Plonk - v0.7.4

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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl over 4 years ago

Plonk - v0.7.3

Added

• Add add_alias method to Profile.
• Add discviscosity, alphashakurasunyaev, epicyclicfrequency, midplanestokesnumber profiles.
• Add utils vectorarraynames like dustarraynames.
• 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 toomreQ profile to toomreq.
• 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: numberofpixels -> numpixels and densityweighted -> 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.setgravitationalparameter to Snap.setcentralbody. A central body is required to calculate orbital dynamics quantities, e.g. eccentricity, on the particles.
• Refactored plonk.loadsnap. Much of the code that was in the phantom reader module was, in fact, more general. Now, some of that code lives in Snap.loadsnap which requires defining three functions in the reader modules: snappropertiesandunits, snaparrayregistry, and snapsink_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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.7.2

Added

• Add label argument to Profile.plot.
• Add dustarraynames 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 basearrayname to baseprofilename.
• Change interpolate to return dimensionful quantity.
• Moved utils functions from each sub-package to modules in utils sub-package.
• Moved animation, animationparticles, animationprofiles 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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.7.1

Added

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

Changed

• Renamed subsnapsbytype to subsnapsasdict.
• Renamed unitsdefaults to arrayunits.
• 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 "stddevshading" 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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.7.0

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 plotsmoothinglength function to plot the smoothing length on particles, or accretion radius on sink particles.
• Added prettyarrayname 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 plotsnaps to VisualizeSimulation and visualizesim.
• 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 prettyarrayname 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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.1.0

Initial release.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.2.0

Changed

• Use KDEpy for interpolation.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.6.2

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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.6.1

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.availablearrays does not reference sink particles; see Snap.sinks.availablearrays.
• 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.numparticlesof_type.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.6.0

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 availablearrays method of Snap has additional arguments to see all sub-arrays on particles, e.g. `velocityxanddustfraction001`.
• 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 radiusmin and radiusmax 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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.5.3

Fixed

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

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.5.2

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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.5.1

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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl almost 6 years ago

Plonk - v0.5.0

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: dusttype → subtype: this allows for Phantom boundary particle sub-types.

Removed

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

Scientific Software - Peer-reviewed - Python
Published by dmentipl about 6 years ago

Plonk - v0.4.1

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. 'dustfraction' not 'dustfrac' and 'velocitydivergence' not 'divv'.

Removed

• Remove Evolution object in favour of pandas DataFrame.

Scientific Software - Peer-reviewed - Python
Published by dmentipl about 6 years ago

Plonk - v0.4.0

Added

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

Scientific Software - Peer-reviewed - Python
Published by dmentipl about 6 years ago

Plonk - v0.3.1

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.

Scientific Software - Peer-reviewed - Python
Published by dmentipl about 6 years ago

Plonk - v0.3.0

Changed

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

Scientific Software - Peer-reviewed - Python
Published by dmentipl over 6 years ago

Plonk - v.0.2.1

Added

• Add the JOSS paper describing the code.

Scientific Software - Peer-reviewed - Python
Published by dmentipl over 6 years ago