general

name	general
description	[WHAT] Canonical engineering standards every `scitex-*` package and research project must follow — 3-layer architecture cascade, dependency/version pinning, local-state directory layout (`~/.scitex/<pkg-short>/` and `<project>/.scitex/<pkg-short>/`), repo layout (src/tests/scripts/examples), the five interfaces (Python API → CLI → MCP → Skills → optional HTTP) with their delegation rules and the noun-verb CLI convention, README/Sphinx docs, version-control workflow plus `scitex-dev ecosystem …` release automation, skill-authoring rules (layout, editable-vs-wheel install, public-vs-private), and the periodic quality checklist. Use as the single entry point for creating, auditing, reviewing, or releasing any SciTeX package. [WHEN] Creating, auditing, reviewing, or releasing any SciTeX package, or onboarding a research repo to ecosystem standards. [HOW] Read SKILL.md as the index, then drill into the per-category sub-dirs (`01_ecosystem/`, `02_package/`, `03_interface/`, `04_docs/`, `05_development/`, `09_quality/`), each with its own `SKILL.md` index, for the relevant tier.
tags	["scitex-general"]
user-invocable	false
primary_interface	mixed
interfaces	{"python":"0-3","cli":"0-3","mcp":"0-3","skills":3,"http":0}

SciTeX General Standards

pip install scitex — standards for all ecosystem packages.

(Interface star ratings live on each interface section header below, not in a single summary callout. See 03_interface/04_skills/13_standard-template.md.)

Sub-skills

Read in this order when building or auditing a package. Each section presupposes the ones above it.

Three tiers of concerns:

• §1 — Ecosystem-wide rules (cross-package conventions every scitex-* repo follows): cascade hierarchy, dependency pinning, module-vs-standalone decisions, env-var prefix, re-export bridge, local-state directory layout. Audience: anyone touching any scitex-* package.
• §2–§5 — Per-package concerns (how to build, document, and ship a single scitex-* repo): package layout, the five interfaces (Skills authoring is now §3.4 under Interfaces), docs, release flow. Audience: package authors.
• §8 — Ecosystem quality (cross-package periodic audits): failure playbook, quality checklist. Audience: ecosystem maintainers.

Research-project usage (@stx.session, CONFIG, SDIR_OUT/SDIR_RUN) lives in ../scientific/ — that is research-methodology, not package engineering.

1. Ecosystem-wide rules — what every scitex-* package must follow

• 01_ecosystem/01_upstream-and-downstream.md — 3-layer cascade, test scope, cascade pattern
• 01_ecosystem/02_dependency-and-version-pinning.md — Dependency hygiene, optional extras, version-pinning rules
• 01_ecosystem/03_modules-and-standalone-packages.md — Module vs standalone package boundaries
• 01_ecosystem/04_environment-variables.md — SCITEX_<MODULE_NAME>_* prefix rule; mandates per-package NN_env-vars.md leaf
• 01_ecosystem/05_re-export.md — Umbrella scitex.<name> thin-re-export pattern + lazy-import guard
• 01_ecosystem/06_dot_scitex_directory.md — <project>/.scitex/<pkg-short>/ + ~/.scitex/<pkg-short>/ layout, precedence, SCITEX_DIR, PathManager
• 01_ecosystem/07_license-and-cla.md — AGPL-3.0-only SPDX policy, CLA workflow template, signatures/cla.json shape (object, not bare array), pull_request_target base-branch trap, bootstrap + audit recipes
• 01_ecosystem/08_linter-plugins.md — Each package ships its own lint rules via the scitex_dev.linter.plugins entry point; scitex-dev linter aggregates. Engine in scitex_dev.linter (formerly scitex-linter); rules live next to the API they enforce. Doc-block linting (.md/.rst/.ipynb) and ecosystem-wide lint sweep.
• 01_ecosystem/10_research-project-type.md — project-type: research — research repos are NOT pip packages; the auditor SKIPS publish rules (PyPI/RTD/codecov/badges/CHANGELOG/CLA) and KEEPS the universal ones (RP-2xx scripts↔tests/scripts mirror, TQ/NM, line budgets, audit-all gate). CI = single Python + pytest + scitex-dev linter.

