | …lls/coding/optimize-for-gpu/references/installation.md | 21 | COMMENT | |
| LOW | …ysics/pymatgen/references/transformations_workflows.md | 301 | relax = MPRelaxSet(slab) | COMMENT |
| LOW | …training/accelerate/references/megatron-integration.md | 421 | # checkpoint-1000/ | COMMENT |
| LOW | backend/cli/skills/ml-training/rwkv/SKILL.md | 141 | ### Workflow 4: RWKV vs Transformer comparison | COMMENT |
| LOW | …/skills/ml-training/gptq/references/troubleshooting.md | 61 | # Requantize with better calibration | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 201 | # Example 1: Evaluate a trained model | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 221 | # watch_agent( | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 241 | # model_path="./models/best_model/best_model.zip", | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 141 | algorithm=PPO, | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 161 | # algorithm=DQN, | COMMENT |
| LOW | …ining/stable-baselines3/scripts/custom_env_template.py | 61 | # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...]) | COMMENT |
| LOW | …gging-face-model-trainer/references/gguf_conversion.md | 61 | ### 3. ✅ Include All Dependencies | COMMENT |
| LOW | …ace-model-trainer/references/reliability_principles.md | 161 | # /// | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 1 | #!/usr/bin/env python3 | COMMENT |
| LOW | …ugging-face-model-trainer/scripts/train_sft_example.py | 1 | #!/usr/bin/env python3 | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1841 | # The name of the chat template to use for training, following values are supported: | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1881 | # message_property_mappings={'role':'role', 'content':'content'}) If a property exists | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1901 | # Roles to train on. The tokens from these roles will be considered for the loss. | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2001 | # will raise an error. This is the default. | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2041 | # 'from' is loaded from input dataset and used as 'role', while 'value' is loaded and | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2061 | # all EOS tokens, turn (default): train on the EOS token at the end of each trainable | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2121 | # `datasets`. The same applies to the `test_datasets` option and the | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2181 | COMMENT | |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2221 | # Mapping of properties from the input dataset to the chat template. (default: | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2241 | temperature: float | None | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2341 | bf16: Literal['auto'] | bool | None = auto | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2381 | max_prompt_len: int | None | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2541 | # sequence into two equal-sized subsequences, or set to 4 to split into four equal-sized | COMMENT |
| 62 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| CRITICAL | evals/launch/capture.ts | 501 | `observable=${result.result.completion.observableComplete ? "complete" : "incomplete"} · ${result.result.observabl | CODE |
| CRITICAL | evals/cadence-harness/run.ts | 293 | jobs = await unwrap<Json[]>(input.client.settings.compute.jobs.list()) | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 94 | subscriptions.push(p.managers.structure.selection.events.changed.subscribe(syncSelection)) | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 95 | subscriptions.push(p.managers.structure.selection.events.additionsHistoryUpdated.subscribe(syncSelection)) | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 96 | subscriptions.push(p.managers.structure.measurement.behaviors.state.subscribe(syncMeasurements)) | CODE |
| CRITICAL | backend/cli/test/session/context-preflight.test.ts | 104 | message.info.error.data.message.includes("No provider request was sent"), | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 658 | core.trainers.grpo.sampler.SequenceParallelRepeatRandomSampler.set_epoch(epoch) | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 1795 | core.trainers.grpo.trainer.AxolotlGRPOSequenceParallelTrainer.get_train_dataloader( | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 4690 | core.trainers.dpo.trainer.AxolotlDPOTrainer.push_to_hub(*args, **kwargs) | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 4892 | core.trainers.mixins.scheduler.SchedulerMixin.create_scheduler( | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 1131 | # Check if quality is acceptable | STRING |
| LOW | …g-face-tool-builder/references/find_models_by_paper.sh | 93 | # Check if the input looks like an arXiv ID (format: YYYY.NNNNN or YYYY.NNNNNNN) | COMMENT |
