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Plasmapy v0.6.0 (2021-03-14)

Backwards Incompatible Changes

  • The State namedtuple was changed to the ~plasmapy.particles.IonicFraction class. (Note: #1046 subsequently changed that to ~plasmapy.particles.IonicLevel). (#796)
  • Now, when the ~plasmapy.particles.IonizationState class is provided with an ion, the ionic fraction for that ion is set to 100% for the corresponding element or isotope. (#796)
  • AtomicError was renamed to ~plasmapy.particles.exceptions.ParticleError and MissingAtomicDataError was renamed to ~plasmapy.particles.exceptions.MissingParticleDataError. (#796)
  • In plasmapy.particles, the IonizationStates class was renamed to ~plasmapy.particles.IonizationStateCollection. Argument n of IonizationStates was changed to n0 in ~plasmapy.particles.IonizationStateCollection. (#796)
  • Moved and refactored error message formatting functionality from plasmapy.utils.error_messages to plasmapy.utils.code_repr. (#920)
  • Renamed the available "methods" for computing the Coulomb logarithm in an attempt to make the names more explicit. This is implemented using the method keyword for functions ~plasmapy.formulary.collisions.Coulomb_logarithm and ~plasmapy.formulary.collisions.impact_parameter, and then propogated throughout the functionality in plasmapy.formulary.collisions. (#962)
  • Add dependency pandas >= 1.0.0. Modify xarray dependency to be xarray >= 0.14.0. (#963)
  • The ~plasmapy.plasma.grids.AbstractGrid property ~plasmapy.plasma.grids.AbstractGrid.grid is now dimensioned (has units) and cannot be accessed if all dimensions do not share the same units. (#981)
  • Renamed attribute is_uniform_grid on ~plasmapy.plasma.grids.AbstractGrid to is_uniform. (#981)
  • Drop Python 3.6 support. (#987)
  • The __getitem__ method of ~plasmapy.plasma.grids.AbstractGrid now returns a ~astropy.units.Quantity array instead of a reference to a xarray.DataArray. (#1027)
  • Renamed IonicFraction to ~plasmapy.particles.ionization_state.IonicLevel. This lays groundwork for future changes, where that class is going to become more than a fraction. (#1046)

Deprecations and Removals

  • The particle attribute of ~plasmapy.particles.particle_class.Particle has been deprecated in favor of the new symbol attribute. The particle attribute now issues a FutureWarning to indicate that it will be removed in a future release. (#984)

