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Plasmapy 0.8.1 (2022-07-05)

Backwards Incompatible Changes

  • In ~plasmapy.diagnostics.thomson.spectral_density, the arguments Te and Ti have been renamed T_e and T_i and are now required :term:`keyword-only` arguments. (#974)
  • Moved the grid_resolution attribute from ~plasmapy.plasma.grids.AbstractGrid to ~plasmapy.plasma.grids.CartesianGrid and ~plasmapy.plasma.grids.NonUniformCartesianGrid separately. This fixes a potential future bug, because this attribute is only valid as written when all axes share the same units. (#1295)
  • Changed the behavior of the __repr__ method of |CustomParticle| to display the symbol as well if it was provided. (#1397)
  • Removed a block of code that printed out special particle properties when plasmapy.particles.special_particles (renamed to plasmapy.particles._special_particles) was executed. (#1440)
  • Renamed plasmapy.particles.elements to plasmapy.particles._elements, plasmapy.particles.isotopes to plasmapy.particles._isotopes, plasmapy.particles.parsing to plasmapy.particles._parsing, and plasmapy.particles.special_particles to plasmapy.particles._special_particles. Consequently, these modules are no longer part of PlasmaPy's public API. Most of these modules did not contain any public objects, except for plasmapy.particles.special_particles.ParticleZoo which was renamed to plasmapy.particles._special_particles.particle_zoo and removed from the public API. (#1440)
  • The parameters Z and mass_numb to |Particle| are now :term:`keyword-only`. (#1456)

Deprecations and Removals

  • Officially deprecated plasmapy.formulary.parameters and scheduled its permanent removal for the v0.9.0 release. (#1453)
  • Dropped support for Python 3.7 in accordance with the deprecation policy laid out in NumPy Enhancement Proposal 29. (#1465)
  • The [all] option when using pip_ to install plasmapy is now deprecated and may be removed in a future release. Packages that were previously optional (|h5py|_, |lmfit|, |mpmath|_, and |numba|_) are now installed by default when running pip install plasmapy. To install all packages required for code development of PlasmaPy, instead run pip install plasmapy[developer]. (#1482)
  • Removed plasmapy.optional_deps. (#1482)