| LOW | …g-face-tool-builder/references/find_models_by_paper.sh | 133 | # Check if we got a valid response | COMMENT |
| LOW⚡ | …ills/databases/uspto-database/scripts/patent_search.py | 281 | # Print results | COMMENT |
| LOW⚡ | …s/databases/gene-database/scripts/batch_gene_lookup.py | 281 | # Output results | STRING |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 224 | # Check if any keyword matches | COMMENT |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 418 | # Output results | COMMENT |
| LOW⚡ | …ls/databases/brenda-database/scripts/brenda_queries.py | 219 | # Check if our target product is in the products list | COMMENT |
| LOW | …ls/databases/brenda-database/scripts/brenda_queries.py | 589 | # Check if organism might be thermophilic based on name | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 301 | # Check if substrate is in the reactants | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 316 | # Check if product is mentioned in substrate data (limited approach) | COMMENT |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 192 | # Check if it's in the database | COMMENT |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 394 | # Check if current metabolite is a starting material | COMMENT |
| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 40 | # Check if at limit | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 222 | # Check if we've hit max_results | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 226 | # Check if there are more pages | COMMENT |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 158 | # Check if we've reached the max or there are no more results | COMMENT |
| LOW | …kills/core/schematics/scripts/generate_schematic_ai.py | 712 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …i/skills/core/paper-writing/scripts/validate_format.py | 180 | # Print results | COMMENT |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 162 | # Check if input is a file | COMMENT |
| LOW⚡ | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 61 | # Check if DiffDock CLI is available | COMMENT |
| LOW | …ls/chemistry/admet-prediction/scripts/compare_drugs.py | 523 | # Print results | STRING |
| LOW | …i/skills/chemistry/diffdock/scripts/analyze_results.py | 36 | # Check if this is a single complex or batch results | COMMENT |
| LOW | …skills/chemistry/diffdock/scripts/prepare_batch_csv.py | 130 | # Check if it's a file path or SMILES | COMMENT |
| LOW⚡ | …skills/chemistry/binding-affinity/scripts/consensus.py | 131 | # Check if it's rescore or interactions | COMMENT |
| LOW | …kills/chemistry/deepchem/scripts/predict_solubility.py | 150 | # Display results | COMMENT |
| LOW | …kills/chemistry/denovo-design/scripts/generate_sbdd.py | 205 | # Check if this residue matches any specified | COMMENT |
| LOW | …li/skills/chemistry/rdkit/scripts/similarity_search.py | 288 | # Output results | STRING |
| LOW | …skills/chemistry/rdkit/scripts/molecular_properties.py | 131 | # Output results | COMMENT |
| LOW | …li/skills/chemistry/pocket-detection/scripts/detect.py | 735 | # Print results | STRING |
| LOW | …er/get-available-resources/scripts/detect_resources.py | 155 | # Check if running on Apple Silicon | COMMENT |
| LOW | …/other/iso-13485-certification/scripts/gap_analyzer.py | 208 | # Read file content (simple text reading) | COMMENT |
| LOW | …/other/iso-13485-certification/scripts/gap_analyzer.py | 231 | # Check if any keyword appears in the document | COMMENT |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 314 | # Check if majority answer matches original and meets threshold | COMMENT |
| LOW | …ills/other/hugging-face-jobs/scripts/finepdfs-stats.py | 423 | # Print results | STRING |
| LOW | …s/other/labarchive-integration/scripts/setup_config.py | 167 | # Check if config already exists | COMMENT |
| LOW | …end/cli/skills/coding/pymc/scripts/model_comparison.py | 104 | # Check if difference is significant relative to SE | COMMENT |
| LOW⚡ | …lls/coding/timesfm-forecasting/scripts/check_system.py | 388 | # Check if GPU is available | COMMENT |
| LOW | …ding/statistical-analysis/scripts/assumption_checks.py | 453 | # Check if grouped data | COMMENT |
| LOW | …ills/coding/torch_geometric/scripts/visualize_graph.py | 159 | # Check if all edges have their reverse | COMMENT |
| LOW | …/skills/coding/pymoo/scripts/many_objective_example.py | 44 | # Print results summary | COMMENT |
| LOW | …kills/coding/pymoo/scripts/single_objective_example.py | 45 | # Print results | COMMENT |
