v0.100.2

Release Notes — v0.100.2

Released: 2026-09-08

A documentation release. The Springer book chapter built on proteusPy is now
published, and this release exists to say so where it matters most: on PyPI.

Why this release exists

pyproject.toml sets readme = "README.md", so the README is rendered as the
project's long description on PyPI — and PyPI does not allow the metadata of an
already-published release to be edited. The 0.100.1 page therefore still
announced the chapter as "going to print" and "in press," and linked the book
DOI, which resolves to a landing page that never names the chapter. Uploading a
new version is the only way to correct that.

No library code changed. Nothing under proteusPy/ differs from v0.100.1,
and no runtime dependency moved, so upgrading changes nothing about how the
package behaves.

What changed

The chapter is published. Structural Analysis of Disulfide Bonds in the
RCSB Protein Data Bank Using proteusPy is out as chapter 2, pp. 15–32, of
Functional Disulphide Bonds: Methods and Protocols, 2nd edition, edited by
Philip J. Hogg (Methods in Molecular Biology, vol. 3016; Springer US / Humana
Press, New York, NY, 2026). Print ISBN 978-1-0716-5157-5, eBook ISBN
978-1-0716-5158-2.

Every citation in the repository now points at the chapter DOI,
10.1007/978-1-0716-5158-2_2. The previously used 10.1007/978-1-0716-5158-2
is the book DOI; it survives only as an explicit book-level SpringerLink
pointer. docs/suchanek_disulfide_chapter_2026.pdf is relabelled from a
pre-publication PDF to the author's accepted manuscript, now that a version of
record exists.

Machine-readable citation. CITATION.cff gains the chapter under
references:, so GitHub's "Cite this repository" panel and downstream citation
tooling surface it alongside the software. preferred-citation is deliberately
unchanged and still names the JOSS paper, which remains the correct citation
for the package itself. CFF 1.2.0 has no book-chapter reference type, so the
entry uses type: generic with the containing work expressed structurally:
collection-title for the series, volume/volume-title for the book, and
section for the chapter. The file validates against the CFF 1.2.0 schema.

Tooling fix. scripts/rebuild-kg.sh called pycodekg build-lancedb, a
subcommand retired along with LanceDB, so the script failed outright on its
second step. It now calls build-index, the sqlite-vec equivalent, which takes
the same --repo/--wipe flags. This is repository tooling and is not part of
the distributed package.

Repository maintenance. The fleet knowledge-graph packages were relocked to
current PyPI versions — doc-kg 0.22.0, pycode-kg 0.23.1, ftree-kg 0.14.0,
with kgmodule-utils 0.18.0 as a transitive resolution. These live in the
optional kg Poetry group, which is dev-only and never ships in the wheel, so
pip install proteusPy is unaffected. .pre-commit-config.yaml gained a
top-level exclude: '^old/', and .gitignore dropped stale lancedb/ rules
that named a path nothing produces since the sqlite-vec migration.

Upgrading

$ pip install --upgrade proteusPy

Nothing to do. There are no API changes, no behavioural changes, and no
migration steps.