2. Package — how does this scitex-* package's repo live on disk?

Project structure split into one leaf per top-level directory:

• 02_package/01_project-structure-root.md — Repo-root rules, allowed files, forbidden top-level dirs, ./docs/, ./templates/ wheel-vs-git, anti-patterns, pre-release checklist
• 02_package/02_project-structure-src.md — src/<pkg>/ layout, absolute imports, cascade direction (umbrella scitex is the only forbidden import from src/), public/private filename convention
• 02_package/03_project-structure-scripts.md — ./scripts/ for maintenance + scientific analysis (not shipped); graduation to examples/ or src/
• 02_package/04_project-structure-makefile.md — ./scripts/makefile/ per-target dispatcher pattern + canonical target inventory
• 02_package/05_project-structure-examples.md — Numbered examples + _out/ artefacts committed + 00_run_all.sh + matched tests/examples/test_*.py
• 02_package/06_project-structure-tests.md — tests/<pkg>/ mandatory parent, allowed subdirs, public/private mirroring, allowed root meta-tests, audit-project rules
• 02_package/07_github-actions.md — CI, PyPI publish, CLA, reusable workflow patterns
• 02_package/08_quality.md — Repository-level quality (AGPL, Four Freedoms, README rules, GitHub setup)
• 02_package/09_browser-automation-debugging.md — Playwright debug-artifact capture for every browser-automation file (PA-305 rule)
• 02_package/10_dev-venv-isolation.md — Real isolated <pkg-root>/.venv/ per peer (no symlinks to ~/.venv); CI-parity local dev setup; scitex-dev ecosystem install --venv per-package (default)
• 02_package/11_ci-and-codecov.md — CI test.yml + codecov.yml + badge wiring; if: always() so coverage uploads on failure
• 02_package/12_no-mocks.md — No unittest.mock/pytest-mock/monkeypatch, no exceptions; replacement menu (inject + fake → real collaborator → delete); enforced by STX-NM001/002/003 (linter, error) + PA-306 (auditor)
• 02_package/13_test-quality.md — TQ family — every test must satisfy: descriptive name (≥3 words after test_), AAA marker comments (# Arrange/# Act/# Assert in order), exactly one assertion. Enforced by STX-TQ001-007 (linter, error/warning).

3. Interfaces — how do users and agents touch this package?

• 03_interface/00_overview.md — Five interfaces: overview and delegation chain
• 03_interface/01_python-api/ — Minimal API, __all__, lazy imports, NumPy docstrings, version strategy (split into per-section files; start at SKILL.md)
• 03_interface/02_cli/ — Required sub-commands, flags, noun-verb convention, AI-friendly rules (split into per-section files; start at SKILL.md)
• 03_interface/03_mcp/SKILL.md — fastmcp, tool naming, reproducibility, standard commands
• 03_interface/04_skills/ — _skills/ layout, SKILL.md format, registration, export, frontmatter, public-vs-private (split into per-section files; start at SKILL.md)
• 03_interface/05_http-api/ (split into per-section files; start at SKILL.md) — Optional FastAPI delegation

4. Documentation — how does this package become understandable?

• 04_docs/01_readme.md — Standard README template, sections, badges, footer
• 04_docs/02_sphinx.md — Sphinx docs, conf.py, troubleshooting
• 04_docs/03_rtd.md — Read the Docs onboarding, .readthedocs.yaml, build config
• 04_docs/04_robust-ci.md — Robust docs-CI: keep sphinx-build -W strict while defending the 4 benign failure modes (docstring reST noise → suppress_warnings=["docutils"]; GH006 commit-back → continue-on-error; missing-peer autodoc → autodoc_mock_imports; math → sphinx.ext.mathjax)

5. Development — version control, periodic audits, release

• 05_development/01_version-control.md — Branches, tags, release waves, release gates (core workflow)
• 05_development/02_periodic-audits.md — Run audit-all continuously while editing — cron / tmux / agent loops, JSON contract for programmatic consumers, Claude Code CronCreate / ScheduleWakeup / Monitor mechanisms
• 05_development/03_release-automation.md — Automation commands, ecosystem sync CLI, MCP tools, Python API
• 05_development/06_subprocess-coverage.md — Subprocess coverage wiring (parallel + COVERAGE_PROCESS_START + .pth shim) — unlocks 10-20 points when tests spawn python -m children
• 05_development/07_demo-smoke-tests.md — Parametrised smoke test over every _demo_*.py and __main__-bearing _test_*.py module — catches NameError, removed APIs, tuple-unpack bugs
• 05_development/08_coverage-push-playbook.md — End-to-end playbook for taking a package 30% → 90% Codecov without omit shortcuts (subprocess wiring → demo smoke → tree-API feedback → refactor → long-tail unit tests)
• 05_development/09_ecosystem-tq-migration.md — Per-peer migration playbook for the no-mocks + test-quality rules. Canonical four-pass sequence (NM → TQ003 → TQ002 → TQ007), subagent dispatch template, verification gate, common gotchas (importorskip placeholders, smoke-import theater, watchdog tests, state-leak), and the rollback contract.

9. Ecosystem quality — periodic cross-package audits, run when something feels off

• 09_quality/00_crash-early-crash-loud.md — Fail-fast discipline: surface errors immediately and loudly, no silent fallbacks
• 09_quality/01_failure-playbook.md — Severity-tagged cookbook of ecosystem failure modes
• 09_quality/02_checklist.md — Strategic /speak-and-call runbook with append-only log

Scratch

• 40_playground.md — Scratch notes