Features

  • Created the ~plasmapy.simulation.abstractions.AbstractNormalizations class to serve as an abstract interface for future classes that represent normalizations. (#859)
  • Create the analysis sub-package plasmapy.analysis.swept_langmuir for analysis code related to analyzing swept Langmuir traces. Sub-package is initiated with functionality for calculating the floating potential, ~plasmapy.analysis.swept_langmuir.floating_potential.find_floating_potential. (#889)
  • Added a proton radiography diagnostic module containing a tool for generating synthetic proton radiographs from simulated or calculated fields using a particle tracking algorithm. (#895)
  • Created new grid objects for representing plasma quantities as functions of space. (#909)
  • Added functions in plasmapy.utils.code_repr to reproduce strings that represent a call to a method or attribute of an object. These functions are used, for example, in error messages. (#920)
  • Add the function :func:`~plasmapy.dispersion.two_fluid_dispersion.two_fluid_dispersion_solution` to plasmapy.dispersion, which gives an analytical solution to the dispersion relation as derived by P. M. Bellan 2012 (DOI: 10.1029/2012JA017856). (#932)
  • Refactor out the ~plasmapy.simulation.particle_integrators.boris_push tracking integrator algorithm from ~plasmapy.simulation.particletracker.ParticleTracker. (#953)
  • For plasmapy.plasma.grids functionality, add better support for recognizing and handling physical quantities (e.g. spatial position, magnetic field, etc.) added to a grid object. (#963)
  • For plasmapy.plasma.grids functionality, improve interpolation performance on non-uniform grids. (#963)
  • Added the ~plasmapy.formulary.drifts.diamagnetic_drift function to ~plasmapy.formulary.drifts. (#966)
  • Add properties ~plasmapy.plasma.grids.AbstractGrid.grid_resolution and ~plasmapy.plasma.grids.AbstractGrid.quantities to ~plasmapy.plasma.grids.AbstractGrid. (#981)
  • Make several speed improvements to the functionality in ~plasmapy.plasma.grids, including the addition of keyword persistent to ~plasmapy.plasma.grids.AbstractGrid (and child class) methods ~plasmapy.plasma.grids.AbstractGrid.nearest_neighbor_interpolator and ~plasmapy.plasma.grids.AbstractGrid.volume_averaged_interpolator. This keyword allows the interpolators to assume the last grid setup and contents if input arguments have not changed. (#981)
  • Add methods ~plasmapy.plasma.grids.AbstractGrid.on_grid and ~plasmapy.plasma.grids.AbstractGrid.vector_intersects to ~plasmapy.plasma.grids.AbstractGrid. (#981)
  • The ~plasmapy.particles.particle_class.Particle class now contains an attribute named symbol that is intended to replace particle. The symbol attribute has been added as a property to ~plasmapy.particles.particle_class.AbstractParticle, ~plasmapy.particles.particle_class.CustomParticle, and ~plasmapy.particles.particle_class.DimensionlessParticle. (#984)
  • Added new can_be_zero check parameter to ~plasmapy.utils.decorators.checks.CheckValues and its dependents ( ~plasmapy.utils.decorators.checks.check_values, ~plasmapy.utils.decorators.validators.ValidateQuantities, ~plasmapy.utils.decorators.validators.validate_quantities). (#999)
  • Both plasmapy.particles.CustomParticle and plasmapy.particles.DimensionlessParticle now allow users to define a custom symbol via the symbol keyword argument, which can then be accessed by the symbol attribute in each of these classes. (#1015)
  • The greater than (>) operator can now be used between ~plasmapy.particles.Particle and/or ~plasmapy.particles.ParticleList instances to get the nuclear reaction energy. (#1017)
  • Create plasmapy.particles.ParticleList as a list-like collection for instances of plasmapy.particles.Particle and plasmapy.particles.CustomParticle. Adding ~plasmapy.particles.Particle and/or ~plasmapy.particles.CustomParticle instances will now create a ~plasmapy.particles.ParticleList. (#1017)
  • Added method ~plasmapy.plasma.grids.AbstractGrid.require_quantities to ~plasmapy.plasma.grids.AbstractGrid that verifies a list of quantities is present on the grid. Method is also incorported into ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph. (#1027)
  • Added the ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph.add_wire_mesh() method to ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph to allow the creation of synthetic proton radiographs that include a wire mesh reference grid. (#1049)
  • Created a function, ~plasmapy.formulary.mathematics.rot_a_to_b, that calculates the rotation matrix that will rotate one 3D vector onto another. (#1054)
  • Made ~plasmapy.plasma.grids.AbstractGrid.is_uniform a properly-documented public attribute of ~plasmapy.plasma.grids.AbstractGrid. (#1072)

Bug Fixes

  • Fixed a minus sign bug in the Particle Tracker simulation that caused the E×B drift to go in the incorrect direction. (#953)
  • Bugfix :meth:`plasmapy.analysis.fit_functions.Linear.root_solve` to handle the case where the slope is zero and no finite roots exist. (#959)
  • Fixed a bug that prevented nested iterations of a single ~plasmapy.particles.IonizationState or ~plasmapy.particles.IonizationStateCollection instance. (#1025)
  • Fixed a bug in grids.py for non-uniform grids that arose when xarray upgraded to v0.17.0 (#1027)
  • In ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph, adaptive dt now calculates the cyclotron period using the provided particle charge and mass (previously assumed protons). (#1035)
  • In ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph, the adaptive timestep algorithm now works when particles are provided using ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph.load_particles. (#1035)
  • In ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph, removed highly deflected particles so the call of ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph.max_deflection does not raise an exception. (#1035)

