v0.100.4

Release Notes -- v0.100.4

Released: 2026-10-05

A maintenance release. It fixes a dependency that a clean install was
missing, corrects the torsional energy equation as written in the
documentation, and moves the turtle classes to the standalone turtlend
package. The public API is unchanged and every computed value is the same.

What changed

Clean installs can load the full database. pyarrow was used but never
declared, so Load_PDB_SS(subset=False) failed on a fresh install with
ModuleNotFoundError. It is now a main dependency.

The energy equation in the docs is corrected. The Disulfide docstring
and the DisulfideAnalysis notebook gave the chi5 term a coefficient of 1.0.
The code has always used 2.0 for both chi1 and chi5, so no energy changes;
only the written equation was wrong. The API documentation is regenerated to
match.

Turtle3D, TurtleND and Vector3D now come from turtlend. proteusPy
and WaveRider each carried a copy of these classes; the turtlend package is
now the single source. The old import paths still work, and built structures
are identical to nine decimal places. This also brings in three Turtle3D
fixes made in turtlend.

Repository housekeeping. The kg Poetry group and the FileTreeKG index are
gone, the ruff and pytest floors match the rest of the fleet, the README
gains a version badge and an APA citation, and stale "Last revision" date lines
are removed from source headers.

Upgrading

Run pip install -U proteusPy. The upgrade pulls in turtlend and pyarrow.
No code changes are needed.

---

Full changelog: CHANGELOG.md