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Michael Milton edited this page Oct 10, 2023 · 2 revisions

Note, this applies to the Pydantic version of the codebase (https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/47)

Structure

The repo is divided into two python packages: core (the core processing and CLI) and plugin (the Napari GUI). Within each directory is:

  • The python package
  • pyproject.toml, the package metadata, and
  • tests/, which contains the tests

Installation

From the repository root:

pip install -e core -e plugin

Technologies

Pydantic

Used for defining the parameter sets, performing parameter validation and conversion. These models live in core/lls_core/models. Note, lls_core uses Pydantic 1.X, which has a different API to Pydantic 2.X. You can find relevant documentation here: https://docs.pydantic.dev/1.10/

Xarray

Used for all image representations, where they are treated as multidimensional arrays with dimensional labels (X, Y, Z etc). Refer to: https://xarray.pydata.org/.

Typer

The CLI is defined using Typer: https://typer.tiangolo.com/.

magicgui and magicclass

These packages are used to define the GUI, which you can find in plugin/napari_lattice. magicclass builds on magicgui by providing the @magicclass decorator which turns a Python class into a GUI.

Adding a new parameter

Whenever a new parameter is added, the following components need to be updated:

  • Add the parameter to the Pydantic models
  • Add the parameter to the CLI (core/lls_core/cmds/__main__.py), and define mapping between CLI and Pydantic using the CLI_PARAM_MAP
  • Add the field to the GUI in plugin/napari_lattice/fields.py
  • Define the new processing logic in core/lls_core/models/lattice_data.py

An example of this can be found in this commit: https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/47/commits/16b28fec307f19e73b8d55e677621082037b2710.

Testing

The tests are run using pytest. To install the testing dependencies, use pip install -e 'core[testing]' -e 'plugin[testing]' Since there are two separate packages, you will have to specify the location of each test directory. To run all the tests, use pytest core/tests/ plugin/tests from the root directory.

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