Pycontrails

Features

- Add Apache-2 LICENSE and NOTICE files (21)
- Add [CONTRIBUTING](https://github.com/contrailcirrus/pycontrails/blob/main/CONTRIBUTING.md) document
- Update documentation website [py.contrails.org](https://py.contrails.org).
Includes `install` and `develop` guides, update citations
and many other small improvements (19).
- Initiate the [Github Discussion](https://github.com/contrailcirrus/pycontrails/discussions) forum (#22).

Fixes

- Fix erroneous docstrings in `emissions.py` (25)

Internals

- Add Github action to push to `pypi` on tag (3)
- Replace `flake8` with `ruff` linter
- Add `nb-clean` to pre-commit hooks for example notebooks
- Add `doc8` rst linter and pre-commit hook

Breaking changes

- Change default value of `epsilon` parameter in method `MetDataArray.to_polygon_feature` from 0.15 to 0.0.
- Change the polygon simplification algorithm. The new implementation uses `shapely.buffer` and doesn't try to preserve the topology of the simplified polygon. This change may result in slightly different polygon geometries.

Internals

- Add `depth` parameter to `MetDataArray.to_polygon_feature` to control the depth of the contour searching.
- Add experimental `convex_hull` parameter to `MetDataArray.to_polygon_feature` to control whether to take the convex hull of each contour.
- Warn if `iso_value` is not specified in `MetDataArray.to_polygon_feature`.

Fixes

- Consolidate three redundant implementations of standardizing variables into a single `met.standardize_variables`.
- Ensure simplified polygons returned by `MetDataArray.to_polygon_feature` are disjoint. While non-disjoint polygons don't violate the GeoJSON spec, they can cause problems in some applications.

Internals

- Add citations for ISA calculations
- Abstract functionality to convert a Dataset or DataArray to longitude coordinates `[-180, 180)` into `core.met.shift_longitude`. Add tests for method.
- Add auto-formatting checks to CI testing

ACCF integration updates

Fixes

- Fixes ability to evaluate ACCF model over a `MetDataset` grid by passing in tuple of (dims, data) when assigning data
- Fixes minor issues with ACCF configuration and allows more configuration options
- Updates example ACCF notebook with example of how to set configuration options when evaluating ACCFs over a grid

Features

- Include "rhi" and "iwc" variables in `CocipGrid` verbose outputs.

Breaking changes

- Update CoCiP unit test static results for breaking changes in tau cirrus calculation. The relative difference in pinned energy forcing values is less than 0.001%.

Fixes

- Fix geopotential height gradient calculation in the `tau_cirrus` module. When calculating finite differences along the vertical axis, the tau cirrus model previously divided the top and bottom differences by 2. To numerically approximate the derivative at the top and bottom levels, these differences should have actually been divided by 1. The calculation now uses `np.gradient` to calculate the derivative along the vertical axis, which handles this correctly.
- Make tau cirrus calculation slightly more performant.
- Include a warning in the suspect `IFS._calc_geopotential` implementation.

Internals

- Remove `_deprecated.tau_cirrus_alt`. This function is now the default `tau_cirrus` calculation. The original `tau_cirrus` calculation is still available in the `_deprecated` module.
- Run `flake8` over test modules.


Release

> ``pycontrails`` is tagged and pushed to [pypi](https://pypi.org/project/pycontrails/) through GitHub Actions.

1. Ensure all changes to be released are committed and pushed to `main`.
1. Ensure [Unit tests](https://github.com/contrailcirrus/pycontrails/actions/workflows/test.yaml) and [Doc / Notebook tests](https://github.com/contrailcirrus/pycontrails/actions/workflows/doctest.yaml) have passed on `main`.
The [Release Action](https://github.com/contrailcirrus/pycontrails/actions/workflows/release.yaml) will fail if these actions have not completed successfully.
1. Review and update the [CHANGELOG](CHANGELOG.md).
Ensure the most recent entry is for the tag about to be released.
1. Create a [new release on Github](https://github.com/contrailcirrus/pycontrails/releases).
Double check that the release tag is consistent and consecutive with
the previous release tag following [PEP 440](https://peps.python.org/pep-0440/#version-scheme).
This often but not always agrees with [Semantic Versioning](https://semver.org/).
1. Copy the CHANGELOG content for the release into the *Description*.
1. Publish the new release.
This will create a tag on `main` and trigger the [Release Action](https://github.com/contrailcirrus/pycontrails/actions/workflows/release.yaml).
1. Confirm that the release is successfully deployed to [PyPI](https://pypi.org/project/pycontrails/).
1. Confirm that the documentation is successfully deployed to [py.contrails.org](https://py.contrails.org).