CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Types of changes:

• Added for new features.
• Changed for changes in existing functionality.
• Deprecated for soon-to-be removed features.
• Removed for now removed features.
• Fixed for any bug fixes.
• Security in case of vulnerabilities.

[Unreleased]

[0.7.4] - 2021-10-13

Changed

• Moved from Travis CI to GitHub actions for tests/CI.
• Moved to src layout.
• Version is now set in src/plonk/__init__.py which is read in setup.cfg.
• Update MANIFEST.in.
• Renamed master branch to main. Changes reflected in docs.
• Restructure docs, including changing from reStructuredText to Markdown using myst-parser.

[0.7.3] - 2020-08-28

Added

• Add add_alias method to Profile.
• Add disc_viscosity, alpha_shakura_sunyaev, epicyclic_frequency, midplane_stokes_number profiles.
• Add utils vector_array_names like dust_array_names.
• Add plotting of multiple dust or vector profiles.
• Add extra test data to complement the test suite.
• Add function to set missing header values on converted Phantom-HDF5 files.

Changed

• Renamed toomre_Q profile to toomre_q.
• Use cache context manager to generate some Snap attributes so as to not cache some arrays in memory.
• Some profiles have been removed when making non-radial profiles.
• The analysis.total module now uses sink particles in computing summed quantities.
• Moved some quantities from particles to discs as they are not generic but appropriate for discs simulations.
• Rename interpolate arguments: number_of_pixels -> num_pixels and density_weighted -> weighted. And weighted is a named argument (i.e. not just caught with **kwargs) to image, vector, and interpolate
• Rename load_ev to load_time_series.
• Rename load_sim to load_simulation.
• Replaced Snap.set_gravitational_parameter to Snap.set_central_body. A central body is required to calculate orbital dynamics quantities, e.g. eccentricity, on the particles.
• Refactored plonk.load_snap. Much of the code that was in the phantom reader module was, in fact, more general. Now, some of that code lives in Snap.load_snap which requires defining three functions in the reader modules: snap_properties_and_units, snap_array_registry, and snap_sink_registry
• Use figshare to host sample datasets not Anaconda Cloud.

Deprecated

• load_ev is deprecated in favour of load_time_series.
• load_sim is deprecated in favour of load_simulation.

Fixed

• Fix units labels in Profile.plot.
• Fix units of internal energy.
• Fix bugs in rotation to face-on and edge-on.
• Fix bugs in disc position and inclination angles.

[0.7.2] - 2020-08-23

Added

• Add label argument to Profile.plot.
• Add dust_array_names utility function. This makes a list of array names broken into sub-species.
• Add plonk.animate function to provide a common interface to animation functions.
• Always cache arrays during plotting using the caching context manager.
• Added function name to logging messages.

Changed

• Analysis particles functions with dust quantites are now for the dust "mixture method" (i.e. 1-fluid).
• Remove '_tot' as an array suffix for dust arrays. This was causing confusion as it makes no sense to sum stopping times.
• Rename base_array_name to base_profile_name.
• Change interpolate to return dimensionful quantity.
• Moved utils functions from each sub-package to modules in utils sub-package.
• Moved animation, animation_particles, animation_profiles from plonk namespace to plonk.visualize namespace.
• Renamed animation to animation_images.

Fixed

• Fix bug in setting default units for dimensionless arrays.
• Fix bugs in Profile related to units.
• Fix bug in std dev shading in Profile.plot.

[0.7.1] - 2020-08-21

Added

• Use a TOML config file to configure options.
• Add default_units and set_units on Snap and Profile.
• Sinks are iterable.
• Plot error bars on profiles.

Changed

• Renamed subsnaps_by_type to subsnaps_as_dict.
• Renamed units_defaults to array_units.
• Name mapping, units, aliases are no longer hard coded and are now in config.toml.
• If no units specified in image/plot/vector functions then use the default units on the Snap if available.
• Renamed some analysis.particles functions.
• Sinks analysis functions take a Sinks object as arguments.
• Profile.plot "std_dev_shading" argument changed to "std", and now is a string not a bool.

Fixed

• Fixed bug in using Snap for snaps with no sinks.
• Fixed bug in accessing a single Sink if a np.int rather than int was passed in.
• Fixed bug in reading Phantom datasets without knowing units.