Features

  • ~plasmapy.diagnostics.thomson.spectral_density and ~plasmapy.diagnostics.thomson.spectral_density_model now support ~plasmapy.particles.particle_collections objects as input to the ions keywords. (#974)
  • Created a :term:`lite-function` for ~plasmapy.diagnostics.thomson.spectral_density, ~plasmapy.diagnostics.thomson.spectral_density_lite. (#974)
  • Added a fitting function for 1D spectra, ~plasmapy.diagnostics.thomson.spectral_density_model, to the Thomson scattering diagnostic module. (#974)
  • Created function plasmapy.formulary.parameters.thermal_speed_coefficients to support plasmapy.formulary.parameters.thermal_speed_lite usage by calculating the various thermal speed coefficients. plasmapy.formulary.parameters.thermal_speed_coefficients is also bound to plasmapy.formulary.parameters.thermal_speed as the coefficients attribute. (#1145)
  • Created decorator ~plasmapy.utils.decorators.lite_func.bind_lite_func for handling the binding of :term:`lite-functions` and any supporting functions to a parent function. (#1145)
  • Introduced the concept of :term:`lite-functions`, by creating the lite-function plasmapy.formulary.parameters.thermal_speed_lite, which is a simplified and Numba_ jitted version of plasmapy.formulary.parameters.thermal_speed. These functions are intended for computational use and as such have no validation of input or output values. plasmapy.formulary.parameters.thermal_speed_lite is also bound to plasmapy.formulary.parameters.thermal_speed as the lite attribute. (#1145)
  • Added the :file:`hollweg_.py` module to the ~plasmapy.dispersion.numerical subpackage to numerically solve the dispersion relation using Hollweg's method :cite:p:`hollweg:1999,bellan:2012`. (#1189)
  • Implemented non-breaking speed improvements on the methods ~plasmapy.plasma.grids.CartesianGrid.nearest_neighbor_interpolator and ~plasmapy.plasma.grids.CartesianGrid.volume_averaged_interpolator for ~plasmapy.plasma.grids.CartesianGrid. The new interpolators now require that the grid axes be sorted, which is always true for uniform grids. Added a new test to ensure this stays true. (#1295)
  • Refactored the interpolator methods on objects defined in ~plasmapy.plasma.grids. All interpolators are now defined in the subclasses of ~plasmapy.plasma.grids.AbstractGrid. Calling the interpolator methods on ~plasmapy.plasma.grids.AbstractGrid raises a NotImplementedError exception. (#1295)
  • Created :term:`lite-function` plasmapy.formulary.parameters.plasma_frequency_lite. (#1308)
  • Added the ~plasmapy.particles.particle_class.molecule function to build |CustomParticle| objects from a str representing a molecule symbol. (#1309)
  • Added the ~plasmapy.particles.particle_collections.ParticleList.is_category method for |ParticleList| objects. This method is analogous to the ~plasmapy.particles.particle_class.Particle.is_category method for |Particle| objects. (#1378)
  • Created the prototype analysis tool plasmapy.analysis.nullpoint for finding the null points in a vector space using the trilinear interpolation method of :cite:t:`haynes:2007`. (#1383)
  • Created plasmapy.formulary.lengths to contain length related plasma parameters, and migrated ~plasmapy.formulary.lengths.Debye_length, ~plasmapy.formulary.lengths.gyroradius, and ~plasmapy.formulary.lengths.inertial_length from plasmapy.formulary.parameters to the new module. Related aliases were also migrated. (#1434)
  • Created plasmapy.formulary.frequencies to contain frequency related plasma parameters, and migrated ~plasmapy.formulary.frequencies.gyrofrequency, ~plasmapy.formulary.frequencies.plasma_frequency, ~plasmapy.formulary.frequencies.plasma_frequency_lite, ~plasmapy.formulary.frequencies.lower_hybrid_frequency, and ~plasmapy.formulary.frequencies.upper_hybrid_frequency from plasmapy.formulary.parameters to the new module. Related aliases were also migrated. (#1439)
  • Migrated ~plasmapy.formulary.dimensionless.Debye_number, and ~plasmapy.formulary.dimensionless.Hall_parameter from plasmapy.formulary.parameters to plasmapy.formulary.dimensionless. Related aliases were also migrated. (#1444)
  • Created plasmapy.formulary.speeds to contain frequency related plasma parameters, and migrated ~plasmapy.formulary.speeds.Alfven_speed, ~plasmapy.formulary.speeds.ion_sound_speed, ~plasmapy.formulary.speeds.kappa_thermal_speed, ~plasmapy.formulary.speeds.thermal_speed, ~plasmapy.formulary.speeds.thermal_speed_coefficients, and ~plasmapy.formulary.speeds.thermal_speed_lite from plasmapy.formulary.parameters to the new module. Related aliases were also migrated. (#1448)
  • Created plasmapy.formulary.misc to contain functionality for miscellaneous plasma parameters, and migrated ~plasmapy.formulary.misc._grab_charge, ~plasmapy.formulary.misc.Bohm_diffusion, ~plasmapy.formulary.misc.magnetic_energy_density, ~plasmapy.formulary.misc.magnetic_pressure, ~plasmapy.formulary.misc.mass_density, and ~plasmapy.formulary.misc.thermal_pressure from plasmapy.formulary.parameters to the new module. Related aliases were also migrated. (#1453)
  • Created :term:`lite-functions` ~plasmapy.dispersion.dispersionfunction.plasma_dispersion_func_lite and ~plasmapy.dispersion.dispersionfunction.plasma_dispersion_func_deriv_lite for ~plasmapy.dispersion.dispersionfunction.plasma_dispersion_func and ~plasmapy.dispersion.dispersionfunction.plasma_dispersion_func_deriv respectively. (#1473)
  • Created :term:`lite-function` plasmapy.formulary.dielectric.permittivity_1D_Maxwellian_lite for plasmapy.formulary.dielectric.permittivity_1D_Maxwellian. (#1476)
  • Added the :file:`stix_.py` module to the ~plasmapy.dispersion.analytical subpackage which contains the Stix cold-plasma dispersion solution :func:`~plasmapy.dispersion.analytical.stix_.stix`, :cite:p:`stix:1992,bellan:2012`. (#1511)
  • Particle("Li").ionize() no longer results in a ~plasmapy.particles.exceptions.ChargeError. Instead, ionization of a neutral atom is assumed. (#1514)
  • Created the |ParticleListLike| typing construct and added :term:`particle-list-like` to the |glossary|. (#1528)
  • Added a null point classifier function which determines the type of a given 3D magnetic null point. (#1554)
  • Added support for arbitrarily shaped input arrays to the function plasmapy.formulary.collisions.impact_parameter. (#1604)

