Merge v2.3.0

[thomaszwagerman]

Circumventing signature error in #100

MeshiPhi Pull Request Template

Date: 30/12/2025
Version Number: 2.3.0

Description of change

Version release branch, v2.3.0

Testing:

• Ensure pytest can be run from the main directory, changing filepaths in relevant tests.
• Refactored test to reduce duplication and remove non-relevant items under /tests to other parts of the package. Consolidate constants in conftest.py.
• Enable avoiding running slow tests: pytest -m "not slow" and running tests in parallel with pytest-xdg: pytest -n auto.
• Updated TestEnvMesh to use temporary file instead of /resources (TestEnvMesh::test_to_tif fails due to module and file errors #99).
• Add Github actions to run tests on Python versions 3.11- 3.14.
• Add pytest-coverage output to tests with addopts.

Quality of life/code:

• Replace all instances of logging.*() with the logger module.
• Replace all instances of assert with appropriate AssertionError (Use of assert #77).
• Add the Meshiphi version number to the meshes ([Feature Request] Include MeshiPhi package version in meshes #86).
• Convert Nan to None when converting to json, to help with Postgres ingestion (Use of NaN in mesh.json output files #95).
• Add Github actions to automatically build docs on PRs and merge with main.
• Add .pre-commit hook to check and re-format code with ruff.
• Add usage section to README.
• Add CONTRIBUTING.md, CHANGELOG.md and CITATION.cff.
• Consolidate package, test, dev, docs dependencies in pyproject.toml.

Fixes # (issue)

Fixes #77, fixes #86, fixes #95, fixes #99, fixes #109.

[thomaszwagerman]

Slowly becoming Not A Big Fan™ of these version branches. A large number of (pretty trivial) changes becomes very hard for anybody to review.

[thomaszwagerman]

Although the number of lines looks scary, this is a combination of the linting + replacing every logger call. A lot of empty lines and reformatting.

[thomaszwagerman]

typehints changes are more involved in terms of code changes, I suggest that goes in a later version

[davidwyld]

LGTM. LGTM.