smappy-microclaw

SMAPpy's single-molecule localization fitting as a MicroClaw skill package: MicroClaw acquires, and SMAPpy fits the dataset as it is written, with the reconstruction growing in SMAPpy's own window.

operation	what it does
self_check	fits simulated frames and builds SMAPpy's GUI offscreen; run by MicroClaw at install
fit_and_view	opens SMAPpy on the dataset with the fit running (opens_window, protocol 1.1); the window stays open after the job
fit_ndtiff	the same fit without a window, for a computer without a desktop

Both fits write locs.hdf5 to the job's output folder, wait out pauses in the acquisition, and finish when MicroClaw says the writer is done. What the agent is told is in package/SKILL.md; the parameters are in package/manifest.json.

Layout

package/                     the release, zipped as it is
  manifest.json              source manifest (pack adds artifact, assets, locks)
  SKILL.md                   what MicroClaw's agent reads
  smappy_microclaw/
    runner.py                the microclaw.analysis.v1 protocol, stdlib only
    fitting.py               parameters onto SMAPpy's fitters, the camera check
locks/pylock.win_amd64.toml  the environment MicroClaw installs
requirements.in              what the lock is compiled from
tests/                       the worker driven as MicroClaw drives it

The fit itself is SMAPpy's: smappy.gui.live_session (the GUI on a fit another program controls) and the Fit plugins' Context.stop and writer_finished. This package is only the protocol and the mapping.

Developing

pip install -e ../SMAPpy            # or smappy-smlm from PyPI
PYTHONPATH=../microclaw python -m pytest tests -q -n 4

microclaw must be importable for the tests: every line the worker prints is checked with MicroClaw's own validate_worker_message.

The lock, after a change to requirements.in:

uv pip compile --no-config --python-version 3.12 --python-platform x86_64-pc-windows-msvc requirements.in -o locks/pylock.win_amd64.toml

Releasing

Bump version in package/manifest.json, push the tag v<version>; the release workflow packs, signs (MICROCLAW_PUBLISHER_KEY) and publishes package.zip and release.json, and release.json then goes to Micro-Claw/package-catalog by PR. See MicroClaw's publishing guide.