SSoQE-Reproducible_Analytical_Pipelines

Imported from SSoQE/SSoQE-Reproducible_Analytical_Pipelines (AGENTS.md). Install upstream with npx skills add SSoQE/SSoQE-Reproducible_Analytical_Pipelines. Copyright stays with the author.

SSoQE repository instructions

Canonical revision: 3c2bef030301c329763989b75c20b2c607370b2b

Repository profile: template-lecture

Before substantive work, read the canonical router and its task-relevant core, R, Quarto, branding, and profile modules. Also read the local .ai/repository.md when present. Local guidance may add compatible rules but may not weaken canonical safety, privacy, reproducibility, or branding.

Mandatory baseline

• Treat this as an independent repository. Inspect its instructions, Git status, and established commands before editing.
• Treat implementation as authorization for local unstaged edits only. Never create or switch branches, stage, commit, push, open or edit a pull request, or merge without explicit authorization for that specific action. Permission for one action never authorizes the next.
• Preserve all unrelated tracked and untracked work. Do not disclose private repository names, unpublished information, personal data, or credentials.
• Apply standards prospectively; do not clean up unrelated teaching material.
• For R, prefer tidyverse clarity, native |>, explicit namespaces, snake_case, immutable raw inputs, here::here(), explicit seeds, one reusable function per file, roxygen documentation, and focused tests. Store every .R file under R/ or a suitable subdirectory of R/; never under scripts/. Keep R source lines at or below 80 characters where practical, including R code inside Quarto or R Markdown cells. The limit does not apply to Markdown prose, YAML, or prose paragraphs in .qmd files.
• Do not install packages or restore dependencies during normal analysis or rendering. Do not rely on interactive state.
• SSoQE repositories are R-first. Do not add Python scripts, Python environments, or Python dependencies unless the user explicitly requests an exception for that repository.
• For Quarto, keep each Markdown paragraph on one physical source line, edit source, and use the repository render command. Never hand-edit generated HTML, Markdown, theme files, or copied publication output.
• SSoQE colors are #F2F4F2, #1F2937, #155560, #509A8E, #A1C3B3, and #C2A337; fonts are Plus Jakarta Sans, Space Grotesk, and JetBrains Mono. SSOQE_logo3 is the current SSoQE logo used by the website and lecture materials. Preserve its proportions, colors, and accessible contrast.
• These are technical instructions. Do not invent pedagogical requirements or lesson-stage workflows.

Profile-specific rule

• Render the presentation through the repository wrapper, normally R/render.R. Edit theme JSON and run R/generate_theme.R; do not hand-edit generated theme or publication files.