Add GeRM detector mock class, plus unit tests for GeRM detector and all edxd scans by jwlodek · Pull Request #109 · NSLS2/hextools

Jakub Wlodek (jwlodek) · 2026-10-23T17:12:35Z

No description provided.

…ll edxd scans

pixi.lock re-solved from main's lock for the merged pixi.toml (keeps main's pins, e.g. ntnda-qt-viewer 778e714). Assisted-by: copilot:claude-opus-5-5

… scans Jakub: the sweep on main is correct, so edxd_calib_scan is back to main's version apart from its EdxdCalibration tiled_specs, and its tests follow main's behaviour (the zero-span check went with the reverted sweep). The calibration fixture puts z1's starting velocity rather than mocking it: the plan restores the velocity's setpoint, which a mocked value leaves at 0 (on the IOC, VELO's setpoint is its value). The auto-exporter now exports EdxdCalibration runs with export_edxd_run_to_h5, the same layout as EDXD scans; before, calibration runs logged 'no exporter registered'. Assisted-by: copilot:claude-opus-5-5

Anthony Sligar (sligara7) · 2026-10-28T21:14:19Z

Updated (AJ asked):

Merged main (177a274); pixi.lock re-solved from main's lock for the merged pixi.toml, so main's pins stay (e.g. ntnda-qt-viewer 778e714).
edxd_calib_scan is back to main's sweep, as you said; only its EdxdCalibration tiled_specs remains from this PR. The calib tests follow main's behaviour, and the zero-span test went with the old sweep. The fixture now puts z1's starting velocity: reset_positions_decorator restores the velocity's setpoint, which a mocked value leaves at 0 in mock mode (on the IOC the setpoint is the PV value).
Calibration runs now export with export_edxd_run_to_h5 (same layout as EDXD scans): EXPORTERS had no EdxdCalibration entry, so they logged "no exporter registered".

Full suite passes against the locked deps (mock only).

Copilot

🟡 Changes recommended

Critical sweep-timing and mock-file reuse defects can falsely mark partially unmeasured calibrations as successful and cause later runs to reference earlier runs’ frames.

3 open issues

What changed in this PR

Adds a file-writing GeRM detector mock and broad EDXD test coverage, supporting simulated acquisition and GUI use without hardware.

Changes:

Simulates GeRM spectra, file output, shutter gating, and live frames.
Adds EDXD metadata and revises calibration sweeps and state restoration.
Improves GUI history, plotting, narration, and development environments.

File	Description
`tests/tomography/test_radiography.py`	Uses shared detector-state setup.
`tests/test_nl_msg_hook.py`	Tests checkpoint deduplication and message handling.
`tests/test_edxd.py`	Adds coverage for EDXD plans and cleanup.
`tests/gui/test_plan_history.py`	Tests history persistence, clearing, and default paths.
`tests/detectors/test_phantom.py`	Uses shared detector-state setup.
`tests/detectors/test_germ.py`	Tests mock spectra, files, callbacks, and shutters.
`tests/conftest.py`	Adds GeRM and shared environment fixtures.
`src/hextools/utils/nl_msg_hook.py`	Deduplicates checkpoints and accepts raw or serialized messages.
`src/hextools/profiles/collection.py`	Configures mock storage and interactive session behavior.
`src/hextools/gui/plan_status.py`	Adds plot toolbars and history clearing.
`src/hextools/gui/misc/tabbed_detectors_widget.py`	Adds direct frame delivery to viewers.
`src/hextools/gui/__main__.py`	Connects mock frames and enables default history persistence.
`src/hextools/edxd.py`	Adds Tiled specs and revises calibration motion.
`src/hextools/detectors/germ.py`	Implements the GeRM acquisition mock.
`pixi.toml`	Consolidates GUI dependencies and task defaults.
`docs/getting_started.md`	Updates environment and task instructions.
`docs/developer.md`	Simplifies development commands.
`.github/workflows/ci.yml`	Uses the configured type-check task.

_{Review effort: Balanced}

Copilot

🟡 Changes recommended

Disabling test pulses mid-acquisition erases previously collected pulse counts from subsequent updates and the saved frame, creating a critical data-integrity defect.

