chore(deps): strip leaf packages from dependencies, restore extras-only model (closes #326)

[ywatanabe1989]

Summary

Closes #326. Strips the 30+ scitex-* leaf packages from [project].dependencies so pip install scitex becomes core-minimal (8 entries) and the documented scitex[<module>] / scitex[all] opt-in model actually works.

Root cause

[project].dependencies silently grew to 38 entries — every scitex-* leaf was duplicated there alongside its own [project.optional-dependencies].<name> extras entry. Result: every pip install scitex pulled the entire ecosystem as REQUIRED deps, ignoring the documented opt-in model. Network cost, install time, and ABI-tagged C-extension wheel churn for users who only need one module.

Bucket assignments

Operator decisions (Telegram msg 664, 661, 660, 2026-06-09):

Core ([project].dependencies) — 8 entries:

• numpy / pandas / PyYAML / tqdm / packaging / natsort — every scitex helper touches at least one; near-universal in the Python scientific stack.
• scitex-config==0.3.6 — env / config loader (scitex.helpers.load_scitex_env delegates here; required even before any module is imported).
• scitex-dev>=0.17.8 — operator-confirmed core: "コアに scitex-dev は必要だと思います、サイテクスコンフィグあればどうせ入りますが" (Telegram msg 664). Pulls in the audit / skill discovery machinery + the project's quality-rule corpus.

Moved to [project.optional-dependencies]:

• All scitex-* leaves (~30 packages): each already had a <name> extra entry. 7 of them (benchmark, context, cv, introspect, msword, os, tex) were inconsistently missing their own wheel pin — added here so pip install scitex[benchmark] actually installs scitex-benchmark.
• bs4 / beautifulsoup4 — only used by helpers/_optional_deps.py check_optional_deps wrapper for the scholar stack; already declared in [scholar] / [io] where it's actually needed (operator confirmed: "コア不要、optional 扱い").
• figrecipe / scitex-ui — already in [plt] / [ui] extras.

[all] extra unchanged — already aggregates via scitex[<name>] self-references, so pip install scitex[all] still produces the bare-equivalent of the pre-refactor install for users who want everything.

Test plan

• CI pytest matrix (3.11/3.12/3.13) installs via pip install -e ".[all,dev]" (already the existing fallback chain); should still resolve the same wheel set.
• pip install scitex on a fresh venv resolves only the 8 core entries (verify the size shrink).
• pip install scitex[stats,io] resolves the documented per-module extras.
• scitex.helpers.load_scitex_env() still works (scitex-config in core).
• scitex-dev CLI still discoverable post-install (scitex-dev in core).
• Lazy-attrs imports like scitex.audio, scitex.cv, etc. raise a friendly ImportError pointing at pip install scitex[<name>] when the corresponding extra is not installed (verified via _AVAILABLE flags + existing _install_guide.py).

Notes

• DRAFT — operator-SSoT repo; NOT merging. Operator reviews the bucket assignments + merges when ready. Lead-confirmed flow: PR open only, no auto-merge on scitex-python.
• Companion PR chore(deps): bump scitex-dev pin to >=0.17.8 (stop CI flood) #323 (scitex-dev pin bump to >=0.17.8) and PR ci(quality): scitex-io simple template — audit target = scitex (stop CI flood) #325 (umbrella quality workflow → scitex-io simple template) are sibling fixes from the same 2026-06-09 CI flood triage.
• Library-side 0.17.8 PR (PS-170 warn-only + load_registry triple-path): fix(audit): CI 0.17.8 emergency — PS-170 warn-only + load_registry triple-path scitex-dev#146