x01dcandClaude Sonnet 5
c3877ecdef
Ports flomni's zero_deg_reference_at_each_subtomo to lamni's "8 equally spaced sub-tomograms" mode: an extra dedicated projection at exactly 0 degrees before every sub-tomogram where the rotation naturally passes back through 0, plus one final shot once the tomogram completes, for tracking radiation damage over a long acquisition. lamni's tomo_type 2/3 already had the equivalent (golden_projections_at_0_deg_for_damage_estimation, byte-for-byte identical to flomni's) -- only tomo_type 1 was missing. _subtomo_starts_near_zero() uses subtomo_number % 2 (every odd sub-tomogram) rather than flomni's 360-mode subtomo_number % 4 == 1 -- confirmed against lamni's actual rotation behavior rather than derived from the position-array math, which doesn't cleanly split odd/even. The GUI (tomo_params.py) needed no new UI code: _build_type1_section() already gated this control on a per-setup has_zero_deg_reference flag, so enabling it for lamni was just flipping that flag plus adding the param name/default, mirroring flomni's entries exactly. 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.