add jabs-cli command for converting jabs pose file to nwb pose file

[gbeane]

Add jabs-cli convert-to-nwb command

Summary

• Adds a new convert-to-nwb subcommand to jabs-cli for converting JABS pose estimation files (any version, v2-v8) to NWB format
• Implements the conversion logic in a new src/jabs/scripts/cli/convert_to_nwb.py module, separate from the Click command wiring in cli.py
• leverages new PoseData->nwb adapter from jabs.io
• Adds per-file ruff ignores (D301, D412) for cli.py to allow Click's \b docstring escape convention for help text formatting

Usage

Convert to a single NWB file (all identities)

jabs-cli convert-to-nwb session_pose_est_v6.h5 session.nwb

Write one NWB file per identity

jabs-cli convert-to-nwb session_pose_est_v6.h5 session.nwb --per-identity

Override the NWB session description

jabs-cli convert-to-nwb session_pose_est_v6.h5 session.nwb --session-description "My experiment"

Notes

• ndx-pose recomends one nwb file per subject. This is specified using the --per-identity option. We also support a non-standard format for including all mice in one nwb file. TODO: investigate ndx-multisubject instead (likely implemented as a follow up pull request).
• Pose format version is auto-detected from the filename (e.g. _pose_est_v6.h5) via the existing open_pose_file factory — no need to specify the version manually
• FPS, scale (cm_per_pixel), static objects, and external identity names are all read directly from the pose file; no manual overrides are needed or exposed
• Optional attributes not present in older formats (static_objects, external_identities, cm_per_pixel) are handled with safe fallbacks so all versions convert cleanly

[Copilot]

Pull request overview

This PR adds a convert-to-nwb subcommand to the jabs-cli tool that converts JABS pose estimation HDF5 files (v2–v8) into NWB format. It separates the conversion logic into convert_to_nwb.py and wires it into the CLI via cli.py, and adds a ruff.toml per-file ignore entry to accommodate Click's \b docstring escape convention.

Changes:

• Adds src/jabs/scripts/cli/convert_to_nwb.py with pose_to_pose_data and run_conversion helpers for converting PoseEstimation objects to PoseData and writing NWB files.
• Registers the new convert-to-nwb Click command in cli.py, wiring up input_path, output, --per-identity, and --session-description parameters.
• Updates ruff.toml with per-file linting ignores (D301, D412) for cli.py to allow Click's \b help-text formatting.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
src/jabs/scripts/cli/convert_to_nwb.py	Core conversion logic: builds PoseData from any PoseEstimation object and calls jabs.io.save
src/jabs/scripts/cli/cli.py	New convert-to-nwb Click command wired to run_conversion
ruff.toml	Per-file ruff ignores to allow Click \b docstring formatting in cli.py

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 12 out of 13 changed files in this pull request and generated 3 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 13 out of 14 changed files in this pull request and generated no new comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 13 out of 14 changed files in this pull request and generated 2 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 14 out of 15 changed files in this pull request and generated 1 comment.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.