x01dcandClaude Sonnet 5
bdb0d25f90
progress["projection"]/["subtomo_projection"]/["subtomo_total_projections"]/ ["total_projections"] are otherwise only ever set inside sub_tomo_scan()'s per-point loop. The zero_deg_reference_at_each_subtomo pre/post shots call _tomo_scan_at_angle() directly, bypassing that -- so the printed progress showed whatever was left over from a previous scan/subtomo instead of a value that made sense for the shot. Confirmed live: a fresh scan's first reference shot printed a stale "Projection: 9 / Total: 32" from an earlier run. Same bug exists in flomni.py (this was ported from there faithfully, bug included) -- flagged in OPEN_ISSUES.md but not touched, out of this branch's scope. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01QLrD7sVYGLAzsQjLVJpCgt
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.