Swiftest

New Features

- Introduced new classes `swiftest.data.SwiftestDataArray` and `swiftest.data.SwiftestDataset`. These are extensions of [xarray.DataArray](https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html) and [xarray.Dataset](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html), respectively. These are now used to define the internal data storage attributes, like `swiftest.Simulation.data`, `swiftest.Simulation.init_cond`, `swiftest.Simulation.collisions`, and `swiftest.Simulation.encounters`, as well as methods `swiftest.SwiftestDataset.xv2el` and `swiftest.SwiftestDataset.el2xv`. [GH24](https://github.com/MintonGroup/swiftest/issues/24)

- Added binding modules and started writing code to connect the Fortran `el2xv` and `xv2el` to Python and removed the Python implementation of these functions. This allows the Python code to call the same Fortran functions for converting state vectors to orbital elements and back again that the core Swiftest code uses, which are nearly identical to the original implementations of these functions written by Martin Duncan in 1992. The functions themselves are accessible via `swiftest.core.el2xv` and `swiftest.core.xv2el`.

- The `swiftest.Simulation.add_solar_system_body` and `swiftest.Simulation.add_body` methods have been overhauled to make selecting the central body in a more consistent way. Central bodies are now chosen automatically to be the most massive body in the system, and the all other bodies' position and velocity vectors are translated to the central body's frame. We also include a new argument to these functions called `align_to_central_body_rotation` which can be used to rotate bodies into a frame that is aligned with the central body's rotation vector. This is useful for using `swiftest.Simulation.add_solar_system_body` to set bodies other than the Sun to be the central body, as otherwise it aligns all bodies to the ecliptic. See the documentation on planetocentric initial conditions for details of how this works.

Bug Fixes

- Fixed a problem with length check when passing `ephemeris_id` and `name` as scalars.
- Added an explicit status variable when adding bodies to ensure that they get counted properly.

Internal Changes

- Updated initial conditions generators to catch more bad or inconsistent inputs and added more tests to cover these cases.
- Updated build script environment variables to help make the MacOS build more robust.
- Improved the efficiency of the `init_cond.solar_system_horizons` function when fetching physical parameters. It can now accept a jpl HorizonsClass object as an argument so that it can re-use a previous query to look for physical parameters, and only execute a new query on an `altid` if they are not found.
- Switched from using `iso_fortran_env` to `iso_c_binding` for basic type definitions in order to make it easier to expose the Fortran library API to Python.

Documentation

- Added a new documentation page to demonstrate the use of the standalone executable.
- Added a new documentation page for setting planetocentric initial conditions.

Bug Fixes

- Fixed issue causing the `get_solar_system_body` method to break when using astroquery 0.4.7. Switched to using the `ephemerides_async` method instead of getting the `raw_response` attribute. [GH19](https://github.com/MintonGroup/swiftest/issues/19)

Bug Fixes
- Fixed problem that was causing the standalone swiftest console executable to not be found on the path when installing from wheel. This has been fixed by wrapping the executable in a Python wrapper called `cli.py` that is used to generate an executable script.
- Fixed a bug that that was causing a file read error when reading a copied initial conditions file. This was caused by the file not being closed after being read.

Breaking Changes
- The binary executable has been refactored from `swiftest_driver` to `swiftest`

Internal Changes
- Addressed an issue where the latest OS X update broke dependency builds, ensuring environment compatibility.
- Streamlined code structure by refactoring `simulation_class` to `simulation`.
- Refactored `_bindings` module to `core`. In a future we plan to develop a more extensive core API exposing some of the lower level integration functions from the Fortran side into the Python module.
- Removed outdated JOSS paper draft rendering workflow and specific CI/CD action on push to optimize development processes.
- Skipped building the Python 3.12 wheel for linux aarch64 in cibuildwheel due to missing h5py, addressing compatibility issues.
- Modified the dependency build scripts to skip tests when building dependent libraries (namely HDF5, NetCDF-C, and NetCDF-Fortran) in order to speed up the wheel generation on github actions.

Documentation
- Updated development status and primary repository location to keep the community informed.

New Features

- Incorporation of [SHTOOLS](https://shtools.github.io/SHTOOLS/) for incorporating gravitational harmonics coefficients into the central body gravity field calculations.
- Introduction of rotation matrix calculations for non-z-axis central body rotation vectors, supporting more accurate precession effects.
- Enhancement of the netCDF output capabilities, including the addition of dimension-coordinates for c_lm arrays and support for spherical harmonics parameters.

Bug Fixes

- Fixed a bug that was causing the spin poles of massive bodies to be calculated incorrectly when pulling ephemerides from JPL/Horizons using [swiftest.Simulation.add_solar_system_body](https://swiftest.readthedocs.io/en/latest/generated/swiftest.Simulation.add_solar_system_body.html)
- Correction of various typos and minor bugs across the documentation and codebase, improving clarity and accuracy.
- Fixing of floating underflow errors and adjustments to normalization calculations to reduce computational errors.

Documentation

- Major updates to user guides and API documentation.

Breaking changes

- Support for ``python 3.8`` has been dropped and the minimum versions of some dependencies were changed.

| Package | Old | New |
|-------------|--------|--------|
| python | 3.8 | 3.9 |
| numpy | 1.24.3 | 1.26.4 |
| scipy | 1.10.1 | 1.12.0 |

| h5netcdf | 1.1 | 1.3.0 |
| h5py | 3.9 | 3.10.0 |

Improvements to the documentation and documentation build process.
* Docstrings in the Python project files have been formatted for better rendering and numerous small inconsistencies and errors have been corrected.
* Restructured the project so that the Fortran code does not have to be compiled when generating documentation for swiftest.readthedocs.io.
* Refactored many swiftest.io functions to indicate that they are not part of the public API.
* Added a more comprehensive list of sections to the API page.