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scripts/ - Quick Reference

Root-level scripts are generic orchestrators for the research pipeline. They coordinate setup, tests, analysis, rendering, validation, copying, LLM review, and executive reporting without implementing project-specific business logic.

Entry Points

Shell

./run.sh
./run.sh --pipeline --resume
./run.sh --all-projects --pipeline
./secure_run.sh --project code_project

Python

uv run python scripts/execute_pipeline.py --project code_project --core-only
uv run python scripts/execute_multi_project.py --no-llm
uv run python scripts/07_generate_executive_report.py

Pipeline Stages

Stage Script Responsibility
00 00_setup_environment.py Validate Python, dependencies, build tools, and directories
01 01_run_tests.py Run infrastructure and project tests with coverage gates
02 02_run_analysis.py Discover and run projects/{name}/scripts/
03 03_render_pdf.py Render manuscripts to PDF
04 04_validate_output.py Validate PDFs, markdown, and integrity reports
05 05_copy_outputs.py Copy final deliverables to output/
06 06_llm_review.py Generate LLM reviews or translations when Ollama is available
07 07_generate_executive_report.py Build multi-project executive summaries and dashboards

execute_pipeline.py also supports single-stage execution with keys such as setup, tests, analysis, render_pdf, validate, copy, llm_reviews, llm_translations, and executive_report.

Key Files

  • bash_utils.sh - shared shell helpers used by run.sh and secure_run.sh
  • execute_pipeline.py - single-project pipeline runner
  • execute_multi_project.py - multi-project pipeline runner
  • generate_active_projects_doc.py - regenerates docs/_generated/active_projects.md
  • audit_filepaths.py - repository filepath and reference audit
  • organize_executive_outputs.py - reorganizes executive report outputs by file type
  • manage_workspace.py - workspace management helper
  • show_project_info.py - project metadata helper (used by run.sh interactive menu)
  • verify_no_mocks.py - checks tests for mock usage

Output Names

  • projects/{name}/output/reports/pipeline_report.{json,html,md}
  • projects/{name}/output/reports/test_results.{json,md}
  • projects/{name}/output/reports/validation_report.{json,md}
  • projects/{name}/output/reports/log_summary.txt
  • output/executive_summary/consolidated_report.{json,html,md}
  • output/executive_summary/dashboard.{png,pdf,html}

Notes

  • Project-specific analysis scripts belong in projects/{name}/scripts/.
  • The root scripts stay generic and work with any active project discovered from projects/.
  • Use uv run for the Python entry points.

See Also