Consolidate packaging metadata into pyproject.toml

[dave-doty]

Packaging metadata is spread across four files, three of which are legacy setuptools/distutils formats:

file	contents	status
setup.py	all real metadata: name, version, deps, author, URLs, long_description	imperative, PEP 517 discourages it
setup.cfg	only [metadata] description_file = README.md	dead — setup.py already sets long_description, so this does nothing
MANIFEST	a tracked file whose first line reads # file GENERATED by distutils, do NOT edit	stale build artifact, checked in by accident
doc/requirements.txt	Sphinx docs dependencies	separate file, hand-synced with install_requires

Consolidate all of it into a single declarative PEP 621 pyproject.toml.

Because setup.py goes away, check_pypi_packaging.yml can no longer build with python setup.py sdist bdist_wheel, so it moves to python -m build — the PEP 517 front end release.yml already uses. That subsumes #326, which therefore does not need doing separately.

Where the version lives

Decision: version under [project] in pyproject.toml is the single source of truth, and scadnano.__version__ is read back from the installed distribution's metadata via importlib.metadata. Bumping a release is a one-line edit.

This replaces the previous arrangement, where the truth was a __version__ string literal in scadnano/scadnano.py that setup.py and doc/conf.py each parsed with their own copy of an extract_version() helper that searched for a magic trailing comment and split the line on =.

An earlier draft of this issue proposed keeping the literal in source and having pyproject.toml read it via dynamic + version = {attr = "scadnano.__version__"}. That attribute path was wrong — scadnano/__init__.py does from scadnano.scadnano import *, and import * skips names beginning with an underscore, so scadnano.__version__ did not exist at all. Fixed separately by exporting it explicitly.

Consequence: installation becomes mandatory

Reading the version from distribution metadata means import scadnano requires the package to be installed. Copying scadnano.py into a working directory and importing it with nothing installed — previously a documented, supported workflow — now raises PackageNotFoundError. That is intended: scadnano becomes a normal pip-installed package. It requires retiring that workflow from README.md and CONTRIBUTING.md, and fixing 21 example scripts that import origami_rectangle and modifications as top-level modules (which only resolves when the package directory itself is on sys.path, so those were already broken for every pip-installed user).

Consequence: stale metadata under editable installs

pip install -e . makes the source live, not the metadata. pip writes scadnano-<version>.dist-info/METADATA once, at install time, with the version baked into the directory name. Bump the version without reinstalling and scadnano.__version__ keeps reporting the old value — which is then written into the "version" field of every .sc file produced.

Two ways to handle it were considered:

• A. Detect it. A test asserting scadnano.__version__ equals the pyproject.toml version, turning silent staleness into an immediate failure naming the fix.
• B. Avoid it. Keep the literal in scadnano.py and have pyproject.toml read it via dynamic + attr:. Eliminates the problem entirely, since an editable install reads the live source — but re-enables importing from a bare checkout, undoing the mandatory-install property above.

Going with A. The window is narrow (between bumping and reinstalling), pip install -e . takes seconds, and run_unit_tests.yml installs immediately before running the suite, so the guard cannot fire spuriously in CI.

Also worth fixing while in there

• tests_require is silently ignored. setup.py passes tests_require=['openpyxl'], which setuptools no longer recognizes — it warns UserWarning: Unknown distribution option: 'tests_require' on every build. Becomes a tests extra. Noted previously in check_pypi_packaging.yml uses deprecated python setup.py sdist bdist_wheel #326.
• doc/requirements.txt folds in as a docs extra, so Read the Docs and the Docs Check workflow install one declared list instead of two hand-synced ones.
• MANIFEST should be deleted and gitignored. It is a generated distutils artifact, not MANIFEST.in, and nothing reads it.
• CI never installed the package. run_unit_tests.yml installed only openpyxl and tabulate and relied on the source tree being importable — exactly the workflow being removed. It needs pip install -e .[tests].
• check_pypi_packaging.yml built the artifacts and threw them away. It should install the built wheel into a clean virtualenv and import it from a directory containing no source tree, asserting the version matches and a design serializes. Running from the repo root proves nothing: the flat layout means the checkout shadows the installed package. (A fuller fix for that shadowing is move the package to a src/ layout so tests exercise the installed package #345.)

Verifying the migration

Compare artifacts before and after:

• python -m build produces scadnano-<version>.tar.gz and scadnano-<version>-py3-none-any.whl, and the wheel contains __init__.py, scadnano.py, modifications.py, origami_rectangle.py.
• twine check dist/* passes, confirming the README still renders on PyPI — worth checking explicitly, since long_description_content_type='text/markdown; variant=GFM' carries over into readme.content-type and a mistake there is only visible on the PyPI page.
• Expect metadata to move to the modern PEP 621/639 spellings: Home-page → Project-URL, Author/Author-email combined, License: MIT → License-Expression: MIT. One field is genuinely lost: Download-URL, which was an f-string interpolating the version into a GitHub archive zip. That cannot be expressed in static TOML, and PyPI does not use it.