Improved Documentation

  • Add narrative documentation on ionization state functionality. (#796)
  • Added description to :func:`~plasmapy.formulary.parameters.Hall_parameter` signature and equation in docstrings. (#934)
  • Updated documentation for the plasmapy.particles and plasmapy.utils subpackages. (#942)
  • Improves documentation of plasmapy/formulary/quantum.py by cleaning up docstrings of contained functionality. (#951)
  • Update all docstrings associated with computing the Coulomb logarithm and the possible methods of calculation. (#962)
  • Add two Jupyter notebooks for functionality contained in plasmapy.plasma.grids: grids_cartesian.ipynb and grids_nonuniform.ipynb. (#963)
  • Added the ExB drift notebook, which demonstrates the analytical solution for the drift and the implementation of the corresponding formulary drift functions, ~plasmapy.formulary.drifts.force_drift and ~plasmapy.formulary.drifts.ExB_drift. (#971)
  • Describe what constitutes a valid representation of a particle in the docstring for the plasmapy.particles.particle_class.ParticleLike typing construct. (#985)
  • Put the docstring for plasmapy.particles.Particle.is_category into numpydoc format. (#1039)
  • Adds formulas (which were missing) to the docstrings of ~plasmapy.formulary.dimensionless.quantum_theta and ~plasmapy.formulary.dimensionless.beta. (#1041)
  • Add live rendering of changelog entries on documentation builds, based on sphinx-changelog. (#1052)
  • Created an example notebook demonstrating how the ~plasmapy.diagnostics.proton_radiography.SyntheticProtonRadiograph class can be used to generate synthetic proton radiographs with arbitrary source profiles. Add code documentation links to all proton radiograph notebooks. (#1054)
  • Update formatting and broken sphinx.ext.intersphinx links in plasmapy.formulary docstrings. (#1058)
  • Make minor fixes in plasmapy.particles docstrings. (#1064)
  • Organize the layout of the example Jupyter notebooks on the Read the Docs example page. (#1066)
  • Fix formatting and broken sphinx.ext.intersphinx links in docstrings in various places in the code base. Improve installation instructions in the docs; the subpackage stability matrix, and funding acknowledgments. (#1076)

Trivial/Internal Changes

  • Removed colorama as a dependency. (#920)
  • Moved remaining CI from CircleCI to GitHub Actions. (#996)
  • Add notebook CI through nbqa. (#997)
  • Remove lambda expressions from plasmapy.particles and plasmapy.utils. (#1013)
  • Add unicode particle aliases for electrons ("β-", "β⁻"), muons ("μ-", "μ⁻"), anti-muons ("μ+", "μ⁺"), tau particles ("τ", "τ-", "τ⁻"), anti-tau particles ("τ+", "τ⁺") electron neutrinos ("ν_e"), muon neutrinos ("ν_μ"), tau neutrinos ("ν_τ"), and alpha particles ("α"). (#1036)
  • A set containing all valid particle categories may now be accessed via plasmapy.particles.Particle.is_category.valid_categories. (#1039)
  • Properly handled warnings in test_proton_radiography.py (#1050)

Plasmapy v0.5.0 (2020-12-09)

Backwards Incompatible Changes

  • Created plasmapy.dispersion in accordance with PlasmaPy Enhancement Proposal 7 (PLEP 7) and migrated the dispersion functionality (dispersionfunction.py) from plasmapy.formulary to plasmapy.dispersion. (#910)
  • Removed default values for the ion and particle arguments of functions contained in plasmapy.formulary.parameters, in accordance with issue [#453](PlasmaPy#453), and updated all relevant calls to modified functionality. (#911)
  • Moved test helper exceptions from plasmapy.utils.pytest_helpers to plasmapy.tests.helpers. (#919)
  • Update :func:`plasmapy.formulary.parameters.mass_density` so it calculates the mass density for a specific particle from a given number density. Original function calculated the total mass density (ion + electron). (#957)