| LOW | …skills/coding/pymoo/scripts/multi_objective_example.py | 36 | # Print results summary | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 128 | # Check if first column looks like benchmark names | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 138 | # Check if there are numeric values in the table | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 281 | # Check if first column header suggests model names | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 286 | # Check if remaining headers look like benchmarks | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 301 | # Check if data rows have numeric values in most columns (except first) | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 346 | # Check if first column header is empty/generic (indicates benchmarks in rows) | COMMENT |
| LOW | …ining/stable-baselines3/scripts/custom_env_template.py | 135 | # Check if goal is reached | COMMENT |
| LOW | …i/skills/ml-training/pufferlib/scripts/env_template.py | 102 | # Check if episode is done | COMMENT |
| LOW | …ills/biology/synthetic-biology/scripts/gene_circuit.py | 250 | # Check if this is a new steady state | COMMENT |
| LOW | …kills/biology/clinical-imaging/scripts/ciliary_beat.py | 154 | # Check if signal has variance (cilia must be beating) | COMMENT |
| LOW | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 313 | # Print results | STRING |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 61 | # Check if start and end are integers | COMMENT |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 168 | # Check if any files were provided | STRING |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 180 | # Print results | STRING |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 417 | # Check if workflow was specified | STRING |
| LOW⚡ | …/biology/treatment-plans/scripts/check_completeness.py | 295 | # Read file | STRING |
| LOW⚡ | …/biology/treatment-plans/scripts/check_completeness.py | 305 | # Display results | STRING |
| 15 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | evals/cadence-harness/prepare.ts | 162 | `# Better search and parallelism backlog\n\nUpdated after each three-run batch. Items stay here when the trajector | CODE |
| MEDIUM | backend/cli/test/tool/question.test.ts | 187 | // header: "This Header is Definitely More Than Thirty Characters Long", | COMMENT |
| MEDIUM | …et-research-reports/scripts/generate_market_visuals.py | 15 | # Generate all 28 visuals (for comprehensive coverage) | STRING |
| MEDIUM | …ills/visualization/matplotlib/scripts/plot_template.py | 317 | """Create a comprehensive figure with multiple subplots.""" | STRING |
| MEDIUM⚡ | …abases/brenda-database/scripts/brenda_visualization.py | 690 | """Generate a comprehensive set of plots for an enzyme.""" | STRING |
| MEDIUM⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 820 | """Generate a comprehensive pathway report.""" | STRING |
| MEDIUM | …kills/core/schematics/scripts/generate_schematic_ai.py | 115 | # Scientific diagram best practices prompt template | COMMENT |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 423 | "composite_score": entry["score"], # just use raw score | CODE |
| MEDIUM⚡ | …chemistry/admet-prediction/scripts/predict_toxicity.py | 69 | # AMES mutagenicity: comprehensive structural alert library (~30 patterns) | COMMENT |
| MEDIUM | …skills/chemistry/rdkit/scripts/molecular_properties.py | 26 | """Calculate comprehensive molecular properties.""" | STRING |
| MEDIUM | …/other/iso-13485-certification/scripts/gap_analyzer.py | 250 | """Generate comprehensive gap analysis report.""" | STRING |
| MEDIUM | …/other/hugging-face-jobs/scripts/generate-responses.py | 94 | """Create a comprehensive dataset card documenting the generation process.""" | STRING |
| MEDIUM | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 349 | """Create a comprehensive dataset card for a supported method.""" | STRING |
| MEDIUM | …/skills/scholar-evaluation/scripts/calculate_scores.py | 148 | """Generate comprehensive evaluation report.""" | STRING |
| MEDIUM | …ding/statistical-analysis/scripts/assumption_checks.py | 186 | # Levene's test (robust to non-normality) | COMMENT |
| MEDIUM | …ding/statistical-analysis/scripts/assumption_checks.py | 533 | # Run comprehensive check | COMMENT |
| MEDIUM | …ogy/treatment-plans/scripts/validate_treatment_plan.py | 179 | """Display comprehensive validation results.""" | STRING |
| MEDIUM | …/biology/flow-cytometry-analysis/scripts/cell_cycle.py | 122 | # Filter out extreme outliers for robust peak detection | COMMENT |
| MEDIUM | …ology/clinical-reports/scripts/validate_case_report.py | 192 | """Generate comprehensive validation report.""" | STRING |
| MEDIUM | …ls/biology/pharmacology-wetlab/scripts/western_blot.py | 84 | # Simple equal-width fallback (robust for most gel images) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 242 | # Example usage | COMMENT |
| LOW | …databases/drugbank-database/scripts/drugbank_helper.py | 328 | # Example usage | COMMENT |
| LOW⚡ | …abases/brenda-database/scripts/brenda_visualization.py | 752 | # Example usage | COMMENT |