Bug Fixes

  • Fixed a bug in the _make_grid method of ~plasmapy.plasma.grids.AbstractGrid that would fail to smoothly handle invalid user input if the start, stop, or num keywords were not the correct type. (#1295)
  • Fixed a bug with |Particle| where Particle("p+") == Particle("H", Z=1, mass_numb=1) led to a |ParticleError|. (#1366)
  • For plasmapy.formulary.parameters.gyroradius, updated the default keyword arguments and conditional for issuing the ~plasmapy.utils.exceptions.PlasmaPyFutureWarning. This addresses the incorrect behavior where a ValueError is raised if an array is passed to the deprecated keyword T_i. (#1430)
  • Exposed plasmapy.formulary.misc to the plasmapy.formulary namespace. (#1471)
  • Replaced misuse of max_exp_bias - max_exp_bias with max_exp_bias - min_exp_bias when creating seed parameters for the bimaxwellian fit function inside :func:`~plasmapy.diagnostics.langmuir.get_electron_temperature`. (#1487)
  • Corrected the improper inversion of the electron temperature for the non-bimaxwellian case for :func:`~plasmapy.diagnostics.langmuir.get_electron_temperature`. The electron temperature, and not the slope, is a fit parameter of the curve used by :func:`~plasmapy.diagnostics.langmuir.get_electron_temperature`, so there is no need for the inversion. The returned value is now the electron temperature and not its reciprocal. (#1487)
  • Exposed the ~plasmapy.analysis and ~plasmapy.dispersion subpackages to the plasmapy namespace. (#1512)
  • Changed the :meth:`~plasmapy.analysis.fit_functions.Linear.curve_fit` method on plasmapy.analysis.fit_functions.Linear so that the arbitrary keyword arguments get passed to scipy.stats.linregress. Previously, :meth:`~plasmapy.analysis.fit_functions.Linear.curve_fit` had accepted arbitrary keyword arguments but did not pass them along to ~scipy.stats.linregress. (#1518)
  • Fixed a bug in :func:`~plasmapy.dispersion.numerical.hollweg_.hollweg` that did not allow for arguments theta and k to simultaneously be arrays. (#1529)
  • Fixed the Z dependence in ~plasmapy.formulary.collisions.fundamental_electron_collision_freq, by replacing n_e with n_i while calling ~plasmapy.formulary.collisions.collision_frequency. (#1546)
  • Updated the regular expression matching used by ~plasmapy.particles.particle_class.Particle to parse and identify a :term:`particle-like` string. This fixes the bug where a string with a trailing space (e.g. "Ar ") was converted into a negatively charged ion (e.g. "Ar -1"). (#1555)
  • Exposed plasmapy.formulary.radiation and functions therein to the plasmapy.formulary namespace. (#1572)

