Plonk

Added

- Snap.sinks attribute has more features.
- Cross section interpolation in a non-xy plane specified by a normal vector to the plane.
- Snap.rotate can be set by an axis vector and angle as opposed to a scipy Rotation object.
- discs module to analysis.
- filters module to analysis to set SubSnaps easily.
- 'id' array on Snap to help track particles.
- Function to plot the smoothing length as a circle.
- Profile method to generate a function from a profile to help create particle filters, for example.
- Simulation method to create a particle array over the whole simulation.

Changed

- Snap.available_arrays does not reference sink particles; see Snap.sinks.available_arrays.
- Profile.plot units are now consistent with visualize functions.
- Dust profiles in Profile are now distinguished by whether they are mixture (dust/gas) particles or dust-only particles.

Fixed

- Setting origin in extra quantities.
- All analysis functions have better physical units support.
- Bug in Snap.num_particles_of_type.

Added

- Added plot and particle_plot as methods of the Snap class. This allows for plotting with `snap.plot(quantity='quantity')` as opposed to `plonk.visualize.plot(snap=snap, quantity='quantity)`.
- Axis and colorbars have labels by default now, including units.
- The to_dataframe Snap method now indicates units in the column names, e.g. `position [au]`.
- The available_arrays method of Snap has additional arguments to see all sub-arrays on particles, e.g. `velocity_x` and `dust_fraction_001`.
- Added to examples and quick-start in documentation.
- Added method to re-open a closed Snap file.

Changed

- Physical units are turned on by default on Snap objects. All particle and sink arrays have units (provided by Pint).
- The units attribute of Snap and Simulation now only has core units, i.e. length, time, mass, and magnetic field.
- Some extra quantities have been renamed.
- Extra quantities are available on Snap objects by default.
- The arguments radius_min and radius_max in Profile have been renamed cmin and cmax to reflect that profiles are not just radial.

Fixed

- Fixed setting pressure from Phantom equation of states.

Fixed

- Fixed major bug in setting extra dust arrays on a Snap.

Added

- Change log.
- Cartesian profiles in y- and z-direction, in addition to x-direction which was already implemented.

Changed

- Do not raise exception in extra_quantities and physical_units if already set.
- Scikit-image and tqdm are no longer required dependencies.
- Conda environment renamed from plonk-dev to plonk.
- Refactor Plonk namespace. Fewer modules are directly imported.

Added

- Analysis functions for sink particles.
- Function to animate particle plots.
- Different colours per particle type in particle plots.
- Tqdm progress bar for animation.

Changed

- Use Matplotlib consistent argument names in particle_plot.

Fixed

- Fix bug in standard deviation shading in Profile.

Added

- Neighbour finding via kd-tree.
- Compute SPH derivatives using kd-tree.
- IPython tab completion for Snap arrays and Profile profiles.
- Profile can have ndim==1 which gives a linear profile, useful for box calculations.
- Option to turn off caching of particle arrays, so that they are always read from file.
- Write derived arrays to HDF5 file, and read arrays from that file onto a Snap.
- Added logging of warning and other information messages.

Changed

- Generalize sub-types: dust_type → sub_type: this allows for Phantom boundary particle sub-types.

Removed

- Remove `Visualization` class in favour of just returning matplotlib's Axes and Figure objects.