| LOW⚡ | …ls/databases/brenda-database/scripts/brenda_queries.py | 813 | # Example usage | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 1028 | # Example usage | COMMENT |
| LOW | …skills/databases/string-database/scripts/string_api.py | 357 | # Example usage | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 293 | # Example usage | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 325 | # Example usage | COMMENT |
| LOW | …s/databases/chembl-database/scripts/example_queries.py | 254 | # Example usage | COMMENT |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 196 | # Example usage | COMMENT |
| LOW | …ases/opentargets-database/scripts/query_opentargets.py | 370 | # Example usage | STRING |
| LOW | …end/cli/skills/coding/pymc/scripts/model_comparison.py | 358 | # Example usage | STRING |
| LOW | …nd/cli/skills/coding/pymc/scripts/model_diagnostics.py | 268 | # Example usage | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 9 | # Usage: | COMMENT |
| LOW | …ding/statistical-analysis/scripts/assumption_checks.py | 521 | # Example usage | COMMENT |
| LOW | …nd/cli/skills/coding/simpy/scripts/resource_monitor.py | 320 | # Example usage | COMMENT |
| LOW | …lls/coding/scikit-learn/scripts/clustering_analysis.py | 338 | # Example usage | COMMENT |
| LOW | …coding/scikit-learn/scripts/classification_pipeline.py | 230 | # Example usage | COMMENT |
| LOW | …decision-support/scripts/generate_survival_analysis.py | 433 | # Example usage: | COMMENT |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 323 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 375 | # Example usage: | COMMENT |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 412 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 501 | # Example usage: | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | frontend/ui/src/components/select.tsx | 28 | "placeholder", | CODE |
| LOW | …nd/workspace/src/components/prompt-placeholder.test.ts | 25 | expect(source).not.toContain('setStore("placeholder"') | CODE |
| LOW | …rkspace/src/components/settings/network-domain.test.ts | 16 | "user@example.org", | CODE |
| LOW | frontend/docs/test/navigation.test.ts | 27 | expect(resolveLink("mailto:help@example.org", route)).toBe("mailto:help@example.org") | CODE |
| LOW⚡ | backend/cli/test/science/crossref.test.ts | 62 | for (const url of urls) expect(url.searchParams.get("mailto")).toBe("lab@example.org") | CODE |
| LOW⚡ | backend/cli/test/science/crossref.test.ts | 68 | process.env.OPENALEX_MAILTO = "openalex@example.org" | CODE |
| LOW⚡ | backend/cli/test/science/crossref.test.ts | 70 | expect(fallback[0]!.searchParams.get("mailto")).toBe("openalex@example.org") | CODE |
| LOW⚡ | backend/cli/test/science/crossref.test.ts | 73 | process.env.CROSSREF_MAILTO = "crossref@example.org" | CODE |
| LOW⚡ | backend/cli/test/science/crossref.test.ts | 75 | expect(explicit[0]!.searchParams.get("mailto")).toBe("crossref@example.org") | CODE |
| LOW | backend/cli/test/cli/run-attach.test.ts | 65 | const token = "run-attach-dummy-token" | CODE |
| LOW | backend/cli/test/cli/run-attach.test.ts | 188 | for (const supplied of [undefined, "wrong-dummy-token"]) { | CODE |
| LOW | backend/cli/test/cli/run-attach.test.ts | 193 | expect(result.stdout + result.stderr).not.toContain("wrong-dummy-token") | CODE |
| LOW | …nd/cli/test/session/harness-units/deliverables.test.ts | 332 | expect(results["todo.md"][0]).toContain("placeholder") | CODE |
| LOW | backend/cli/skills/llm-tools/dspy/SKILL.md | 363 | print(result.person.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/dspy/references/modules.md | 236 | print(result.person.name) # "John Doe" | CODE |
| LOW | …nd/cli/skills/llm-tools/langchain/references/agents.md | 137 | ("placeholder", "{agent_scratchpad}"), | CODE |
| LOW | backend/cli/skills/llm-tools/outlines/SKILL.md | 83 | print(user.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 75 | print(user.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 641 | "name": "John Doe", | STRING |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 683 | "name": "John Doe", | CODE |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 13 | email="user@example.com", | STRING |
| LOW | …/writing/pptx-posters/assets/poster_html_template.html | 206 | <div id="chart1" class="placeholder" style="width: 100%; height: 400pt;"></div> | CODE |
| LOW | …riting/pptx-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | backend/cli/skills/writing/latex-posters/SKILL.md | 1083 | - [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.) | CODE |
| LOW | …/skills/writing/latex-posters/scripts/review_poster.sh | 179 | echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)" | CODE |
| LOW | …iting/latex-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | backend/cli/src/auth/index.ts | 11 | export const OAUTH_DUMMY_KEY = "synsc-oauth-dummy-key" | CODE |