Improved Documentation

Trivial/Internal Changes

  • Streamlined ~plasmapy.utils.decorators.helpers.preserve_signature such that it only binds __signature__ to the wrapped function, i.e. it no longer touches any other attribute of the wrapped function. (#1145)
  • Moved all tests associated with calculating the thermal speed from test file :file:`plasmapy/formulary/tests/test_parameters.py` to :file:`plasmapy/formulary/tests/test_thermal_speed.py`. (#1145)
  • Applied reST_ substitutions for plasmapy.particles and |ParticleTracker| in the narrative documentation. (#1158)
  • Added csslint to the pre-commit_ configuration to check the formatting and style of CSS_ files. (#1287)
  • Added Python 3.10 to the `GitHub Actions`_ test suite. (#1292)
  • Parametrized tests for plasmapy.formulary.parameters.ion_sound_speed. (#1313)
  • Added cron tests of the development versions of matplotlib_ and SciPy_, while changing the cadence of cron tests to be run approximately fortnightly. (#1333)
  • Applied pytest.warns in several tests to catch warnings that are being issued during execution of the test suite. (#1345)
  • Split the tests running on pull requests into multiple stages. The various pytest_ test environments, including code coverage, now run conditionally given successful execution of a basic test environment and the linter checks. This change also prevents code coverage prompts from appearing twice, with incomplete information on the first time. (#1350)
  • Added a helper function that takes an iterable and creates a dict with physical types as keys and the corresponding objects from that iterable as values. This change updates the minimum required version of Astropy_ to 4.3.1. (#1360)
  • Added the module plasmapy.particles._factory which contains a private function that accepts arguments that can be provided to |Particle|, |CustomParticle|, or |ParticleList| and returns the appropriate instance of one of those three classes. (#1365)
  • Used the extract method refactoring pattern on the initialization of |Particle| objects. (#1366, #1368)
  • Refactored tests in plasmapy.particles. (#1369)
  • |CustomParticle| and |DimensionlessParticle| no longer emit a warning when the charge and/or mass is not provided and got assigned a value of |nan| in the appropriate units. (#1399)
  • Added unit test cases for manual entry of vector values in order to improve code coverage in the null point finder. (#1427)
  • Consolidated and parametrized tests associated with plasmapy.formulary.parameters.gyroradius. (#1430)
  • Within plasmapy.particles modules, the _elements, _isotopes, _parsing, and _special_particles modules are now imported directly. Before this, objects within these modules were typically imported. (#1440)
  • Renamed objects within the source code for plasmapy.particles to conform with PEP 8 naming conventions (e.g., ParticleZooClass → ParticleZoo, ParticleZoo → particle_zoo, and Particles → particles). (#1440)
  • Applied automated refactorings from Sourcery to plasmapy.utils. (#1463)
  • Applied automated refactorings from Sourcery to plasmapy.plasma. (#1464)
  • Bumped the minimum version of h5py to 3.0.0. (#1465)
  • Changed the raised exception to ImportError (from a general Exception) when attempting to import plasmapy from a Python version below the minimum supported version. (#1465)
  • Added a workflow to label pull requests based on size. (#1467, #1492)
  • Separated plasmapy.analysis.nullpoint.null_point_find into two functions named ~plasmapy.analysis.nullpoint.null_point_find and plasmapy.analysis.nullpoint.uniform_null_point_find. ~plasmapy.analysis.nullpoint.null_point_find finds the null points of a vector space whose values are manually entered. plasmapy.analysis.nullpoint.uniform_null_point_find finds the null points of a uniform vector space whose values are generated by a function provided by the user. (#1477)
  • Applied automated refactorings from Sourcery to plasmapy.particles. (#1479)
  • Applied automated refactorings from Sourcery to plasmapy.formulary. (#1480)
  • Bumped the minimum versions of |mpmath|_ to 1.2.1, numpy to 1.19.0, pandas to 1.0.0, pytest to 5.4.0, scipy to 1.5.0, and |xarray|_ to 0.15.0. (#1482)
  • Moved |h5py|_, |lmfit|_, |mpmath|_, and |numba|_ out of the extras requirements category and into the install requirements category. These packages are now installed when running pip install plasmapy. (#1482)
  • Added dlint, flake8_, flake8-absolute-import, flake8-rst-docstrings, flake8-use-fstring, pydocstyle_, and pygments_ into the tests requirements category and pre-commit_ into the extras requirements category. These dependencies are not required for basic installation with pip_. (#1482)
  • Updated :file:`docs/environment.yml` to use pip_ to install all requirements specified by :file:`requirements.txt` when creating a Conda_ environment. (#1482)
  • Used codespell to fix typos. (#1493)
  • Used contextlib.suppress to suppress exceptions, instead of try & except blocks. (#1494)
  • Added a pre-commit_ hook that transforms relative imports to absolute imports, except in :file:`docs/plasmapy_sphinx`. (#1499)
  • Added a test that import plasmapy does not raise an exception. (#1501)
  • Added a GitHub Action for codespell, and updated the corresponding tox_ environment to print out contextual information. (#1530)
  • Added :file:`plasmapy/utils/units_definitions.py` to precompute units which were applied to optimize functionality in :file:`plasmapy/formulary/distribution.py`. (#1531)
  • Replaced except Exception clauses in formulary, particles, and utils with specific exception statements. (#1541)
  • Added tests for passing array valued k and theta arguments to :func:`~plasmapy.dispersion.numerical.hollweg_.hollweg`, which was an added feature in :pr:`1529`. (#1549)
  • Added flake8-implicit-str-concat and flake8-mutable as extensions for flake8_. (#1557)
  • Added flake8-simplify as an extension for flake8_. (#1558)
  • Applied automated refactorings from Sourcery to plasmapy.dispersion. (#1562)
  • Applied automated refactorings from Sourcery to plasmapy.diagnostics. (#1563)
  • Applied automated refactorings from Sourcery to plasmapy.analysis. (#1564)
  • Removed an extraneous print statement from ~plasmapy.formulary.collisions.collision_frequency that activated when the colliding particles were both electrons. (#1570)
  • Changed the type hints for z_mean in plasmapy.formulary.collisions functions from astropy.units.dimensionless_unscaled to ~numbers.Real. Consequently, z_mean will no longer be processed by ~plasmapy.utils.decorators.validators.validate_quantities. Previously, z_mean issued a warning when a real number was provided instead of a dimensionless |Quantity|. (#1570)
  • Updated the version of black_ to 22.3.0 in PlasmaPy's pre-commit_ configuration. This update included a formatting change where spaces around power operators were removed for sufficiently simple operands (e.g., a ** b → a**b). (#1582)
  • Renamed units_definitions to _units_definitions and units_helpers to _units_helpers in plasmapy.utils to mark these modules as private. (#1587)
  • Updated the :file:`codemeta.json` file with metadata for the version 0.8.1 release. (#1606)

