Fix audit findings in the deprecated paths, mocks, CI, and README

[rly]

Motivation

A repo-wide Claude Code audit turned up a broken deprecated code path, three CI/test defects, and a set of documentation and packaging errors. This fixes the ones that affect correctness or are cheap and unambiguous.

Correctness

PoseEstimation built from the deprecated nodes and edges arguments could not be written. The Skeleton constructed from them is reachable only from that PoseEstimation object, so the link has no target in the NWBFile and io.write() fails with OrphanContainerBuildError. The constructor now raises with an explanation of what to build instead. Construct mode is unchanged, so files written before ndx-pose 0.2.0, which store nodes and edges on the PoseEstimation group, still read as before.

Making the old path work would require a schema change (a Skeleton child inside PoseEstimation, which the spec does not allow and which conflicts with keeping skeletons in a Skeletons container), so this converts a confusing failure at write time into an actionable one at construction. It is listed under Breaking changes in the CHANGELOG.

An empty devices list no longer raises a DeprecationWarning. An empty list carries no device, so it is not a use of the deprecated behavior.

Tests and CI

• test_example_usage.py runs the examples with sys.executable rather than whatever python resolves to on PATH, from the repository root rather than the working directory, and removes the NWB file even when an example fails. The tests now pass when pytest is invoked from an unrelated directory, which they did not before.
• The Windows wheel installation step sources the venv activation script. Running activate.bat under bash leaves the venv inactive, so the step was installing into and importing from the outer environment, where ndx-pose was already present, and passed unconditionally.
• Checkout no longer fetches full history for tags. The version comes from pyproject.toml; there is no VCS-based versioning.

Fixtures

The default pose_estimation_series of mock_PoseEstimation hold (x, y) positions in pixel space, matching the single camera view a PoseEstimation object represents. They previously held (x, y, z) data labelled pixels. The per-camera views in the MultiCameraPoseEstimation roundtrip test are updated for the same reason.

Packaging and docs

• license is the SPDX expression BSD-3-Clause (PEP 639), with LICENSE.txt in license-files. Verified in the built wheel: License-Expression: BSD-3-Clause, License-File: LICENSE.txt, and the file is bundled under dist-info/licenses/.
• .gitignore negates *.nwb for src/pynwb/tests/back_compat/. Those fixtures are tracked, so a new one would otherwise need git add -f.
• PoseEstimation's class docstring describes the single camera view scoping, matching the schema and README.
• README: the mermaid init directive in both diagrams had a mismatched quote ("primaryBorderColor') that made it invalid; PoseTraining had a stray third angle bracket; MultiCameraPoseEstimation used source_software_version where PoseEstimation used the dataset__attribute form; SkeletonInstance pointed at Skeleton with the containment arrow despite being a link; and the labeled_video link had no relationship line.

Testing

• pytest src/pynwb/tests: 60 passed, 309 subtests passed
• ruff check src/ examples/: passes
• Confirmed by hand that new construction with nodes/edges raises and that 0.1.1_poseestimation_nodes_edges.nwb still reads back its skeleton nodes with no unexpected warnings.

Not included

The audit also flagged items left alone here: the nodes/edges entries in __nwbfields__ being inert, the setters raising ValueError rather than AttributeError, black and ruff both being configured with neither enforced in CI, pre-commit in the dev group with no config, the stale src/matnwb sdist exclusion, the empty [tool.pytest.ini_options], and the unedited ndx-template placeholders in docs/source/.

🤖 Generated with Claude Code