Development

Development#

Setup#

git clone https://github.com/MillerBrainObservatory/mbo_utilities.git
cd mbo_utilities
uv sync --all-extras

Testing#

Tests use synthetic data by default.

There are additional tests for filetype-specific properties that use tiffs e.g. raw scanimage tiffs.

# run all tests
uv run pytest tests/ -v

# run specific test file
uv run pytest tests/test_arrays.py -v

# for CI: run only synthetic data tests
uv run pytest tests/test_arrays.py tests/test_to_video.py -v -k "synthetic or Synthetic"

# keep output files
KEEP_TEST_OUTPUT=1 uv run pytest tests/

Test structure:

  • tests/conftest.py - fixtures for synthetic 3D/4D data, temp files, comparison helpers

  • tests/test_arrays.py - array class tests (indexing, protocols, volume detection)

  • tests/test_roundtrip.py - format conversion tests

  • tests/test_to_video.py - video export tests

Code Formatting#

ruff for formatting and linting.

# format code
uv tool run ruff format .

# check linting
uv tool run ruff check .

# fix auto-fixable issues
uv tool run ruff check --fix .

## Building Docs

```bash
uv pip install "mbo_utilities[docs]"
cd docs
uv run make clean
uv run make html
Contents