Plasmapy v0.7.0 (2021-11-18)

Backwards Incompatible Changes

  • Removed alias tfds_ to plasmapy.dispersion.two_fluid_dispersion.two_fluid_dispersion_solution, with the reasoning behind the removal outlined in the pull request. (#1101)
  • Removed the Tracker.synthetic_radiograph() method and created the standalone function :func:`~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph` in its place. This new function takes either a ~plasmapy.diagnostics.charged_particle_radiography.Tracker object or a dictionary equivalent to ~plasmapy.diagnostics.charged_particle_radiography.Tracker.results_dict. (#1134)
  • Renamed subpackage plasmapy.diagnostics.proton_radiography to plasmapy.diagnostics.charged_particle_radiography, and renamed the SyntheticProtonRadiograph class within that module to ~plasmapy.diagnostics.charged_particle_radiography.Tracker. (#1134)
  • ~plasmapy.diagnostics.charged_particle_radiography.Tracker no longer supports making changes to an instantiated object and re-running the simulation. Subsequent simulations should be performed by instantiating a new ~plasmapy.diagnostics.charged_particle_radiography.Tracker object and running its simulation. (#1134)
  • For ~plasmapy.plasma.grids.CartesianGrid the ~plasmapy.plasma.grids.CartesianGrid.volume_averaged_interpolator now returns numpy.nan values for any interpolation not bounded by the grid points. (#1173)
  • Renamed file :file:`two_fluid_dispersion.py` to :file:`two_fluid_.py` and moved it into the plasmapy.dispersion.analytical subpackage. The function two_fluid_dispersion_solution() contained within that file was renamed to ~plasmapy.dispersion.analytical.two_fluid_.two_fluid. (#1208)
  • Changed |ParticleList| so that if it is provided with no arguments, then it creates an empty |ParticleList|. This behavior is analogous to how list and tuple work. (#1223)
  • Changed the behavior of |Particle| in equality comparisons. Comparing a |Particle| with an object that is not :term:`particle-like` will now return False instead of raising a TypeError. (#1225)
  • Changed the behavior of ~plasmapy.particles.particle_class.CustomParticle so that it returns False when compared for equality with another type. Previously, a TypeError was raised. (#1315)

Deprecations and Removals

  • In plasmapy.particles, use of the term "integer charge" has been deprecated in favor of the term "charge number". The ~plasmapy.particles.particle_class.Particle.integer_charge attribute of |Particle| has been deprecated in favor of ~plasmapy.particles.particle_class.Particle.charge_number. The ~plasmapy.particles.ionization_state.IonicLevel.integer_charge attribute of |IonicLevel| (formerly IonicFraction) has been deprecated in favor of ~plasmapy.particles.ionization_state.IonicLevel.charge_number. The ~plasmapy.particles.ionization_state.IonizationState.integer_charges attribute of |IonizationState| has been deprecated in favor of ~plasmapy.particles.ionization_state.IonizationState.charge_numbers. (#1136)
  • The particle attribute of |Particle| has been removed after having been deprecated in 0.6.0. (#1146)
  • Use more generalized keyword argument T instead of T_i in plasmapy.formulary.parameters.gyroradius. The T_i argument has been deprecated and will be removed in a subsequent release. (#1210)