Features

  • Added a function to calculate the power spectrum of thermal bremsstrahlung emitted by a Maxwellian plasma. (#892)
  • Added support for multiple electron components to diagnostics.thomson.spectral_density. Also fixed a bug for multiple ion populations. (#893)
  • Add dependency pygments >= 2.4.1. (#898)
  • Create the plasmapy.analysis package as per PLEP-7 and initialize the package with the ~plasmapy.analysis.fit_functions module. Fit functions are designed to wrap together an analytical function, a curve fitter, uncertainty propagation, and a root solver to make curve fitting a little less painful. (#908)
  • Created a new subpackage, plasmapy.tests.helpers, to contain test helper functionality. (#919)
  • Create decorator ~plasmapy.utils.decorators.helpers.modify_docstring, which allows for programmatically prepending and/or appending a docstring. (#943)

Bug Fixes

Improved Documentation

  • Improved the release guide after the release of 0.4.0. (#872)
  • Add various improvements to the documentation.
    • Replace home link with the plasmapy logo.
    • Add module and index navigation links to sidebar header.
    • Replace raw html on the main page that simulates a nbgallery with a real nbgallery directive.
    • Move link to view page source code from the header to footer.
    • Add link to footer the jumps the user back to the top of the page.
    • Create and add custom CSS stylesheet.
    • Create _templates directory and templates to customize page elements. (#875)
  • Add static stub files to docs/api_static so all modules of plasmapy are indexed. This is necessary to expose all of plasmapy since not all modules are indexed in the narrative documentation. (#878)
  • Decompose sub-package plasmapy/utils/roman/ into the plasmapy/utils/roman.py file. Move definition of roman specific Exceptions into plasmapy.utils.exceptions. (#883)
  • Replaced references to Riot.im with references to Element.io or Matrix, as appropriate, following their recent rebranding. (#891)
  • Update the information on how to cite PlasmaPy, including in the release guide. (#900)

Trivial/Internal Changes

  • Apply isort to entire codebase, bringing it back to the pre-commit hook suite. (#857)
  • Expand package metadata contained in codemeta.json, following the CodeMeta standard. (#902)
  • Changed remaining instances of @u.quantity_input to @validate_quantities in response to issue #880. (#905)
  • Switched from Azure Pipelines to GitHub Actions for PR tests to make things easier for contributors. Moved away from Travis CI for test cron jobs. (#952)

Plasmapy v0.4.0 (2020-07-20)

Backwards Incompatible Changes

Features

  • Added units to reprs of .formulary.magnetostatics classes. (#743)

  • Create prototype abstract interfaces for plasma simulations (#753)

  • Created classes to represent custom and dimensionless particles in plasmapy.particles. (#755)

  • Create :func:`~plasmapy.formulary.relativity.relativistic_energy` function, which uses the established :func:`~plamsapy.formulary.relativity.Lorentz_factor` function to aid in the calculation of the relativistic energy of an object. (#805)

  • Create :func:`~plasmapy.formulary.dimensionless.Reynolds_number` function. (#815)

  • Create :func:`~plasmapy.formulary.dimensionless.Mag_Reynolds` function. (#820)

  • Create :func:`~plasmapy.formulary.parameters.Bohm_diffusion` function. (#830)

  • Added a new diagnostics module thomson containing a function spectral_density that calculates Thomson scattering spectra for Maxwellian plasmas in both the collective and non-collective regimes. As a followup to PR #835, set the minimal required Numpy version to 1.18.1 to finally fix unit dropping bugs. (#831)

  • Revised parameters.thermal_speed to support 1D and 2D distributions as well as 3D, and added an example notebook for this function. (#850)

  • Create plasmapy/formulary/ionization.py Create :func:`~plasmapy.formulary.ionization.Z_bal` function. (#851)

  • Create :func:`~plasmapy.formulary.ionization.Saha` function. (#860)