6 open issues

_{Review effort: Balanced}

…est jobs GeRM mock: the last step sleeps only the remaining exposure; test pulses accumulate with the settings active in each step, so turning them off mid-count keeps the pulses already counted. --mock: the GeRM viewer is built in callback mode (push_frame), so it never subscribes to the real GeRM PV, and frames reach viewers through push_frame, which drops them while stopped. Profile: %mov/%movr (HEXBlueskyMagics) put back RE.waiting_hook, so the GUI's progress bars survive them; mock detectors get UUID file names, so two runs in one second cannot share a file. CI: with the GUI extra now in the py3xx envs, tests/gui ran in the unit-test jobs too, where a GUI test's IPython shell broke test_resume_button_resumes_a_paused_plan[shell] and leftover Qt objects segfaulted test_dclm on 3.12; tests/gui runs only in the GUI job again. Assisted-by: copilot:claude-opus-5-5

Copilot

🔵 Needs a closer look

The tests and coverage tasks run GUI and non-GUI suites in one process, retaining the documented Qt garbage-collection crash risk and requiring separate pytest processes with combined coverage.

No open issues 🎉

1 previously missed issue

In code that hasn't changed since last review

Split GUI and non-GUI tests into separate coverage processes

pixi.toml:162

The tests task runs GUI and non-GUI tests in one process, retaining the Qt garbage-collection crash documented in .github/workflows/ci.yml:82–84. The coverage task at line 169 has the same issue. Split both tasks into separate pytest processes and append the GUI coverage so reports still include both suites.

6 resolved since last review

_{Review effort: Balanced}

Jakub Wlodek (jwlodek) and others added 8 commits October 23, 2026 13:12

Add GeRM detector mock class, plus unit tests for GeRM detector and a…

f8012e1

…ll edxd scans

Update mock germ behavior

9664f55

Merge with upstream

3d8759c

Improvements to plots, plan history, and germ mock

bc14b83

Use standard locations for plan history file

840a0d5

Placate linte

b181885

Simplify list of environments, placate linter

e5ba21a

Merge upstream/main into mock-germ

177a274

pixi.lock re-solved from main's lock for the merged pixi.toml (keeps main's pins, e.g. ntnda-qt-viewer 778e714). Assisted-by: copilot:claude-opus-5-5

Anthony Sligar (sligara7) marked this pull request as ready for review October 28, 2026 21:08

Copilot AI balanced review requested due to automatic review settings October 28, 2026 21:08

Copilot started reviewing on behalf of Anthony Sligar (sligara7) October 28, 2026 21:09

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Copilot AI reviewed Oct 28, 2026

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Comment thread src/hextools/detectors/germ.py Resolved

Comment thread src/hextools/gui/__main__.py Resolved

Comment thread src/hextools/gui/misc/tabbed_detectors_widget.py Resolved

Copilot AI balanced review requested due to automatic review settings October 28, 2026 21:17

Copilot started reviewing on behalf of Jakub Wlodek (jwlodek) October 28, 2026 21:17

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Copilot AI reviewed Oct 28, 2026

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Comment thread src/hextools/detectors/germ.py Resolved

Comment thread src/hextools/profiles/collection.py Resolved

Comment thread src/hextools/profiles/collection.py Resolved

Copilot AI balanced review requested due to automatic review settings October 28, 2026 21:43

Copilot started reviewing on behalf of Jakub Wlodek (jwlodek) October 28, 2026 21:44

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Anthony Sligar (sligara7) merged commit c5d557a into NSLS2:main Oct 28, 2026
6 checks passed

This was referenced Oct 29, 2026

Fix HEX slit values, EDXD recovery and manual shutter exclusion #126

Merged

Simplify filters, SampleSmall, FE Aperture. Rework filters.yml into beamline constants.yml #125

Merged

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Add GeRM detector mock class, plus unit tests for GeRM detector and all edxd scans - #109

Add GeRM detector mock class, plus unit tests for GeRM detector and all edxd scans#109
Anthony Sligar (sligara7) merged 10 commits into
NSLS2:mainfrom
jwlodek:mock-germ

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Jakub Wlodek (jwlodek) commented Oct 23, 2026

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