Features

  • Add the ~plasmapy.particles.ionization_state.IonizationState.average_ion method to |IonizationState|. (#1028)
  • Added the ~plasmapy.particles.ionization_state_collection.IonizationStateCollection.average_ion method to |IonizationStateCollection|. (#1028)
  • Added the plasmapy.formulary.mathematics.Chandrasekhar_G function, which is helpful in neoclassical transport theory. This change was reverted in #1233. (#1084)
  • Enabled slicing of |IonizationState| instances to return a list of |IonicLevel| instances. (#1130)
  • |IonizationState| instances can now be compared to an |IonizationState| of a different element without raising an exception. (#1130)
  • Allowed len to be used on |IonizationState| instances. (#1130)
  • |IonicLevel| and |IonizationState| now accept an additional, optional ion temperature argument for each of the ionic levels. (#1130)
  • Added the :meth:`~plasmapy.diagnostics.charged_particle_radiography.Tracker.save_results` method to ~plasmapy.diagnostics.charged_particle_radiography.Tracker for saving results to the :file:`.npz` file format (see numpy.lib.format for details on the file format). (#1134)
  • Added the plasmapy.utils.decorators.deprecation module. The module includes ~plasmapy.utils.decorators.deprecation.deprecated, which is a decorator that is based on astropy.utils.decorators.deprecated. (#1136)
  • Created the ~plasmapy.particles.ionization_state.IonizationState.to_list method of |IonizationState| to provide a |ParticleList| instance that contains the different ionic levels. (#1154)
  • The behavior of the function plasmapy.formulary.parameters.gyroradius has been changed. If numpy.nan values are provided for T_i or Vperp, then instead of raising a slightly misleading error, numpy.nan in the appropriate units is returned. (#1187)
  • Added the ~plasmapy.particles.particle_collections.ParticleList.average_particle method to |ParticleList|. This method returns a particle with the mean mass and charge of the |ParticleList|. The use_rms_charge and use_rms_mass keyword arguments make this method calculate the root mean square charge and mass, respectively. The abundances keyword argument allows the calculation of the mean or root mean square to be weighted. (#1204)
  • Restructured the plasmapy.dispersion subpackage by creating the ~plasmapy.dispersion.analytical subpackage to contain functionality related to analytical dispersion solutions. (#1208)
  • Implemented __eq__, __ne__ and __hash__ to allow |CustomParticle| instances to be used as dict keys. (#1216)
  • Added the ~plasmapy.particles.particle_collections.ionic_levels function to create a |ParticleList| initialized with different ionic levels of an element or isotope. (#1223)

Bug Fixes

  • Made |Particle| instances pickleable. (#1122)
  • Fixed the behavior of plasmapy.formulary.mathematics.Chandrasekhar_G at very small and very large argument values. This change was reverted in #1233. (#1125)
  • Running ~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph with the keyword optical_density=True will now return numpy.inf where the source profile intensity is zero. Previously, an incorrect value was returned since zero entries were replaced with values of 1 before taking the logarithm. (#1134)
  • Fixed a bug in the volume-averaged interpolator for ~plasmapy.plasma.grids.CartesianGrid (~plasmapy.plasma.grids.CartesianGrid.volume_averaged_interpolator). The old method miss interpreted where the interpolation point was inside the nearest neighbor cell volume. So, if an interpolation point was at the lower bounds of the nearest neighbor cell volume, then the position was flipped and interpreted as being at the upper bounds of the cell volume, and visa-versa. (#1173)
  • Fixed the normalization of the wavevector in the Thomson spectral density function, :func:`~plasmapy.diagnostics.thomson.spectral_density`. The previous version was not properly normalizing the wavevector to unity. (#1190)
  • Reverted most of #1084 and #1125, removing our implementation of the Chandrasekhar G function (for now!). This function may get brought back at a later date, once we have an implementation we numerically trust. (#1233)