  • Added aliases (with trailing underscores) for parameters in the formulary:

    • plasmapy.formulary.dimensionless.Reynolds_number -> ~plasmapy.formulary.dimensionless.Re_
    • plasmapy.formulary.dimensionless.Mag_Reynolds -> ~plasmapy.formulary.dimensionless.Rm_
    • plasmapy.formulary.drifts.ExB_drift -> ~plasmapy.formulary.drifts.veb_
    • plasmapy.formulary.drifts.force_drift -> ~plasmapy.formulary.drifts.vfd_
    • plasmapy.formulary.parameters.mass_density -> ~plasmapy.formulary.parameters.rho_
    • plasmapy.formulary.parameters.Afven_speed -> ~plasmapy.formulary.parameters.va_
    • plasmapy.formulary.parameters.ion_sound_speed -> ~plasmapy.formulary.parameters.cs_
    • plasmapy.formulary.parameters.thermal_speed -> ~plasmapy.formulary.parameters.vth_
    • plasmapy.formulary.parameters.thermal_pressure -> ~plasmapy.formulary.parameters.pth_
    • plasmapy.formulary.parameters.kappa_thermal_speed -> ~plasmapy.formulary.parameters.vth_kappa_
    • plasmapy.formulary.parameters.inertial_length -> ~plasmapy.formulary.parameters.cwp_
    • plasmapy.formulary.parameters.Hall_parameter -> ~plasmapy.formulary.parameters.betaH_
    • plasmapy.formulary.parameters.gyrofrequency -> ~plasmapy.formulary.parameters.oc_, ~plasmapy.formulary.parameters.wc_
    • plasmapy.formulary.parameters.gyroradius -> ~plasmapy.formulary.parameters.rc_, ~plasmapy.formulary.parameters.rhoc_
    • plasmapy.formulary.parameters.plasma_frequency -> ~plasmapy.formulary.parameters.wp_
    • plasmapy.formulary.parameters.Debye_length -> ~plasmapy.formulary.parameters.lambdaD_
    • plasmapy.formulary.parameters.Debye_number -> ~plasmapy.formulary.parameters.nD_
    • plasmapy.formulary.parameters.magnetic_pressure -> ~plasmapy.formulary.parameters.pmag_
    • plasmapy.formulary.parameters.magnetic_energy_density -> ~plasmapy.formulary.parameters.ub_
    • plasmapy.formulary.parameters.upper_hybrid_frequency -> ~plasmapy.formulary.parameters.wuh_
    • plasmapy.formulary.parameters.lower_hybrid_frequency -> ~plasmapy.formulary.parameters.wlh_
    • plasmapy.formulary.parameters.Bohm_diffusion -> ~plasmapy.formulary.parameters.DB_
    • plasmapy.formulary.quantum.deBroglie_wavelength -> ~plasmapy.formulary.quantum.lambdaDB_
    • plasmapy.formulary.quantum.thermal_deBroglie_wavelength -> ~plasmapy.formulary.quantum.lambdaDB_th_
    • plasmapy.formulary.quantum.Fermi_energy -> ~plasmapy.formulary.quantum.Ef_ (#865)

  • Add json_dumps method to ~plasmapy.particles.particle_class.AbstractParticle to convert a particle object into a JSON string. Add json_dump method to ~plasmapy.particles.particle_class.AbstractParticle to serialize a particle object and writes it to a file. Add JSON decoder ~plasmapy.particles.serialization.ParticleJSONDecoder to deserialize JSON objects into particle objects. Add plasmapy.particles.serialization.json_loads_particle function to convert JSON strings to particle objects (using ~plasmapy.particles.serialization.ParticleJSONDecoder). Add plasmapy.particles.json_load_particle function to deserialize a JSON file into a particle object (using ~plasmapy.particles.serialization.ParticleJSONDecoder). (#836)

