x01dcandClaude Sonnet 5
abc2a3d041
Add tomo_queue_reacquire(job_index, projection_number) to the shared TomoQueueMixin: reopens any queue job (even an already-"done" one) at an earlier projection than its own recorded progress, and resets every job queued after it -- tomo and command jobs alike -- to "pending", so a following tomo_queue_resume() (a new alias for tomo_queue_execute(), added for naming symmetry with tomo_scan_resume()) re-runs everything from there forward in order. Reuses the existing tomo_scan_resume() machinery by writing the requested resume point into the shared progress global var, rather than adding new parameters to tomo_scan()/tomo_queue_execute(). Guards against clobbering another job's progress if one is already "incomplete"/"running" elsewhere in the queue. A flat projection number is used as the resume-point unit for all three tomo_types, including type 1 (8 equally-spaced sub-tomograms), via a new per-setup _resolve_type1_projection() that maps it to (subtomo_start, start_angle). flomni's version reuses its existing _subtomo_angle_plan(); lamni's inline angle math in sub_tomo_scan() was extracted into an analogous _subtomo_angle_plan() static method first (behavior-preserving -- verified against the existing angle-math test suite) so both setups share the same pattern. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Getting Started with Testing using pytest
BEC is using the pytest framework. It can be installed via
pip install pytest
in your python environment.
We note that pytest is part of the optional-dependencies [dev] of the plugin package.
Introduction
Tests in this package should be stored in the tests directory.
We suggest to sort tests of different submodules, i.e. scans or devices in the respective folder structure, and to folow a naming convention of <test_module_name.py>.
It is mandatory for test files to begin with test_ for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
pytest -v --random-order ./tests
Note, the python environment needs to be active.
The additional arg -v allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument --random-order instructs pytest to run the tests in random order, which is the default in the CI pipelines.
Test examples
Writing tests can be quite specific for the given function. We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes. A very useful class to enable isolated testing is MagicMock. In addition, we also recommend to take a look at the How-to guides from pytest.