Improved Documentation

  • Improved consistency of documentation style and made reST_ fixes in several subpackages. (#1073)
  • Added a pre-release section to the release guide. This section now includes steps for having a feature freeze about a week before the release, followed by a code freeze about two days before the release. (#1081)
  • Created the Sphinx_ extension package plasmapy_sphinx and used it to replace `sphinx_automodapi`_. plasmapy_sphinx creates directives :rst:dir:`automodapi` and :rst:dir:`automodsumm` to replace the same directives defined by `sphinx_automodapi`_. The documentation was updated so the slight syntax differences in the newly defined directives will still render the same as before. (#1105)
  • The term "integer charge" has been replaced in the documentation with the term "charge number". (#1136)
  • Implemented a framework to define and use common Sphinx substitutions across the narrative documentation and docstrings. These substitutions are defined in :file:`docs/common_links.rst`. (#1147)
  • Began a project glossary at :file:`docs/glossary.rst`. (#1149)
  • Changed the default branch name to main. Locations in the code and documentation that referred to the default branch of PlasmaPy (and certain other packages) were changed to reflect the new name (including, for example, in the development guide in the documentation). (#1150)
  • Updated information on how to write and build documentation in the development guide. (#1156)
  • Updated information on how to write and run tests in the contributor guide. (#1163)
  • Created an outline of a page in the development guide to describe the workflow required to contribute to PlasmaPy. (#1178)
  • Added brief description about the physics of the upper-hybrid resonance to the docstring of the function plasmapy.formulary.parameters.upper_hybrid_frequency. (#1180)
  • Added a brief description about the physics of the lower-hybrid resonance to the docstring of the function plasmapy.formulary.parameters.lower_hybrid_frequency. (#1181)
  • Made the function plasmapy.formulary.parameters.gyrofrequency more general by removing the indications that it might only work for ions. (#1183)
  • Make plasmapy.analysis.fit_functions.AbstractFitFunction.FitParamTuple a property to fix the documentation build warning caused by the release of Sphinx_ v4.1.0. (#1199)
  • Included a step in the release guide to update Binder requirements so that the release of PlasmaPy on PyPI_ gets installed when opening example notebooks from the stable and release branches of the online documentation. (#1205)
  • Updated the documentation guide to include updates to tox_ environments for building the documentation. (#1206)
  • Fixed numerous broken reST_ links in prior changelogs. (#1207)
  • Improve the docstring for plasmapy.online_help. (#1213)
  • Renamed "Development Guide" to "Contributor Guide", and temporarily removed the incomplete :file:`docs/development/workflow.rst` from the toctree of the Contributor Guide. (#1217)
  • Fixed a typo in the docstring of plasmapy.formulary.parameters.Alfven_speed. (#1218)
  • Fixed broken reST_ links in docstrings for aliases in plasmapy.formulary. (#1238)
  • Fixed multiple broken and redirected links. (#1257)
  • Updated the documentation guide to include a description on how to add and cite references to PlasmaPy's global bibliography BibTeX_ file, :file:`docs/bibliography.bib`. (#1263)
  • Added sphinxcontrib-bibtex_ as a Sphinx_ extension to enable references to be stored in a BibTeX_ file. (#1263)
  • Began a documentation-wide bibliography page. (#1263)
  • Updated documentation guide to describe where formulae should go in docstrings and how to use glossary entries. (#1264)
  • Updated and fixed hyperlinks in the documentation. (#1267)
  • Adopted the "xcode" code highlighting style for pygments_ to increase color contrast and improve web accessibility. (#1268)
  • Updated the feedback and communication page. (#1272)
  • Updated the requirements for the documentation build to include no restrictions on docutils and sphinx_rtd_theme >= 1.0.0. docutils == 0.17 is not compatible with sphinx_rtd_theme < 1.0 (see #1107 and #1230). (#1275)
  • Added a screenshot of the link for the `Read the Docs`_ preview of the documentation for a pull request. (#1298)
  • Incorporated citations in the ~plasmapy.dispersion.analytical.two_fluid_.two_fluid docstring into the PlasmaPy bibliography framework. (#1301)

