x01dcandClaude Sonnet 5
0a12d4892f
Take one real 0-degree projection at the very start of every new tomogram (subtomo_number=1, included in reconstruction like any grid projection), independent of zero_deg_reference_at_each_subtomo / golden_projections_at_0_deg_for_damage_estimation -- gives an immediate radiation-damage baseline even when those flags are off. Placed right after Flomni's existing collect_empty_frames() step; LamNI gets the same 0-deg shot but no flat-field step, since it has no way to retract the sample out of the beam. Omny intentionally left as a follow-up (not implemented here). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0132KBoxsovfcMNRGJhS1Pbw
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.