Ichthyop

New features

- Adding a first version of orientation, based on Romain Chaput's thesis. **To be improved**
- Documentation conversion from Sphinx to Quarto.
- Adding the possibility to fix the random seed to insure reproducibility of the results.
- Adding additional unit tests (`TestGetParameter.java`, `TestReefAction.java`, `TestVmDistribution.java`)
- Adding the possibility to read Stockes velocity in `Roms3dCommon.java`

Bug fix

- In `MigrationAction.java`, in case of constant depth, check if the particle is below the sea-bed. If so, the particle does not move.

Bug fix

- Correction of `BuoyancyAction.java`: correction of the ovoid calculation (minor axis was used twice) (cf. 71).

Bug fix

- Correction of `Mercator2dDataset.java` to take into account data either in float or double. Use `Index` object instead of `copyToNDJavaArray`

New features

- Possibility to define the number of particles released per area
- Sphinx documentation is now included in the repository
- Update of the different plugins and dependencies

Bug fix

- If the `units` attribute is not found in the NetCDF file, then the `time_of_origin` parameter is used. **Must be in the NETCDF standards, i.e `seconds since YYYY-MM-DD HH:MM`**
- Adding serial parameters with the console did not work properly when hidden parameters were effectively hidden. The button is therefore activated only when hidden parameters are shown.
- Correction of a bug in the Preview. When zones were modified, preview was not updated accordingly. Now it is the case.
- In `MigrationAction.java`, correction of the check on whether the particle destination depth is below the sea-bed. Comparison with bathymetry is now used instead of depth at `k=0`, which only workd on sigma models (ROMS and MARS)
- In some cases, the bouncing algorithm fails and particle may advect over land (if wind drift is activated). Now, if the bouncing algorithm fails, particle is killed.
- Change in the resource encoding. Move from `ISO-8859-1` to `UTF-8`

Bug fix

- Correction in the reading of vertical scale variables in `Mercator_3D`. Management of the case where it is a 1D variable.
- Forcing compilation and target to Java 11 in `pom.xml`

New features

- Adding the reading of noleap calendars.
- Possibility to select the NetCDF output format (usefull for Windows users).
- Adding some unit tests (NetCDF time)
- Adding the possibility to save density maps instead of trajectories.
- Adding saving of a `drifter` variable in order to use for mapping
- Adding possibility to use NetCDF file compression (new set of parameters)

Bug fix

- Consideration of the case where HH:mm:ss is not provided in units (issues 22)
- Consideration of the case where time is provided as HH:mm instead of HH:mm:ss (issue 32)
- If NetCDF time cannot be properly read in NetCDF (wrong units), use the string provided in the `time_origin` parameter.
- Adding the case when time units is in `minutes since ...`
- Correct a bug in the writting of time in the Ichthyop console.