Bug Fixes

  • Fix incorrect use of pkg.resources when defining plasmapy.__version__. Add setuptools to package dependencies. Add a definition of __version__ for developers using source files. (#774)
  • Repair notebook links that are defined in the nbsphinx_prolog sphinx configuration variable. (#828)
  • Increase the required Astropy version from 3.1 to 4.0, Numpy from 1.14 to 1.16.6, Scipy from 0.19 to 1.2 and lmfit from 0.9.7 to 1.0.1. This fixes long-standing issues with Numpy operations dropping units from AstroPy quantities. (#835)

Improved Documentation

    • Added documentation to file test_converters (#756)
    • Updated installation instructions. (#772)
  • Reorder documentation page (#777)
  • Fix failing documentation build due to duplicate docstrings for ParticleTracker.kinetic_energy_history and incompatibility of sphinx-automodapi with sphinx v3.0.0. (#780)
  • Automate definition of documentation release and version in docs/conf.py with plasmapy.__version__. (#781)
  • Add a docstring to __init__.py in plasmapy.formulary. (#788)
  • Replaced sphinx-gallery with nbsphinx, turning .py example files into .ipynb files and allowing for easier example submission. (#792)
  • Linked various instances of classes and functions in the .ipynb examples in docs/notebooks/ to the respective API docs. (#825)
  • Fixed a few documentation formatting errors. (#827)
  • Add notes on the PlasmaPy benchmarks repository to documentation. (#841)
  • Improve readability of the plasmapy.formulary page by replacing the toctree list with a cleaner reST table. (#867)

Trivial/Internal Changes

  • Remove mutable arguments from Particle.is_category method. (#751)
  • Remove all occurrences of default mutable arguments (#754)
  • Handle ModuleNotFoundError when trying to import __version__ but setuptools_scm has not generated the version.py file. This commonly happens during development when plasmapy is not installed in the python environment. (#763)
  • Updated pep8speaks/flake8 configuration and added .pre-commit-config.yaml to simplify automated style checks during development. (#770)
  • Removes some lint from setup.py and setup.cfg. Use pkg_resources for version checking in code. Remove version.py file in favor of pkg_resources. (#771)
  • Default settings for isort were set to be consistent with default settings for black. (#773)
  • Update community meeting and funding information in docs. (#784)
  • Improved pull request template to include more information about changelog entries. (#843)
  • Added GitHub actions that apply pre-commit and flake8 (separately) to incoming pull requests. (#845)
  • Apply pre-commit hooks to entire repository, so that GitHub actions do not shout at contributors needlessly. (#846)
  • Update :class:`~plasmapy.particles.particle_class.CustomParticle` so input parameters mass and charge can accept string representations of astropy Quantities. (#862)

Plasmapy v0.3.0 (2020-01-25)

Backwards Incompatible Changes

  • Create simulation subpackage; move Species particle tracker there; rename to particletracker (#665)
  • Changed plasmapy.classes.Species to plasmapy.simulation.ParticleTracker (#668)
  • Move pytest helper functionality from plasmapy.utils to ~plasmapy.utils.pytest_helpers (#674)
  • Move plasmapy.physics, plasmapy.mathematics and plasmapy.transport into the common plasmapy.formulary subpackage (#692)
  • Change ClassicalTransport methods into attributes (#705)

Deprecations and Removals

  • Remove parameters_cython.pyx, switching to Numba for the future of computationally intensive code in PlasmaPy (#650)
  • Remove plasmapy.constants, which was a thin wrapper around astropy.constants with no added value (#651)

Features

  • Generalize ion_sound_speed function to work for all values of k^2 \lambda_{D}^2 (i.e. not just in the non-dispersive limit). (#700)
  • Optimize add__magnetostatics for a 16x speedup in tests! (#703)

Bug Fixes

  • Define preserve_signature decorator to help IDEs parse signatures of decorated functions. (#640)
  • Fix Pytest deprecations of message argument to raise and warn functions. (#666)
  • Fix h5py warning in OpenPMD module, opening files in read mode by default (#717)

Improved Documentation

Trivial/Internal Changes