| LOW | backend/cli/src/harness/deliverables.ts | 34 | const PLACEHOLDER = /\b(?:TODO|TBD|FIXME|placeholder|dummy|lorem ipsum|xxx+|fill me|to be filled|<insert)\b/i | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | …ls/chemistry/molecule-visualization/scripts/draw_2d.py | 106 | # Create the drawer | COMMENT |
| MEDIUM | …ls/chemistry/hypogenic/references/config_template.yaml | 116 | # Define a custom function in your code to parse specific output formats | COMMENT |
| MEDIUM | …ering/hugging-face-datasets/scripts/dataset_manager.py | 55 | # Create a basic README.md with metadata if it doesn't exist | COMMENT |
| MEDIUM | …ering/hugging-face-datasets/scripts/dataset_manager.py | 358 | # Create a newline-delimited JSON string | COMMENT |
| MEDIUM | …ills/coding/torch_geometric/scripts/visualize_graph.py | 155 | # Create a set of edges and reverse edges | COMMENT |
| MEDIUM | …/skills/coding/pymoo/scripts/many_objective_example.py | 19 | # Define the problem - DTLZ2 with 5 objectives | COMMENT |
| MEDIUM | …kills/coding/pymoo/scripts/single_objective_example.py | 21 | # Define the problem - Sphere function (sum of squares) | COMMENT |
| MEDIUM | …skills/coding/pymoo/scripts/multi_objective_example.py | 18 | # Define the problem - ZDT1 (bi-objective) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/sdk/python/openscience/client.py | 306 | CODE | |
| LOW | evals/science-harness/campaign.py | 102 | CODE | |
| LOW | …lls/databases/fred-economic-data/scripts/fred_query.py | 113 | CODE | |
| LOW | …lls/databases/fred-economic-data/scripts/fred_query.py | 162 | CODE | |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 22 | CODE | |
| LOW | …core/scientific-visualization/scripts/figure_export.py | 149 | CODE | |
| LOW | …core/scientific-visualization/scripts/figure_export.py | 323 | CODE | |
| LOW | …ore/scientific-visualization/scripts/image_metadata.py | 468 | CODE | |
| LOW | …i/skills/chemistry/pkpd-modeling/scripts/ddi_static.py | 77 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 541 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 811 | CODE | |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 172 | CODE | |
| LOW | …ills/coding/torch_geometric/scripts/visualize_graph.py | 27 | CODE | |
| LOW | backend/cli/skills/physics/openpiv/scripts/runner.py | 22 | CODE | |
| LOW | …ing/hugging-face-evaluation/scripts/inspect_vllm_uv.py | 49 | CODE | |
| LOW | …g/hugging-face-evaluation/scripts/lighteval_vllm_uv.py | 45 | CODE | |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 24 | CODE | |
| LOW | …ls/biology/molecular-cloning/scripts/design_primers.py | 87 | CODE | |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 416 | CODE | |
| LOW | …y/neuropixels-analysis/scripts/preprocess_recording.py | 15 | CODE | |
| LOW | …s/biology/pharmacology-wetlab/scripts/dose_response.py | 215 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/sdk/python/openscience/__init__.py | 13 | __all__ = [ | CODE |
| LOW | …/cli/skills/chemistry/pkpd-modeling/scripts/_common.py | 311 | __all__ = [ | CODE |
| LOW | …/cli/skills/chemistry/pkpd-modeling/scripts/_models.py | 654 | __all__ = [ | CODE |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 61 | logger = logging.getLogger(__name__) | CODE |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 80 | logger = logging.getLogger(__name__) | CODE |
| LOW | …ills/other/hugging-face-jobs/scripts/finepdfs-stats.py | 53 | logger = logging.getLogger(__name__) | CODE |
| LOW | …ent-parsing/xlsx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | …kend/cli/skills/document-parsing/pptx/scripts/clean.py | 233 | def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None: | CODE |
| LOW | …ent-parsing/pptx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | …skills/document-parsing/docx/scripts/accept_changes.py | 14 | logger = logging.getLogger(__name__) | CODE |
| LOW | …ent-parsing/docx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | backend/cli/skills/ml-training/deepspeed/SKILL.md | 73 | **Pattern 7:** DeepSpeed Configuration JSON Contents Batch Size Related Parameters Optimizer Parameters Scheduler Parame | CODE |
| HIGH | backend/cli/skills/ml-training/pytorch-fsdp/SKILL.md | 35 | **Pattern 2:** Distributed communication package - torch.distributed# Created On: Jul 12, 2017 | Last Updated On: Sep 04 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | backend/cli/skills/writing/latex-posters/SKILL.md | 121 | The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | …/hugging-face-datasets/examples/training_examples.json | 111 | "content": "Great! I've fixed the missing config file issue. Your Node.js app should now start without crashing. | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/sdk/python/tests/test_client.py | 64 | def handle_request(self): | CODE |