[0.7.0] - 2020-08-17

Added

• Added plonk.image to make image plots (with interpolation and then matplotlib imshow).
• Added plonk.vector to make vector plots (with interpolation and then matplotlib quiver).
• Added plot_smoothing_length function to plot the smoothing length on particles, or accretion radius on sink particles.
• Added pretty_array_name function to prettify array names.
• Added visualize_sim as a method on Simulation objects.
• Allow getting subsets of Sinks.
• Added ax_kwargs to plotting functions for passing to ax.set.
• Added xlim, ylim on visualize.plot.
• Added units_dict function to return a units dictionary for passing to plotting functions.
• Added bulk load and unload functions on Snap for loading/unloading multiple arrays into/out-of memory.
• Add context manager for caching arrays on Snap.
• Added public methods on Snap: family for accessing particle families, and array for accessing particle arrays. These are already accessible via getitem but this makes the underlying methods available.
• Add function to add missing units to array on Snap.

Changed

• Removed plonk.particle_plot in favour of plonk.plot.
• Changed plonk.plot to produce particle plots
• Renamed MultiVisualization and plot_snaps to VisualizeSimulation and visualize_sim.
• Changed units system from cgs to SI.
• Simplified animation functions by only allowing one axes per animation.
• Changed default units to more conventional SI units, e.g. Pascal for pressure and Joule for energy.
• Simplified tree and neighbours functions on Snap. Now there is only one tree for a Snap. If you want a tree for just, say, dust particles, then first create a SubSnap and get the tree on that.
• Changed _Sinks into Sinks, i.e. a public class.
• All plotting functions/methods use the same argument for setting units.
• Renamed Snap.available_arrays argument "all" to "verbose".
• Changed Snap.units to Snap.code_units.
• Use pretty_array_name for plots labels.
• Rename Snap.unset to Snap.reset and allow for unloading cached arrays.
• When setting Snap.cache_arrays to False, no longer unload currently cached arrays.

Fixed

• Fixed writing Snap.to_dataframe units.

[0.6.2] - 2020-08-11

Changed

• Use setup.cfg for setuptools, and pyproject.toml (and setup.cfg) for config of tools.
• Version is set in setup.cfg and imported into plonk via importlib_metadata.
• Changed API documentation.
• Moved sph module from utils sub-package to analysis.

Deprecated

• plonk.particle_plot will be removed.
• plonk.plot will change from image plots to particle plots, and plonk.image and plonk.vector will be added to replace plonk.plot.
• Default units will change from cgs to SI.

Fixed

• Fixed bug in Profile with getting number of mixture dust species.
• Fixed bugs in animation functions (due to making physical units on by default).
• Fixed issues with colorbar size matching height of plots.

[0.6.1] - 2020-08-09

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.

[0.6.0] - 2020-08-05

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.

[0.5.3] - 2020-07-28

Fixed

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

[0.5.2] - 2020-07-28

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.

[0.5.1] - 2020-07-11

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.

[0.5.0] - 2020-04-20

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.

[0.4.1] - 2020-03-24

Added

• Add scatter plots, i.e. particle plots with variable color and size markers.
• Add extra_quantities method to easily calculate extra quantities on the snapshot.
• Allow for setting array units, whether the array is rotatable, and whether it is a dust on derived arrays.
• Profiles are automatically generated from any 1d Snap quantity.
• Access individual dust quantities on profiles via '_001', etc.
• Read Phantom equation of state information to get pressure, sound speed, temperature.
• Add extra Snap quantities, e.g. Stokes number.
• Add extra profiles, e.g. Toomre Q.
• Allow accessing components of Snap quantities via '_x', etc.
• Calculate standard deviation on profiles.

Changed

• Use verbose names for all snapshot quantities, e.g. 'dust_fraction' not 'dustfrac' and 'velocity_divergence' not 'divv'.

Removed

• Remove Evolution object in favour of pandas DataFrame.

[0.4.0] - 2020-03-15

Added

• Add physical units on the Snap object.
• Physical units are compatible with all visualization and analysis modules.

[0.3.1] - 2020-03-06

Added

• Add many analysis functions.
• Animations of visualizations.

Changed

• Make it easier to add profiles to Profile
• Make plonk.visualize.plot easier to use.

Fixed

• Fix bug in Snap.rotate not rotating sink particles.

[0.3.0] - 2019-12-07

Changed

• Interpolation functions are now written in Python and JIT-compiled with Numba.

[0.2.1] - 2019-11-27

Added

• Add the JOSS paper describing the code.

[0.2.0] - 2019-11-06

Changed

• Use KDEpy for interpolation.

[0.1.0] - 2019-06-28

• Initial release.