Dependency cleanup (PR 1 of 3): packaging truth — extras [extras]/[test]/[dev], drop setup.py and sortedcollections

[DLWoodruff]

This is the first of three PRs implementing the dependency cleanup designed in doc/designs/dependency_cleanup_design.md (included in this PR). Phase 2 will switch the CI runners to install via the new extras; phase 3 will add attempt_import guards to the four opt-in modules that currently crash on import when their optional package is missing.

What this PR does

• Deletes setup.py. It has been dead weight since 0.14.0: pyproject.toml is authoritative (pip, editable installs, and the publish workflow all use it), while setup.py still said version 0.13.2.dev0 with its own diverged dependency lists.

• Drops sortedcollections from the hard dependencies — it is imported nowhere in the repository (leftover from removed code). The true hard dependencies are just numpy and pyomo>=6.4.

• Drops the unused alias extras scipy, pandas, plot (each just installed one identically-named package; nothing in the repo, docs, or CI used them, and pip only warns on unknown extras so stale external installs don't break).

• Adds three purposeful extras (extras may reference other extras of the same project):

  • extras — every pip-safe optional feature of the library itself: scipy (confidence intervals, prox approx, kkt), pandas (rho CSV, wtracker, phtracker), matplotlib (plotting), dill (pickled bundles), mip (MPS/LP/SMPS input).
  • test — extras plus pytest, coverage, addheader (imported by test_headers.py), and gridx-egret (UC tests/examples).
  • dev — test plus doc plus ruff; the contributor one-stop shop: pip install -e ".[mpi,dev]".

  Solvers (cplex/gurobipy/xpress) and proprietary-bridge packages (gams, amplpy) are deliberately in no extra — licensing decisions. mpi4py stays only in [mpi] because pip-installing it fails without an MPI toolchain.

• Updates the install docs (README, quick_start.rst, install_mpi.rst — which now documents what each extra enables — and CLAUDE.md).

Verification

• Fresh venv: pip install --dry-run -e ".[dev]" resolves correctly (all nested extras expand; no sortedcollections).
• pip install -e . --no-deps rebuilds fine without setup.py; import mpisppy and the console scripts work.
• ruff check clean; mpisppy/tests/test_sputils.py passes (136 tests); cd doc && make html builds clean.
• Repo-wide grep: no remaining references to setup.py, sortedcollections, or the dropped alias extras.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.33%. Comparing base (3749661) to head (1051791).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #811   +/-   ##
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  Coverage   76.33%   76.33%           
=======================================
  Files         170      170           
  Lines       22628    22628           
=======================================
  Hits        17274    17274           
  Misses       5354     5354           

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