Trivial/Internal Changes

  • Simplified handling of package dependencies. Removed duplicated requirements files and centralized them instead. Developer dependencies can now be installed with either pip install plasmapy[developer] or pip install -r requirements.txt. (#789)
  • Reconfigured flake8_ settings in CI. (#1062)
  • Added pydocstyle_ to continuous integration (CI), to hopefully make writing prettier docstrings easier. (#1062)
  • Added flake8-rst-docstrings to catch reST_ formatting errors in documentation in the linter stage of CI. (#1062)
  • Added pytest-regressions to testing dependencies, to make regression tests a little easier to write. (#1084)
  • Fixed a minor error in the \mathbf{E} \times \mathbf{B} drift notebook. (#1088)
  • Upgrade nbqa to latest available version (0.6.0). (#1104)
  • Moved our custom `pre-commit`_ style testing suite to pre-commit.ci, taking advantage of the new pre-commit.ci autofix command that allows manually calling for pre-commit to be run by typing that command as a comment to a pull request. (#1106)
  • Added tests using hypothesis_. (#1125)
  • Added to :file:`setup.cfg` the configuration flake8.per-file-ignores=plasmapy/formulary/__init__.py:F403 to ignore warnings resulting from imports like from xx import *. (#1127)
  • Re-enabled several flake8_ checks by removing the following codes from the flake8.extend-ignore configuration in :file:`setup.cfg`: D100, D102, D103, D104, D200, D210, D301, D401, D407, D409, D412, E712, E713, F403, F541, RST213, RST306, and RST902. Addressed any failed linter checks from this modification. (#1127)
  • ~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph now determines the default detector size to be the smallest detector plane centered on the origin that includes all particles. (#1134)
  • Added ion velocity input to the :file:`thomson.ipynb` diagnostics notebook. (#1171)
  • Added tox_ and removed pytest_ as extra requirements. (#1195)
  • Updated tox_ test environments for building the documentation. Added the build_docs_nitpicky environment to check for broken reST_ links. (#1206)
  • Added the --keep-going flag to the build_docs* tox_ environments with the -W option so that test failures will not stop after the first warning (that is treated as an error). (#1206)
  • Make queries to plasmapy.online_help for "quantity" or "quantities" redirect to the help page for astropy.units (which was already the case for "unit" and "units"). (#1213)
  • Bumped the Python_ version for `Read the Docs`_ builds from 3.7 to 3.8. (#1248)
  • Refactored :file:`plasmapy/dispersion/tests/test_dispersion.py` to use hypothesis_ for property based testing. (#1249)
  • Defined redirects to allow and anchors to avoid checking when using Sphinx_ to verify that hyperlinks are correct via make linkcheck. (#1267)
  • Replaced usage of eval inside |IonizationStateCollection| with getattr. (#1280)
  • Added using dlint to the linters testing environment in :file:`tox.ini` as a static analysis tool to search for security issues. (#1280)
  • Enabled using flake8-use-fstring in the linters testing environment in :file:`tox.ini` to enforce usage of formatted string literals (f-strings). (#1281)
  • Switched usage of str.format to formatted string literals (f-strings) in several files. (#1281)
  • Added flake8-absolute-import to the linters tox_ environment. (#1283)
  • Removed unused imports, and changed several imports from relative to absolute. (#1283)
  • Added `pre-commit`_ hooks to auto-format :file:`.ini`, :file:`.toml`, and :file:`.yaml` files, and applied changes from those hooks to existing files. (#1284)
  • Changed the validated units for the theta input argument of ~plasmapy.dispersion.analytical.two_fluid_.two_fluid from degrees to radians. (#1301)
  • Replaced usage of distutils.version.StrictVersion with packaging.version.Version because distutils has been deprecated. As part of this change, packaging has been added as a dependency. (#1306)
  • Increased the minimum version of matplotlib to 3.3.0 and updated plasmapy.diagnostics.langmuir.swept_probe_analysis to be compatible with matplotlib 3.5.0. (#1334)

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 propagated 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 incorporated 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 :file:`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 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 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

  • Allowed implicit conversions of AstroPy units in inputs and outputs of validated functions to happen without warnings. Most notably, this removes warnings on eV inputs to temperature fields. (#886)
  • Update plasmapy.formulary.parameters.Alfven_speed to properly use the updated plasmapy.formulary.parameters.mass_density and maintain the same behavior. Also add handling of the ion input keyword, so |Particle| and the |Particle| convertible representations can be used as inputs. (#957)

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:`~plasmapy.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 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